Starting phenix.real_space_refine
on Thu Jul 24 07:20:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mjs_23883/07_2025/7mjs_23883.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mjs_23883/07_2025/7mjs_23883.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2025/7mjs_23883.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2025/7mjs_23883.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2025/7mjs_23883.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2025/7mjs_23883.cif"
  }
  resolution = 3.03
  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=   0.022
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       1      5.49       5
     S      26      5.16       5
     C    3618      2.51       5
     N     878      2.21       5
     O    1013      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5536
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1018
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 2, 'TRANS': 129}
    Chain: "L"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 863
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 6, 'TRANS': 106}
    Chain: "X"
      Number of atoms: 3592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3592
          Classifications: {'peptide': 458}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 438}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "X"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 63
          Unusual residues: {'NAG': 2, 'ZGS': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.69, per 1000 atoms: 0.85
  Number of scatterers: 5536
  At special positions: 0
  Unit cell: (69.72, 69.72, 131.14, 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      26     16.00
     P       1     15.00
     O    1013      8.00
     N     878      7.00
     C    3618      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X 207 " - pdb=" SG  CYS X 460 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG X 602 " - " ASN X 227 "
      " NAG X 603 " - " ASN X 218 "
  Time building additional restraints: 1.37
  Conformation dependent library (CDL) restraints added in 797.3 milliseconds
  

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1300

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 6 sheets defined
      54.8% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'X' and resid 37 through 42
      removed outlier: 3.526A  pdb=" N   LEU X  42 " --> pdb=" O   VAL X  38 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 42 through 47
      removed outlier: 3.594A  pdb=" N   VAL X  46 " --> pdb=" O   LEU X  42 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLY X  47 " --> pdb=" O   CYS X  43 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'X' and resid 42 through 47'
    Processing helix  chain 'X' and resid 47 through 69
      removed outlier: 4.666A  pdb=" N   TYR X  51 " --> pdb=" O   GLY X  47 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLN X  52 " --> pdb=" O   GLY X  48 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   GLN X  63 " --> pdb=" O   GLY X  59 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   ILE X  64 " --> pdb=" O   PHE X  60 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 73 through 99
      removed outlier: 3.630A  pdb=" N   ASP X  92 " --> pdb=" O   ASP X  88 " (cutoff:3.500A)
      Proline residue:  X  93  - end of helix
    Processing helix  chain 'X' and resid 110 through 127
      removed outlier: 3.884A  pdb=" N   ILE X 114 " --> pdb=" O   LEU X 110 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR X 118 " --> pdb=" O   ILE X 114 " (cutoff:3.500A)
      Proline residue:  X 119  - end of helix
    Processing helix  chain 'X' and resid 137 through 162
      removed outlier: 3.534A  pdb=" N   TRP X 141 " --> pdb=" O   GLY X 137 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TYR X 142 " --> pdb=" O   GLN X 138 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE X 145 " --> pdb=" O   TRP X 141 " (cutoff:3.500A)
      Proline residue:  X 159  - end of helix
    Processing helix  chain 'X' and resid 163 through 168
      removed outlier: 4.385A  pdb=" N   SER X 168 " --> pdb=" O   THR X 164 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 170 through 202
      removed outlier: 3.599A  pdb=" N   VAL X 200 " --> pdb=" O   GLN X 196 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS X 202 " --> pdb=" O   GLN X 198 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 218 through 223
      removed outlier: 4.088A  pdb=" N   ALA X 222 " --> pdb=" O   ASN X 218 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 228 through 264
    Processing helix  chain 'X' and resid 281 through 289
      removed outlier: 3.673A  pdb=" N   MET X 289 " --> pdb=" O   LEU X 285 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 291 through 322
      removed outlier: 4.163A  pdb=" N   THR X 320 " --> pdb=" O   ALA X 316 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 328 through 354
      Proline residue:  X 345  - end of helix
    Processing helix  chain 'X' and resid 355 through 366
      removed outlier: 3.973A  pdb=" N   TYR X 361 " --> pdb=" O   LYS X 357 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 366 through 377
      removed outlier: 4.321A  pdb=" N   PHE X 370 " --> pdb=" O   SER X 366 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   VAL X 375 " --> pdb=" O   LEU X 371 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 380 through 417
      removed outlier: 3.620A  pdb=" N   TYR X 385 " --> pdb=" O   LEU X 381 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE X 386 " --> pdb=" O   VAL X 382 " (cutoff:3.500A)
      Proline residue:  X 402  - end of helix
      Proline residue:  X 407  - end of helix
    Processing helix  chain 'X' and resid 425 through 453
      removed outlier: 3.628A  pdb=" N   THR X 438 " --> pdb=" O   PHE X 434 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 463 through 473
    Processing helix  chain 'X' and resid 475 through 489
    Processing helix  chain 'X' and resid 490 through 492
      No H-bonds generated for 'chain 'X' and resid 490 through 492'
    Processing helix  chain 'X' and resid 497 through 505
      removed outlier: 4.238A  pdb=" N   GLU X 501 " --> pdb=" O   GLU X 497 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15
      removed outlier: 3.621A  pdb=" N   SER H 102 " --> pdb=" O   SER H  36 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ILE H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   TYR H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR H  60 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15
      removed outlier: 6.781A  pdb=" N   CYS H  99 " --> pdb=" O   TRP H 122 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   TRP H 122 " --> pdb=" O   CYS H  99 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ARG H 101 " --> pdb=" O   ASP H 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.368A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 108 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55
      removed outlier: 5.739A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    969 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: 1.79

  Time building geometry restraints manager: 1.60 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 836
        1.31 -     1.44: 1687
        1.44 -     1.56: 3112
        1.56 -     1.69: 3
        1.69 -     1.82: 39
  Bond restraints: 5677
  Sorted by residual:
  bond pdb=" C18 ZGS X 601 "
       pdb=" O20 ZGS X 601 "
    ideal  model  delta    sigma   weight residual
    1.345  1.416 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" N   VAL X 226 "
       pdb=" CA  VAL X 226 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.042 1.19e-02 7.06e+03 1.22e+01
  bond pdb=" C32 ZGS X 601 "
       pdb=" N31 ZGS X 601 "
    ideal  model  delta    sigma   weight residual
    1.500  1.441  0.059 2.00e-02 2.50e+03 8.73e+00
  bond pdb=" N   ASN X 227 "
       pdb=" CA  ASN X 227 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.22e-02 6.72e+03 7.72e+00
  bond pdb=" N   THR X 217 "
       pdb=" CA  THR X 217 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.036 1.32e-02 5.74e+03 7.24e+00
  ... (remaining 5672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 7623
        2.57 -     5.14: 79
        5.14 -     7.71: 15
        7.71 -    10.28: 2
       10.28 -    12.85: 1
  Bond angle restraints: 7720
  Sorted by residual:
  angle pdb=" N   CYS X 460 "
        pdb=" CA  CYS X 460 "
        pdb=" C   CYS X 460 "
      ideal   model   delta    sigma   weight residual
     114.31  108.51    5.80 1.29e+00 6.01e-01 2.02e+01
  angle pdb=" O26 ZGS X 601 "
        pdb=" P25 ZGS X 601 "
        pdb=" O27 ZGS X 601 "
      ideal   model   delta    sigma   weight residual
     121.97  109.12   12.85 3.00e+00 1.11e-01 1.83e+01
  angle pdb=" N   PHE X 219 "
        pdb=" CA  PHE X 219 "
        pdb=" C   PHE X 219 "
      ideal   model   delta    sigma   weight residual
     113.23  108.29    4.94 1.24e+00 6.50e-01 1.59e+01
  angle pdb=" C   THR X 217 "
        pdb=" CA  THR X 217 "
        pdb=" CB  THR X 217 "
      ideal   model   delta    sigma   weight residual
     111.06  117.68   -6.62 1.89e+00 2.80e-01 1.23e+01
  angle pdb=" C   VAL H  15 "
        pdb=" N   GLN H  16 "
        pdb=" CA  GLN H  16 "
      ideal   model   delta    sigma   weight residual
     120.97  111.17    9.80 2.84e+00 1.24e-01 1.19e+01
  ... (remaining 7715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 3001
       17.64 -    35.28: 264
       35.28 -    52.91: 45
       52.91 -    70.55: 14
       70.55 -    88.19: 3
  Dihedral angle restraints: 3327
    sinusoidal: 1289
      harmonic: 2038
  Sorted by residual:
  dihedral pdb=" CB  CYS X 207 "
           pdb=" SG  CYS X 207 "
           pdb=" SG  CYS X 460 "
           pdb=" CB  CYS X 460 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -31.66  -54.34     1      1.00e+01 1.00e-02 4.00e+01
  dihedral pdb=" CA  ASN L  96 "
           pdb=" C   ASN L  96 "
           pdb=" N   GLN L  97 "
           pdb=" CA  GLN L  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.23  -23.77     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" C   THR X 217 "
           pdb=" N   THR X 217 "
           pdb=" CA  THR X 217 "
           pdb=" CB  THR X 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.98    9.98     0      2.50e+00 1.60e-01 1.59e+01
  ... (remaining 3324 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.198: 881
       0.198 -    0.396: 3
       0.396 -    0.595: 0
       0.595 -    0.793: 0
       0.793 -    0.991: 1
  Chirality restraints: 885
  Sorted by residual:
  chirality pdb=" C1  NAG X 603 "
            pdb=" ND2 ASN X 218 "
            pdb=" C2  NAG X 603 "
            pdb=" O5  NAG X 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.41   -0.99 2.00e-01 2.50e+01 2.46e+01
  chirality pdb=" C1  NAG X 602 "
            pdb=" ND2 ASN X 227 "
            pdb=" C2  NAG X 602 "
            pdb=" O5  NAG X 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.03   -0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" CA  THR X 217 "
            pdb=" N   THR X 217 "
            pdb=" C   THR X 217 "
            pdb=" CB  THR X 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.30    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 882 not shown)

  Planarity restraints: 953
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG X 602 "   -0.114 2.00e-02 2.50e+03   9.38e-02 1.10e+02
        pdb=" C7  NAG X 602 "    0.033 2.00e-02 2.50e+03
        pdb=" C8  NAG X 602 "   -0.086 2.00e-02 2.50e+03
        pdb=" N2  NAG X 602 "    0.150 2.00e-02 2.50e+03
        pdb=" O7  NAG X 602 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG X 603 "    0.091 2.00e-02 2.50e+03   7.74e-02 7.48e+01
        pdb=" C7  NAG X 603 "   -0.015 2.00e-02 2.50e+03
        pdb=" C8  NAG X 603 "   -0.023 2.00e-02 2.50e+03
        pdb=" N2  NAG X 603 "   -0.125 2.00e-02 2.50e+03
        pdb=" O7  NAG X 603 "    0.073 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L  44 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.45e+00
        pdb=" N   PRO L  45 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO L  45 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO L  45 "    0.022 5.00e-02 4.00e+02
  ... (remaining 950 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 999
        2.76 -     3.30: 5470
        3.30 -     3.83: 9160
        3.83 -     4.37: 11223
        4.37 -     4.90: 19596
  Nonbonded interactions: 46448
  Sorted by model distance:
  nonbonded pdb=" O   SER H  66 "
            pdb=" NH1 ARG H  70 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OG  SER H  58 "
            pdb=" O   PHE X 213 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   GLY X 363 "
            pdb=" OG  SER X 366 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" NH1 ARG H  41 "
            pdb=" OD1 ASP H  93 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OH  TYR H 105 "
            pdb=" OG  SER L  92 "
     model   vdw
     2.333 3.040
  ... (remaining 46443 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 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:                  0.000
  Normalize map: mean=0, sd=1:             2.620
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.940
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
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      :  0.005   0.071   5682  Z= 0.270
  Angle     :  0.781  13.101   7732  Z= 0.428
  Chirality :  0.057   0.991    885
  Planarity :  0.006   0.094    951
  Dihedral  : 14.033  88.191   2018
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.15 %
  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: -3.02 (0.26), residues: 695
  helix: -1.42 (0.23), residues: 341
  sheet: -2.47 (0.41), residues: 114
  loop : -2.35 (0.34), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP X 349 
 HIS   0.003   0.001   HIS X 291 
 PHE   0.015   0.002   PHE X 318 
 TYR   0.014   0.001   TYR X 146 
 ARG   0.002   0.000   ARG L  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01681 (    2)
  link_NAG-ASN         : angle       6.98969 (    6)
  hydrogen bonds       : bond        0.12120 (  331)
  hydrogen bonds       : angle       6.90881 (  969)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       0.76706 (    6)
  covalent geometry    : bond        0.00543 ( 5677)
  covalent geometry    : angle       0.75615 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.543 
Fit side-chains
REVERT: H   46 LYS cc_start: 0.8527 (mttp) cc_final: 0.8312 (mttp)
REVERT: H   49 GLU cc_start: 0.7553 (tt0) cc_final: 0.7207 (tt0)
REVERT: L   46 LYS cc_start: 0.8591 (mttt) cc_final: 0.8258 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1709
  time to fit residues: 25.2235
Evaluate side-chains
  93 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0370
   chunk 54 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
H 112 GLN
L  38 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 240 ASN
X 290 ASN
X 291 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.143001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.125110 restraints weight = 6974.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.94
r_work: 0.3409 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5682  Z= 0.146
  Angle     :  0.562   7.980   7732  Z= 0.294
  Chirality :  0.043   0.296    885
  Planarity :  0.004   0.040    951
  Dihedral  :  6.439  59.030    839
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.81 %
    Favored  : 88.18 %
  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: -1.33 (0.30), residues: 695
  helix:  0.10 (0.27), residues: 345
  sheet: -1.90 (0.44), residues: 103
  loop : -1.69 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP X 349 
 HIS   0.006   0.001   HIS X 291 
 PHE   0.015   0.001   PHE X 318 
 TYR   0.015   0.001   TYR X 492 
 ARG   0.002   0.000   ARG H  70 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00838 (    2)
  link_NAG-ASN         : angle       3.47693 (    6)
  hydrogen bonds       : bond        0.04519 (  331)
  hydrogen bonds       : angle       5.11006 (  969)
  SS BOND              : bond        0.00354 (    3)
  SS BOND              : angle       0.85705 (    6)
  covalent geometry    : bond        0.00313 ( 5677)
  covalent geometry    : angle       0.55387 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.594 
Fit side-chains
REVERT: H   49 GLU cc_start: 0.8237 (tt0) cc_final: 0.8031 (tt0)
REVERT: L   46 LYS cc_start: 0.8993 (mttt) cc_final: 0.8700 (mttp)
  outliers start: 6
  outliers final: 5
  residues processed: 104
  average time/residue: 0.1560
  time to fit residues: 22.0945
Evaluate side-chains
  97 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue  429 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0470
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0270
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.145543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127317 restraints weight = 6941.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.05
r_work: 0.3436 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5682  Z= 0.123
  Angle     :  0.534   7.404   7732  Z= 0.276
  Chirality :  0.042   0.251    885
  Planarity :  0.004   0.044    951
  Dihedral  :  5.581  56.469    839
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.49 %
    Favored  : 86.15 %
  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: -0.53 (0.31), residues: 695
  helix:  0.75 (0.28), residues: 349
  sheet: -1.53 (0.45), residues: 103
  loop : -1.33 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP X 349 
 HIS   0.002   0.000   HIS H  38 
 PHE   0.015   0.001   PHE X 318 
 TYR   0.019   0.001   TYR H  33 
 ARG   0.001   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00760 (    2)
  link_NAG-ASN         : angle       2.98676 (    6)
  hydrogen bonds       : bond        0.04092 (  331)
  hydrogen bonds       : angle       4.72439 (  969)
  SS BOND              : bond        0.00739 (    3)
  SS BOND              : angle       0.97513 (    6)
  covalent geometry    : bond        0.00265 ( 5677)
  covalent geometry    : angle       0.52723 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.599 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.9026 (mttt) cc_final: 0.8704 (mttp)
REVERT: X  170 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7294 (mm-30)
REVERT: X  240 ASN cc_start: 0.8765 (m-40) cc_final: 0.8382 (m-40)
  outliers start: 14
  outliers final: 10
  residues processed: 110
  average time/residue: 0.1624
  time to fit residues: 23.8674
Evaluate side-chains
  108 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue   69 VAL
Chi-restraints excluded: chain X residue  190 VAL
Chi-restraints excluded: chain X residue  230 HIS
Chi-restraints excluded: chain X residue  464 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.142967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.124279 restraints weight = 7143.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.08
r_work: 0.3398 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5682  Z= 0.175
  Angle     :  0.565   6.848   7732  Z= 0.294
  Chirality :  0.043   0.251    885
  Planarity :  0.004   0.044    951
  Dihedral  :  5.567  56.051    839
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 13.18 %
    Favored  : 83.28 %
  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: -0.44 (0.31), residues: 695
  helix:  0.80 (0.27), residues: 349
  sheet: -1.38 (0.45), residues: 103
  loop : -1.30 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 122 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.016   0.001   PHE X 318 
 TYR   0.026   0.002   TYR X 492 
 ARG   0.002   0.000   ARG X 458 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00613 (    2)
  link_NAG-ASN         : angle       2.79768 (    6)
  hydrogen bonds       : bond        0.04469 (  331)
  hydrogen bonds       : angle       4.75904 (  969)
  SS BOND              : bond        0.00411 (    3)
  SS BOND              : angle       0.88273 (    6)
  covalent geometry    : bond        0.00393 ( 5677)
  covalent geometry    : angle       0.55998 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.600 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.9031 (mttt) cc_final: 0.8716 (mttp)
REVERT: X  170 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7369 (mm-30)
REVERT: X  240 ASN cc_start: 0.8795 (m-40) cc_final: 0.8436 (m-40)
REVERT: X  297 LEU cc_start: 0.8708 (tt) cc_final: 0.8450 (tp)
  outliers start: 21
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1351
  time to fit residues: 21.5197
Evaluate side-chains
  116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  124 GLN
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue   69 VAL
Chi-restraints excluded: chain X residue  190 VAL
Chi-restraints excluded: chain X residue  230 HIS
Chi-restraints excluded: chain X residue  429 SER
Chi-restraints excluded: chain X residue  464 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0970
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
L  39 GLN
X 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.141207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.124639 restraints weight = 7238.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.78
r_work: 0.3380 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5682  Z= 0.145
  Angle     :  0.548   7.064   7732  Z= 0.283
  Chirality :  0.043   0.241    885
  Planarity :  0.004   0.044    951
  Dihedral  :  5.431  54.574    839
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.19 %
    Favored  : 82.43 %
  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: -0.20 (0.32), residues: 695
  helix:  0.98 (0.28), residues: 351
  sheet: -1.29 (0.46), residues: 103
  loop : -1.17 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.015   0.001   PHE X 318 
 TYR   0.023   0.001   TYR X 492 
 ARG   0.002   0.000   ARG X 458 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00610 (    2)
  link_NAG-ASN         : angle       2.66124 (    6)
  hydrogen bonds       : bond        0.04258 (  331)
  hydrogen bonds       : angle       4.65612 (  969)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       0.85843 (    6)
  covalent geometry    : bond        0.00322 ( 5677)
  covalent geometry    : angle       0.54262 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.544 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.8943 (mttt) cc_final: 0.8636 (mttp)
REVERT: X  170 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7367 (mm-30)
REVERT: X  240 ASN cc_start: 0.8733 (m-40) cc_final: 0.8386 (m-40)
REVERT: X  297 LEU cc_start: 0.8662 (tt) cc_final: 0.8431 (tp)
  outliers start: 20
  outliers final: 15
  residues processed: 117
  average time/residue: 0.1363
  time to fit residues: 22.0028
Evaluate side-chains
  117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  109 ILE
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue   69 VAL
Chi-restraints excluded: chain X residue  190 VAL
Chi-restraints excluded: chain X residue  230 HIS
Chi-restraints excluded: chain X residue  288 VAL
Chi-restraints excluded: chain X residue  429 SER
Chi-restraints excluded: chain X residue  464 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.141081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.124312 restraints weight = 7223.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.84
r_work: 0.3365 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5682  Z= 0.151
  Angle     :  0.551   6.943   7732  Z= 0.286
  Chirality :  0.043   0.239    885
  Planarity :  0.004   0.044    951
  Dihedral  :  5.360  54.397    839
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.03 %
    Favored  : 81.76 %
  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: -0.09 (0.32), residues: 695
  helix:  1.07 (0.28), residues: 351
  sheet: -1.21 (0.46), residues: 103
  loop : -1.13 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.016   0.001   PHE X 318 
 TYR   0.023   0.001   TYR X 492 
 ARG   0.002   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00593 (    2)
  link_NAG-ASN         : angle       2.55710 (    6)
  hydrogen bonds       : bond        0.04303 (  331)
  hydrogen bonds       : angle       4.62080 (  969)
  SS BOND              : bond        0.00324 (    3)
  SS BOND              : angle       0.84201 (    6)
  covalent geometry    : bond        0.00335 ( 5677)
  covalent geometry    : angle       0.54669 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.613 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.8964 (mttt) cc_final: 0.8666 (mttp)
REVERT: X  240 ASN cc_start: 0.8737 (m-40) cc_final: 0.8389 (m-40)
REVERT: X  472 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8092 (mt)
  outliers start: 19
  outliers final: 16
  residues processed: 114
  average time/residue: 0.1406
  time to fit residues: 22.1799
Evaluate side-chains
  119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  109 ILE
Chi-restraints excluded: chain L residue  112 THR
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue   43 CYS
Chi-restraints excluded: chain X residue   69 VAL
Chi-restraints excluded: chain X residue  190 VAL
Chi-restraints excluded: chain X residue  288 VAL
Chi-restraints excluded: chain X residue  429 SER
Chi-restraints excluded: chain X residue  464 SER
Chi-restraints excluded: chain X residue  472 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
X 423 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.140940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.124105 restraints weight = 7217.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.85
r_work: 0.3365 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5682  Z= 0.157
  Angle     :  0.559   6.834   7732  Z= 0.290
  Chirality :  0.043   0.236    885
  Planarity :  0.004   0.044    951
  Dihedral  :  5.376  54.427    839
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.71 %
    Favored  : 80.57 %
  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: -0.07 (0.32), residues: 695
  helix:  1.08 (0.28), residues: 351
  sheet: -1.16 (0.46), residues: 103
  loop : -1.12 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.015   0.001   PHE X 318 
 TYR   0.030   0.001   TYR X 492 
 ARG   0.002   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00594 (    2)
  link_NAG-ASN         : angle       2.49187 (    6)
  hydrogen bonds       : bond        0.04306 (  331)
  hydrogen bonds       : angle       4.65149 (  969)
  SS BOND              : bond        0.00507 (    3)
  SS BOND              : angle       1.49280 (    6)
  covalent geometry    : bond        0.00350 ( 5677)
  covalent geometry    : angle       0.55391 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.534 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.8981 (mttt) cc_final: 0.8689 (mttp)
REVERT: X  240 ASN cc_start: 0.8725 (m-40) cc_final: 0.8379 (m-40)
REVERT: X  418 PRO cc_start: 0.8864 (Cg_endo) cc_final: 0.8657 (Cg_exo)
REVERT: X  472 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8014 (mt)
  outliers start: 22
  outliers final: 17
  residues processed: 116
  average time/residue: 0.1464
  time to fit residues: 23.4153
Evaluate side-chains
  122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  109 ILE
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue   43 CYS
Chi-restraints excluded: chain X residue   69 VAL
Chi-restraints excluded: chain X residue  190 VAL
Chi-restraints excluded: chain X residue  230 HIS
Chi-restraints excluded: chain X residue  288 VAL
Chi-restraints excluded: chain X residue  429 SER
Chi-restraints excluded: chain X residue  464 SER
Chi-restraints excluded: chain X residue  472 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0030
   chunk 41 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5990

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.142257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.125757 restraints weight = 7186.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.78
r_work: 0.3392 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5682  Z= 0.134
  Angle     :  0.544   7.104   7732  Z= 0.282
  Chirality :  0.043   0.229    885
  Planarity :  0.004   0.043    951
  Dihedral  :  5.262  53.794    839
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.71 %
    Favored  : 80.74 %
  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:  0.07 (0.32), residues: 695
  helix:  1.22 (0.28), residues: 351
  sheet: -1.12 (0.46), residues: 103
  loop : -1.08 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.015   0.001   PHE X 318 
 TYR   0.029   0.001   TYR X 492 
 ARG   0.003   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00613 (    2)
  link_NAG-ASN         : angle       2.38369 (    6)
  hydrogen bonds       : bond        0.04113 (  331)
  hydrogen bonds       : angle       4.57526 (  969)
  SS BOND              : bond        0.00393 (    3)
  SS BOND              : angle       1.09412 (    6)
  covalent geometry    : bond        0.00293 ( 5677)
  covalent geometry    : angle       0.53987 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.548 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.8983 (mttt) cc_final: 0.8702 (mttp)
REVERT: X  240 ASN cc_start: 0.8730 (m-40) cc_final: 0.8400 (m-40)
REVERT: X  418 PRO cc_start: 0.8859 (Cg_endo) cc_final: 0.8653 (Cg_exo)
REVERT: X  472 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7666 (mt)
  outliers start: 21
  outliers final: 18
  residues processed: 117
  average time/residue: 0.1352
  time to fit residues: 22.1280
Evaluate side-chains
  121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  109 ILE
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue   43 CYS
Chi-restraints excluded: chain X residue   69 VAL
Chi-restraints excluded: chain X residue  190 VAL
Chi-restraints excluded: chain X residue  230 HIS
Chi-restraints excluded: chain X residue  285 LEU
Chi-restraints excluded: chain X residue  288 VAL
Chi-restraints excluded: chain X residue  429 SER
Chi-restraints excluded: chain X residue  464 SER
Chi-restraints excluded: chain X residue  472 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0170
   chunk 51 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
X 423 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.142406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.125877 restraints weight = 7196.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.77
r_work: 0.3391 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5682  Z= 0.139
  Angle     :  0.544   7.303   7732  Z= 0.282
  Chirality :  0.043   0.225    885
  Planarity :  0.004   0.043    951
  Dihedral  :  5.219  54.097    839
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.39 %
    Favored  : 80.24 %
  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:  0.19 (0.32), residues: 695
  helix:  1.29 (0.28), residues: 356
  sheet: -1.02 (0.47), residues: 103
  loop : -1.06 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.015   0.001   PHE X 318 
 TYR   0.028   0.001   TYR X 492 
 ARG   0.002   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00607 (    2)
  link_NAG-ASN         : angle       2.29628 (    6)
  hydrogen bonds       : bond        0.04117 (  331)
  hydrogen bonds       : angle       4.55007 (  969)
  SS BOND              : bond        0.00381 (    3)
  SS BOND              : angle       0.94289 (    6)
  covalent geometry    : bond        0.00305 ( 5677)
  covalent geometry    : angle       0.54047 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.561 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.8974 (mttt) cc_final: 0.8675 (mttp)
REVERT: X  240 ASN cc_start: 0.8724 (m-40) cc_final: 0.8387 (m-40)
  outliers start: 20
  outliers final: 19
  residues processed: 113
  average time/residue: 0.1542
  time to fit residues: 24.1133
Evaluate side-chains
  122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  109 ILE
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue   43 CYS
Chi-restraints excluded: chain X residue   69 VAL
Chi-restraints excluded: chain X residue  190 VAL
Chi-restraints excluded: chain X residue  230 HIS
Chi-restraints excluded: chain X residue  285 LEU
Chi-restraints excluded: chain X residue  288 VAL
Chi-restraints excluded: chain X residue  423 HIS
Chi-restraints excluded: chain X residue  429 SER
Chi-restraints excluded: chain X residue  464 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0020
   chunk 7 optimal weight:    0.0980
   chunk 16 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
X 423 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.147014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.128548 restraints weight = 6909.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.07
r_work: 0.3451 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5682  Z= 0.119
  Angle     :  0.538   8.121   7732  Z= 0.277
  Chirality :  0.042   0.220    885
  Planarity :  0.004   0.043    951
  Dihedral  :  5.141  53.543    839
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.23 %
    Favored  : 79.90 %
  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:  0.39 (0.32), residues: 695
  helix:  1.46 (0.28), residues: 356
  sheet: -0.88 (0.49), residues: 103
  loop : -1.01 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.004   0.001   HIS X 423 
 PHE   0.014   0.001   PHE X 318 
 TYR   0.028   0.001   TYR X 492 
 ARG   0.004   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00620 (    2)
  link_NAG-ASN         : angle       2.22478 (    6)
  hydrogen bonds       : bond        0.03943 (  331)
  hydrogen bonds       : angle       4.46846 (  969)
  SS BOND              : bond        0.00399 (    3)
  SS BOND              : angle       0.84534 (    6)
  covalent geometry    : bond        0.00254 ( 5677)
  covalent geometry    : angle       0.53464 ( 7720)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.548 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.9020 (mttt) cc_final: 0.8708 (mttp)
REVERT: X  240 ASN cc_start: 0.8770 (m-40) cc_final: 0.8341 (m-40)
REVERT: X  418 PRO cc_start: 0.8874 (Cg_endo) cc_final: 0.8640 (Cg_exo)
  outliers start: 17
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1302
  time to fit residues: 20.0706
Evaluate side-chains
  117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    8 VAL
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue  109 ILE
Chi-restraints excluded: chain L residue  113 VAL
Chi-restraints excluded: chain X residue   69 VAL
Chi-restraints excluded: chain X residue  190 VAL
Chi-restraints excluded: chain X residue  230 HIS
Chi-restraints excluded: chain X residue  285 LEU
Chi-restraints excluded: chain X residue  288 VAL
Chi-restraints excluded: chain X residue  423 HIS
Chi-restraints excluded: chain X residue  429 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 59 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.146346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.127966 restraints weight = 7027.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.09
r_work: 0.3445 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5682  Z= 0.130
  Angle     :  0.548   7.832   7732  Z= 0.282
  Chirality :  0.042   0.218    885
  Planarity :  0.004   0.043    951
  Dihedral  :  5.119  53.835    839
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.23 %
    Favored  : 79.90 %
  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:  0.42 (0.32), residues: 695
  helix:  1.46 (0.28), residues: 357
  sheet: -0.83 (0.49), residues: 103
  loop : -0.98 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.015   0.001   PHE X 318 
 TYR   0.027   0.001   TYR X 492 
 ARG   0.003   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00594 (    2)
  link_NAG-ASN         : angle       2.17974 (    6)
  hydrogen bonds       : bond        0.03985 (  331)
  hydrogen bonds       : angle       4.45382 (  969)
  SS BOND              : bond        0.00402 (    3)
  SS BOND              : angle       0.79904 (    6)
  covalent geometry    : bond        0.00285 ( 5677)
  covalent geometry    : angle       0.54465 ( 7720)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3368.83 seconds
wall clock time: 58 minutes 47.21 seconds (3527.21 seconds total)