Starting phenix.real_space_refine
on Tue Mar  3 12:05:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sof_25269/03_2026/7sof_25269.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sof_25269/03_2026/7sof_25269.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sof_25269/03_2026/7sof_25269.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sof_25269/03_2026/7sof_25269.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sof_25269/03_2026/7sof_25269.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sof_25269/03_2026/7sof_25269.cif"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.045
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      13      5.16       5
     C    2426      2.51       5
     N     611      2.21       5
     O     685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3735
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 730
          Classifications: {'peptide': 105}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 7, 'TRANS': 97}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "H"
      Number of atoms: 916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 916
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 7, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1966
          Classifications: {'peptide': 258}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 13, 'TRANS': 244}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 171
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'PHE:plan': 1, 'ASP:plan': 7, 'ARG:plan': 2, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 77
    Chain: "B"
      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 dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 0.98, per 1000 atoms: 0.26
  Number of scatterers: 3735
  At special positions: 0
  Unit cell: (73.341, 91.044, 77.556, 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      13     16.00
     O     685      8.00
     N     611      7.00
     C    2426      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.02

  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 B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 282 "
      " NAG A1303 " - " ASN A 165 "
      " NAG A1304 " - " ASN A 234 "
      " NAG A1305 " - " ASN A 149 "
      " NAG A1306 " - " ASN A  17 "
      " NAG B   1 " - " ASN A 122 "
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 89.6 milliseconds
  

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  912

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 6 sheets defined
      4.7% alpha, 38.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'L' and resid 78 through 82
      removed outlier: 3.797A  pdb=" N   GLU L  82 " --> pdb=" O   THR L  79 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 65 through 67
      No H-bonds generated for 'chain 'H' and resid 65 through 67'
    Processing helix  chain 'H' and resid 88 through 92
    Processing helix  chain 'A' and resid 294 through 303
    Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11
      removed outlier: 6.529A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 104 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   TRP L  34 " --> pdb=" O   VAL L  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 11 through 12
    current: chain 'H' and resid 48 through 54
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 59 through 61
    current: chain 'H' and resid 108 through 115
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 108 through 115
    current: chain 'A' and resid 116 through 121
      removed outlier: 6.601A  pdb=" N   VAL A 126 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   TYR A 170 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ILE A 128 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   PHE A 168 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   VAL A 130 " --> pdb=" O   CYS A 166 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER A 162 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   CYS A 136 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   TYR A 160 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP A 138 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   ARG A 158 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   PHE A 140 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   GLU A 156 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   ASP A 142 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      removed outlier: 5.299A  pdb=" N   LYS A 154 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   TYR A 144 " --> pdb=" O   TRP A 152 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   TRP A 152 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 27 through 31
      removed outlier: 8.484A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 55
      removed outlier: 3.711A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)

    116 hydrogen bonds defined for protein.
    288 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: 0.39

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 730
        1.33 -     1.45: 971
        1.45 -     1.57: 2117
        1.57 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3834
  Sorted by residual:
  bond pdb=" NE  ARG A 246 "
       pdb=" CZ  ARG A 246 "
    ideal  model  delta    sigma   weight residual
    1.326  1.369 -0.043 1.10e-02 8.26e+03 1.50e+01
  bond pdb=" NE  ARG A  78 "
       pdb=" CZ  ARG A  78 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.41e+01
  bond pdb=" N   ILE L  94 "
       pdb=" CA  ILE L  94 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.19e-02 7.06e+03 8.85e+00
  bond pdb=" C5  NAG A1303 "
       pdb=" O5  NAG A1303 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.31e+00
  bond pdb=" C5  NAG A1305 "
       pdb=" O5  NAG A1305 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.17e+00
  ... (remaining 3829 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 4327
        1.49 -     2.99: 734
        2.99 -     4.48: 108
        4.48 -     5.98: 52
        5.98 -     7.47: 27
  Bond angle restraints: 5248
  Sorted by residual:
  angle pdb=" C   GLN H  41 "
        pdb=" N   PRO H  42 "
        pdb=" CA  PRO H  42 "
      ideal   model   delta    sigma   weight residual
     119.66  125.79   -6.13 7.30e-01 1.88e+00 7.05e+01
  angle pdb=" C   ASN A  81 "
        pdb=" N   PRO A  82 "
        pdb=" CA  PRO A  82 "
      ideal   model   delta    sigma   weight residual
     120.03  127.20   -7.17 9.90e-01 1.02e+00 5.24e+01
  angle pdb=" C   GLY H   8 "
        pdb=" N   PRO H   9 "
        pdb=" CA  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     119.76  126.99   -7.23 1.03e+00 9.43e-01 4.93e+01
  angle pdb=" C   ASP A 138 "
        pdb=" N   PRO A 139 "
        pdb=" CA  PRO A 139 "
      ideal   model   delta    sigma   weight residual
     119.76  126.70   -6.94 1.00e+00 1.00e+00 4.82e+01
  angle pdb=" C   ARG L  53 "
        pdb=" N   PRO L  54 "
        pdb=" CA  PRO L  54 "
      ideal   model   delta    sigma   weight residual
     119.85  126.83   -6.98 1.01e+00 9.80e-01 4.78e+01
  ... (remaining 5243 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.32: 2273
       21.32 -    42.64: 44
       42.64 -    63.96: 5
       63.96 -    85.28: 7
       85.28 -   106.60: 4
  Dihedral angle restraints: 2333
    sinusoidal: 916
      harmonic: 1417
  Sorted by residual:
  dihedral pdb=" C   THR L  93 "
           pdb=" N   THR L  93 "
           pdb=" CA  THR L  93 "
           pdb=" CB  THR L  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.33   10.33     0      2.50e+00 1.60e-01 1.71e+01
  dihedral pdb=" CA  GLY H 105 "
           pdb=" C   GLY H 105 "
           pdb=" N   GLU H 106 "
           pdb=" CA  GLU H 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.62   20.38     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.89  106.60     1      3.00e+01 1.11e-03 1.37e+01
  ... (remaining 2330 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 447
       0.070 -    0.139: 136
       0.139 -    0.209: 29
       0.209 -    0.278: 4
       0.278 -    0.348: 10
  Chirality restraints: 626
  Sorted by residual:
  chirality pdb=" C1  BMA B   3 "
            pdb=" O4  NAG B   2 "
            pdb=" C2  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.52    0.12 2.00e-02 2.50e+03 3.71e+01
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.47    0.07 2.00e-02 2.50e+03 1.13e+01
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.62    0.35 2.00e-01 2.50e+01 3.03e+00
  ... (remaining 623 not shown)

  Planarity restraints: 659
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  96 "    0.034 2.00e-02 2.50e+03   1.80e-02 6.45e+00
        pdb=" CG  TYR H  96 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  96 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  96 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  96 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  96 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  96 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H  96 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY H 105 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.75e+00
        pdb=" C   GLY H 105 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLY H 105 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU H 106 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1303 "   -0.026 2.00e-02 2.50e+03   2.12e-02 5.61e+00
        pdb=" C7  NAG A1303 "   -0.003 2.00e-02 2.50e+03
        pdb=" C8  NAG A1303 "   -0.016 2.00e-02 2.50e+03
        pdb=" N2  NAG A1303 "    0.035 2.00e-02 2.50e+03
        pdb=" O7  NAG A1303 "    0.010 2.00e-02 2.50e+03
  ... (remaining 656 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 2165
        3.03 -     3.50: 3156
        3.50 -     3.97: 6049
        3.97 -     4.43: 6775
        4.43 -     4.90: 11258
  Nonbonded interactions: 29403
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A 146 "
            pdb=" N   LYS A 147 "
     model   vdw
     2.563 3.200
  nonbonded pdb=" O   PRO H  14 "
            pdb=" OG1 THR H  15 "
     model   vdw
     2.593 3.040
  nonbonded pdb=" N   ASN A 148 "
            pdb=" O   ASN A 148 "
     model   vdw
     2.603 2.496
  nonbonded pdb=" N   THR H  10 "
            pdb=" N   LEU H  11 "
     model   vdw
     2.608 2.560
  nonbonded pdb=" OD1 ASP H 113 "
            pdb=" N   VAL H 114 "
     model   vdw
     2.625 3.120
  ... (remaining 29398 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:             10.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.300
  Find NCS groups from input model:        0.010
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
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      :  0.010   0.062   3848  Z= 0.575
  Angle     :  1.320   7.472   5285  Z= 0.869
  Chirality :  0.080   0.348    626
  Planarity :  0.005   0.024    652
  Dihedral  : 11.425 106.597   1406
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 1.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.22 %
  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 are not related in a simple way.
  whole:  0.64 (0.38), residues: 474
  helix:  0.56 (1.75), residues: 11
  sheet:  1.23 (0.35), residues: 207
  loop : -0.24 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  40 
 TYR   0.034   0.005   TYR H  96 
 PHE   0.014   0.003   PHE A 220 
 TRP   0.019   0.004   TRP L  90 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.01013 ( 3834)
  covalent geometry    : angle       1.30778 ( 5248)
  SS BOND              : bond        0.00544 (    5)
  SS BOND              : angle       1.93358 (   10)
  hydrogen bonds       : bond        0.16819 (  116)
  hydrogen bonds       : angle       7.97272 (  288)
  link_BETA1-4         : bond        0.05715 (    2)
  link_BETA1-4         : angle       2.83908 (    6)
  link_NAG-ASN         : bond        0.05510 (    7)
  link_NAG-ASN         : angle       2.65280 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.082 
Fit side-chains
REVERT: L   36 GLN cc_start: 0.8889 (tt0) cc_final: 0.8627 (tt0)
REVERT: H    3 THR cc_start: 0.7351 (t) cc_final: 0.7149 (m)
REVERT: H   62 SER cc_start: 0.8441 (t) cc_final: 0.8090 (p)
REVERT: H  124 SER cc_start: 0.6718 (p) cc_final: 0.6437 (t)
REVERT: A  154 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8075 (ttpp)
REVERT: A  258 TRP cc_start: 0.7459 (m-90) cc_final: 0.7187 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0717
  time to fit residues: 7.7321
Evaluate side-chains
  63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
L  49 GLN
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.182044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.149621 restraints weight = 4141.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.150291 restraints weight = 3045.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.153392 restraints weight = 2977.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.153992 restraints weight = 2188.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.157952 restraints weight = 1979.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3848  Z= 0.167
  Angle     :  0.621   5.554   5285  Z= 0.323
  Chirality :  0.047   0.174    626
  Planarity :  0.005   0.052    652
  Dihedral  :  8.418  64.032    704
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  1.27 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  7.35 %
    Favored  : 91.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.94 (0.39), residues: 474
  helix:  1.82 (1.56), residues: 11
  sheet:  1.33 (0.36), residues: 214
  loop : -0.02 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 102 
 TYR   0.025   0.002   TYR L  48 
 PHE   0.016   0.002   PHE A  55 
 TRP   0.010   0.001   TRP H 103 
 HIS   0.002   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 3834)
  covalent geometry    : angle       0.59870 ( 5248)
  SS BOND              : bond        0.00678 (    5)
  SS BOND              : angle       1.98766 (   10)
  hydrogen bonds       : bond        0.03898 (  116)
  hydrogen bonds       : angle       6.23752 (  288)
  link_BETA1-4         : bond        0.00468 (    2)
  link_BETA1-4         : angle       2.44869 (    6)
  link_NAG-ASN         : bond        0.00271 (    7)
  link_NAG-ASN         : angle       1.95867 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  154 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8169 (ttpp)
REVERT: A  258 TRP cc_start: 0.8002 (m-90) cc_final: 0.7587 (m-90)
  outliers start: 5
  outliers final: 2
  residues processed: 68
  average time/residue: 0.0703
  time to fit residues: 5.8419
Evaluate side-chains
  62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain H residue   83 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0000
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 37 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0770
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.3942

-------------------------------------------------------------------------------
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 = 0.4124 r_free = 0.4124 target = 0.191102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.159165 restraints weight = 4091.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.162242 restraints weight = 3203.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.164338 restraints weight = 2634.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.164969 restraints weight = 1995.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.165319 restraints weight = 1858.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3848  Z= 0.123
  Angle     :  0.566   5.752   5285  Z= 0.287
  Chirality :  0.045   0.167    626
  Planarity :  0.004   0.048    652
  Dihedral  :  6.296  39.538    704
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  8.82 %
    Favored  : 89.12 %
  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 are not related in a simple way.
  whole:  0.87 (0.39), residues: 474
  helix:  2.81 (1.63), residues: 11
  sheet:  1.31 (0.35), residues: 214
  loop : -0.16 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 102 
 TYR   0.020   0.001   TYR L  48 
 PHE   0.011   0.001   PHE A  55 
 TRP   0.006   0.001   TRP H 103 
 HIS   0.002   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3834)
  covalent geometry    : angle       0.55070 ( 5248)
  SS BOND              : bond        0.00285 (    5)
  SS BOND              : angle       1.21644 (   10)
  hydrogen bonds       : bond        0.03358 (  116)
  hydrogen bonds       : angle       5.84155 (  288)
  link_BETA1-4         : bond        0.00665 (    2)
  link_BETA1-4         : angle       2.48266 (    6)
  link_NAG-ASN         : bond        0.00345 (    7)
  link_NAG-ASN         : angle       1.53409 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8296 (ttpp)
REVERT: A  258 TRP cc_start: 0.8229 (m-90) cc_final: 0.7720 (m-90)
  outliers start: 7
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0865
  time to fit residues: 6.2813
Evaluate side-chains
  62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  210 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0570
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
L  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.161955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.129957 restraints weight = 4300.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.131097 restraints weight = 3567.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.132692 restraints weight = 3594.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.133348 restraints weight = 2716.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.134619 restraints weight = 2375.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3848  Z= 0.189
  Angle     :  0.588   5.131   5285  Z= 0.303
  Chirality :  0.046   0.167    626
  Planarity :  0.005   0.051    652
  Dihedral  :  5.260  37.112    704
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  :  8.24 %
    Favored  : 87.65 %
  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 are not related in a simple way.
  whole:  0.42 (0.38), residues: 474
  helix:  3.05 (1.63), residues: 11
  sheet:  1.00 (0.36), residues: 190
  loop : -0.35 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  53 
 TYR   0.017   0.002   TYR L  48 
 PHE   0.013   0.002   PHE A 157 
 TRP   0.007   0.001   TRP A 258 
 HIS   0.003   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 3834)
  covalent geometry    : angle       0.57344 ( 5248)
  SS BOND              : bond        0.00398 (    5)
  SS BOND              : angle       1.61876 (   10)
  hydrogen bonds       : bond        0.03472 (  116)
  hydrogen bonds       : angle       5.73456 (  288)
  link_BETA1-4         : bond        0.00675 (    2)
  link_BETA1-4         : angle       2.13354 (    6)
  link_NAG-ASN         : bond        0.00232 (    7)
  link_NAG-ASN         : angle       1.53044 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: L    2 TYR cc_start: 0.8715 (t80) cc_final: 0.8325 (t80)
REVERT: A  154 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8348 (ttpp)
  outliers start: 14
  outliers final: 10
  residues processed: 64
  average time/residue: 0.0718
  time to fit residues: 5.5284
Evaluate side-chains
  62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  284 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.158460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.126956 restraints weight = 4372.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.128703 restraints weight = 3760.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.129824 restraints weight = 3676.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.130536 restraints weight = 2762.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.131600 restraints weight = 2421.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3848  Z= 0.202
  Angle     :  0.598   7.527   5285  Z= 0.302
  Chirality :  0.046   0.165    626
  Planarity :  0.004   0.047    652
  Dihedral  :  5.397  38.001    704
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  :  9.12 %
    Favored  : 87.06 %
  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 are not related in a simple way.
  whole:  0.35 (0.39), residues: 474
  helix:  3.23 (1.64), residues: 11
  sheet:  0.78 (0.36), residues: 191
  loop : -0.25 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 158 
 TYR   0.016   0.002   TYR A 265 
 PHE   0.013   0.002   PHE A 238 
 TRP   0.007   0.001   TRP H 115 
 HIS   0.004   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 3834)
  covalent geometry    : angle       0.58433 ( 5248)
  SS BOND              : bond        0.00380 (    5)
  SS BOND              : angle       1.60694 (   10)
  hydrogen bonds       : bond        0.03529 (  116)
  hydrogen bonds       : angle       5.75854 (  288)
  link_BETA1-4         : bond        0.00662 (    2)
  link_BETA1-4         : angle       1.96160 (    6)
  link_NAG-ASN         : bond        0.00267 (    7)
  link_NAG-ASN         : angle       1.57026 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8229 (mtp85)
REVERT: A  154 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8362 (ttpp)
REVERT: A  258 TRP cc_start: 0.8197 (m-90) cc_final: 0.7610 (m-90)
  outliers start: 13
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0887
  time to fit residues: 6.3892
Evaluate side-chains
  62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   66 HIS
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  210 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0030
   chunk 11 optimal weight:    0.0870
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.2166

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.178929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.146601 restraints weight = 4341.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.146512 restraints weight = 3139.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.148775 restraints weight = 3008.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.149473 restraints weight = 2309.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.150243 restraints weight = 2075.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3848  Z= 0.093
  Angle     :  0.539   7.941   5285  Z= 0.266
  Chirality :  0.044   0.160    626
  Planarity :  0.004   0.042    652
  Dihedral  :  4.995  35.857    704
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.76 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.40 (0.39), residues: 474
  helix:  3.26 (1.65), residues: 11
  sheet:  0.89 (0.36), residues: 195
  loop : -0.32 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 158 
 TYR   0.015   0.001   TYR L  48 
 PHE   0.010   0.001   PHE A  55 
 TRP   0.006   0.001   TRP H 103 
 HIS   0.004   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 3834)
  covalent geometry    : angle       0.52676 ( 5248)
  SS BOND              : bond        0.00263 (    5)
  SS BOND              : angle       1.19143 (   10)
  hydrogen bonds       : bond        0.03001 (  116)
  hydrogen bonds       : angle       5.45836 (  288)
  link_BETA1-4         : bond        0.00574 (    2)
  link_BETA1-4         : angle       1.97854 (    6)
  link_NAG-ASN         : bond        0.00326 (    7)
  link_NAG-ASN         : angle       1.41432 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8275 (ttpp)
REVERT: A  258 TRP cc_start: 0.8123 (m-90) cc_final: 0.7606 (m-90)
  outliers start: 7
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0796
  time to fit residues: 5.8657
Evaluate side-chains
  60 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  131 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0570
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0470
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.159551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.127653 restraints weight = 4429.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.127156 restraints weight = 4470.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.129526 restraints weight = 4012.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.129846 restraints weight = 3157.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.131280 restraints weight = 2722.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3848  Z= 0.151
  Angle     :  0.561   7.470   5285  Z= 0.280
  Chirality :  0.045   0.166    626
  Planarity :  0.004   0.044    652
  Dihedral  :  5.039  36.785    704
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 12.06 %
    Favored  : 84.71 %
  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 are not related in a simple way.
  whole:  0.39 (0.39), residues: 474
  helix:  3.25 (1.64), residues: 11
  sheet:  0.80 (0.36), residues: 191
  loop : -0.23 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 158 
 TYR   0.015   0.001   TYR A 265 
 PHE   0.012   0.002   PHE A  55 
 TRP   0.005   0.001   TRP H 115 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3834)
  covalent geometry    : angle       0.54888 ( 5248)
  SS BOND              : bond        0.00331 (    5)
  SS BOND              : angle       1.40960 (   10)
  hydrogen bonds       : bond        0.03121 (  116)
  hydrogen bonds       : angle       5.40989 (  288)
  link_BETA1-4         : bond        0.00525 (    2)
  link_BETA1-4         : angle       1.90653 (    6)
  link_NAG-ASN         : bond        0.00249 (    7)
  link_NAG-ASN         : angle       1.40115 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8661 (ttpt) cc_final: 0.8304 (ttpp)
REVERT: A  258 TRP cc_start: 0.8200 (m-90) cc_final: 0.7626 (m-90)
  outliers start: 11
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0849
  time to fit residues: 6.3840
Evaluate side-chains
  62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  284 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0000
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.159078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.127545 restraints weight = 4383.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127732 restraints weight = 4290.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.130053 restraints weight = 4167.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.130224 restraints weight = 2985.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.130700 restraints weight = 2763.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3848  Z= 0.135
  Angle     :  0.555   7.911   5285  Z= 0.276
  Chirality :  0.045   0.163    626
  Planarity :  0.004   0.043    652
  Dihedral  :  4.979  36.451    704
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 11.76 %
    Favored  : 84.71 %
  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 are not related in a simple way.
  whole:  0.35 (0.39), residues: 474
  helix:  3.16 (1.65), residues: 11
  sheet:  0.79 (0.36), residues: 191
  loop : -0.27 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.015   0.001   TYR A 265 
 PHE   0.016   0.001   PHE A  55 
 TRP   0.005   0.001   TRP H 115 
 HIS   0.003   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3834)
  covalent geometry    : angle       0.54282 ( 5248)
  SS BOND              : bond        0.00291 (    5)
  SS BOND              : angle       1.34913 (   10)
  hydrogen bonds       : bond        0.03051 (  116)
  hydrogen bonds       : angle       5.36549 (  288)
  link_BETA1-4         : bond        0.00539 (    2)
  link_BETA1-4         : angle       1.86897 (    6)
  link_NAG-ASN         : bond        0.00275 (    7)
  link_NAG-ASN         : angle       1.37932 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8307 (ttpp)
REVERT: A  258 TRP cc_start: 0.8223 (m-90) cc_final: 0.7672 (m-90)
  outliers start: 12
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0823
  time to fit residues: 6.1221
Evaluate side-chains
  63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  284 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 31 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    0.1980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.157327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.126400 restraints weight = 4456.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.126072 restraints weight = 4444.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.128494 restraints weight = 4396.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.128717 restraints weight = 3200.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.129281 restraints weight = 2943.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3848  Z= 0.153
  Angle     :  0.581   8.161   5285  Z= 0.286
  Chirality :  0.045   0.165    626
  Planarity :  0.004   0.043    652
  Dihedral  :  5.034  36.920    704
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 12.35 %
    Favored  : 84.41 %
  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 are not related in a simple way.
  whole:  0.25 (0.39), residues: 474
  helix:  3.52 (1.72), residues: 11
  sheet:  0.73 (0.36), residues: 191
  loop : -0.37 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 158 
 TYR   0.015   0.001   TYR A 265 
 PHE   0.020   0.002   PHE A  55 
 TRP   0.006   0.001   TRP H 115 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3834)
  covalent geometry    : angle       0.56967 ( 5248)
  SS BOND              : bond        0.00315 (    5)
  SS BOND              : angle       1.41756 (   10)
  hydrogen bonds       : bond        0.03147 (  116)
  hydrogen bonds       : angle       5.39298 (  288)
  link_BETA1-4         : bond        0.00506 (    2)
  link_BETA1-4         : angle       1.83509 (    6)
  link_NAG-ASN         : bond        0.00256 (    7)
  link_NAG-ASN         : angle       1.38777 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8316 (ttpp)
REVERT: A  258 TRP cc_start: 0.8288 (m-90) cc_final: 0.7720 (m-90)
  outliers start: 11
  outliers final: 10
  residues processed: 60
  average time/residue: 0.0960
  time to fit residues: 6.9668
Evaluate side-chains
  62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  284 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 31 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.158575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.127988 restraints weight = 4430.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.128262 restraints weight = 4384.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.130710 restraints weight = 4116.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.130612 restraints weight = 3112.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.131217 restraints weight = 2837.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3848  Z= 0.152
  Angle     :  0.565   7.672   5285  Z= 0.280
  Chirality :  0.045   0.159    626
  Planarity :  0.004   0.042    652
  Dihedral  :  5.032  36.991    704
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 11.76 %
    Favored  : 84.71 %
  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 are not related in a simple way.
  whole:  0.14 (0.39), residues: 474
  helix:  3.09 (1.69), residues: 11
  sheet:  0.67 (0.36), residues: 191
  loop : -0.44 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 158 
 TYR   0.015   0.001   TYR A 265 
 PHE   0.018   0.002   PHE A  55 
 TRP   0.006   0.001   TRP H 115 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3834)
  covalent geometry    : angle       0.55336 ( 5248)
  SS BOND              : bond        0.00323 (    5)
  SS BOND              : angle       1.42229 (   10)
  hydrogen bonds       : bond        0.03072 (  116)
  hydrogen bonds       : angle       5.38461 (  288)
  link_BETA1-4         : bond        0.00512 (    2)
  link_BETA1-4         : angle       1.81429 (    6)
  link_NAG-ASN         : bond        0.00264 (    7)
  link_NAG-ASN         : angle       1.37369 (   21)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: L   60 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7460 (mtm180)
REVERT: A  154 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8307 (ttpp)
REVERT: A  258 TRP cc_start: 0.8252 (m-90) cc_final: 0.7699 (m-90)
  outliers start: 12
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0849
  time to fit residues: 6.4853
Evaluate side-chains
  65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  284 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0970
   chunk 40 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 9 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.159177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.127074 restraints weight = 4349.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.127684 restraints weight = 3838.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.129317 restraints weight = 4003.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.130051 restraints weight = 2900.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.130362 restraints weight = 2625.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3848  Z= 0.128
  Angle     :  0.580  10.432   5285  Z= 0.279
  Chirality :  0.045   0.159    626
  Planarity :  0.004   0.045    652
  Dihedral  :  4.930  36.217    704
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 12.35 %
    Favored  : 84.41 %
  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 are not related in a simple way.
  whole:  0.17 (0.39), residues: 474
  helix:  3.64 (1.73), residues: 11
  sheet:  0.68 (0.36), residues: 191
  loop : -0.44 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 158 
 TYR   0.015   0.001   TYR A 265 
 PHE   0.021   0.001   PHE A  55 
 TRP   0.005   0.001   TRP H 103 
 HIS   0.003   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3834)
  covalent geometry    : angle       0.56936 ( 5248)
  SS BOND              : bond        0.00278 (    5)
  SS BOND              : angle       1.29570 (   10)
  hydrogen bonds       : bond        0.02975 (  116)
  hydrogen bonds       : angle       5.28859 (  288)
  link_BETA1-4         : bond        0.00503 (    2)
  link_BETA1-4         : angle       1.80766 (    6)
  link_NAG-ASN         : bond        0.00276 (    7)
  link_NAG-ASN         : angle       1.35283 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1007.28 seconds
wall clock time: 17 minutes 56.61 seconds (1076.61 seconds total)