Starting phenix.real_space_refine
on Fri Aug 22 15:47:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1d_41810/08_2025/8u1d_41810.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1d_41810/08_2025/8u1d_41810.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1d_41810/08_2025/8u1d_41810.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1d_41810/08_2025/8u1d_41810.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1d_41810/08_2025/8u1d_41810.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1d_41810/08_2025/8u1d_41810.map"
  }
  resolution = 4.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
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      35      5.16       5
     C    3195      2.51       5
     N     882      2.21       5
     O     997      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5109
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3310
          Classifications: {'peptide': 421}
          Link IDs: {'PTRANS': 18, 'TRANS': 402}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 969
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "J"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 816
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.36, per 1000 atoms: 0.27
  Number of scatterers: 5109
  At special positions: 0
  Unit cell: (89.64, 84.24, 85.32, 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      35     16.00
     O     997      8.00
     N     882      7.00
     C    3195      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 119 " - pdb=" SG  CYS A 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 157 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 239 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 296 " - pdb=" SG  CYS A 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 378 " - pdb=" SG  CYS A 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 385 " - pdb=" SG  CYS A 418 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  23 " - pdb=" SG  CYS J  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 386 "
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 181.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1212

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 14 sheets defined
      13.8% alpha, 35.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 70
    Processing helix  chain 'A' and resid 71 through 73
      No H-bonds generated for 'chain 'A' and resid 71 through 73'
    Processing helix  chain 'A' and resid 99 through 115
      removed outlier: 4.125A  pdb=" N   GLN A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 126
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 3.644A  pdb=" N   ILE A 141 " --> pdb=" O   ASN A 138 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE A 142 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 138 through 142'
    Processing helix  chain 'A' and resid 205 through 209
      removed outlier: 3.518A  pdb=" N   VAL A 208 " --> pdb=" O   CYS A 205 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER A 209 " --> pdb=" O   PRO A 206 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 205 through 209'
    Processing helix  chain 'A' and resid 334 through 350
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 3.826A  pdb=" N   THR A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
      removed outlier: 3.571A  pdb=" N   PHE A 391 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ASN A 392 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 388 through 392'
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'I' and resid 28 through 32
      removed outlier: 4.220A  pdb=" N   TYR I  32 " --> pdb=" O   PHE I  29 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 83 through 87
      removed outlier: 3.967A  pdb=" N   THR I  87 " --> pdb=" O   SER I  84 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86
      removed outlier: 3.637A  pdb=" N   SER A 243 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   VAL A 245 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ILE A 225 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 224 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 94
    Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174
    Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203
      removed outlier: 6.377A  pdb=" N   VAL A 200 " --> pdb=" O   ALA A 433 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   TYR A 435 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   THR A 202 " --> pdb=" O   TYR A 435 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261
      removed outlier: 6.556A  pdb=" N   LEU A 260 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 292 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 290 " (cutoff:3.500A)
      removed outlier: 11.117A  pdb=" N   GLU A 290 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261
      removed outlier: 6.556A  pdb=" N   LEU A 260 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 292 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 290 " (cutoff:3.500A)
      removed outlier: 11.117A  pdb=" N   GLU A 290 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU A 295 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE A 382 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 307
      removed outlier: 6.898A  pdb=" N   ASN A 301 " --> pdb=" O   VAL A 322 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   VAL A 322 " --> pdb=" O   ASN A 301 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   THR A 303 " --> pdb=" O   GLY A 321 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 361
      removed outlier: 6.928A  pdb=" N   ASN A 357 " --> pdb=" O   GLU A 464 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   PHE A 466 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR A 359 " --> pdb=" O   PHE A 466 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 3 through 6
      removed outlier: 3.527A  pdb=" N   LEU I  82 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 57 through 58
      removed outlier: 6.056A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER I 102 " --> pdb=" O   ARG I  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 57 through 58
      removed outlier: 6.056A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 5 through 6
      removed outlier: 3.800A  pdb=" N   ASP J  70 " --> pdb=" O   SER J  67 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER J  67 " --> pdb=" O   ASP J  70 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 10 through 13
      removed outlier: 6.064A  pdb=" N   LEU J  11 " --> pdb=" O   ASP J 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'J' and resid 53 through 54
      removed outlier: 6.542A  pdb=" N   ALA J  46 " --> pdb=" O   GLN J  37 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   GLN J  37 " --> pdb=" O   ALA J  46 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ILE J  48 " --> pdb=" O   TRP J  35 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    420 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: 0.68

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1654
        1.34 -     1.46: 1222
        1.46 -     1.59: 2297
        1.59 -     1.71: 0
        1.71 -     1.83: 48
  Bond restraints: 5221
  Sorted by residual:
  bond pdb=" N   ASP A  78 "
       pdb=" CA  ASP A  78 "
    ideal  model  delta    sigma   weight residual
    1.460  1.487 -0.027 7.10e-03 1.98e+04 1.46e+01
  bond pdb=" N   ILE A 271 "
       pdb=" CA  ILE A 271 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.11e-02 8.12e+03 1.02e+01
  bond pdb=" N   VAL A 281 "
       pdb=" CA  VAL A 281 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.19e-02 7.06e+03 1.00e+01
  bond pdb=" N   VAL A  65 "
       pdb=" CA  VAL A  65 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.12e+00
  bond pdb=" N   VAL A 286 "
       pdb=" CA  VAL A 286 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.24e-02 6.50e+03 8.07e+00
  ... (remaining 5216 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 6546
        1.85 -     3.70: 447
        3.70 -     5.55: 58
        5.55 -     7.40: 24
        7.40 -     9.25: 10
  Bond angle restraints: 7085
  Sorted by residual:
  angle pdb=" N   LYS A  63 "
        pdb=" CA  LYS A  63 "
        pdb=" C   LYS A  63 "
      ideal   model   delta    sigma   weight residual
     113.28  107.17    6.11 1.22e+00 6.72e-01 2.50e+01
  angle pdb=" N   ILE J  29 "
        pdb=" CA  ILE J  29 "
        pdb=" C   ILE J  29 "
      ideal   model   delta    sigma   weight residual
     112.17  107.96    4.21 9.50e-01 1.11e+00 1.96e+01
  angle pdb=" N   VAL A  68 "
        pdb=" CA  VAL A  68 "
        pdb=" C   VAL A  68 "
      ideal   model   delta    sigma   weight residual
     113.16  106.66    6.50 1.49e+00 4.50e-01 1.90e+01
  angle pdb=" C   PRO I  41 "
        pdb=" N   ARG I  42 "
        pdb=" CA  ARG I  42 "
      ideal   model   delta    sigma   weight residual
     121.54  129.09   -7.55 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" CB  GLN I  39 "
        pdb=" CG  GLN I  39 "
        pdb=" CD  GLN I  39 "
      ideal   model   delta    sigma   weight residual
     112.60  119.26   -6.66 1.70e+00 3.46e-01 1.54e+01
  ... (remaining 7080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 2836
       17.29 -    34.58: 248
       34.58 -    51.87: 59
       51.87 -    69.16: 6
       69.16 -    86.46: 4
  Dihedral angle restraints: 3153
    sinusoidal: 1264
      harmonic: 1889
  Sorted by residual:
  dihedral pdb=" CA  GLU A 429 "
           pdb=" C   GLU A 429 "
           pdb=" N   VAL A 430 "
           pdb=" CA  VAL A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.51   22.49     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CB  CYS J  23 "
           pdb=" SG  CYS J  23 "
           pdb=" SG  CYS J  88 "
           pdb=" CB  CYS J  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.77  -37.77     1      1.00e+01 1.00e-02 2.01e+01
  dihedral pdb=" CA  MET A 434 "
           pdb=" C   MET A 434 "
           pdb=" N   TYR A 435 "
           pdb=" CA  TYR A 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.78   22.22     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 3150 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 617
       0.071 -    0.143: 138
       0.143 -    0.214: 30
       0.214 -    0.285: 3
       0.285 -    0.357: 1
  Chirality restraints: 789
  Sorted by residual:
  chirality pdb=" CB  VAL A 208 "
            pdb=" CA  VAL A 208 "
            pdb=" CG1 VAL A 208 "
            pdb=" CG2 VAL A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" CB  ILE A 326 "
            pdb=" CA  ILE A 326 "
            pdb=" CG1 ILE A 326 "
            pdb=" CG2 ILE A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  GLU J  81 "
            pdb=" N   GLU J  81 "
            pdb=" C   GLU J  81 "
            pdb=" CB  GLU J  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 786 not shown)

  Planarity restraints: 910
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER J  94 "   -0.047 5.00e-02 4.00e+02   7.11e-02 8.09e+00
        pdb=" N   PRO J  95 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO J  95 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO J  95 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP I 103 "   -0.015 2.00e-02 2.50e+03   1.54e-02 5.92e+00
        pdb=" CG  TRP I 103 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP I 103 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP I 103 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP I 103 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP I 103 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP I 103 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP I 103 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP I 103 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP I 103 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN J  79 "    0.037 5.00e-02 4.00e+02   5.55e-02 4.92e+00
        pdb=" N   PRO J  80 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO J  80 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO J  80 "    0.031 5.00e-02 4.00e+02
  ... (remaining 907 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1334
        2.80 -     3.33: 4531
        3.33 -     3.85: 8162
        3.85 -     4.38: 8702
        4.38 -     4.90: 15210
  Nonbonded interactions: 37939
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 103 "
            pdb=" OD2 ASP A 107 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OG  SER J  14 "
            pdb=" OD2 ASP J  17 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG  SER A 479 "
            pdb=" OE1 GLU A 480 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   PHE I 100E"
            pdb=" OH  TYR J  36 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   GLN J   3 "
            pdb=" OG  SER J  26 "
     model   vdw
     2.347 3.040
  ... (remaining 37934 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 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:             2.730
  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:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.580
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
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      :  0.006   0.056   5230  Z= 0.359
  Angle     :  1.057   9.252   7104  Z= 0.611
  Chirality :  0.064   0.357    789
  Planarity :  0.007   0.071    909
  Dihedral  : 13.613  86.455   1917
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  7.94 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  1.22 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.32 (0.30), residues: 642
  helix: -2.35 (0.52), residues: 57
  sheet: -0.76 (0.36), residues: 189
  loop : -1.87 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG J  42 
 TYR   0.033   0.003   TYR A 330 
 PHE   0.012   0.002   PHE A 210 
 TRP   0.038   0.003   TRP I 103 
 HIS   0.016   0.002   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 5221)
  covalent geometry    : angle       1.05494 ( 7085)
  SS BOND              : bond        0.00597 (    8)
  SS BOND              : angle       1.86133 (   16)
  hydrogen bonds       : bond        0.17849 (  149)
  hydrogen bonds       : angle       7.12534 (  420)
  link_NAG-ASN         : bond        0.01644 (    1)
  link_NAG-ASN         : angle       1.01020 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8241 (p) cc_final: 0.7914 (t)
REVERT: A  396 MET cc_start: 0.6848 (ppp) cc_final: 0.6359 (ppp)
REVERT: I    3 HIS cc_start: 0.8035 (t-90) cc_final: 0.7531 (t-90)
REVERT: I   12 LYS cc_start: 0.8432 (mptt) cc_final: 0.8214 (mmtt)
REVERT: I   80 MET cc_start: 0.8926 (ttt) cc_final: 0.8424 (ttp)
REVERT: J    2 ILE cc_start: 0.7936 (mp) cc_final: 0.7277 (mp)
REVERT: J    4 MET cc_start: 0.7089 (mpp) cc_final: 0.6824 (mpp)
REVERT: J   58 VAL cc_start: 0.8674 (t) cc_final: 0.8212 (t)
  outliers start: 3
  outliers final: 1
  residues processed: 139
  average time/residue: 0.0576
  time to fit residues: 10.5217
Evaluate side-chains
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.143960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.119888 restraints weight = 11957.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.123596 restraints weight = 7585.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.126255 restraints weight = 5402.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.128068 restraints weight = 4196.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.129425 restraints weight = 3474.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5230  Z= 0.135
  Angle     :  0.597   6.417   7104  Z= 0.321
  Chirality :  0.043   0.139    789
  Planarity :  0.005   0.053    909
  Dihedral  :  6.063  50.141    725
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.30 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.31), residues: 642
  helix: -0.79 (0.67), residues: 52
  sheet: -0.45 (0.39), residues: 166
  loop : -1.45 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J  42 
 TYR   0.015   0.002   TYR I  32 
 PHE   0.015   0.001   PHE A 233 
 TRP   0.017   0.002   TRP I  50 
 HIS   0.005   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5221)
  covalent geometry    : angle       0.59441 ( 7085)
  SS BOND              : bond        0.00523 (    8)
  SS BOND              : angle       1.34277 (   16)
  hydrogen bonds       : bond        0.04017 (  149)
  hydrogen bonds       : angle       6.07384 (  420)
  link_NAG-ASN         : bond        0.00253 (    1)
  link_NAG-ASN         : angle       0.60577 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8677 (p) cc_final: 0.8411 (t)
REVERT: A  122 LEU cc_start: 0.9140 (tp) cc_final: 0.8910 (tp)
REVERT: A  396 MET cc_start: 0.6713 (ppp) cc_final: 0.6316 (ppp)
REVERT: I    3 HIS cc_start: 0.8021 (t-90) cc_final: 0.7820 (t-90)
REVERT: I    4 LEU cc_start: 0.8241 (mt) cc_final: 0.8029 (mt)
REVERT: I   80 MET cc_start: 0.8975 (ttt) cc_final: 0.8471 (ttp)
REVERT: J    2 ILE cc_start: 0.8191 (mp) cc_final: 0.7518 (mp)
REVERT: J   79 GLN cc_start: 0.8065 (pp30) cc_final: 0.7841 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0644
  time to fit residues: 10.1376
Evaluate side-chains
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0770
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.142471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.118077 restraints weight = 12037.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.121666 restraints weight = 7806.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.124165 restraints weight = 5687.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.126025 restraints weight = 4494.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.127296 restraints weight = 3750.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5230  Z= 0.141
  Angle     :  0.595   6.012   7104  Z= 0.318
  Chirality :  0.042   0.141    789
  Planarity :  0.004   0.048    909
  Dihedral  :  5.914  50.285    725
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.39 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.32), residues: 642
  helix:  0.32 (0.76), residues: 46
  sheet: -0.21 (0.38), residues: 186
  loop : -1.39 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG J  42 
 TYR   0.016   0.002   TYR I  32 
 PHE   0.024   0.002   PHE J  83 
 TRP   0.015   0.001   TRP I  50 
 HIS   0.004   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5221)
  covalent geometry    : angle       0.59215 ( 7085)
  SS BOND              : bond        0.00404 (    8)
  SS BOND              : angle       1.22558 (   16)
  hydrogen bonds       : bond        0.03690 (  149)
  hydrogen bonds       : angle       5.71141 (  420)
  link_NAG-ASN         : bond        0.00348 (    1)
  link_NAG-ASN         : angle       1.16047 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8677 (p) cc_final: 0.8408 (t)
REVERT: A  145 MET cc_start: 0.2716 (mtt) cc_final: 0.2355 (mtt)
REVERT: A  396 MET cc_start: 0.6782 (ppp) cc_final: 0.6458 (ppp)
REVERT: A  426 MET cc_start: 0.7002 (tmm) cc_final: 0.6409 (tmm)
REVERT: I    4 LEU cc_start: 0.8356 (mt) cc_final: 0.8061 (mt)
REVERT: I   71 ARG cc_start: 0.8982 (ppt170) cc_final: 0.8449 (ptt90)
REVERT: I   80 MET cc_start: 0.8975 (ttt) cc_final: 0.8653 (ttp)
REVERT: J    2 ILE cc_start: 0.8379 (mp) cc_final: 0.7862 (mp)
REVERT: J   79 GLN cc_start: 0.8108 (pp30) cc_final: 0.7880 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0617
  time to fit residues: 9.4102
Evaluate side-chains
  94 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    0.1980
   chunk 44 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** I   6 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 = 0.3876 r_free = 0.3876 target = 0.143037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.118458 restraints weight = 11988.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.122108 restraints weight = 7728.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.124564 restraints weight = 5590.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.126453 restraints weight = 4429.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.127716 restraints weight = 3675.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5230  Z= 0.130
  Angle     :  0.596  11.945   7104  Z= 0.311
  Chirality :  0.042   0.149    789
  Planarity :  0.004   0.047    909
  Dihedral  :  6.002  54.585    725
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.07 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.32), residues: 642
  helix:  0.05 (0.73), residues: 53
  sheet: -0.12 (0.38), residues: 186
  loop : -1.42 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J  42 
 TYR   0.012   0.001   TYR A 330 
 PHE   0.014   0.001   PHE A 233 
 TRP   0.013   0.001   TRP I  50 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5221)
  covalent geometry    : angle       0.59452 ( 7085)
  SS BOND              : bond        0.00380 (    8)
  SS BOND              : angle       1.09703 (   16)
  hydrogen bonds       : bond        0.03555 (  149)
  hydrogen bonds       : angle       5.67496 (  420)
  link_NAG-ASN         : bond        0.00350 (    1)
  link_NAG-ASN         : angle       1.07843 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8700 (p) cc_final: 0.8448 (t)
REVERT: A  321 GLN cc_start: 0.8610 (mp-120) cc_final: 0.8122 (pm20)
REVERT: A  396 MET cc_start: 0.6698 (ppp) cc_final: 0.6351 (ppp)
REVERT: A  434 MET cc_start: 0.8146 (ttm) cc_final: 0.7680 (tpp)
REVERT: I    4 LEU cc_start: 0.8192 (mt) cc_final: 0.7958 (mt)
REVERT: I   13 GLU cc_start: 0.8214 (mp0) cc_final: 0.7953 (mp0)
REVERT: I   71 ARG cc_start: 0.8988 (ppt170) cc_final: 0.8462 (ptt90)
REVERT: I   80 MET cc_start: 0.9017 (ttt) cc_final: 0.8497 (ttp)
REVERT: J   79 GLN cc_start: 0.8129 (pp30) cc_final: 0.7734 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0577
  time to fit residues: 8.8213
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 20 optimal weight:    0.3980
   chunk 59 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0980
   chunk 51 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** I   6 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 = 0.3876 r_free = 0.3876 target = 0.143118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.118550 restraints weight = 12041.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.122138 restraints weight = 7722.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.124710 restraints weight = 5575.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.126550 restraints weight = 4368.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.127854 restraints weight = 3640.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5230  Z= 0.134
  Angle     :  0.582   5.744   7104  Z= 0.310
  Chirality :  0.042   0.136    789
  Planarity :  0.004   0.048    909
  Dihedral  :  6.101  59.477    725
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.23 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.33 (0.32), residues: 642
  helix:  0.24 (0.72), residues: 53
  sheet: -0.10 (0.37), residues: 191
  loop : -1.50 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG J  42 
 TYR   0.025   0.002   TYR J  87 
 PHE   0.015   0.001   PHE A 233 
 TRP   0.013   0.001   TRP I  50 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5221)
  covalent geometry    : angle       0.58016 ( 7085)
  SS BOND              : bond        0.00357 (    8)
  SS BOND              : angle       1.08733 (   16)
  hydrogen bonds       : bond        0.03570 (  149)
  hydrogen bonds       : angle       5.60468 (  420)
  link_NAG-ASN         : bond        0.00409 (    1)
  link_NAG-ASN         : angle       1.11039 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8710 (p) cc_final: 0.8445 (t)
REVERT: A  321 GLN cc_start: 0.8568 (mp-120) cc_final: 0.8260 (pm20)
REVERT: A  347 LYS cc_start: 0.8419 (pttt) cc_final: 0.8120 (tptp)
REVERT: A  426 MET cc_start: 0.6947 (tmm) cc_final: 0.6269 (tmm)
REVERT: A  434 MET cc_start: 0.8118 (ttm) cc_final: 0.7611 (tpp)
REVERT: I    3 HIS cc_start: 0.8058 (t-90) cc_final: 0.7685 (t-90)
REVERT: I    4 LEU cc_start: 0.8279 (mt) cc_final: 0.7889 (mt)
REVERT: I   71 ARG cc_start: 0.9003 (ppt170) cc_final: 0.8486 (ptt90)
REVERT: I   80 MET cc_start: 0.9016 (ttt) cc_final: 0.8440 (ttp)
REVERT: J   79 GLN cc_start: 0.8127 (pp30) cc_final: 0.7786 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0639
  time to fit residues: 9.6168
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 63 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** I   6 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 = 0.3850 r_free = 0.3850 target = 0.141665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.117902 restraints weight = 12061.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.121264 restraints weight = 7786.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.123799 restraints weight = 5671.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.125562 restraints weight = 4456.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.126772 restraints weight = 3721.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5230  Z= 0.146
  Angle     :  0.606   5.764   7104  Z= 0.321
  Chirality :  0.043   0.149    789
  Planarity :  0.004   0.051    909
  Dihedral  :  5.827  48.639    725
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.92 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.32), residues: 642
  helix:  0.20 (0.71), residues: 53
  sheet: -0.14 (0.38), residues: 196
  loop : -1.50 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J  42 
 TYR   0.011   0.002   TYR I  91 
 PHE   0.012   0.001   PHE A 233 
 TRP   0.013   0.001   TRP I  50 
 HIS   0.006   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5221)
  covalent geometry    : angle       0.60456 ( 7085)
  SS BOND              : bond        0.00417 (    8)
  SS BOND              : angle       1.13602 (   16)
  hydrogen bonds       : bond        0.03454 (  149)
  hydrogen bonds       : angle       5.62662 (  420)
  link_NAG-ASN         : bond        0.00528 (    1)
  link_NAG-ASN         : angle       0.98813 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8758 (p) cc_final: 0.8530 (t)
REVERT: A  104 MET cc_start: 0.8673 (tpp) cc_final: 0.7877 (tpt)
REVERT: A  116 LEU cc_start: 0.9598 (mm) cc_final: 0.9260 (mt)
REVERT: A  347 LYS cc_start: 0.8346 (pttt) cc_final: 0.8051 (tptp)
REVERT: A  396 MET cc_start: 0.6482 (ppp) cc_final: 0.6172 (ppp)
REVERT: A  426 MET cc_start: 0.6930 (tmm) cc_final: 0.6687 (tmm)
REVERT: A  434 MET cc_start: 0.8117 (ttm) cc_final: 0.7479 (tpp)
REVERT: I    3 HIS cc_start: 0.8124 (t-90) cc_final: 0.7759 (t-90)
REVERT: I    4 LEU cc_start: 0.8314 (mt) cc_final: 0.7931 (mt)
REVERT: I   71 ARG cc_start: 0.8983 (ppt170) cc_final: 0.8558 (ptt90)
REVERT: I   80 MET cc_start: 0.9035 (ttt) cc_final: 0.8539 (ttp)
REVERT: J   38 GLN cc_start: 0.8256 (tp40) cc_final: 0.7979 (tp-100)
REVERT: J   79 GLN cc_start: 0.8054 (pp30) cc_final: 0.7638 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0590
  time to fit residues: 8.8099
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 1 optimal weight:    8.9990
   chunk 29 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** I   6 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 = 0.3823 r_free = 0.3823 target = 0.139047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.113187 restraints weight = 12484.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.116761 restraints weight = 8023.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.119282 restraints weight = 5855.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.121041 restraints weight = 4654.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.122137 restraints weight = 3936.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5230  Z= 0.145
  Angle     :  0.597   5.892   7104  Z= 0.315
  Chirality :  0.042   0.142    789
  Planarity :  0.004   0.048    909
  Dihedral  :  5.548  35.674    725
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.07 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.32), residues: 642
  helix:  0.23 (0.71), residues: 54
  sheet: -0.19 (0.38), residues: 198
  loop : -1.53 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG J  24 
 TYR   0.011   0.001   TYR I  91 
 PHE   0.011   0.001   PHE A 233 
 TRP   0.017   0.001   TRP I  47 
 HIS   0.005   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5221)
  covalent geometry    : angle       0.59541 ( 7085)
  SS BOND              : bond        0.00396 (    8)
  SS BOND              : angle       1.13029 (   16)
  hydrogen bonds       : bond        0.03459 (  149)
  hydrogen bonds       : angle       5.49661 (  420)
  link_NAG-ASN         : bond        0.00554 (    1)
  link_NAG-ASN         : angle       0.93695 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8737 (p) cc_final: 0.8464 (t)
REVERT: A  116 LEU cc_start: 0.9606 (mm) cc_final: 0.9302 (mt)
REVERT: A  347 LYS cc_start: 0.8460 (pttt) cc_final: 0.8185 (tptp)
REVERT: A  396 MET cc_start: 0.6614 (ppp) cc_final: 0.6278 (ppp)
REVERT: A  426 MET cc_start: 0.6979 (tmm) cc_final: 0.6766 (tmm)
REVERT: A  434 MET cc_start: 0.8059 (ttm) cc_final: 0.7419 (tpp)
REVERT: I    3 HIS cc_start: 0.8092 (t-90) cc_final: 0.7647 (t-90)
REVERT: I    4 LEU cc_start: 0.8257 (mt) cc_final: 0.7900 (mt)
REVERT: I   71 ARG cc_start: 0.9025 (ppt170) cc_final: 0.8463 (ptt90)
REVERT: I   80 MET cc_start: 0.8978 (ttt) cc_final: 0.8354 (ttp)
REVERT: J   79 GLN cc_start: 0.8111 (pp30) cc_final: 0.7623 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0482
  time to fit residues: 7.2192
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0370
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** I   6 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 = 0.3833 r_free = 0.3833 target = 0.140754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.117074 restraints weight = 11975.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.120481 restraints weight = 7717.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.122889 restraints weight = 5597.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.124586 restraints weight = 4415.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.125716 restraints weight = 3707.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5230  Z= 0.137
  Angle     :  0.607   6.685   7104  Z= 0.318
  Chirality :  0.043   0.171    789
  Planarity :  0.004   0.047    909
  Dihedral  :  5.442  29.977    725
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.23 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.32), residues: 642
  helix:  0.37 (0.72), residues: 54
  sheet: -0.22 (0.38), residues: 198
  loop : -1.55 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J  24 
 TYR   0.019   0.002   TYR A 435 
 PHE   0.018   0.001   PHE J  62 
 TRP   0.012   0.001   TRP I  50 
 HIS   0.004   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5221)
  covalent geometry    : angle       0.60558 ( 7085)
  SS BOND              : bond        0.00397 (    8)
  SS BOND              : angle       1.11546 (   16)
  hydrogen bonds       : bond        0.03475 (  149)
  hydrogen bonds       : angle       5.48374 (  420)
  link_NAG-ASN         : bond        0.00532 (    1)
  link_NAG-ASN         : angle       0.93423 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8823 (p) cc_final: 0.8596 (t)
REVERT: A  116 LEU cc_start: 0.9606 (mm) cc_final: 0.9357 (mt)
REVERT: A  347 LYS cc_start: 0.8324 (pttt) cc_final: 0.8058 (tptp)
REVERT: A  396 MET cc_start: 0.6552 (ppp) cc_final: 0.6228 (ppp)
REVERT: A  426 MET cc_start: 0.7079 (tmm) cc_final: 0.6866 (tmm)
REVERT: A  435 TYR cc_start: 0.8272 (t80) cc_final: 0.8023 (t80)
REVERT: I    3 HIS cc_start: 0.8146 (t-90) cc_final: 0.7754 (t-90)
REVERT: I    4 LEU cc_start: 0.8356 (mt) cc_final: 0.8033 (mt)
REVERT: I   71 ARG cc_start: 0.9025 (ppt170) cc_final: 0.8568 (ptt90)
REVERT: I   80 MET cc_start: 0.9055 (ttt) cc_final: 0.8579 (ttp)
REVERT: J   79 GLN cc_start: 0.8076 (pp30) cc_final: 0.7312 (pp30)
REVERT: J   81 GLU cc_start: 0.9223 (pp20) cc_final: 0.7685 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0457
  time to fit residues: 6.7733
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   chunk 17 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0980
   chunk 18 optimal weight:    0.0970
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I   6 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 = 0.3862 r_free = 0.3862 target = 0.142643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.118668 restraints weight = 11644.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.122195 restraints weight = 7374.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.124670 restraints weight = 5290.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.126447 restraints weight = 4147.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.127490 restraints weight = 3436.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5230  Z= 0.107
  Angle     :  0.588   6.016   7104  Z= 0.305
  Chirality :  0.043   0.163    789
  Planarity :  0.004   0.047    909
  Dihedral  :  5.154  27.739    725
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.92 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.32), residues: 642
  helix:  0.50 (0.73), residues: 54
  sheet: -0.21 (0.38), residues: 196
  loop : -1.56 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I  71 
 TYR   0.016   0.001   TYR A 435 
 PHE   0.014   0.001   PHE J  62 
 TRP   0.010   0.001   TRP I  50 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5221)
  covalent geometry    : angle       0.58621 ( 7085)
  SS BOND              : bond        0.00356 (    8)
  SS BOND              : angle       1.03391 (   16)
  hydrogen bonds       : bond        0.03214 (  149)
  hydrogen bonds       : angle       5.41773 (  420)
  link_NAG-ASN         : bond        0.00448 (    1)
  link_NAG-ASN         : angle       0.93001 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8820 (p) cc_final: 0.8589 (t)
REVERT: A  116 LEU cc_start: 0.9624 (mm) cc_final: 0.9129 (mp)
REVERT: A  347 LYS cc_start: 0.8305 (pttt) cc_final: 0.8066 (tptp)
REVERT: A  396 MET cc_start: 0.6519 (ppp) cc_final: 0.6262 (ppp)
REVERT: A  434 MET cc_start: 0.7892 (tpp) cc_final: 0.7639 (tpp)
REVERT: I    4 LEU cc_start: 0.8328 (mt) cc_final: 0.8084 (mt)
REVERT: I   12 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8128 (mmmm)
REVERT: I   80 MET cc_start: 0.9094 (ttt) cc_final: 0.8646 (ttp)
REVERT: J   79 GLN cc_start: 0.8107 (pp30) cc_final: 0.7634 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0488
  time to fit residues: 7.0957
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0170
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** I   6 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 = 0.3828 r_free = 0.3828 target = 0.140599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.117144 restraints weight = 12127.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.120518 restraints weight = 7867.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.122841 restraints weight = 5725.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.124482 restraints weight = 4518.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.125517 restraints weight = 3785.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5230  Z= 0.143
  Angle     :  0.630   9.512   7104  Z= 0.327
  Chirality :  0.043   0.161    789
  Planarity :  0.005   0.073    909
  Dihedral  :  5.249  27.235    725
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.85 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.32), residues: 642
  helix:  0.39 (0.72), residues: 54
  sheet: -0.25 (0.37), residues: 196
  loop : -1.57 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG I  71 
 TYR   0.011   0.002   TYR A 352 
 PHE   0.027   0.002   PHE J  83 
 TRP   0.015   0.001   TRP I  50 
 HIS   0.006   0.001   HIS I  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5221)
  covalent geometry    : angle       0.62764 ( 7085)
  SS BOND              : bond        0.00360 (    8)
  SS BOND              : angle       1.27572 (   16)
  hydrogen bonds       : bond        0.03557 (  149)
  hydrogen bonds       : angle       5.36658 (  420)
  link_NAG-ASN         : bond        0.00544 (    1)
  link_NAG-ASN         : angle       0.86268 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8888 (p) cc_final: 0.8670 (t)
REVERT: A  116 LEU cc_start: 0.9620 (mm) cc_final: 0.9269 (mp)
REVERT: A  347 LYS cc_start: 0.8338 (pttt) cc_final: 0.8097 (tptp)
REVERT: A  396 MET cc_start: 0.6638 (ppp) cc_final: 0.6376 (ppp)
REVERT: I    3 HIS cc_start: 0.8124 (t-90) cc_final: 0.7761 (t-90)
REVERT: I    4 LEU cc_start: 0.8425 (mt) cc_final: 0.8052 (mt)
REVERT: I   80 MET cc_start: 0.9077 (ttt) cc_final: 0.8630 (ttp)
REVERT: J   38 GLN cc_start: 0.8230 (tp-100) cc_final: 0.8019 (tp-100)
REVERT: J   79 GLN cc_start: 0.7965 (pp30) cc_final: 0.7266 (pp30)
REVERT: J   83 PHE cc_start: 0.8138 (m-80) cc_final: 0.7820 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0498
  time to fit residues: 7.5933
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0770
   chunk 2 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** I   6 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 = 0.3842 r_free = 0.3842 target = 0.141053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.117903 restraints weight = 11801.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.121302 restraints weight = 7531.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.123692 restraints weight = 5407.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.125360 restraints weight = 4226.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.126538 restraints weight = 3513.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5230  Z= 0.134
  Angle     :  0.620   8.219   7104  Z= 0.321
  Chirality :  0.043   0.157    789
  Planarity :  0.004   0.072    909
  Dihedral  :  5.208  30.544    725
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.39 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.32), residues: 642
  helix:  0.35 (0.72), residues: 54
  sheet: -0.25 (0.38), residues: 196
  loop : -1.53 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG I  71 
 TYR   0.012   0.002   TYR I  54 
 PHE   0.033   0.002   PHE J  83 
 TRP   0.012   0.001   TRP I  50 
 HIS   0.004   0.001   HIS I  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5221)
  covalent geometry    : angle       0.61820 ( 7085)
  SS BOND              : bond        0.00375 (    8)
  SS BOND              : angle       1.09574 (   16)
  hydrogen bonds       : bond        0.03413 (  149)
  hydrogen bonds       : angle       5.36990 (  420)
  link_NAG-ASN         : bond        0.00520 (    1)
  link_NAG-ASN         : angle       0.86849 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 880.77 seconds
wall clock time: 15 minutes 55.96 seconds (955.96 seconds total)