Starting phenix.real_space_refine
on Sat May 10 10:33:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bvq_44941/05_2025/9bvq_44941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bvq_44941/05_2025/9bvq_44941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bvq_44941/05_2025/9bvq_44941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bvq_44941/05_2025/9bvq_44941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bvq_44941/05_2025/9bvq_44941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bvq_44941/05_2025/9bvq_44941.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      25      5.16       5
     C    3906      2.51       5
     N     977      2.21       5
     O    1067      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5977
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5490
          Classifications: {'peptide': 665}
          Link IDs: {'PTRANS': 35, 'TRANS': 629}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 293
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 2, 'TRANS': 32}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 110
          Unusual residues: {'6PL': 2, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   6PL A 801 " occ=0.60
      ... (44 atoms not shown)
      pdb=" P   6PL A 801 " occ=0.60
    residue:
      pdb=" N   6PL A 802 " occ=0.60
      ... (48 atoms not shown)
      pdb=" P   6PL A 802 " occ=0.60
  Time building chain proxies: 4.44, per 1000 atoms: 0.74
  Number of scatterers: 5977
  At special positions: 0
  Unit cell: (86.7626, 85.8773, 108.896, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     P       2     15.00
     O    1067      8.00
     N     977      7.00
     C    3906      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 450 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM 5851  O5  NAG D   1 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 803 " - " ASN A 459 "
      " NAG B   1 " - " ASN A 570 "
      " NAG C   1 " - " ASN A 550 "
      " NAG D   1 " - " ASN A 605 "
  Time building additional restraints: 1.45
  Conformation dependent library (CDL) restraints added in 856.3 milliseconds
  

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 3 sheets defined
      55.3% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 39
    Processing helix  chain 'A' and resid 41 through 46
    Processing helix  chain 'A' and resid 47 through 55
    Processing helix  chain 'A' and resid 61 through 79
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.537A  pdb=" N   LYS A  91 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 132
    Processing helix  chain 'A' and resid 134 through 153
      Proline residue:  A 145  - end of helix
      removed outlier: 3.747A  pdb=" N   ASP A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 157
      removed outlier: 3.777A  pdb=" N   TRP A 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 154 through 157'
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 4.209A  pdb=" N   PHE A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET A 174 " --> pdb=" O   GLN A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 3.509A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 218
      removed outlier: 3.776A  pdb=" N   LEU A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 244
      removed outlier: 3.863A  pdb=" N   LEU A 232 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   SER A 233 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A 234 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS A 235 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   TRP A 236 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   LEU A 237 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      Proline residue:  A 240  - end of helix
    Processing helix  chain 'A' and resid 246 through 254
    Processing helix  chain 'A' and resid 256 through 270
      removed outlier: 4.024A  pdb=" N   LEU A 270 " --> pdb=" O   ALA A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 294
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 308 through 311
    Processing helix  chain 'A' and resid 314 through 321
      removed outlier: 3.823A  pdb=" N   LYS A 318 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 319 " --> pdb=" O   TRP A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 377
      removed outlier: 3.539A  pdb=" N   ALA A 364 " --> pdb=" O   HIS A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 380
      No H-bonds generated for 'chain 'A' and resid 378 through 380'
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.700A  pdb=" N   TYR A 387 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 455
    Processing helix  chain 'A' and resid 456 through 459
      removed outlier: 3.596A  pdb=" N   ASN A 459 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 456 through 459'
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 4.111A  pdb=" N   LYS A 515 " --> pdb=" O   PRO A 511 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLN A 517 " --> pdb=" O   ARG A 513 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 627
    Processing helix  chain 'A' and resid 638 through 644
    Processing helix  chain 'A' and resid 653 through 674
    Processing helix  chain 'A' and resid 676 through 709
      removed outlier: 3.598A  pdb=" N   ARG A 680 " --> pdb=" O   PRO A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 724
    Processing helix  chain 'P' and resid 33 through 38
      removed outlier: 3.725A  pdb=" N   GLN P  38 " --> pdb=" O   PRO P  34 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 479 through 480
      removed outlier: 3.661A  pdb=" N   GLN A 479 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   HIS A 410 " --> pdb=" O   TRP A 470 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   SER A 472 " --> pdb=" O   HIS A 408 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   HIS A 408 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   ILE A 413 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   TYR A 425 " --> pdb=" O   LEU P  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 534
      removed outlier: 6.573A  pdb=" N   CYS A 598 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   THR A 551 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 543
      removed outlier: 3.614A  pdb=" N   VAL A 560 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    816 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: 1.56

  Time building geometry restraints manager: 1.71 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1008
        1.33 -     1.45: 1734
        1.45 -     1.57: 3357
        1.57 -     1.69: 4
        1.69 -     1.81: 42
  Bond restraints: 6145
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.77e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.41e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.35e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.35e+00
  ... (remaining 6140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 8109
        1.21 -     2.42: 167
        2.42 -     3.63: 45
        3.63 -     4.84: 5
        4.84 -     6.04: 4
  Bond angle restraints: 8330
  Sorted by residual:
  angle pdb=" N   VAL P  30 "
        pdb=" CA  VAL P  30 "
        pdb=" C   VAL P  30 "
      ideal   model   delta    sigma   weight residual
     112.96  110.14    2.82 1.00e+00 1.00e+00 7.97e+00
  angle pdb=" N   PRO P  34 "
        pdb=" CA  PRO P  34 "
        pdb=" C   PRO P  34 "
      ideal   model   delta    sigma   weight residual
     110.70  113.08   -2.38 1.22e+00 6.72e-01 3.80e+00
  angle pdb=" CA  PRO P  34 "
        pdb=" C   PRO P  34 "
        pdb=" N   PRO P  35 "
      ideal   model   delta    sigma   weight residual
     117.93  120.18   -2.25 1.20e+00 6.94e-01 3.51e+00
  angle pdb=" CA  VAL P  30 "
        pdb=" C   VAL P  30 "
        pdb=" O   VAL P  30 "
      ideal   model   delta    sigma   weight residual
     119.29  120.74   -1.45 8.40e-01 1.42e+00 2.99e+00
  angle pdb=" N   PHE A 268 "
        pdb=" CA  PHE A 268 "
        pdb=" C   PHE A 268 "
      ideal   model   delta    sigma   weight residual
     112.90  115.13   -2.23 1.31e+00 5.83e-01 2.89e+00
  ... (remaining 8325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.96: 3573
       24.96 -    49.92: 96
       49.92 -    74.88: 27
       74.88 -    99.85: 8
       99.85 -   124.81: 17
  Dihedral angle restraints: 3721
    sinusoidal: 1670
      harmonic: 2051
  Sorted by residual:
  dihedral pdb=" C2  NAG C   1 "
           pdb=" C1  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C5  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   61.85 -124.81     1      3.00e+01 1.11e-03 1.68e+01
  dihedral pdb=" C1  NAG C   1 "
           pdb=" C5  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C6  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -68.78 -120.06     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" C1  NAG C   1 "
           pdb=" C5  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C4  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   55.88 -119.99     1      3.00e+01 1.11e-03 1.60e+01
  ... (remaining 3718 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.332: 898
       0.332 -    0.664: 2
       0.664 -    0.996: 3
       0.996 -    1.329: 0
       1.329 -    1.661: 2
  Chirality restraints: 905
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.02   -1.38 2.00e-02 2.50e+03 4.73e+03
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.48   -0.92 2.00e-02 2.50e+03 2.13e+03
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.70   -0.70 2.00e-02 2.50e+03 1.21e+03
  ... (remaining 902 not shown)

  Planarity restraints: 1038
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 570 "    0.003 2.00e-02 2.50e+03   5.51e-02 3.79e+01
        pdb=" CG  ASN A 570 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 570 "   -0.050 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 570 "    0.094 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "   -0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 550 "   -0.046 2.00e-02 2.50e+03   5.28e-02 3.49e+01
        pdb=" CG  ASN A 550 "    0.021 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 550 "    0.015 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 550 "    0.080 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.069 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 459 "   -0.008 2.00e-02 2.50e+03   1.90e-02 4.51e+00
        pdb=" CG  ASN A 459 "    0.005 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 459 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 459 "    0.034 2.00e-02 2.50e+03
        pdb=" C1  NAG A 803 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1035 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 460
        2.74 -     3.28: 5532
        3.28 -     3.82: 9313
        3.82 -     4.36: 10638
        4.36 -     4.90: 19258
  Nonbonded interactions: 45201
  Sorted by model distance:
  nonbonded pdb=" O   ASP A  60 "
            pdb=" OH  TYR A 200 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   SER A 228 "
            pdb=" NE2 HIS A 256 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OD2 ASP A 153 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" NH1 ARG A 704 "
            pdb=" OE2 GLU A 719 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" OD1 ASP A 417 "
            pdb=" OG1 THR A 461 "
     model   vdw
     2.351 3.040
  ... (remaining 45196 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.60 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:                  0.010
  Normalize map: mean=0, sd=1:             2.130
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.320
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
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      :  0.004   0.200   6153  Z= 0.210
  Angle     :  1.392  55.479   8353  Z= 0.496
  Chirality :  0.096   1.661    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 15.642 124.808   2398
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  4.59 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.33), residues: 692
  helix:  1.34 (0.28), residues: 348
  sheet:  1.62 (0.58), residues: 73
  loop : -0.65 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 406 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.11272 (    4)
  link_NAG-ASN         : angle      24.34865 (   12)
  link_BETA1-4         : bond        0.06797 (    3)
  link_BETA1-4         : angle      28.34613 (    9)
  hydrogen bonds       : bond        0.13855 (  286)
  hydrogen bonds       : angle       5.67442 (  816)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.42604 (    2)
  covalent geometry    : bond        0.00273 ( 6145)
  covalent geometry    : angle       0.47055 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8528 (mt) cc_final: 0.8313 (mp)
REVERT: A  115 MET cc_start: 0.8407 (mmt) cc_final: 0.7898 (mmt)
REVERT: A  180 TRP cc_start: 0.7480 (t60) cc_final: 0.7112 (t-100)
REVERT: A  680 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.6993 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6959 (p90)
  outliers start: 10
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2879
  time to fit residues: 39.7295
Evaluate side-chains
  59 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0570
   chunk 27 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0010
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5304

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

Flipped N/Q/H residues before XYZ refinement:
P  38 GLN
P  44 HIS
P  97 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.133375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.096110 restraints weight = 9210.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.69
r_work: 0.3007 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6153  Z= 0.125
  Angle     :  0.660  11.560   8353  Z= 0.291
  Chirality :  0.042   0.290    905
  Planarity :  0.005   0.049   1034
  Dihedral  : 14.584  78.579   1011
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  6.96 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.34), residues: 692
  helix:  1.82 (0.29), residues: 355
  sheet:  1.73 (0.58), residues: 73
  loop : -0.37 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 315 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 285 
 ARG   0.006   0.001   ARG A 671 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00761 (    4)
  link_NAG-ASN         : angle       6.34367 (   12)
  link_BETA1-4         : bond        0.00920 (    3)
  link_BETA1-4         : angle       2.23908 (    9)
  hydrogen bonds       : bond        0.04197 (  286)
  hydrogen bonds       : angle       4.17340 (  816)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.23361 (    2)
  covalent geometry    : bond        0.00278 ( 6145)
  covalent geometry    : angle       0.61135 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.8594 (mmp) cc_final: 0.8392 (mmp)
REVERT: A  180 TRP cc_start: 0.7843 (t60) cc_final: 0.7262 (t-100)
REVERT: A  663 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8511 (tp-100)
REVERT: A  680 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.6851 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6690 (p90)
  outliers start: 6
  outliers final: 1
  residues processed: 65
  average time/residue: 0.2639
  time to fit residues: 21.7528
Evaluate side-chains
  57 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 58 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.087148 restraints weight = 9201.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.83
r_work: 0.2863 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6153  Z= 0.158
  Angle     :  0.594   7.888   8353  Z= 0.275
  Chirality :  0.042   0.251    905
  Planarity :  0.005   0.051   1034
  Dihedral  : 12.397  75.336   1011
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.91 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.34), residues: 692
  helix:  1.99 (0.29), residues: 355
  sheet:  1.82 (0.59), residues: 73
  loop : -0.34 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 315 
 HIS   0.007   0.001   HIS P  44 
 PHE   0.008   0.001   PHE A 684 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.007   0.000   ARG A 671 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00332 (    4)
  link_NAG-ASN         : angle       4.35170 (   12)
  link_BETA1-4         : bond        0.00424 (    3)
  link_BETA1-4         : angle       1.95312 (    9)
  hydrogen bonds       : bond        0.04337 (  286)
  hydrogen bonds       : angle       3.98029 (  816)
  SS BOND              : bond        0.00077 (    1)
  SS BOND              : angle       0.19974 (    2)
  covalent geometry    : bond        0.00371 ( 6145)
  covalent geometry    : angle       0.56787 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LYS cc_start: 0.9068 (tppt) cc_final: 0.8821 (tppt)
REVERT: A  180 TRP cc_start: 0.7849 (t60) cc_final: 0.7178 (t-100)
REVERT: A  183 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8270 (m-30)
REVERT: A  417 ASP cc_start: 0.8213 (t0) cc_final: 0.7838 (t0)
REVERT: A  619 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8596 (tm-30)
REVERT: A  663 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8534 (tp-100)
REVERT: A  680 ARG cc_start: 0.7747 (mtp-110) cc_final: 0.6879 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6629 (p90)
  outliers start: 8
  outliers final: 1
  residues processed: 63
  average time/residue: 0.2271
  time to fit residues: 18.7203
Evaluate side-chains
  56 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0570
   chunk 16 optimal weight:    0.0970
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.4096

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.093427 restraints weight = 9438.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.74
r_work: 0.2967 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6153  Z= 0.105
  Angle     :  0.579  10.729   8353  Z= 0.259
  Chirality :  0.042   0.279    905
  Planarity :  0.004   0.051   1034
  Dihedral  : 11.099  65.200   1011
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.75 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.34), residues: 692
  helix:  2.21 (0.29), residues: 355
  sheet:  1.79 (0.59), residues: 73
  loop : -0.28 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.005   0.001   HIS P  44 
 PHE   0.008   0.001   PHE P  90 
 TYR   0.012   0.001   TYR A 285 
 ARG   0.007   0.000   ARG A 671 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00413 (    4)
  link_NAG-ASN         : angle       4.43488 (   12)
  link_BETA1-4         : bond        0.00502 (    3)
  link_BETA1-4         : angle       1.69984 (    9)
  hydrogen bonds       : bond        0.03722 (  286)
  hydrogen bonds       : angle       3.80332 (  816)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.10580 (    2)
  covalent geometry    : bond        0.00227 ( 6145)
  covalent geometry    : angle       0.55252 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 TRP cc_start: 0.7811 (t60) cc_final: 0.7162 (t-100)
REVERT: A  183 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8264 (m-30)
REVERT: A  229 MET cc_start: 0.8825 (mtt) cc_final: 0.8438 (mtt)
REVERT: A  619 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8511 (tm-30)
REVERT: A  663 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8516 (tp-100)
REVERT: A  680 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.6857 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6644 (p90)
  outliers start: 8
  outliers final: 3
  residues processed: 66
  average time/residue: 0.2281
  time to fit residues: 19.8239
Evaluate side-chains
  60 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0020
   chunk 39 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.9392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.123590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.085470 restraints weight = 9405.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.83
r_work: 0.2847 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2846 r_free = 0.2846    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2846
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6153  Z= 0.158
  Angle     :  0.600  10.444   8353  Z= 0.274
  Chirality :  0.043   0.324    905
  Planarity :  0.004   0.052   1034
  Dihedral  : 11.528  96.758   1011
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.70 %
    Favored  : 90.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.34), residues: 692
  helix:  2.23 (0.29), residues: 355
  sheet:  1.94 (0.59), residues: 71
  loop : -0.23 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 198 
 HIS   0.005   0.001   HIS P  44 
 PHE   0.010   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.004   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01426 (    4)
  link_NAG-ASN         : angle       4.92990 (   12)
  link_BETA1-4         : bond        0.00382 (    3)
  link_BETA1-4         : angle       1.59429 (    9)
  hydrogen bonds       : bond        0.04187 (  286)
  hydrogen bonds       : angle       3.81402 (  816)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.14673 (    2)
  covalent geometry    : bond        0.00371 ( 6145)
  covalent geometry    : angle       0.56902 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8361 (m-30)
REVERT: A  236 TRP cc_start: 0.8680 (p-90) cc_final: 0.8469 (p-90)
REVERT: A  285 TYR cc_start: 0.8310 (t80) cc_final: 0.8022 (t80)
REVERT: A  417 ASP cc_start: 0.8254 (t0) cc_final: 0.7879 (t0)
REVERT: A  520 LYS cc_start: 0.8532 (tppp) cc_final: 0.8308 (tttm)
REVERT: A  619 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8482 (tm-30)
REVERT: A  663 GLN cc_start: 0.8923 (tp-100) cc_final: 0.8543 (tp-100)
REVERT: A  671 ARG cc_start: 0.9430 (tmm-80) cc_final: 0.8985 (ttp80)
REVERT: A  680 ARG cc_start: 0.7754 (mtp-110) cc_final: 0.6885 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7168 (OUTLIER) cc_final: 0.6592 (p90)
  outliers start: 8
  outliers final: 4
  residues processed: 65
  average time/residue: 0.2154
  time to fit residues: 18.5115
Evaluate side-chains
  64 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0980
   chunk 68 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.124163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.086149 restraints weight = 9252.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.83
r_work: 0.2855 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6153  Z= 0.124
  Angle     :  0.554   9.714   8353  Z= 0.254
  Chirality :  0.040   0.233    905
  Planarity :  0.004   0.048   1034
  Dihedral  : 10.763  96.130   1011
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.49 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.34), residues: 692
  helix:  2.35 (0.29), residues: 355
  sheet:  1.90 (0.59), residues: 71
  loop : -0.26 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00450 (    4)
  link_NAG-ASN         : angle       4.21827 (   12)
  link_BETA1-4         : bond        0.00346 (    3)
  link_BETA1-4         : angle       1.46870 (    9)
  hydrogen bonds       : bond        0.03872 (  286)
  hydrogen bonds       : angle       3.73949 (  816)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       0.12324 (    2)
  covalent geometry    : bond        0.00286 ( 6145)
  covalent geometry    : angle       0.52923 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8269 (t0)
REVERT: A  183 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8375 (m-30)
REVERT: A  236 TRP cc_start: 0.8671 (p-90) cc_final: 0.8467 (p-90)
REVERT: A  285 TYR cc_start: 0.8309 (t80) cc_final: 0.8007 (t80)
REVERT: A  417 ASP cc_start: 0.8297 (t0) cc_final: 0.7891 (t0)
REVERT: A  520 LYS cc_start: 0.8517 (tppp) cc_final: 0.8308 (tttm)
REVERT: A  619 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: A  663 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8537 (tp-100)
REVERT: A  680 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.6895 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6650 (p90)
  outliers start: 7
  outliers final: 3
  residues processed: 65
  average time/residue: 0.2241
  time to fit residues: 19.2173
Evaluate side-chains
  63 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 36 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    0.3980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.123400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.085501 restraints weight = 9366.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 2.83
r_work: 0.2857 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6153  Z= 0.120
  Angle     :  0.548  10.550   8353  Z= 0.252
  Chirality :  0.040   0.205    905
  Planarity :  0.004   0.048   1034
  Dihedral  : 10.805 107.882   1011
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.81 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.34), residues: 692
  helix:  2.56 (0.29), residues: 348
  sheet:  1.90 (0.59), residues: 71
  loop : -0.09 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.017   0.001   TYR A 458 
 ARG   0.003   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01067 (    4)
  link_NAG-ASN         : angle       4.80110 (   12)
  link_BETA1-4         : bond        0.00363 (    3)
  link_BETA1-4         : angle       1.40537 (    9)
  hydrogen bonds       : bond        0.03748 (  286)
  hydrogen bonds       : angle       3.69712 (  816)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.07892 (    2)
  covalent geometry    : bond        0.00271 ( 6145)
  covalent geometry    : angle       0.51551 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8304 (t0)
REVERT: A  183 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8374 (m-30)
REVERT: A  285 TYR cc_start: 0.8317 (t80) cc_final: 0.7826 (t80)
REVERT: A  619 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8480 (tm-30)
REVERT: A  663 GLN cc_start: 0.8903 (tp-100) cc_final: 0.7761 (tp-100)
REVERT: A  667 GLN cc_start: 0.9584 (mt0) cc_final: 0.9134 (mt0)
REVERT: A  680 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.6915 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8207 (tp40) cc_final: 0.8001 (tp40)
REVERT: P   94 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6663 (p90)
  outliers start: 8
  outliers final: 3
  residues processed: 67
  average time/residue: 0.2328
  time to fit residues: 20.0868
Evaluate side-chains
  67 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 58 optimal weight:    0.2980
   chunk 1 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0170
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.124759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.086706 restraints weight = 9359.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.87
r_work: 0.2861 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6153  Z= 0.109
  Angle     :  0.534   9.131   8353  Z= 0.249
  Chirality :  0.039   0.157    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 10.351 106.362   1011
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.81 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.34), residues: 692
  helix:  2.62 (0.29), residues: 348
  sheet:  1.96 (0.59), residues: 70
  loop :  0.00 (0.42), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.006   0.001   PHE A 684 
 TYR   0.021   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00558 (    4)
  link_NAG-ASN         : angle       4.04962 (   12)
  link_BETA1-4         : bond        0.00403 (    3)
  link_BETA1-4         : angle       1.38773 (    9)
  hydrogen bonds       : bond        0.03685 (  286)
  hydrogen bonds       : angle       3.66914 (  816)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.04213 (    2)
  covalent geometry    : bond        0.00245 ( 6145)
  covalent geometry    : angle       0.50992 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8300 (t0)
REVERT: A  183 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8387 (m-30)
REVERT: A  417 ASP cc_start: 0.8256 (t0) cc_final: 0.7821 (t0)
REVERT: A  619 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8477 (tm-30)
REVERT: A  663 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8543 (tp-100)
REVERT: A  680 ARG cc_start: 0.7789 (mtp-110) cc_final: 0.6916 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8171 (tp40) cc_final: 0.7960 (tp40)
REVERT: P   94 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6666 (p90)
  outliers start: 7
  outliers final: 4
  residues processed: 65
  average time/residue: 0.2326
  time to fit residues: 19.4471
Evaluate side-chains
  67 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0770
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 68 optimal weight:    0.1980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.4338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.124485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.086655 restraints weight = 9350.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 2.84
r_work: 0.2875 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6153  Z= 0.105
  Angle     :  0.553   9.203   8353  Z= 0.256
  Chirality :  0.039   0.166    905
  Planarity :  0.004   0.045   1034
  Dihedral  : 10.419 108.723   1011
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.60 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.34), residues: 692
  helix:  2.63 (0.29), residues: 349
  sheet:  2.02 (0.59), residues: 70
  loop : -0.07 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.006   0.001   PHE A 684 
 TYR   0.026   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00897 (    4)
  link_NAG-ASN         : angle       4.65181 (   12)
  link_BETA1-4         : bond        0.00450 (    3)
  link_BETA1-4         : angle       1.41150 (    9)
  hydrogen bonds       : bond        0.03550 (  286)
  hydrogen bonds       : angle       3.61907 (  816)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.03790 (    2)
  covalent geometry    : bond        0.00233 ( 6145)
  covalent geometry    : angle       0.52272 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8284 (t0)
REVERT: A  183 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8378 (m-30)
REVERT: A  619 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8509 (tm-30)
REVERT: A  663 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8382 (tp-100)
REVERT: A  667 GLN cc_start: 0.9585 (mt0) cc_final: 0.9380 (mt0)
REVERT: A  680 ARG cc_start: 0.7798 (mtp-110) cc_final: 0.6923 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8203 (tp40) cc_final: 0.7992 (tp40)
REVERT: P   94 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6669 (p90)
  outliers start: 6
  outliers final: 3
  residues processed: 65
  average time/residue: 0.2240
  time to fit residues: 18.7663
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0770
   chunk 66 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.5738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.124042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.086114 restraints weight = 9324.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.85
r_work: 0.2867 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2872
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2872 r_free = 0.2872    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2872 r_free = 0.2872    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2872
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6153  Z= 0.114
  Angle     :  0.538   8.549   8353  Z= 0.251
  Chirality :  0.039   0.153    905
  Planarity :  0.004   0.043   1034
  Dihedral  : 10.335 110.550   1011
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.60 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.34), residues: 692
  helix:  2.60 (0.29), residues: 349
  sheet:  1.99 (0.58), residues: 71
  loop : -0.06 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.006   0.001   PHE A 684 
 TYR   0.026   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00334 (    4)
  link_NAG-ASN         : angle       3.76016 (   12)
  link_BETA1-4         : bond        0.00360 (    3)
  link_BETA1-4         : angle       1.39982 (    9)
  hydrogen bonds       : bond        0.03628 (  286)
  hydrogen bonds       : angle       3.63180 (  816)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.02261 (    2)
  covalent geometry    : bond        0.00262 ( 6145)
  covalent geometry    : angle       0.51772 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8295 (t0)
REVERT: A  183 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8377 (m-30)
REVERT: A  459 ASN cc_start: 0.7583 (t0) cc_final: 0.7290 (t0)
REVERT: A  619 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8526 (tm-30)
REVERT: A  663 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8381 (tp-100)
REVERT: A  667 GLN cc_start: 0.9578 (mt0) cc_final: 0.9370 (mt0)
REVERT: A  680 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.6928 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8203 (tp40) cc_final: 0.7994 (tp40)
REVERT: P   94 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6642 (p90)
  outliers start: 6
  outliers final: 3
  residues processed: 65
  average time/residue: 0.2267
  time to fit residues: 18.8705
Evaluate side-chains
  67 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.122141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.084143 restraints weight = 9441.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 2.85
r_work: 0.2835 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6153  Z= 0.148
  Angle     :  0.563   9.652   8353  Z= 0.263
  Chirality :  0.040   0.158    905
  Planarity :  0.004   0.045   1034
  Dihedral  : 10.376 111.994   1011
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.60 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.34), residues: 692
  helix:  2.52 (0.29), residues: 349
  sheet:  1.73 (0.58), residues: 73
  loop : -0.06 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.009   0.001   PHE A 286 
 TYR   0.024   0.001   TYR A 285 
 ARG   0.002   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    4)
  link_NAG-ASN         : angle       3.64296 (   12)
  link_BETA1-4         : bond        0.00340 (    3)
  link_BETA1-4         : angle       1.38442 (    9)
  hydrogen bonds       : bond        0.04125 (  286)
  hydrogen bonds       : angle       3.71880 (  816)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.06704 (    2)
  covalent geometry    : bond        0.00351 ( 6145)
  covalent geometry    : angle       0.54482 ( 8330)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3009.47 seconds
wall clock time: 52 minutes 51.62 seconds (3171.62 seconds total)