Starting phenix.real_space_refine
on Fri Aug 22 13:00:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ral_24365/08_2025/7ral_24365.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ral_24365/08_2025/7ral_24365.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ral_24365/08_2025/7ral_24365.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ral_24365/08_2025/7ral_24365.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ral_24365/08_2025/7ral_24365.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ral_24365/08_2025/7ral_24365.cif"
  }
  resolution = 3.7
  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=   0.021
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      14      5.16       5
     C    1825      2.51       5
     N     487      2.21       5
     O     521      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2847
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 862
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "L"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 663
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 6, 'TRANS': 92}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 1308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1308
          Classifications: {'peptide': 171}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 10, 'TRANS': 160}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.06, per 1000 atoms: 0.37
  Number of scatterers: 2847
  At special positions: 0
  Unit cell: (61.95, 77.7, 61.95, 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      14     16.00
     O     521      8.00
     N     487      7.00
     C    1825      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
  Time building additional restraints: 0.24
  Conformation dependent library (CDL) restraints added in 119.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  702

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 10 sheets defined
      11.8% alpha, 37.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 74 through 77
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.568A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 4.723A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.598A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 123 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   THR H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ARG H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 123 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 116 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   TRP H 116 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 114 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASP H 114 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 15 through 20
      removed outlier: 4.481A  pdb=" N   SER H  16 " --> pdb=" O   SER H  85 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 105 through 107
      removed outlier: 3.727A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 23
    Processing sheet with id=AA7, first strand: chain 'L' and resid 47 through 50
      removed outlier: 6.564A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ASN L 101 " --> pdb=" O   ASP L  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 47 through 50
      removed outlier: 6.564A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.462A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454

    114 hydrogen bonds defined for protein.
    261 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: 0.46

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 569
        1.32 -     1.45: 847
        1.45 -     1.58: 1470
        1.58 -     1.71: 12
        1.71 -     1.84: 18
  Bond restraints: 2916
  Sorted by residual:
  bond pdb=" NE  ARG L  63 "
       pdb=" CZ  ARG L  63 "
    ideal  model  delta    sigma   weight residual
    1.326  1.384 -0.058 1.10e-02 8.26e+03 2.78e+01
  bond pdb=" CB  LEU L 110 "
       pdb=" CG  LEU L 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.611 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" NE  ARG H  50 "
       pdb=" CZ  ARG H  50 "
    ideal  model  delta    sigma   weight residual
    1.326  1.362 -0.036 1.10e-02 8.26e+03 1.08e+01
  bond pdb=" CB  TYR L  38 "
       pdb=" CG  TYR L  38 "
    ideal  model  delta    sigma   weight residual
    1.512  1.441  0.071 2.20e-02 2.07e+03 1.03e+01
  bond pdb=" CG  ASP B 398 "
       pdb=" OD1 ASP B 398 "
    ideal  model  delta    sigma   weight residual
    1.249  1.190  0.059 1.90e-02 2.77e+03 9.54e+00
  ... (remaining 2911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 3296
        1.80 -     3.59: 547
        3.59 -     5.39: 106
        5.39 -     7.19: 26
        7.19 -     8.98: 2
  Bond angle restraints: 3977
  Sorted by residual:
  angle pdb=" C   GLN B 498 "
        pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     119.56  128.54   -8.98 1.02e+00 9.61e-01 7.76e+01
  angle pdb=" C   ARG L  56 "
        pdb=" N   PRO L  57 "
        pdb=" CA  PRO L  57 "
      ideal   model   delta    sigma   weight residual
     120.03  127.11   -7.08 9.90e-01 1.02e+00 5.12e+01
  angle pdb=" C   ALA B 520 "
        pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
      ideal   model   delta    sigma   weight residual
     119.56  126.54   -6.98 1.02e+00 9.61e-01 4.68e+01
  angle pdb=" C   GLY L  99 "
        pdb=" N   PRO L 100 "
        pdb=" CA  PRO L 100 "
      ideal   model   delta    sigma   weight residual
     119.76  126.15   -6.39 1.03e+00 9.43e-01 3.85e+01
  angle pdb=" N   SER L  54 "
        pdb=" CA  SER L  54 "
        pdb=" CB  SER L  54 "
      ideal   model   delta    sigma   weight residual
     111.79  104.82    6.97 1.20e+00 6.94e-01 3.37e+01
  ... (remaining 3972 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 1619
       17.78 -    35.57: 57
       35.57 -    53.35: 9
       53.35 -    71.14: 2
       71.14 -    88.92: 3
  Dihedral angle restraints: 1690
    sinusoidal: 582
      harmonic: 1108
  Sorted by residual:
  dihedral pdb=" CB  GLU B 406 "
           pdb=" CG  GLU B 406 "
           pdb=" CD  GLU B 406 "
           pdb=" OE1 GLU B 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.92  -88.92     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  119.87  -26.87     1      1.00e+01 1.00e-02 1.04e+01
  dihedral pdb=" CA  ARG H  98 "
           pdb=" CB  ARG H  98 "
           pdb=" CG  ARG H  98 "
           pdb=" CD  ARG H  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  105.43  -45.43     3      1.50e+01 4.44e-03 8.17e+00
  ... (remaining 1687 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 312
       0.079 -    0.159: 94
       0.159 -    0.238: 20
       0.238 -    0.317: 4
       0.317 -    0.397: 4
  Chirality restraints: 434
  Sorted by residual:
  chirality pdb=" CB  VAL H   2 "
            pdb=" CA  VAL H   2 "
            pdb=" CG1 VAL H   2 "
            pdb=" CG2 VAL H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.03    0.40 2.00e-01 2.50e+01 3.93e+00
  chirality pdb=" C2  NAG B1301 "
            pdb=" C1  NAG B1301 "
            pdb=" C3  NAG B1301 "
            pdb=" N2  NAG B1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CG  LEU L 110 "
            pdb=" CB  LEU L 110 "
            pdb=" CD1 LEU L 110 "
            pdb=" CD2 LEU L 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.92    0.33 2.00e-01 2.50e+01 2.75e+00
  ... (remaining 431 not shown)

  Planarity restraints: 519
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L 102 "    0.030 2.00e-02 2.50e+03   1.60e-02 6.39e+00
        pdb=" CG  TRP L 102 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TRP L 102 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP L 102 "   -0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP L 102 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP L 102 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP L 102 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L 102 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L 102 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP L 102 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 104 "    0.028 2.00e-02 2.50e+03   1.47e-02 4.35e+00
        pdb=" CG  TYR H 104 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 104 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 104 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 104 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 104 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 104 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR H 104 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  37 "   -0.021 2.00e-02 2.50e+03   1.18e-02 3.45e+00
        pdb=" CG  TRP L  37 "    0.006 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  37 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  37 "    0.014 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  37 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  37 "    0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  37 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  37 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  37 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  37 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 516 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 822
        2.82 -     3.34: 2339
        3.34 -     3.86: 4627
        3.86 -     4.38: 5445
        4.38 -     4.90: 9158
  Nonbonded interactions: 22391
  Sorted by model distance:
  nonbonded pdb=" O   GLY H  27 "
            pdb=" CG1 ILE H  28 "
     model   vdw
     2.298 3.440
  nonbonded pdb=" N   ASP H 114 "
            pdb=" OD1 ASP H 114 "
     model   vdw
     2.477 3.120
  nonbonded pdb=" N   GLY L  30 "
            pdb=" N   ALA L  31 "
     model   vdw
     2.536 2.560
  nonbonded pdb=" OD1 ASN L  28 "
            pdb=" N   ILE L  29 "
     model   vdw
     2.540 3.120
  nonbonded pdb=" OE1 GLU H  46 "
            pdb=" NZ  LYS H  63 "
     model   vdw
     2.565 3.120
  ... (remaining 22386 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:             4.160
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.150
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.081   2922  Z= 0.771
  Angle     :  1.468   8.985   3990  Z= 0.998
  Chirality :  0.086   0.397    434
  Planarity :  0.006   0.037    518
  Dihedral  : 10.313  88.920    973
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 0.56
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.22 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.76 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.43), residues: 373
  helix: -4.68 (0.26), residues: 27
  sheet:  0.49 (0.44), residues: 140
  loop : -0.09 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  98 
 TYR   0.028   0.005   TYR H 104 
 PHE   0.015   0.003   PHE H 113 
 TRP   0.030   0.007   TRP L 102 
 HIS   0.003   0.002   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.01431 ( 2916)
  covalent geometry    : angle       1.46452 ( 3977)
  SS BOND              : bond        0.01804 (    5)
  SS BOND              : angle       2.40214 (   10)
  hydrogen bonds       : bond        0.16198 (  103)
  hydrogen bonds       : angle       9.03477 (  261)
  link_NAG-ASN         : bond        0.05995 (    1)
  link_NAG-ASN         : angle       2.24467 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8236 (mtpt)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0681
  time to fit residues: 8.4492
Evaluate side-chains
  61 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 26 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.2778

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

Flipped N/Q/H residues before XYZ refinement:
H 103 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN
B 460 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.151612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.141947 restraints weight = 4509.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.144801 restraints weight = 2578.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.146457 restraints weight = 1657.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.147743 restraints weight = 1176.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.148660 restraints weight = 853.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   2922  Z= 0.165
  Angle     :  0.660   7.914   3990  Z= 0.346
  Chirality :  0.048   0.138    434
  Planarity :  0.004   0.029    518
  Dihedral  :  4.540  17.470    440
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  2.95 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.57 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.42), residues: 373
  helix: -4.22 (0.61), residues: 27
  sheet:  0.32 (0.41), residues: 147
  loop : -0.27 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  38 
 TYR   0.018   0.002   TYR B 369 
 PHE   0.024   0.002   PHE H  29 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.002   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 2916)
  covalent geometry    : angle       0.64763 ( 3977)
  SS BOND              : bond        0.00743 (    5)
  SS BOND              : angle       2.37818 (   10)
  hydrogen bonds       : bond        0.03418 (  103)
  hydrogen bonds       : angle       6.88623 (  261)
  link_NAG-ASN         : bond        0.00089 (    1)
  link_NAG-ASN         : angle       2.22852 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0634
  time to fit residues: 5.9431
Evaluate side-chains
  70 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  391 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0970
   chunk 0 optimal weight:    0.9980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
H 103 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.128537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.117518 restraints weight = 4699.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.120446 restraints weight = 2696.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.122372 restraints weight = 1750.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.123686 restraints weight = 1228.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124559 restraints weight = 913.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2922  Z= 0.194
  Angle     :  0.647   7.354   3990  Z= 0.337
  Chirality :  0.047   0.132    434
  Planarity :  0.004   0.034    518
  Dihedral  :  4.586  20.815    440
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.49 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 16.93 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.42), residues: 373
  helix: -4.18 (0.67), residues: 27
  sheet:  0.79 (0.44), residues: 130
  loop : -0.25 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 509 
 TYR   0.022   0.002   TYR B 369 
 PHE   0.020   0.002   PHE H  29 
 TRP   0.008   0.001   TRP H 116 
 HIS   0.002   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 2916)
  covalent geometry    : angle       0.64266 ( 3977)
  SS BOND              : bond        0.00368 (    5)
  SS BOND              : angle       1.35456 (   10)
  hydrogen bonds       : bond        0.03426 (  103)
  hydrogen bonds       : angle       6.33900 (  261)
  link_NAG-ASN         : bond        0.00066 (    1)
  link_NAG-ASN         : angle       1.78218 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 LEU cc_start: 0.8501 (pp) cc_final: 0.8276 (pp)
REVERT: L   56 ARG cc_start: 0.5608 (mtm-85) cc_final: 0.4890 (ptm-80)
REVERT: B  430 THR cc_start: 0.8782 (m) cc_final: 0.8197 (p)
REVERT: B  461 LEU cc_start: 0.8182 (mt) cc_final: 0.7829 (mt)
  outliers start: 12
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0571
  time to fit residues: 4.9066
Evaluate side-chains
  65 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0270
   chunk 11 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
H 103 ASN
L  40 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.125941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.115297 restraints weight = 4678.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.117904 restraints weight = 2690.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.119766 restraints weight = 1766.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.121184 restraints weight = 1251.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.122107 restraints weight = 930.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   2922  Z= 0.216
  Angle     :  0.651   6.913   3990  Z= 0.335
  Chirality :  0.047   0.138    434
  Planarity :  0.004   0.037    518
  Dihedral  :  4.698  20.719    440
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.68 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 17.72 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.42), residues: 373
  helix: -4.15 (0.67), residues: 27
  sheet:  0.68 (0.43), residues: 129
  loop : -0.41 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  63 
 TYR   0.019   0.002   TYR B 369 
 PHE   0.022   0.002   PHE H  29 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.002   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 2916)
  covalent geometry    : angle       0.64869 ( 3977)
  SS BOND              : bond        0.00766 (    5)
  SS BOND              : angle       0.99945 (   10)
  hydrogen bonds       : bond        0.03484 (  103)
  hydrogen bonds       : angle       6.28181 (  261)
  link_NAG-ASN         : bond        0.00100 (    1)
  link_NAG-ASN         : angle       1.67854 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 LEU cc_start: 0.8489 (pp) cc_final: 0.8282 (pp)
REVERT: L   56 ARG cc_start: 0.5645 (mtm-85) cc_final: 0.4952 (ptm-80)
REVERT: B  371 SER cc_start: 0.8337 (t) cc_final: 0.8104 (p)
REVERT: B  430 THR cc_start: 0.8810 (m) cc_final: 0.8231 (p)
REVERT: B  461 LEU cc_start: 0.8088 (mt) cc_final: 0.7729 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 68
  average time/residue: 0.0509
  time to fit residues: 4.3608
Evaluate side-chains
  66 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  445 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 33 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0050
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
H 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.124859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114588 restraints weight = 4525.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.117300 restraints weight = 2628.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.119141 restraints weight = 1727.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.120476 restraints weight = 1214.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.121381 restraints weight = 896.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.4719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   2922  Z= 0.257
  Angle     :  0.688   7.630   3990  Z= 0.356
  Chirality :  0.047   0.146    434
  Planarity :  0.005   0.043    518
  Dihedral  :  5.236  23.261    440
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.29 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 18.11 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.41), residues: 373
  helix: -4.10 (0.72), residues: 26
  sheet:  0.37 (0.43), residues: 131
  loop : -0.74 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 454 
 TYR   0.021   0.002   TYR B 369 
 PHE   0.021   0.003   PHE H  29 
 TRP   0.007   0.001   TRP H 107 
 HIS   0.001   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 2916)
  covalent geometry    : angle       0.68553 ( 3977)
  SS BOND              : bond        0.00576 (    5)
  SS BOND              : angle       1.03933 (   10)
  hydrogen bonds       : bond        0.03683 (  103)
  hydrogen bonds       : angle       6.42113 (  261)
  link_NAG-ASN         : bond        0.00141 (    1)
  link_NAG-ASN         : angle       1.72504 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 LEU cc_start: 0.8501 (pp) cc_final: 0.8249 (pp)
REVERT: L   56 ARG cc_start: 0.5910 (mtm-85) cc_final: 0.5217 (ptm-80)
REVERT: B  430 THR cc_start: 0.8823 (m) cc_final: 0.8394 (p)
REVERT: B  441 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7765 (tt)
REVERT: B  461 LEU cc_start: 0.8075 (mt) cc_final: 0.7697 (mt)
  outliers start: 18
  outliers final: 12
  residues processed: 69
  average time/residue: 0.0554
  time to fit residues: 4.7502
Evaluate side-chains
  70 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   75 LEU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  445 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0470
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
H 103 ASN
L  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.126163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.115895 restraints weight = 4555.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.118561 restraints weight = 2615.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.120442 restraints weight = 1711.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.121761 restraints weight = 1199.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.122676 restraints weight = 881.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   2922  Z= 0.219
  Angle     :  0.653   6.705   3990  Z= 0.337
  Chirality :  0.047   0.138    434
  Planarity :  0.005   0.046    518
  Dihedral  :  5.039  22.416    440
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.49 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 20.87 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.41), residues: 373
  helix: -4.17 (0.68), residues: 26
  sheet:  0.31 (0.43), residues: 132
  loop : -0.82 (0.41), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  38 
 TYR   0.019   0.002   TYR B 369 
 PHE   0.023   0.002   PHE H  29 
 TRP   0.006   0.001   TRP H 107 
 HIS   0.001   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 2916)
  covalent geometry    : angle       0.64940 ( 3977)
  SS BOND              : bond        0.00705 (    5)
  SS BOND              : angle       1.31959 (   10)
  hydrogen bonds       : bond        0.03576 (  103)
  hydrogen bonds       : angle       6.42160 (  261)
  link_NAG-ASN         : bond        0.00002 (    1)
  link_NAG-ASN         : angle       1.51816 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: L    5 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8132 (p)
REVERT: L   49 LEU cc_start: 0.8436 (pp) cc_final: 0.8223 (pp)
REVERT: L   56 ARG cc_start: 0.6070 (mtm-85) cc_final: 0.5267 (ptm-80)
REVERT: B  430 THR cc_start: 0.8794 (m) cc_final: 0.8295 (p)
REVERT: B  441 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7823 (tt)
REVERT: B  461 LEU cc_start: 0.7963 (mt) cc_final: 0.7614 (mt)
  outliers start: 13
  outliers final: 9
  residues processed: 69
  average time/residue: 0.0496
  time to fit residues: 4.3369
Evaluate side-chains
  68 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  445 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0770
   chunk 24 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0050
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.3352

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.127277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.116961 restraints weight = 4513.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.119720 restraints weight = 2603.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.121633 restraints weight = 1700.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.123003 restraints weight = 1189.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.123959 restraints weight = 866.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.5024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   2922  Z= 0.163
  Angle     :  0.615   7.812   3990  Z= 0.314
  Chirality :  0.046   0.135    434
  Planarity :  0.004   0.047    518
  Dihedral  :  4.634  20.361    440
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.83 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 22.83 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.41), residues: 373
  helix: -4.19 (0.66), residues: 26
  sheet:  0.37 (0.43), residues: 130
  loop : -0.91 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 403 
 TYR   0.018   0.001   TYR B 369 
 PHE   0.022   0.002   PHE H  29 
 TRP   0.005   0.001   TRP B 436 
 HIS   0.001   0.000   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 2916)
  covalent geometry    : angle       0.61298 ( 3977)
  SS BOND              : bond        0.00516 (    5)
  SS BOND              : angle       1.06662 (   10)
  hydrogen bonds       : bond        0.03324 (  103)
  hydrogen bonds       : angle       6.27964 (  261)
  link_NAG-ASN         : bond        0.00065 (    1)
  link_NAG-ASN         : angle       1.37283 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: H   48 MET cc_start: 0.6204 (mtm) cc_final: 0.5928 (mtm)
REVERT: L    5 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8117 (p)
REVERT: L   49 LEU cc_start: 0.8406 (pp) cc_final: 0.8182 (pp)
REVERT: L   56 ARG cc_start: 0.6026 (mtm-85) cc_final: 0.5176 (ptm-80)
REVERT: B  430 THR cc_start: 0.8779 (m) cc_final: 0.8390 (p)
REVERT: B  461 LEU cc_start: 0.7872 (mt) cc_final: 0.7550 (mt)
  outliers start: 10
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0519
  time to fit residues: 4.2984
Evaluate side-chains
  65 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  445 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0020
   chunk 20 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0370
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.3066

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.130380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.121474 restraints weight = 4517.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.123890 restraints weight = 2687.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.125488 restraints weight = 1760.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.126665 restraints weight = 1244.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.127468 restraints weight = 918.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.5188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2922  Z= 0.148
  Angle     :  0.588   7.814   3990  Z= 0.300
  Chirality :  0.045   0.132    434
  Planarity :  0.004   0.047    518
  Dihedral  :  4.366  18.923    440
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.56 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 22.44 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.41), residues: 373
  helix: -4.23 (0.65), residues: 26
  sheet:  0.26 (0.41), residues: 146
  loop : -1.02 (0.41), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  38 
 TYR   0.018   0.001   TYR B 369 
 PHE   0.021   0.002   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.000   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2916)
  covalent geometry    : angle       0.58594 ( 3977)
  SS BOND              : bond        0.00504 (    5)
  SS BOND              : angle       0.98943 (   10)
  hydrogen bonds       : bond        0.03139 (  103)
  hydrogen bonds       : angle       6.10456 (  261)
  link_NAG-ASN         : bond        0.00058 (    1)
  link_NAG-ASN         : angle       1.36920 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: L    5 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8091 (p)
REVERT: L   49 LEU cc_start: 0.8351 (pp) cc_final: 0.8133 (pp)
REVERT: L   56 ARG cc_start: 0.6022 (mtm-85) cc_final: 0.5267 (ptm-80)
REVERT: B  430 THR cc_start: 0.8768 (m) cc_final: 0.8359 (p)
REVERT: B  461 LEU cc_start: 0.7802 (mt) cc_final: 0.7489 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0474
  time to fit residues: 3.9606
Evaluate side-chains
  68 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  445 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.123835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.113355 restraints weight = 4639.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.116120 restraints weight = 2644.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.118037 restraints weight = 1718.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.119181 restraints weight = 1201.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.120173 restraints weight = 908.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.5338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   2922  Z= 0.217
  Angle     :  0.636   7.231   3990  Z= 0.329
  Chirality :  0.046   0.134    434
  Planarity :  0.005   0.049    518
  Dihedral  :  4.754  23.033    440
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.09 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 22.44 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.41), residues: 373
  helix: -4.23 (0.69), residues: 26
  sheet:  0.24 (0.43), residues: 136
  loop : -0.99 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 403 
 TYR   0.020   0.002   TYR B 369 
 PHE   0.025   0.002   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 2916)
  covalent geometry    : angle       0.63372 ( 3977)
  SS BOND              : bond        0.00567 (    5)
  SS BOND              : angle       1.10742 (   10)
  hydrogen bonds       : bond        0.03442 (  103)
  hydrogen bonds       : angle       6.31263 (  261)
  link_NAG-ASN         : bond        0.00023 (    1)
  link_NAG-ASN         : angle       1.48176 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: L    5 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8166 (p)
REVERT: L   49 LEU cc_start: 0.8433 (pp) cc_final: 0.8214 (pp)
REVERT: L   56 ARG cc_start: 0.6135 (mtm-85) cc_final: 0.5349 (ptm-80)
REVERT: B  430 THR cc_start: 0.8782 (m) cc_final: 0.8353 (p)
REVERT: B  461 LEU cc_start: 0.7845 (mt) cc_final: 0.7528 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0446
  time to fit residues: 3.6614
Evaluate side-chains
  68 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  445 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 14 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
H  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.127218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.117431 restraints weight = 4508.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.119961 restraints weight = 2596.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.121763 restraints weight = 1689.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.123031 restraints weight = 1181.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.123951 restraints weight = 868.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.5470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   2922  Z= 0.223
  Angle     :  0.636   7.087   3990  Z= 0.329
  Chirality :  0.047   0.135    434
  Planarity :  0.005   0.052    518
  Dihedral  :  4.833  23.446    440
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.56 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 22.83 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.33 (0.41), residues: 373
  helix: -4.26 (0.68), residues: 26
  sheet:  0.18 (0.43), residues: 135
  loop : -1.16 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 408 
 TYR   0.020   0.002   TYR B 369 
 PHE   0.026   0.002   PHE H  29 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.000   0.000   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 2916)
  covalent geometry    : angle       0.63375 ( 3977)
  SS BOND              : bond        0.00541 (    5)
  SS BOND              : angle       1.06042 (   10)
  hydrogen bonds       : bond        0.03412 (  103)
  hydrogen bonds       : angle       6.33944 (  261)
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       1.52934 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 LEU cc_start: 0.8377 (pp) cc_final: 0.8157 (pp)
REVERT: L   56 ARG cc_start: 0.6033 (mtm-85) cc_final: 0.5279 (ptm-80)
REVERT: B  430 THR cc_start: 0.8774 (m) cc_final: 0.8353 (p)
REVERT: B  461 LEU cc_start: 0.7824 (mt) cc_final: 0.7513 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0482
  time to fit residues: 3.9324
Evaluate side-chains
  65 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  445 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   chunk 1 optimal weight:    0.0770
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.3538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.128594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.118590 restraints weight = 4434.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.121254 restraints weight = 2557.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.123079 restraints weight = 1661.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.124307 restraints weight = 1161.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.125268 restraints weight = 861.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.5514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   2922  Z= 0.163
  Angle     :  0.593   7.410   3990  Z= 0.303
  Chirality :  0.045   0.134    434
  Planarity :  0.005   0.053    518
  Dihedral  :  4.521  20.858    440
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.29 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 23.23 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.42), residues: 373
  helix: -4.27 (0.66), residues: 26
  sheet:  0.07 (0.42), residues: 147
  loop : -1.26 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 403 
 TYR   0.018   0.001   TYR B 369 
 PHE   0.023   0.002   PHE H  29 
 TRP   0.007   0.001   TRP H 107 
 HIS   0.001   0.000   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 2916)
  covalent geometry    : angle       0.59029 ( 3977)
  SS BOND              : bond        0.00476 (    5)
  SS BOND              : angle       0.95581 (   10)
  hydrogen bonds       : bond        0.03159 (  103)
  hydrogen bonds       : angle       6.18787 (  261)
  link_NAG-ASN         : bond        0.00083 (    1)
  link_NAG-ASN         : angle       1.42249 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 759.48 seconds
wall clock time: 13 minutes 40.61 seconds (820.61 seconds total)