Starting phenix.real_space_refine
on Sun Jul 27 13:10:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dw3_27750/07_2025/8dw3_27750.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dw3_27750/07_2025/8dw3_27750.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2025/8dw3_27750.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2025/8dw3_27750.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2025/8dw3_27750.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2025/8dw3_27750.cif"
  }
  resolution = 4.26
  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=   0.002 sd=   0.019
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: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    5897      2.51       5
     N    1564      2.21       5
     O    1857      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9351
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1140
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 3, 'TRANS': 151}
    Chain: "B"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1521
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 10, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1624
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201}
    Chain: "D"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1715
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215}
    Chain: "H"
      Number of atoms: 1609
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 216, 1607
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 216, 1607
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1646
    Chain: "L"
      Number of atoms: 1703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1703
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 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
  Time building chain proxies: 7.16, per 1000 atoms: 0.77
  Number of scatterers: 9351
  At special positions: 0
  Unit cell: (82.062, 125.712, 174.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    1857      8.00
     N    1564      7.00
     C    5897      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  89 " distance=2.40
    Simple disulfide: pdb=" SG  CYS C 134 " - pdb=" SG  CYS C 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 154 " - pdb=" SG  CYS D 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG E   1 " - " ASN B 343 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.05
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2234

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 23 sheets defined
      15.3% alpha, 31.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 25
      removed outlier: 3.928A  pdb=" N   GLU A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A  24 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 49 through 58
      removed outlier: 4.283A  pdb=" N   LEU A  53 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
      removed outlier: 3.817A  pdb=" N   ASN A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 91
      removed outlier: 3.930A  pdb=" N   LEU A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 103
      removed outlier: 3.747A  pdb=" N   GLU A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 123
      removed outlier: 3.610A  pdb=" N   LEU A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 135
      removed outlier: 4.251A  pdb=" N   VAL A 129 " --> pdb=" O   HIS A 125 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 156
      removed outlier: 3.938A  pdb=" N   ILE A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASN A 156 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 169
      removed outlier: 4.275A  pdb=" N   ALA A 162 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 164 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.543A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.558A  pdb=" N   ALA B 352 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 369
      removed outlier: 3.803A  pdb=" N   VAL B 367 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
      removed outlier: 3.789A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
      removed outlier: 3.869A  pdb=" N   TYR B 421 " --> pdb=" O   LYS B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
      removed outlier: 3.640A  pdb=" N   GLN B 506 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 126
      removed outlier: 3.606A  pdb=" N   LEU C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.724A  pdb=" N   SER D  31 " --> pdb=" O   PRO D  28 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 170 through 172
      No H-bonds generated for 'chain 'D' and resid 170 through 172'
    Processing helix  chain 'D' and resid 199 through 203
      removed outlier: 3.715A  pdb=" N   SER D 202 " --> pdb=" O   PRO D 199 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.602A  pdb=" N   THR H  31 " --> pdb=" O   GLY H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.947A  pdb=" N   GLN H  65 " --> pdb=" O   PRO H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 191 through 193
      No H-bonds generated for 'chain 'H' and resid 191 through 193'
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.989A  pdb=" N   VAL L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 127 through 134
    Processing helix  chain 'L' and resid 189 through 195
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356
      removed outlier: 3.761A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5
      removed outlier: 3.914A  pdb=" N   ARG C  24 " --> pdb=" O   THR C   5 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 39
    Processing sheet with id=AA6, first strand: chain 'C' and resid 34 through 39
    Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 50
    Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 118
    Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 150
    Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.498A  pdb=" N   GLU D  10 " --> pdb=" O   THR D 124 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLY D  33 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ILE D  34 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   TRP D  50 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   TRP D  36 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 138
    Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 138
    Processing sheet with id=AB5, first strand: chain 'D' and resid 165 through 168
      removed outlier: 4.150A  pdb=" N   TYR D 208 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 2 through 5
    Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL H 108 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 128
      removed outlier: 6.630A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL H 185 " --> pdb=" O   HIS H 168 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.121A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.570A  pdb=" N   THR L 108 " --> pdb=" O   TYR L  92 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 120 through 124
      removed outlier: 5.933A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 151 through 156

    336 hydrogen bonds defined for protein.
    864 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: 3.13

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        0.50 -     0.77: 1
        0.77 -     1.04: 0
        1.04 -     1.31: 1548
        1.31 -     1.58: 7967
        1.58 -     1.84: 46
  Bond restraints: 9562
  Sorted by residual:
  bond pdb=" CG  PRO D  28 "
       pdb=" CD  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.503  0.505  0.998 3.40e-02 8.65e+02 8.62e+02
  bond pdb=" CG  PRO C 204 "
       pdb=" CD  PRO C 204 "
    ideal  model  delta    sigma   weight residual
    1.503  1.060  0.443 3.40e-02 8.65e+02 1.70e+02
  bond pdb=" N   PRO D  28 "
       pdb=" CD  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.473  1.589 -0.116 1.40e-02 5.10e+03 6.84e+01
  bond pdb=" CB  PRO D  28 "
       pdb=" CG  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.492  1.844 -0.352 5.00e-02 4.00e+02 4.95e+01
  bond pdb=" N   PRO C 204 "
       pdb=" CD  PRO C 204 "
    ideal  model  delta    sigma   weight residual
    1.473  1.569 -0.096 1.40e-02 5.10e+03 4.73e+01
  ... (remaining 9557 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.56: 12984
        7.56 -    15.11: 14
       15.11 -    22.67: 5
       22.67 -    30.23: 0
       30.23 -    37.79: 1
  Bond angle restraints: 13004
  Sorted by residual:
  angle pdb=" N   PRO D  28 "
        pdb=" CD  PRO D  28 "
        pdb=" CG  PRO D  28 "
      ideal   model   delta    sigma   weight residual
     103.20   65.41   37.79 1.50e+00 4.44e-01 6.35e+02
  angle pdb=" N   PRO C 204 "
        pdb=" CD  PRO C 204 "
        pdb=" CG  PRO C 204 "
      ideal   model   delta    sigma   weight residual
     103.20   81.48   21.72 1.50e+00 4.44e-01 2.10e+02
  angle pdb=" CA  PRO C 204 "
        pdb=" N   PRO C 204 "
        pdb=" CD  PRO C 204 "
      ideal   model   delta    sigma   weight residual
     112.00   94.26   17.74 1.40e+00 5.10e-01 1.61e+02
  angle pdb=" CA  PRO D  28 "
        pdb=" CB  PRO D  28 "
        pdb=" CG  PRO D  28 "
      ideal   model   delta    sigma   weight residual
     104.50   81.83   22.67 1.90e+00 2.77e-01 1.42e+02
  angle pdb=" CA  PRO C  81 "
        pdb=" N   PRO C  81 "
        pdb=" CD  PRO C  81 "
      ideal   model   delta    sigma   weight residual
     112.00   96.12   15.88 1.40e+00 5.10e-01 1.29e+02
  ... (remaining 12999 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.00: 5008
       21.00 -    42.01: 607
       42.01 -    63.01: 88
       63.01 -    84.01: 20
       84.01 -   105.02: 6
  Dihedral angle restraints: 5729
    sinusoidal: 2221
      harmonic: 3508
  Sorted by residual:
  dihedral pdb=" CB  CYS D 154 "
           pdb=" SG  CYS D 154 "
           pdb=" SG  CYS D 210 "
           pdb=" CB  CYS D 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.97   81.97     1      1.00e+01 1.00e-02 8.26e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   16.91   76.09     1      1.00e+01 1.00e-02 7.29e+01
  dihedral pdb=" CB  CYS C 134 "
           pdb=" SG  CYS C 134 "
           pdb=" SG  CYS C 194 "
           pdb=" CB  CYS C 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.05   75.05     1      1.00e+01 1.00e-02 7.12e+01
  ... (remaining 5726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1453
       0.131 -    0.263: 12
       0.263 -    0.394: 2
       0.394 -    0.525: 0
       0.525 -    0.657: 1
  Chirality restraints: 1468
  Sorted by residual:
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-02 2.50e+03 1.77e+02
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 343 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.08e+01
  chirality pdb=" CA  TRP D  50 "
            pdb=" N   TRP D  50 "
            pdb=" C   TRP D  50 "
            pdb=" CB  TRP D  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.08e+00
  ... (remaining 1465 not shown)

  Planarity restraints: 1671
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "   -0.081 2.00e-02 2.50e+03   6.71e-02 5.62e+01
        pdb=" C7  NAG E   1 "    0.020 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "   -0.061 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "    0.108 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 160 "    0.085 5.00e-02 4.00e+02   1.22e-01 2.39e+01
        pdb=" N   PRO D 161 "   -0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO D 161 "    0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO D 161 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  50 "    0.034 2.00e-02 2.50e+03   3.08e-02 2.37e+01
        pdb=" CG  TRP D  50 "   -0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  50 "    0.039 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  50 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  50 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1668 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 233
        2.66 -     3.22: 8587
        3.22 -     3.78: 13725
        3.78 -     4.34: 17656
        4.34 -     4.90: 29133
  Nonbonded interactions: 69334
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 345 "
            pdb=" OG  SER D 109 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   ILE C 106 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   SER C 121 "
            pdb=" NE2 GLN C 124 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" OG  SER B 383 "
            pdb=" OG  SER H 100 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG  SER D 202 "
            pdb=" OE1 GLN D 206 "
     model   vdw
     2.204 3.040
  ... (remaining 69329 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 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ 
 through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 
4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid  \ 
55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ 
d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213))
  selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ 
 through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 
3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through  \ 
58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ 
h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ 
hrough 219))
}

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=1.00
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:             1.170
  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:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.220
  Find NCS groups from input model:        0.210
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
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      :  0.014   0.998   9578  Z= 0.646
  Angle     :  0.965  37.787  13037  Z= 0.532
  Chirality :  0.051   0.657   1468
  Planarity :  0.008   0.122   1670
  Dihedral  : 17.592 105.017   3459
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.71 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 37.69 %
    Favored  : 62.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.89 (0.24), residues: 1209
  helix: -0.33 (0.49), residues: 104
  sheet:  0.37 (0.27), residues: 418
  loop : -1.29 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.082   0.003   TRP D  50 
 HIS   0.005   0.001   HIS A  52 
 PHE   0.025   0.001   PHE L 145 
 TYR   0.041   0.001   TYR L 102 
 ARG   0.003   0.000   ARG L 148 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00913 (    1)
  link_NAG-ASN         : angle       6.00156 (    3)
  link_BETA1-4         : bond        0.00339 (    2)
  link_BETA1-4         : angle       2.06847 (    6)
  hydrogen bonds       : bond        0.14673 (  314)
  hydrogen bonds       : angle       6.46055 (  864)
  SS BOND              : bond        0.10592 (   12)
  SS BOND              : angle       3.49234 (   24)
  covalent geometry    : bond        0.01266 ( 9562)
  covalent geometry    : angle       0.94946 (13004)
  Misc. bond           : bond        0.46470 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8274 (mp) cc_final: 0.7734 (tp)
REVERT: B  489 TYR cc_start: 0.6882 (m-80) cc_final: 0.6449 (m-80)
REVERT: C  117 ILE cc_start: 0.9102 (tt) cc_final: 0.8880 (tt)
REVERT: C  154 LEU cc_start: 0.9124 (tp) cc_final: 0.8874 (pt)
REVERT: D   48 MET cc_start: 0.6484 (mmm) cc_final: 0.6169 (tpp)
REVERT: D  138 LEU cc_start: 0.7749 (tp) cc_final: 0.7006 (mp)
REVERT: D  168 TRP cc_start: 0.7187 (m100) cc_final: 0.6603 (m100)
REVERT: D  210 CYS cc_start: 0.4075 (t) cc_final: 0.2355 (t)
REVERT: H  158 TRP cc_start: 0.7154 (m100) cc_final: 0.6662 (m100)
  outliers start: 1
  outliers final: 1
  residues processed: 205
  average time/residue: 0.2263
  time to fit residues: 63.2901
Evaluate side-chains
  128 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 90 optimal weight:   20.0000
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0040
   chunk 60 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 36 optimal weight:    0.2980
   chunk 56 optimal weight:   40.0000
   chunk 69 optimal weight:    4.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    2.4396

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 450 ASN
C   6 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 206 GLN
D 218 ASN
H 204 HIS
H 208 ASN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 172 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.072697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.057278 restraints weight = 55757.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.058904 restraints weight = 32409.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.060022 restraints weight = 21873.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   9578  Z= 0.159
  Angle     :  0.690   8.090  13037  Z= 0.347
  Chirality :  0.046   0.168   1468
  Planarity :  0.006   0.079   1670
  Dihedral  :  6.490  59.569   1372
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.87 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.04 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    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 (0.25), residues: 1209
  helix: -0.41 (0.46), residues: 119
  sheet:  0.47 (0.27), residues: 415
  loop : -1.26 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  50 
 HIS   0.006   0.001   HIS H 168 
 PHE   0.022   0.002   PHE B 429 
 TYR   0.019   0.002   TYR L 102 
 ARG   0.009   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00994 (    1)
  link_NAG-ASN         : angle       3.62549 (    3)
  link_BETA1-4         : bond        0.00463 (    2)
  link_BETA1-4         : angle       3.10171 (    6)
  hydrogen bonds       : bond        0.03115 (  314)
  hydrogen bonds       : angle       5.51845 (  864)
  SS BOND              : bond        0.00502 (   12)
  SS BOND              : angle       1.41445 (   24)
  covalent geometry    : bond        0.00382 ( 9562)
  covalent geometry    : angle       0.68323 (13004)
  Misc. bond           : bond        0.00088 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 180
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9466 (mp) cc_final: 0.9103 (tp)
REVERT: B  386 LYS cc_start: 0.9030 (mtpp) cc_final: 0.8700 (mtmt)
REVERT: B  389 ASP cc_start: 0.8310 (t70) cc_final: 0.8025 (t0)
REVERT: B  406 GLU cc_start: 0.8434 (pm20) cc_final: 0.8170 (pm20)
REVERT: B  414 GLN cc_start: 0.7925 (tt0) cc_final: 0.7660 (tm-30)
REVERT: B  442 ASP cc_start: 0.8719 (m-30) cc_final: 0.8464 (m-30)
REVERT: B  489 TYR cc_start: 0.7318 (m-80) cc_final: 0.6765 (m-80)
REVERT: C  118 PHE cc_start: 0.8295 (m-80) cc_final: 0.7525 (m-80)
REVERT: D   30 THR cc_start: 0.9185 (p) cc_final: 0.8955 (t)
REVERT: D   46 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8506 (pm20)
REVERT: D   48 MET cc_start: 0.8892 (mmm) cc_final: 0.8333 (tpp)
REVERT: D   87 ARG cc_start: 0.8662 (mpp-170) cc_final: 0.8336 (mtt90)
REVERT: D   94 TYR cc_start: 0.8992 (m-10) cc_final: 0.8596 (m-80)
REVERT: D  108 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8108 (mp0)
REVERT: D  168 TRP cc_start: 0.7722 (m100) cc_final: 0.6874 (m100)
REVERT: D  210 CYS cc_start: 0.7836 (t) cc_final: 0.5186 (t)
REVERT: H  149 TYR cc_start: 0.5484 (p90) cc_final: 0.5246 (p90)
REVERT: H  158 TRP cc_start: 0.7458 (m100) cc_final: 0.7103 (m100)
REVERT: L  142 LEU cc_start: 0.8479 (tp) cc_final: 0.8258 (tp)
  outliers start: 4
  outliers final: 1
  residues processed: 184
  average time/residue: 0.1990
  time to fit residues: 51.9787
Evaluate side-chains
  110 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
H  39 GLN
H  82 GLN
L 130 GLN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.070672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.053720 restraints weight = 92447.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.055837 restraints weight = 44631.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.057272 restraints weight = 27335.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9578  Z= 0.155
  Angle     :  0.626   9.072  13037  Z= 0.314
  Chirality :  0.044   0.140   1468
  Planarity :  0.005   0.046   1670
  Dihedral  :  5.386  32.905   1372
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.04 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.55 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.80 (0.25), residues: 1209
  helix: -0.05 (0.50), residues: 105
  sheet:  0.34 (0.26), residues: 421
  loop : -1.20 (0.24), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  50 
 HIS   0.004   0.001   HIS H 168 
 PHE   0.014   0.002   PHE B 429 
 TYR   0.017   0.001   TYR H  52 
 ARG   0.010   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01006 (    1)
  link_NAG-ASN         : angle       3.26218 (    3)
  link_BETA1-4         : bond        0.00379 (    2)
  link_BETA1-4         : angle       2.99649 (    6)
  hydrogen bonds       : bond        0.02842 (  314)
  hydrogen bonds       : angle       5.29307 (  864)
  SS BOND              : bond        0.00428 (   12)
  SS BOND              : angle       1.35240 (   24)
  covalent geometry    : bond        0.00361 ( 9562)
  covalent geometry    : angle       0.61846 (13004)
  Misc. bond           : bond        0.00152 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 1.027 
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: B  386 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8707 (mtmt)
REVERT: B  402 ILE cc_start: 0.9468 (tp) cc_final: 0.9080 (tp)
REVERT: B  406 GLU cc_start: 0.8460 (pm20) cc_final: 0.7955 (pm20)
REVERT: B  414 GLN cc_start: 0.8864 (tt0) cc_final: 0.8333 (tt0)
REVERT: B  420 ASP cc_start: 0.8970 (t70) cc_final: 0.8710 (t0)
REVERT: B  442 ASP cc_start: 0.8739 (m-30) cc_final: 0.8495 (m-30)
REVERT: C  118 PHE cc_start: 0.8312 (m-80) cc_final: 0.7545 (m-80)
REVERT: D   48 MET cc_start: 0.8830 (mmm) cc_final: 0.8334 (tpp)
REVERT: D   81 MET cc_start: 0.8920 (tmm) cc_final: 0.8669 (tmm)
REVERT: D  108 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8356 (mp0)
REVERT: D  168 TRP cc_start: 0.7832 (m100) cc_final: 0.6986 (m100)
REVERT: D  210 CYS cc_start: 0.7901 (t) cc_final: 0.5371 (t)
REVERT: H  149 TYR cc_start: 0.5669 (p90) cc_final: 0.5352 (p90)
REVERT: H  158 TRP cc_start: 0.7609 (m100) cc_final: 0.7234 (m100)
  outliers start: 2
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1988
  time to fit residues: 45.7578
Evaluate side-chains
  107 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0050
   chunk 0 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   chunk 57 optimal weight:    0.0970
   chunk 63 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 17 optimal weight:    8.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    4.2198

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

Flipped N/Q/H residues before XYZ refinement:
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
** L 161 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 = 0.3490 r_free = 0.3490 target = 0.068339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.052802 restraints weight = 68068.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.054514 restraints weight = 37311.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.055663 restraints weight = 24467.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9578  Z= 0.198
  Angle     :  0.669   9.471  13037  Z= 0.335
  Chirality :  0.044   0.144   1468
  Planarity :  0.005   0.045   1670
  Dihedral  :  5.230  31.876   1372
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.11 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.98 (0.24), residues: 1209
  helix: -0.25 (0.48), residues: 111
  sheet:  0.20 (0.26), residues: 422
  loop : -1.30 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  36 
 HIS   0.007   0.001   HIS H 168 
 PHE   0.016   0.002   PHE B 392 
 TYR   0.030   0.002   TYR H  32 
 ARG   0.005   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00595 (    1)
  link_NAG-ASN         : angle       4.14735 (    3)
  link_BETA1-4         : bond        0.00490 (    2)
  link_BETA1-4         : angle       2.89209 (    6)
  hydrogen bonds       : bond        0.02979 (  314)
  hydrogen bonds       : angle       5.31376 (  864)
  SS BOND              : bond        0.00446 (   12)
  SS BOND              : angle       1.67699 (   24)
  covalent geometry    : bond        0.00445 ( 9562)
  covalent geometry    : angle       0.65971 (13004)
  Misc. bond           : bond        0.00078 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8852 (p0) cc_final: 0.8642 (p0)
REVERT: B  390 LEU cc_start: 0.8648 (pp) cc_final: 0.8273 (pp)
REVERT: B  406 GLU cc_start: 0.8539 (pm20) cc_final: 0.8338 (pm20)
REVERT: B  414 GLN cc_start: 0.8941 (tt0) cc_final: 0.8222 (tm-30)
REVERT: B  516 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: C  118 PHE cc_start: 0.8246 (m-80) cc_final: 0.7548 (m-80)
REVERT: D   48 MET cc_start: 0.8814 (mmm) cc_final: 0.8524 (mmt)
REVERT: D   73 ASP cc_start: 0.9004 (t0) cc_final: 0.8711 (t0)
REVERT: D   81 MET cc_start: 0.8883 (tmm) cc_final: 0.8632 (tmm)
REVERT: D   94 TYR cc_start: 0.8943 (m-10) cc_final: 0.8710 (m-10)
REVERT: D  108 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8764 (mp0)
REVERT: D  168 TRP cc_start: 0.7858 (m100) cc_final: 0.6910 (m100)
REVERT: D  210 CYS cc_start: 0.8050 (t) cc_final: 0.5775 (t)
REVERT: H  158 TRP cc_start: 0.7687 (m100) cc_final: 0.7292 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2029
  time to fit residues: 40.2430
Evaluate side-chains
  100 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0050
   chunk 26 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 66 optimal weight:    7.9990
   chunk 102 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    3.6000

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 116 ASN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.068219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.052721 restraints weight = 67738.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.054405 restraints weight = 37430.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.055533 restraints weight = 24557.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9578  Z= 0.171
  Angle     :  0.651   9.404  13037  Z= 0.324
  Chirality :  0.044   0.207   1468
  Planarity :  0.004   0.043   1670
  Dihedral  :  5.132  33.259   1372
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.53 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.39 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.93 (0.25), residues: 1209
  helix: -0.15 (0.49), residues: 113
  sheet:  0.14 (0.25), residues: 428
  loop : -1.22 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H  33 
 HIS   0.006   0.001   HIS H 168 
 PHE   0.015   0.002   PHE H 170 
 TYR   0.029   0.002   TYR H 180 
 ARG   0.005   0.001   ARG B 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01202 (    1)
  link_NAG-ASN         : angle       6.72743 (    3)
  link_BETA1-4         : bond        0.00464 (    2)
  link_BETA1-4         : angle       2.87159 (    6)
  hydrogen bonds       : bond        0.02816 (  314)
  hydrogen bonds       : angle       5.28485 (  864)
  SS BOND              : bond        0.00411 (   12)
  SS BOND              : angle       1.40468 (   24)
  covalent geometry    : bond        0.00391 ( 9562)
  covalent geometry    : angle       0.63840 (13004)
  Misc. bond           : bond        0.00059 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8895 (p0) cc_final: 0.8692 (p0)
REVERT: B  390 LEU cc_start: 0.8597 (pp) cc_final: 0.8198 (pp)
REVERT: B  402 ILE cc_start: 0.9496 (tp) cc_final: 0.9105 (tp)
REVERT: B  406 GLU cc_start: 0.8570 (pm20) cc_final: 0.8232 (pm20)
REVERT: B  414 GLN cc_start: 0.8874 (tt0) cc_final: 0.8215 (tm-30)
REVERT: B  442 ASP cc_start: 0.8775 (m-30) cc_final: 0.8520 (m-30)
REVERT: B  456 PHE cc_start: 0.6920 (t80) cc_final: 0.6377 (t80)
REVERT: C  175 LEU cc_start: 0.9145 (tp) cc_final: 0.8834 (tt)
REVERT: D   46 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8244 (mp0)
REVERT: D   48 MET cc_start: 0.8739 (mmm) cc_final: 0.8459 (mmt)
REVERT: D  108 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8785 (mp0)
REVERT: D  168 TRP cc_start: 0.7881 (m100) cc_final: 0.6939 (m100)
REVERT: D  210 CYS cc_start: 0.7836 (t) cc_final: 0.5620 (t)
REVERT: H  158 TRP cc_start: 0.7753 (m100) cc_final: 0.7397 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1906
  time to fit residues: 38.6836
Evaluate side-chains
  98 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 44 optimal weight:   20.0000
   chunk 37 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 50 optimal weight:    8.9990
   chunk 88 optimal weight:    0.1980
   chunk 20 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    3.8388

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 206 GLN
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.066930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.051478 restraints weight = 70125.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.053147 restraints weight = 38325.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.054279 restraints weight = 25016.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9578  Z= 0.178
  Angle     :  0.670  13.010  13037  Z= 0.329
  Chirality :  0.045   0.178   1468
  Planarity :  0.004   0.042   1670
  Dihedral  :  5.194  34.668   1372
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.20 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.91 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.93 (0.25), residues: 1209
  helix: -0.13 (0.49), residues: 113
  sheet:  0.20 (0.26), residues: 422
  loop : -1.27 (0.25), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  50 
 HIS   0.006   0.001   HIS H 168 
 PHE   0.015   0.002   PHE H 170 
 TYR   0.019   0.002   TYR H 149 
 ARG   0.005   0.001   ARG D  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00293 (    1)
  link_NAG-ASN         : angle       7.97725 (    3)
  link_BETA1-4         : bond        0.00607 (    2)
  link_BETA1-4         : angle       3.04685 (    6)
  hydrogen bonds       : bond        0.02857 (  314)
  hydrogen bonds       : angle       5.32463 (  864)
  SS BOND              : bond        0.00483 (   12)
  SS BOND              : angle       1.54266 (   24)
  covalent geometry    : bond        0.00401 ( 9562)
  covalent geometry    : angle       0.65294 (13004)
  Misc. bond           : bond        0.00054 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8889 (p0) cc_final: 0.8616 (p0)
REVERT: B  390 LEU cc_start: 0.8526 (pp) cc_final: 0.8137 (pp)
REVERT: B  406 GLU cc_start: 0.8577 (pm20) cc_final: 0.8273 (pm20)
REVERT: B  414 GLN cc_start: 0.8885 (tt0) cc_final: 0.8160 (tm-30)
REVERT: B  458 LYS cc_start: 0.9059 (mmpt) cc_final: 0.8777 (mmmt)
REVERT: D   46 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8248 (mp0)
REVERT: D   48 MET cc_start: 0.8825 (mmm) cc_final: 0.8482 (mtm)
REVERT: D  108 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8849 (mp0)
REVERT: D  168 TRP cc_start: 0.7911 (m100) cc_final: 0.6936 (m100)
REVERT: D  206 GLN cc_start: 0.5433 (OUTLIER) cc_final: 0.5201 (pp30)
REVERT: D  210 CYS cc_start: 0.8137 (t) cc_final: 0.5970 (t)
REVERT: H  158 TRP cc_start: 0.7799 (m100) cc_final: 0.7449 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2156
  time to fit residues: 38.8138
Evaluate side-chains
  85 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 83 optimal weight:    0.0980
   chunk 97 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 99 optimal weight:    8.9990
   chunk 111 optimal weight:    0.0030
   chunk 20 optimal weight:    0.0020
   chunk 75 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.8202

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 116 ASN
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.068136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.052582 restraints weight = 69397.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.054312 restraints weight = 37624.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.055480 restraints weight = 24459.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9578  Z= 0.119
  Angle     :  0.637  11.952  13037  Z= 0.312
  Chirality :  0.044   0.154   1468
  Planarity :  0.004   0.041   1670
  Dihedral  :  4.790  28.981   1372
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.79 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    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 (0.25), residues: 1209
  helix: -0.07 (0.49), residues: 113
  sheet:  0.28 (0.26), residues: 426
  loop : -1.19 (0.25), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP H  33 
 HIS   0.003   0.001   HIS H 168 
 PHE   0.018   0.002   PHE D 114 
 TYR   0.020   0.001   TYR H  52 
 ARG   0.004   0.001   ARG D  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00411 (    1)
  link_NAG-ASN         : angle       5.00828 (    3)
  link_BETA1-4         : bond        0.00594 (    2)
  link_BETA1-4         : angle       2.75779 (    6)
  hydrogen bonds       : bond        0.02654 (  314)
  hydrogen bonds       : angle       5.16312 (  864)
  SS BOND              : bond        0.00362 (   12)
  SS BOND              : angle       1.51760 (   24)
  covalent geometry    : bond        0.00278 ( 9562)
  covalent geometry    : angle       0.62710 (13004)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8892 (p0) cc_final: 0.8619 (p0)
REVERT: B  386 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8804 (ptpt)
REVERT: B  390 LEU cc_start: 0.8490 (pp) cc_final: 0.8094 (pp)
REVERT: B  406 GLU cc_start: 0.8530 (pm20) cc_final: 0.8205 (pm20)
REVERT: B  414 GLN cc_start: 0.8816 (tt0) cc_final: 0.8243 (tt0)
REVERT: B  442 ASP cc_start: 0.8820 (m-30) cc_final: 0.8558 (m-30)
REVERT: B  458 LYS cc_start: 0.8985 (mmpt) cc_final: 0.8767 (mmmt)
REVERT: C  175 LEU cc_start: 0.9139 (tp) cc_final: 0.8759 (tt)
REVERT: D   46 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8235 (mp0)
REVERT: D   48 MET cc_start: 0.8845 (mmm) cc_final: 0.8470 (mtm)
REVERT: D   81 MET cc_start: 0.8952 (tmm) cc_final: 0.8702 (tmm)
REVERT: D  108 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8875 (mp0)
REVERT: D  168 TRP cc_start: 0.7928 (m100) cc_final: 0.7053 (m100)
REVERT: D  210 CYS cc_start: 0.7989 (t) cc_final: 0.5729 (t)
REVERT: H  158 TRP cc_start: 0.7783 (m100) cc_final: 0.7430 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1923
  time to fit residues: 38.7027
Evaluate side-chains
  91 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 114 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   chunk 104 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 118 optimal weight:    0.2980
   chunk 107 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 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 = 0.3497 r_free = 0.3497 target = 0.068221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.053132 restraints weight = 57232.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.054694 restraints weight = 32857.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.055755 restraints weight = 22043.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9578  Z= 0.122
  Angle     :  0.664  13.135  13037  Z= 0.319
  Chirality :  0.045   0.263   1468
  Planarity :  0.004   0.073   1670
  Dihedral  :  4.901  33.694   1372
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.95 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.83 (0.25), residues: 1209
  helix:  0.02 (0.49), residues: 113
  sheet:  0.20 (0.25), residues: 445
  loop : -1.20 (0.25), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 118 
 PHE   0.021   0.001   PHE C  72 
 TYR   0.028   0.001   TYR L 102 
 ARG   0.007   0.001   ARG C  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00183 (    1)
  link_NAG-ASN         : angle      11.95425 (    3)
  link_BETA1-4         : bond        0.00860 (    2)
  link_BETA1-4         : angle       3.11733 (    6)
  hydrogen bonds       : bond        0.02738 (  314)
  hydrogen bonds       : angle       5.13456 (  864)
  SS BOND              : bond        0.00429 (   12)
  SS BOND              : angle       1.41690 (   24)
  covalent geometry    : bond        0.00286 ( 9562)
  covalent geometry    : angle       0.63329 (13004)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8905 (p0) cc_final: 0.8622 (p0)
REVERT: B  386 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8630 (ptpt)
REVERT: B  390 LEU cc_start: 0.8595 (pp) cc_final: 0.8202 (pp)
REVERT: B  406 GLU cc_start: 0.8512 (pm20) cc_final: 0.8167 (pm20)
REVERT: B  414 GLN cc_start: 0.8796 (tt0) cc_final: 0.8223 (tt0)
REVERT: B  442 ASP cc_start: 0.8804 (m-30) cc_final: 0.8527 (m-30)
REVERT: C  175 LEU cc_start: 0.9125 (tp) cc_final: 0.8743 (tt)
REVERT: D   48 MET cc_start: 0.8788 (mmm) cc_final: 0.8275 (mtm)
REVERT: D  108 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8905 (mp0)
REVERT: D  168 TRP cc_start: 0.7835 (m100) cc_final: 0.6975 (m100)
REVERT: D  210 CYS cc_start: 0.7962 (t) cc_final: 0.5595 (t)
REVERT: H  158 TRP cc_start: 0.7762 (m100) cc_final: 0.7414 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2062
  time to fit residues: 41.0524
Evaluate side-chains
  93 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 12 optimal weight:   20.0000
   chunk 95 optimal weight:    7.9990
   chunk 81 optimal weight:    0.0970
   chunk 90 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    3.6184

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 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 = 0.3459 r_free = 0.3459 target = 0.066574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.051646 restraints weight = 57044.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.053161 restraints weight = 32921.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.054168 restraints weight = 22101.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9578  Z= 0.175
  Angle     :  0.679  13.315  13037  Z= 0.332
  Chirality :  0.045   0.192   1468
  Planarity :  0.004   0.040   1670
  Dihedral  :  5.021  33.749   1372
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.20 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.89 (0.25), residues: 1209
  helix:  0.03 (0.49), residues: 113
  sheet:  0.04 (0.24), residues: 451
  loop : -1.16 (0.26), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  33 
 HIS   0.005   0.001   HIS H 168 
 PHE   0.017   0.002   PHE C  72 
 TYR   0.027   0.002   TYR L 102 
 ARG   0.007   0.001   ARG B 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00472 (    1)
  link_NAG-ASN         : angle       9.55323 (    3)
  link_BETA1-4         : bond        0.00608 (    2)
  link_BETA1-4         : angle       2.90731 (    6)
  hydrogen bonds       : bond        0.02880 (  314)
  hydrogen bonds       : angle       5.29691 (  864)
  SS BOND              : bond        0.00570 (   12)
  SS BOND              : angle       1.61110 (   24)
  covalent geometry    : bond        0.00399 ( 9562)
  covalent geometry    : angle       0.65775 (13004)
  Misc. bond           : bond        0.00063 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8867 (p0) cc_final: 0.8576 (p0)
REVERT: B  386 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8782 (ptpt)
REVERT: B  390 LEU cc_start: 0.8589 (pp) cc_final: 0.8215 (pp)
REVERT: B  406 GLU cc_start: 0.8537 (pm20) cc_final: 0.8216 (pm20)
REVERT: B  414 GLN cc_start: 0.8813 (tt0) cc_final: 0.8261 (tt0)
REVERT: D    3 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8151 (tm-30)
REVERT: D   46 GLU cc_start: 0.8202 (mp0) cc_final: 0.7996 (mp0)
REVERT: D   48 MET cc_start: 0.8800 (mmm) cc_final: 0.8312 (mtm)
REVERT: D  108 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8896 (mp0)
REVERT: D  168 TRP cc_start: 0.7834 (m100) cc_final: 0.6955 (m100)
REVERT: D  210 CYS cc_start: 0.8086 (t) cc_final: 0.5800 (t)
REVERT: H   83 TRP cc_start: 0.7840 (m100) cc_final: 0.6983 (m100)
REVERT: H  158 TRP cc_start: 0.7720 (m100) cc_final: 0.7356 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1795
  time to fit residues: 33.4780
Evaluate side-chains
  89 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 106 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 102 optimal weight:    8.9990
   chunk 99 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 98 optimal weight:    7.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 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 = 0.3442 r_free = 0.3442 target = 0.065755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.050443 restraints weight = 69875.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.052092 restraints weight = 37921.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.053186 restraints weight = 24713.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9578  Z= 0.189
  Angle     :  0.699  17.338  13037  Z= 0.341
  Chirality :  0.045   0.181   1468
  Planarity :  0.004   0.040   1670
  Dihedral  :  5.169  33.999   1372
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.19 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.93 (0.25), residues: 1209
  helix:  0.23 (0.51), residues: 106
  sheet: -0.08 (0.24), residues: 451
  loop : -1.14 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  50 
 HIS   0.006   0.001   HIS H 168 
 PHE   0.016   0.002   PHE C  72 
 TYR   0.020   0.002   TYR L 102 
 ARG   0.004   0.001   ARG C  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00259 (    1)
  link_NAG-ASN         : angle       9.22757 (    3)
  link_BETA1-4         : bond        0.00646 (    2)
  link_BETA1-4         : angle       2.89539 (    6)
  hydrogen bonds       : bond        0.03045 (  314)
  hydrogen bonds       : angle       5.35569 (  864)
  SS BOND              : bond        0.00597 (   12)
  SS BOND              : angle       1.67426 (   24)
  covalent geometry    : bond        0.00426 ( 9562)
  covalent geometry    : angle       0.67908 (13004)
  Misc. bond           : bond        0.00073 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8840 (p0) cc_final: 0.8594 (p0)
REVERT: B  386 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8777 (ptpt)
REVERT: B  390 LEU cc_start: 0.8533 (pp) cc_final: 0.8154 (pp)
REVERT: B  406 GLU cc_start: 0.8608 (pm20) cc_final: 0.8292 (pm20)
REVERT: B  414 GLN cc_start: 0.8834 (tt0) cc_final: 0.8301 (tt0)
REVERT: D    3 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8009 (tm-30)
REVERT: D   48 MET cc_start: 0.8812 (mmm) cc_final: 0.8320 (mtm)
REVERT: D  108 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8924 (mp0)
REVERT: D  168 TRP cc_start: 0.7884 (m100) cc_final: 0.7062 (m100)
REVERT: D  210 CYS cc_start: 0.8117 (t) cc_final: 0.5898 (t)
REVERT: H   40 MET cc_start: 0.8663 (mmm) cc_final: 0.8369 (mmt)
REVERT: H   48 MET cc_start: 0.8701 (mpp) cc_final: 0.8496 (mpp)
REVERT: H  158 TRP cc_start: 0.7710 (m100) cc_final: 0.7362 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1780
  time to fit residues: 32.1895
Evaluate side-chains
  84 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 105 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 81 optimal weight:    0.0770
   chunk 43 optimal weight:    2.9990
   overall best weight:    2.0144

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

Flipped N/Q/H residues before XYZ refinement:
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 168 HIS
** L 161 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 = 0.3472 r_free = 0.3472 target = 0.066996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.050727 restraints weight = 93102.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.052706 restraints weight = 45404.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.054013 restraints weight = 27883.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.5136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9578  Z= 0.127
  Angle     :  0.673  15.652  13037  Z= 0.325
  Chirality :  0.045   0.174   1468
  Planarity :  0.004   0.051   1670
  Dihedral  :  4.951  32.806   1372
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.85 (0.25), residues: 1209
  helix:  0.30 (0.52), residues: 106
  sheet:  0.09 (0.25), residues: 439
  loop : -1.17 (0.25), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D 105 
 HIS   0.004   0.001   HIS A  52 
 PHE   0.015   0.001   PHE C  72 
 TYR   0.018   0.001   TYR D  95 
 ARG   0.005   0.001   ARG B 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00161 (    1)
  link_NAG-ASN         : angle       8.50541 (    3)
  link_BETA1-4         : bond        0.00562 (    2)
  link_BETA1-4         : angle       2.93888 (    6)
  hydrogen bonds       : bond        0.02800 (  314)
  hydrogen bonds       : angle       5.25479 (  864)
  SS BOND              : bond        0.00410 (   12)
  SS BOND              : angle       1.35344 (   24)
  covalent geometry    : bond        0.00294 ( 9562)
  covalent geometry    : angle       0.65562 (13004)
  Misc. bond           : bond        0.00019 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3578.29 seconds
wall clock time: 62 minutes 44.48 seconds (3764.48 seconds total)