Starting phenix.real_space_refine
on Thu Jul  2 00:41:28 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7ey4_31377/07_2026/7ey4_31377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ey4_31377/07_2026/7ey4_31377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2026/7ey4_31377.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2026/7ey4_31377.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2026/7ey4_31377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2026/7ey4_31377.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2026/7ey4_31377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2026/7ey4_31377.map"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    3000      2.51       5
     N     772      2.21       5
     O     894      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4683
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 985
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 126}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1465
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "N"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1359
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 8, 'TRANS': 156}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.05, per 1000 atoms: 0.22
  Number of scatterers: 4683
  At special positions: 0
  Unit cell: (62.13, 80.66, 110.09, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      17     16.00
     O     894      8.00
     N     772      7.00
     C    3000      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 131 " - pdb=" SG  CYS N 166 " distance=2.05

  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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    NAG-ASN
      " NAG A   1 " - " ASN N 165 "
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 147.9 milliseconds
  

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1072

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 11 sheets defined
      7.2% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.648A  pdb=" N   ASP H  31 " --> pdb=" O   ARG H  28 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'R' and resid 338 through 343
    Processing helix  chain 'R' and resid 349 through 353
    Processing helix  chain 'R' and resid 365 through 370
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.577A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 410
      removed outlier: 3.653A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 417 through 422
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.923A  pdb=" N   GLU L  70 " --> pdb=" O   PHE L  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.193A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.513A  pdb=" N   SER H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP H  73 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 47
      removed outlier: 4.277A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASN H  35 " --> pdb=" O   ALA H  97 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 50
      removed outlier: 3.668A  pdb=" N   TYR H  50 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'R' and resid 356 through 358
      removed outlier: 3.687A  pdb=" N   ILE R 402 " --> pdb=" O   TYR R 508 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLY R 431 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TYR R 380 " --> pdb=" O   GLY R 431 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   VAL R 433 " --> pdb=" O   LYS R 378 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS R 378 " --> pdb=" O   VAL R 433 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474
    Processing sheet with id=AB1, first strand: chain 'N' and resid 50 through 55
      removed outlier: 3.774A  pdb=" N   ASP N  53 " --> pdb=" O   ARG N 273 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ASP N 287 " --> pdb=" O   LYS N 278 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 63 through 64
  WARNING: can't find start of bonding for strands!
    previous: chain 'N' and resid 63 through 64
    current: chain 'N' and resid 116 through 121
      removed outlier: 4.174A  pdb=" N   ASN N 164 " --> pdb=" O   GLU N 132 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'N' and resid 163 through 164
    current: chain 'N' and resid 200 through 205
      removed outlier: 5.953A  pdb=" N   SER N 205 " --> pdb=" O   PRO N 225 " (cutoff:3.500A)

    103 hydrogen bonds defined for protein.
    252 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.62

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1473
        1.35 -     1.48: 1418
        1.48 -     1.61: 1891
        1.61 -     1.74: 0
        1.74 -     1.88: 21
  Bond restraints: 4803
  Sorted by residual:
  bond pdb=" CA  SER H 107 "
       pdb=" CB  SER H 107 "
    ideal  model  delta    sigma   weight residual
    1.532  1.464  0.067 1.82e-02 3.02e+03 1.37e+01
  bond pdb=" N   CYS N 166 "
       pdb=" CA  CYS N 166 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.58e+00
  bond pdb=" N   PHE N 168 "
       pdb=" CA  PHE N 168 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.22e-02 6.72e+03 7.54e+00
  bond pdb=" CA  SER H 104 "
       pdb=" CB  SER H 104 "
    ideal  model  delta    sigma   weight residual
    1.524  1.491  0.033 1.22e-02 6.72e+03 7.34e+00
  bond pdb=" N   ASP H 105 "
       pdb=" CA  ASP H 105 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.34e-02 5.57e+03 7.04e+00
  ... (remaining 4798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 6374
        2.63 -     5.25: 127
        5.25 -     7.88: 15
        7.88 -    10.50: 1
       10.50 -    13.13: 2
  Bond angle restraints: 6519
  Sorted by residual:
  angle pdb=" N   VAL L  29 "
        pdb=" CA  VAL L  29 "
        pdb=" C   VAL L  29 "
      ideal   model   delta    sigma   weight residual
     111.90  107.22    4.68 8.10e-01 1.52e+00 3.34e+01
  angle pdb=" CA  CYS R 379 "
        pdb=" CB  CYS R 379 "
        pdb=" SG  CYS R 379 "
      ideal   model   delta    sigma   weight residual
     114.40  127.53  -13.13 2.30e+00 1.89e-01 3.26e+01
  angle pdb=" CA  CYS R 432 "
        pdb=" CB  CYS R 432 "
        pdb=" SG  CYS R 432 "
      ideal   model   delta    sigma   weight residual
     114.40  127.18  -12.78 2.30e+00 1.89e-01 3.09e+01
  angle pdb=" N   CYS R 379 "
        pdb=" CA  CYS R 379 "
        pdb=" C   CYS R 379 "
      ideal   model   delta    sigma   weight residual
     108.38  114.13   -5.75 1.35e+00 5.49e-01 1.82e+01
  angle pdb=" N   CYS R 432 "
        pdb=" CA  CYS R 432 "
        pdb=" C   CYS R 432 "
      ideal   model   delta    sigma   weight residual
     108.60  114.65   -6.05 1.46e+00 4.69e-01 1.71e+01
  ... (remaining 6514 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 2470
       16.00 -    32.00: 210
       32.00 -    48.00: 59
       48.00 -    64.01: 11
       64.01 -    80.01: 7
  Dihedral angle restraints: 2757
    sinusoidal: 1068
      harmonic: 1689
  Sorted by residual:
  dihedral pdb=" CA  SER L   7 "
           pdb=" C   SER L   7 "
           pdb=" N   PRO L   8 "
           pdb=" CA  PRO L   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.41   47.59     0      5.00e+00 4.00e-02 9.06e+01
  dihedral pdb=" CB  CYS R 379 "
           pdb=" SG  CYS R 379 "
           pdb=" SG  CYS R 432 "
           pdb=" CB  CYS R 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -10.28  -75.72     1      1.00e+01 1.00e-02 7.23e+01
  dihedral pdb=" CA  CYS R 379 "
           pdb=" C   CYS R 379 "
           pdb=" N   TYR R 380 "
           pdb=" CA  TYR R 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.32  -39.68     0      5.00e+00 4.00e-02 6.30e+01
  ... (remaining 2754 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 624
       0.078 -    0.156: 70
       0.156 -    0.233: 4
       0.233 -    0.311: 2
       0.311 -    0.389: 1
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" C1  BMA A   3 "
            pdb=" O4  NAG A   2 "
            pdb=" C2  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-02 2.50e+03 3.79e+02
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.37   -0.03 2.00e-02 2.50e+03 2.58e+00
  chirality pdb=" CA  CYS R 432 "
            pdb=" N   CYS R 432 "
            pdb=" C   CYS R 432 "
            pdb=" CB  CYS R 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 698 not shown)

  Planarity restraints: 836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.322 2.00e-02 2.50e+03   2.72e-01 9.26e+02
        pdb=" C7  NAG A   1 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.188 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.471 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "   -0.293 2.00e-02 2.50e+03   2.52e-01 7.94e+02
        pdb=" C7  NAG A   2 "    0.063 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "    0.007 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "    0.430 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "   -0.208 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO L   8 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "    0.035 5.00e-02 4.00e+02
  ... (remaining 833 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 180
        2.70 -     3.25: 4472
        3.25 -     3.80: 6731
        3.80 -     4.35: 8835
        4.35 -     4.90: 15297
  Nonbonded interactions: 35515
  Sorted by model distance:
  nonbonded pdb=" OH  TYR N  37 "
            pdb=" O   LEU N  54 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" OD1 ASP N  40 "
            pdb=" OH  TYR N 204 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OH  TYR N  91 "
            pdb=" OE1 GLU N 191 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NH2 ARG H  98 "
            pdb=" OD2 ASP H 117 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" NH2 ARG L  31 "
            pdb=" OE1 GLU R 340 "
     model   vdw
     2.241 3.120
  ... (remaining 35510 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.400
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   4812  Z= 0.328
  Angle     :  0.941  13.127   6540  Z= 0.524
  Chirality :  0.053   0.389    701
  Planarity :  0.014   0.272    835
  Dihedral  : 13.633  80.007   1667
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 13.50 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.34), residues: 563
  helix: -3.57 (0.84), residues: 20
  sheet: -0.83 (0.39), residues: 181
  loop : -2.14 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG N  44 
 TYR   0.024   0.002   TYR H 110 
 PHE   0.028   0.002   PHE H  56 
 TRP   0.016   0.002   TRP R 436 
 HIS   0.001   0.001   HIS N  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00695 /  0.33 ( 4803)
  covalent geometry    : angle       0.90135 /  0.51 ( 6519)
  SS BOND              : bond        0.00982 /  0.42 (    6)
  SS BOND              : angle       4.82403 /  2.12 (   12)
  hydrogen bonds       : bond        0.29872 / 20.16 (  103)
  hydrogen bonds       : angle      10.92957 /  7.19 (  252)
  link_BETA1-4         : bond        0.00559 /  0.27 (    2)
  link_BETA1-4         : angle       3.11479 /  1.53 (    6)
  link_NAG-ASN         : bond        0.02273 /  1.20 (    1)
  link_NAG-ASN         : angle       7.17095 /  3.76 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.128 
Fit side-chains
REVERT: H   74 ASP cc_start: 0.8334 (m-30) cc_final: 0.7991 (m-30)
REVERT: N   54 LEU cc_start: 0.7149 (mp) cc_final: 0.6142 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0773
  time to fit residues: 11.8033
Evaluate side-chains
  98 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 109 ASN
N 164 ASN
N 282 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.144604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.116218 restraints weight = 6581.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.117213 restraints weight = 6065.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.118175 restraints weight = 4859.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.119073 restraints weight = 4132.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.119501 restraints weight = 3733.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4812  Z= 0.200
  Angle     :  0.758   8.783   6540  Z= 0.398
  Chirality :  0.048   0.199    701
  Planarity :  0.005   0.056    835
  Dihedral  :  5.887  43.883    647
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.88 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.60 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.34), residues: 563
  helix: -3.46 (0.93), residues: 20
  sheet: -0.27 (0.40), residues: 182
  loop : -2.10 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  54 
 TYR   0.015   0.002   TYR R 369 
 PHE   0.017   0.002   PHE N 106 
 TRP   0.017   0.002   TRP R 436 
 HIS   0.001   0.000   HIS N  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00467 /  0.20 ( 4803)
  covalent geometry    : angle       0.74557 /  0.39 ( 6519)
  SS BOND              : bond        0.00589 /  0.29 (    6)
  SS BOND              : angle       3.01212 /  1.27 (   12)
  hydrogen bonds       : bond        0.03975 /  2.87 (  103)
  hydrogen bonds       : angle       7.17865 /  4.74 (  252)
  link_BETA1-4         : bond        0.00470 /  0.23 (    2)
  link_BETA1-4         : angle       2.01487 /  1.03 (    6)
  link_NAG-ASN         : bond        0.00480 /  0.25 (    1)
  link_NAG-ASN         : angle       0.94336 /  0.52 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.173 
Fit side-chains
REVERT: H   74 ASP cc_start: 0.8367 (m-30) cc_final: 0.8045 (m-30)
REVERT: R  378 LYS cc_start: 0.7820 (ptpt) cc_final: 0.7605 (ptpp)
REVERT: R  414 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7339 (mm-40)
REVERT: N   64 TRP cc_start: 0.7829 (t60) cc_final: 0.7604 (t60)
  outliers start: 8
  outliers final: 5
  residues processed: 111
  average time/residue: 0.0803
  time to fit residues: 11.0859
Evaluate side-chains
  93 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain N residue   51 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.143661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115472 restraints weight = 6632.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.116276 restraints weight = 5312.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116446 restraints weight = 5064.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.117030 restraints weight = 4432.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.117808 restraints weight = 4046.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4812  Z= 0.213
  Angle     :  0.743   9.370   6540  Z= 0.387
  Chirality :  0.048   0.172    701
  Planarity :  0.006   0.086    835
  Dihedral  :  5.619  42.513    647
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.83 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 12.60 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.34), residues: 563
  helix: -3.48 (0.91), residues: 20
  sheet: -0.31 (0.39), residues: 189
  loop : -2.14 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  44 
 TYR   0.019   0.002   TYR H 110 
 PHE   0.021   0.002   PHE H  56 
 TRP   0.015   0.002   TRP R 436 
 HIS   0.003   0.001   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00511 /  0.21 ( 4803)
  covalent geometry    : angle       0.72682 /  0.38 ( 6519)
  SS BOND              : bond        0.00742 /  0.33 (    6)
  SS BOND              : angle       3.52203 /  1.52 (   12)
  hydrogen bonds       : bond        0.04301 /  3.04 (  103)
  hydrogen bonds       : angle       6.50868 /  4.29 (  252)
  link_BETA1-4         : bond        0.00906 /  0.43 (    2)
  link_BETA1-4         : angle       1.52167 /  0.81 (    6)
  link_NAG-ASN         : bond        0.00380 /  0.20 (    1)
  link_NAG-ASN         : angle       1.56220 /  0.83 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.162 
Fit side-chains
REVERT: L   93 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7625 (m-40)
REVERT: H   74 ASP cc_start: 0.8492 (m-30) cc_final: 0.8130 (m-30)
REVERT: N   52 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7481 (pp30)
  outliers start: 24
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0866
  time to fit residues: 12.2209
Evaluate side-chains
  97 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue   93 ASN
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 43 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0470
   chunk 31 optimal weight:    0.0670
   chunk 8 optimal weight:    0.3980
   chunk 41 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.2816

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.147521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.117441 restraints weight = 6449.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.119469 restraints weight = 5055.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.121051 restraints weight = 4257.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.122083 restraints weight = 3783.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122671 restraints weight = 3473.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4812  Z= 0.124
  Angle     :  0.665   8.074   6540  Z= 0.346
  Chirality :  0.044   0.173    701
  Planarity :  0.005   0.079    835
  Dihedral  :  5.236  38.769    647
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.70 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.00 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.34), residues: 563
  helix: -3.04 (1.01), residues: 20
  sheet: -0.03 (0.40), residues: 184
  loop : -1.95 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  54 
 TYR   0.011   0.001   TYR H 110 
 PHE   0.017   0.001   PHE N  43 
 TRP   0.016   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.12 ( 4803)
  covalent geometry    : angle       0.65192 /  0.34 ( 6519)
  SS BOND              : bond        0.00631 /  0.27 (    6)
  SS BOND              : angle       2.94590 /  1.39 (   12)
  hydrogen bonds       : bond        0.03322 /  2.37 (  103)
  hydrogen bonds       : angle       6.19673 /  4.11 (  252)
  link_BETA1-4         : bond        0.00719 /  0.34 (    2)
  link_BETA1-4         : angle       1.52412 /  0.80 (    6)
  link_NAG-ASN         : bond        0.00103 /  0.05 (    1)
  link_NAG-ASN         : angle       1.28237 /  0.70 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.194 
Fit side-chains
REVERT: H   74 ASP cc_start: 0.8410 (m-30) cc_final: 0.8135 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0872
  time to fit residues: 11.6670
Evaluate side-chains
  93 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  38 GLN
N  81 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.144548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.114364 restraints weight = 6594.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.116198 restraints weight = 5202.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.117685 restraints weight = 4438.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.118540 restraints weight = 3961.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.119386 restraints weight = 3665.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4812  Z= 0.183
  Angle     :  0.689   7.808   6540  Z= 0.360
  Chirality :  0.045   0.157    701
  Planarity :  0.005   0.091    835
  Dihedral  :  5.337  41.765    647
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 19.20 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.35), residues: 563
  helix: -2.99 (0.97), residues: 20
  sheet: -0.06 (0.38), residues: 196
  loop : -1.95 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  54 
 TYR   0.012   0.001   TYR H 110 
 PHE   0.020   0.002   PHE H  56 
 TRP   0.016   0.001   TRP R 436 
 HIS   0.001   0.001   HIS N  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.18 ( 4803)
  covalent geometry    : angle       0.67449 /  0.35 ( 6519)
  SS BOND              : bond        0.00560 /  0.26 (    6)
  SS BOND              : angle       3.15192 /  1.33 (   12)
  hydrogen bonds       : bond        0.03463 /  2.48 (  103)
  hydrogen bonds       : angle       5.99044 /  3.95 (  252)
  link_BETA1-4         : bond        0.00731 /  0.35 (    2)
  link_BETA1-4         : angle       1.45899 /  0.78 (    6)
  link_NAG-ASN         : bond        0.00036 /  0.02 (    1)
  link_NAG-ASN         : angle       1.55041 /  0.84 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.173 
Fit side-chains
REVERT: L   93 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7683 (m-40)
REVERT: H   74 ASP cc_start: 0.8445 (m-30) cc_final: 0.8143 (m-30)
REVERT: N   52 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7660 (pp30)
  outliers start: 20
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0908
  time to fit residues: 12.3750
Evaluate side-chains
  107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue   93 ASN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0770
   chunk 47 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  38 GLN

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 = 0.143015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112057 restraints weight = 6547.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.114258 restraints weight = 5003.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.115491 restraints weight = 4171.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.116899 restraints weight = 3712.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.117597 restraints weight = 3381.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4812  Z= 0.152
  Angle     :  0.676   7.388   6540  Z= 0.352
  Chirality :  0.045   0.163    701
  Planarity :  0.005   0.086    835
  Dihedral  :  5.241  38.621    647
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 19.80 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.34), residues: 563
  helix: -2.73 (1.04), residues: 20
  sheet:  0.12 (0.37), residues: 201
  loop : -2.03 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  54 
 TYR   0.010   0.001   TYR H 110 
 PHE   0.024   0.001   PHE N  43 
 TRP   0.016   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.15 ( 4803)
  covalent geometry    : angle       0.65979 /  0.35 ( 6519)
  SS BOND              : bond        0.00498 /  0.23 (    6)
  SS BOND              : angle       3.21616 /  1.59 (   12)
  hydrogen bonds       : bond        0.03287 /  2.35 (  103)
  hydrogen bonds       : angle       5.92952 /  3.92 (  252)
  link_BETA1-4         : bond        0.00681 /  0.33 (    2)
  link_BETA1-4         : angle       1.51083 /  0.80 (    6)
  link_NAG-ASN         : bond        0.00166 /  0.09 (    1)
  link_NAG-ASN         : angle       1.69841 /  0.92 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.206 
Fit side-chains
REVERT: N   52 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7655 (pp30)
  outliers start: 20
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0859
  time to fit residues: 11.1481
Evaluate side-chains
  101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R 360 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.140379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.110054 restraints weight = 6583.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.111646 restraints weight = 5813.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112474 restraints weight = 4609.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.112890 restraints weight = 4146.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.113202 restraints weight = 3945.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   4812  Z= 0.202
  Angle     :  0.781  20.276   6540  Z= 0.401
  Chirality :  0.047   0.268    701
  Planarity :  0.005   0.079    835
  Dihedral  :  5.409  40.386    647
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 19.40 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.35), residues: 563
  helix: -2.81 (1.02), residues: 20
  sheet:  0.10 (0.38), residues: 201
  loop : -2.03 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  54 
 TYR   0.013   0.001   TYR H 110 
 PHE   0.028   0.002   PHE N  43 
 TRP   0.015   0.002   TRP R 436 
 HIS   0.001   0.001   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00493 /  0.20 ( 4803)
  covalent geometry    : angle       0.75494 /  0.39 ( 6519)
  SS BOND              : bond        0.00844 /  0.34 (    6)
  SS BOND              : angle       4.34821 /  2.82 (   12)
  hydrogen bonds       : bond        0.03619 /  2.59 (  103)
  hydrogen bonds       : angle       6.00461 /  3.97 (  252)
  link_BETA1-4         : bond        0.00754 /  0.36 (    2)
  link_BETA1-4         : angle       1.56192 /  0.85 (    6)
  link_NAG-ASN         : bond        0.00374 /  0.20 (    1)
  link_NAG-ASN         : angle       3.48226 /  1.89 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.194 
Fit side-chains
REVERT: N   44 ARG cc_start: 0.5476 (ttm170) cc_final: 0.4820 (mpt180)
REVERT: N   52 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7769 (pp30)
  outliers start: 22
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0868
  time to fit residues: 11.8998
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  103 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  105 ILE
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.0570
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 31 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.5298

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.142077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.110864 restraints weight = 6627.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.112631 restraints weight = 5730.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113373 restraints weight = 4554.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.114482 restraints weight = 4123.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.114647 restraints weight = 3792.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   4812  Z= 0.157
  Angle     :  0.741  18.151   6540  Z= 0.381
  Chirality :  0.046   0.285    701
  Planarity :  0.005   0.097    835
  Dihedral  :  5.290  38.754    647
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.00 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.35), residues: 563
  helix: -2.71 (1.06), residues: 20
  sheet:  0.16 (0.38), residues: 201
  loop : -1.94 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  54 
 TYR   0.011   0.001   TYR H 110 
 PHE   0.030   0.002   PHE N  43 
 TRP   0.016   0.001   TRP R 436 
 HIS   0.001   0.001   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.16 ( 4803)
  covalent geometry    : angle       0.71845 /  0.37 ( 6519)
  SS BOND              : bond        0.00684 /  0.28 (    6)
  SS BOND              : angle       3.98814 /  2.46 (   12)
  hydrogen bonds       : bond        0.03347 /  2.40 (  103)
  hydrogen bonds       : angle       5.91481 /  3.92 (  252)
  link_BETA1-4         : bond        0.00683 /  0.33 (    2)
  link_BETA1-4         : angle       1.46264 /  0.78 (    6)
  link_NAG-ASN         : bond        0.00097 /  0.05 (    1)
  link_NAG-ASN         : angle       2.69384 /  1.46 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.145 
Fit side-chains
REVERT: L   74 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8386 (p)
REVERT: R  493 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7891 (mm-40)
REVERT: N   44 ARG cc_start: 0.5852 (ttm170) cc_final: 0.4667 (mpt180)
REVERT: N   52 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7680 (pp30)
REVERT: N  237 ARG cc_start: 0.8627 (mtp-110) cc_final: 0.8253 (mtm110)
  outliers start: 18
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0907
  time to fit residues: 11.9636
Evaluate side-chains
  108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  105 ILE
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   chunk 15 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0670
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4318

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R 334 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.143058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.113126 restraints weight = 6558.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.114531 restraints weight = 5991.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114972 restraints weight = 4900.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115850 restraints weight = 4455.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.116074 restraints weight = 4093.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4812  Z= 0.146
  Angle     :  0.732  16.805   6540  Z= 0.377
  Chirality :  0.046   0.259    701
  Planarity :  0.005   0.095    835
  Dihedral  :  5.203  38.186    647
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 23.20 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.35), residues: 563
  helix: -2.48 (1.12), residues: 20
  sheet:  0.32 (0.39), residues: 191
  loop : -1.88 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  54 
 TYR   0.012   0.001   TYR H 110 
 PHE   0.029   0.001   PHE N  43 
 TRP   0.014   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 ( 4803)
  covalent geometry    : angle       0.71327 /  0.37 ( 6519)
  SS BOND              : bond        0.00658 /  0.27 (    6)
  SS BOND              : angle       3.61102 /  2.14 (   12)
  hydrogen bonds       : bond        0.03264 /  2.35 (  103)
  hydrogen bonds       : angle       5.76734 /  3.82 (  252)
  link_BETA1-4         : bond        0.00730 /  0.35 (    2)
  link_BETA1-4         : angle       1.48075 /  0.79 (    6)
  link_NAG-ASN         : bond        0.00189 /  0.10 (    1)
  link_NAG-ASN         : angle       2.26061 /  1.24 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.152 
Fit side-chains
REVERT: L   74 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8405 (p)
REVERT: H   87 ARG cc_start: 0.7703 (ptp-170) cc_final: 0.7491 (ptp-170)
REVERT: R  493 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7873 (mm-40)
REVERT: N   44 ARG cc_start: 0.6082 (ttm170) cc_final: 0.4626 (mpt180)
REVERT: N   52 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7693 (pp30)
REVERT: N  237 ARG cc_start: 0.8603 (mtp-110) cc_final: 0.8228 (mtm110)
  outliers start: 18
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0950
  time to fit residues: 11.9019
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  105 ILE
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0060
   chunk 19 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.143418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.113266 restraints weight = 6614.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.115358 restraints weight = 5915.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.116254 restraints weight = 4768.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116393 restraints weight = 4102.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.117154 restraints weight = 3964.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4812  Z= 0.150
  Angle     :  0.736  15.881   6540  Z= 0.380
  Chirality :  0.046   0.249    701
  Planarity :  0.005   0.093    835
  Dihedral  :  5.148  36.729    647
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 23.40 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.35), residues: 563
  helix: -3.07 (0.87), residues: 26
  sheet:  0.35 (0.39), residues: 188
  loop : -1.78 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  54 
 TYR   0.011   0.001   TYR H 110 
 PHE   0.029   0.001   PHE N  43 
 TRP   0.014   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.15 ( 4803)
  covalent geometry    : angle       0.71987 /  0.37 ( 6519)
  SS BOND              : bond        0.00663 /  0.29 (    6)
  SS BOND              : angle       3.44628 /  1.98 (   12)
  hydrogen bonds       : bond        0.03242 /  2.33 (  103)
  hydrogen bonds       : angle       5.73145 /  3.80 (  252)
  link_BETA1-4         : bond        0.00729 /  0.35 (    2)
  link_BETA1-4         : angle       1.46724 /  0.78 (    6)
  link_NAG-ASN         : bond        0.00180 /  0.09 (    1)
  link_NAG-ASN         : angle       2.00954 /  1.11 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.180 
Fit side-chains
REVERT: L   74 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8403 (p)
REVERT: R  493 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7969 (mm-40)
REVERT: N   52 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7719 (pp30)
REVERT: N  237 ARG cc_start: 0.8609 (mtp-110) cc_final: 0.8247 (mtm110)
  outliers start: 16
  outliers final: 15
  residues processed: 97
  average time/residue: 0.0915
  time to fit residues: 10.8924
Evaluate side-chains
  102 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  105 ILE
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 50 optimal weight:    0.3980
   chunk 35 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0000
   chunk 36 optimal weight:    0.4980
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.2984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.145450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115191 restraints weight = 6585.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.117308 restraints weight = 5930.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.118212 restraints weight = 4672.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.118393 restraints weight = 4154.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.118592 restraints weight = 3957.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.4246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4812  Z= 0.128
  Angle     :  0.708  14.862   6540  Z= 0.365
  Chirality :  0.045   0.232    701
  Planarity :  0.005   0.090    835
  Dihedral  :  4.986  36.136    647
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 24.20 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.35), residues: 563
  helix: -2.98 (0.90), residues: 26
  sheet:  0.39 (0.40), residues: 178
  loop : -1.74 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  54 
 TYR   0.011   0.001   TYR H 110 
 PHE   0.028   0.001   PHE N  43 
 TRP   0.014   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 4803)
  covalent geometry    : angle       0.69371 /  0.36 ( 6519)
  SS BOND              : bond        0.00595 /  0.26 (    6)
  SS BOND              : angle       3.11902 /  1.74 (   12)
  hydrogen bonds       : bond        0.03067 /  2.21 (  103)
  hydrogen bonds       : angle       5.55595 /  3.69 (  252)
  link_BETA1-4         : bond        0.00711 /  0.34 (    2)
  link_BETA1-4         : angle       1.45341 /  0.77 (    6)
  link_NAG-ASN         : bond        0.00197 /  0.10 (    1)
  link_NAG-ASN         : angle       1.71746 /  0.96 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 997.61 seconds
wall clock time: 17 minutes 52.65 seconds (1072.65 seconds total)