Starting phenix.real_space_refine
on Thu Jul  2 10:50:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vbg_43124/07_2026/8vbg_43124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vbg_43124/07_2026/8vbg_43124.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vbg_43124/07_2026/8vbg_43124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vbg_43124/07_2026/8vbg_43124.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vbg_43124/07_2026/8vbg_43124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vbg_43124/07_2026/8vbg_43124.map"
  }
  resolution = 2.4
  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=   0.010
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: 6
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     Mg      2      5.21       5
     S      13      5.16       5
     C    5320      2.51       5
     N    1404      2.21       5
     O    1638      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8417
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4405
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 542, 4400
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 504}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
      Conformer: "B"
        Number of residues, atoms: 542, 4400
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 504}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
          bond proxies already assigned to first conformer: 4512
    Chain: "B"
      Number of atoms: 3219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3219
          Classifications: {'peptide': 396}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 28, 'TRANS': 367}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "F"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 761
          Classifications: {'DNA': 35, 'RNA': 2}
          Modifications used: {'rna3p': 2}
          Link IDs: {'rna3p': 36}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 6
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 2, 'F2A': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.96, per 1000 atoms: 0.23
  Number of scatterers: 8417
  At special positions: 0
  Unit cell: (78.48, 94.32, 121.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      13     16.00
     P      40     15.00
     Mg      2     11.99
     O    1638      8.00
     N    1404      7.00
     C    5320      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 283.0 milliseconds
  

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1774

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      36.6% alpha, 17.4% beta
      13 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 44
    Processing helix  chain 'A' and resid 77 through 84
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 114 through 118
    Processing helix  chain 'A' and resid 121 through 129
      removed outlier: 4.545A  pdb=" N   LYS A 126 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA A 129 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 194 through 211
    Processing helix  chain 'A' and resid 217 through 221
    Processing helix  chain 'A' and resid 253 through 268
    Processing helix  chain 'A' and resid 276 through 282
      removed outlier: 3.767A  pdb=" N   LEU A 282 " --> pdb=" O   GLN A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 4.200A  pdb=" N   GLU A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 383
    Processing helix  chain 'A' and resid 394 through 405
    Processing helix  chain 'A' and resid 473 through 488
    Processing helix  chain 'A' and resid 499 through 507
      removed outlier: 3.507A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'B' and resid 27 through 44
    Processing helix  chain 'B' and resid 77 through 84
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 4.634A  pdb=" N   LYS B 126 " --> pdb=" O   GLU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 129
      No H-bonds generated for 'chain 'B' and resid 127 through 129'
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 160 through 168
      removed outlier: 3.589A  pdb=" N   LYS B 166 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 173
    Processing helix  chain 'B' and resid 194 through 211
      removed outlier: 3.721A  pdb=" N   GLU B 203 " --> pdb=" O   ARG B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 271
      removed outlier: 3.847A  pdb=" N   GLN B 269 " --> pdb=" O   ASN B 265 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ILE B 270 " --> pdb=" O   TRP B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 312
    Processing helix  chain 'B' and resid 363 through 384
    Processing helix  chain 'B' and resid 394 through 402
    Processing helix  chain 'B' and resid 403 through 405
      No H-bonds generated for 'chain 'B' and resid 403 through 405'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 354
      removed outlier: 8.605A  pdb=" N   ASN A 348 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   GLN A 343 " --> pdb=" O   ASN A 348 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   GLN A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362
    Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 465
    Processing sheet with id=AA8, first strand: chain 'A' and resid 464 through 465
    Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49
    Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 64
    Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 183
    Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 253
      removed outlier: 4.361A  pdb=" N   TRP B 252 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 355
      removed outlier: 8.555A  pdb=" N   ASN B 348 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   GLN B 343 " --> pdb=" O   ASN B 348 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   GLN B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ALA B 327 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 415 " (cutoff:3.500A)

    327 hydrogen bonds defined for protein.
    897 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      36 hydrogen bonds
      72 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      29 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1307
        1.30 -     1.43: 2444
        1.43 -     1.57: 4862
        1.57 -     1.70: 77
        1.70 -     1.83: 25
  Bond restraints: 8715
  Sorted by residual:
  bond pdb=" C   GLY B 190 "
       pdb=" N   SER B 191 "
    ideal  model  delta    sigma   weight residual
    1.327  1.458 -0.131 1.47e-02 4.63e+03 7.89e+01
  bond pdb=" O3B F2A A 601 "
       pdb=" PG  F2A A 601 "
    ideal  model  delta    sigma   weight residual
    1.728  1.611  0.117 2.00e-02 2.50e+03 3.45e+01
  bond pdb=" C   GLN A 509 "
       pdb=" O   GLN A 509 "
    ideal  model  delta    sigma   weight residual
    1.233  1.205  0.028 4.80e-03 4.34e+04 3.39e+01
  bond pdb=" C   THR A 107 "
       pdb=" N   VAL A 108 "
    ideal  model  delta    sigma   weight residual
    1.330  1.416 -0.085 1.48e-02 4.57e+03 3.32e+01
  bond pdb=" C   GLU A 302 "
       pdb=" O   GLU A 302 "
    ideal  model  delta    sigma   weight residual
    1.236  1.175  0.062 1.15e-02 7.56e+03 2.88e+01
  ... (remaining 8710 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 11462
        2.49 -     4.98: 471
        4.98 -     7.47: 64
        7.47 -     9.96: 15
        9.96 -    12.45: 6
  Bond angle restraints: 12018
  Sorted by residual:
  angle pdb=" N   ILE B 159 "
        pdb=" CA  ILE B 159 "
        pdb=" C   ILE B 159 "
      ideal   model   delta    sigma   weight residual
     113.10  105.63    7.47 9.70e-01 1.06e+00 5.94e+01
  angle pdb=" CA  ASP A 110 "
        pdb=" C   ASP A 110 "
        pdb=" N   VAL A 111 "
      ideal   model   delta    sigma   weight residual
     116.37  125.38   -9.01 1.19e+00 7.06e-01 5.73e+01
  angle pdb=" C   THR B  84 "
        pdb=" CA  THR B  84 "
        pdb=" CB  THR B  84 "
      ideal   model   delta    sigma   weight residual
     109.89  121.86  -11.97 1.60e+00 3.91e-01 5.60e+01
  angle pdb=" C   THR B 409 "
        pdb=" CA  THR B 409 "
        pdb=" CB  THR B 409 "
      ideal   model   delta    sigma   weight residual
     109.65  122.10  -12.45 1.74e+00 3.30e-01 5.12e+01
  angle pdb=" O   ASP A 110 "
        pdb=" C   ASP A 110 "
        pdb=" N   VAL A 111 "
      ideal   model   delta    sigma   weight residual
     123.27  114.98    8.29 1.18e+00 7.18e-01 4.93e+01
  ... (remaining 12013 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.74: 4538
       28.74 -    57.48: 514
       57.48 -    86.21: 69
       86.21 -   114.95: 5
      114.95 -   143.69: 1
  Dihedral angle restraints: 5127
    sinusoidal: 2378
      harmonic: 2749
  Sorted by residual:
  dihedral pdb=" C   THR A 240 "
           pdb=" N   THR A 240 "
           pdb=" CA  THR A 240 "
           pdb=" CB  THR A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -106.41  -15.59     0      2.50e+00 1.60e-01 3.89e+01
  dihedral pdb=" C   THR B  84 "
           pdb=" N   THR B  84 "
           pdb=" CA  THR B  84 "
           pdb=" CB  THR B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.16   14.16     0      2.50e+00 1.60e-01 3.21e+01
  dihedral pdb=" C   PRO A 537 "
           pdb=" N   PRO A 537 "
           pdb=" CA  PRO A 537 "
           pdb=" CB  PRO A 537 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -107.17  -13.53     0      2.50e+00 1.60e-01 2.93e+01
  ... (remaining 5124 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1160
       0.098 -    0.195: 121
       0.195 -    0.293: 28
       0.293 -    0.391: 4
       0.391 -    0.489: 3
  Chirality restraints: 1316
  Sorted by residual:
  chirality pdb=" C3'  DG F  33 "
            pdb=" C4'  DG F  33 "
            pdb=" O3'  DG F  33 "
            pdb=" C2'  DG F  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.24   -0.49 2.00e-01 2.50e+01 5.97e+00
  chirality pdb=" C3'  DT F  18 "
            pdb=" C4'  DT F  18 "
            pdb=" O3'  DT F  18 "
            pdb=" C2'  DT F  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.31   -0.42 2.00e-01 2.50e+01 4.44e+00
  chirality pdb=" CA  THR B  84 "
            pdb=" N   THR B  84 "
            pdb=" C   THR B  84 "
            pdb=" CB  THR B  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.13    0.39 2.00e-01 2.50e+01 3.89e+00
  ... (remaining 1313 not shown)

  Planarity restraints: 1381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 110 "    0.023 2.00e-02 2.50e+03   4.30e-02 1.85e+01
        pdb=" C   ASP A 110 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   ASP A 110 "    0.026 2.00e-02 2.50e+03
        pdb=" N   VAL A 111 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG F  33 "   -0.059 2.00e-02 2.50e+03   2.29e-02 1.57e+01
        pdb=" N9   DG F  33 "    0.032 2.00e-02 2.50e+03
        pdb=" C8   DG F  33 "    0.020 2.00e-02 2.50e+03
        pdb=" N7   DG F  33 "    0.011 2.00e-02 2.50e+03
        pdb=" C5   DG F  33 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DG F  33 "   -0.020 2.00e-02 2.50e+03
        pdb=" O6   DG F  33 "   -0.022 2.00e-02 2.50e+03
        pdb=" N1   DG F  33 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG F  33 "    0.010 2.00e-02 2.50e+03
        pdb=" N2   DG F  33 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG F  33 "    0.015 2.00e-02 2.50e+03
        pdb=" C4   DG F  33 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 302 "    0.019 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" C   GLU A 302 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   GLU A 302 "    0.025 2.00e-02 2.50e+03
        pdb=" N   LEU A 303 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1378 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 173
        2.65 -     3.22: 7149
        3.22 -     3.78: 14463
        3.78 -     4.34: 20146
        4.34 -     4.90: 31139
  Nonbonded interactions: 73070
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 185 "
            pdb="MG    MG A 602 "
     model   vdw
     2.092 2.170
  nonbonded pdb=" NH2 ARG A 358 "
            pdb=" OE2 GLU B 396 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" N   GLU B 396 "
            pdb=" OE1 GLU B 396 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   LEU A  80 "
            pdb=" OG1 THR A  84 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OD1 ASP A 110 "
            pdb="MG    MG A 602 "
     model   vdw
     2.340 2.170
  ... (remaining 73065 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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.560
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.131   8715  Z= 0.502
  Angle     :  1.088  12.451  12018  Z= 0.746
  Chirality :  0.071   0.489   1316
  Planarity :  0.005   0.043   1381
  Dihedral  : 21.841 143.687   3353
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  3.76 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  7.51 %
    Allowed  : 23.00 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.45 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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: -0.06 (0.28), residues: 931
  helix:  0.94 (0.31), residues: 308
  sheet: -0.47 (0.37), residues: 175
  loop : -0.45 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 277 
 TYR   0.018   0.002   TYR A 501 
 PHE   0.016   0.002   PHE B 171 
 TRP   0.045   0.002   TRP A 406 
 HIS   0.006   0.002   HIS B  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00703 /  0.50 ( 8715)
  covalent geometry    : angle       1.08803 /  0.75 (12018)
  hydrogen bonds       : bond        0.13446 /  9.07 (  361)
  hydrogen bonds       : angle       6.12654 /  4.48 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 84
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (t0)
REVERT: A  454 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6430 (ttpt)
REVERT: A  500 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7951 (mp10)
REVERT: A  537 PRO cc_start: 0.8472 (OUTLIER) cc_final: 0.8195 (Cg_endo)
REVERT: B  242 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.7104 (mt0)
REVERT: B  277 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8106 (tmt-80)
REVERT: B  281 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7718 (mmpt)
  outliers start: 61
  outliers final: 16
  residues processed: 130
  average time/residue: 0.4940
  time to fit residues: 68.1779
Evaluate side-chains
  91 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LYS
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  361 HIS
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  454 LYS
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  537 PRO
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue  211 ARG
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.5276

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 221 HIS
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN
A 539 HIS
B  96 HIS
B 182 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.136067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.102502 restraints weight = 16443.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.53
r_work: 0.3249 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8715  Z= 0.150
  Angle     :  0.606   8.834  12018  Z= 0.327
  Chirality :  0.045   0.270   1316
  Planarity :  0.005   0.076   1381
  Dihedral  : 17.594 140.690   1456
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.09 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 24.58 %
    Favored  : 71.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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:  0.53 (0.28), residues: 931
  helix:  1.59 (0.30), residues: 318
  sheet: -0.36 (0.39), residues: 165
  loop : -0.19 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 358 
 TYR   0.019   0.002   TYR A 457 
 PHE   0.013   0.001   PHE A 440 
 TRP   0.033   0.001   TRP A 406 
 HIS   0.011   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 ( 8715)
  covalent geometry    : angle       0.60587 /  0.33 (12018)
  hydrogen bonds       : bond        0.04126 /  2.79 (  361)
  hydrogen bonds       : angle       4.53650 /  3.24 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 85
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  454 LYS cc_start: 0.7150 (mtmm) cc_final: 0.6255 (ttpt)
REVERT: A  500 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7750 (mp10)
REVERT: A  520 GLN cc_start: 0.8699 (mt0) cc_final: 0.8475 (mt0)
REVERT: B  242 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6851 (mt0)
REVERT: B  277 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8205 (tmt170)
REVERT: B  356 ARG cc_start: 0.7658 (tpm-80) cc_final: 0.7185 (tpp-160)
REVERT: B  425 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7418 (pp)
  outliers start: 32
  outliers final: 13
  residues processed: 111
  average time/residue: 0.4460
  time to fit residues: 52.8146
Evaluate side-chains
  88 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LYS
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  211 ARG
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 89 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  91 GLN
A 494 ASN
** A 500 GLN ** 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 = 0.3837 r_free = 0.3837 target = 0.135258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.101987 restraints weight = 14904.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.40
r_work: 0.3244 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8715  Z= 0.153
  Angle     :  0.568   8.635  12018  Z= 0.307
  Chirality :  0.044   0.294   1316
  Planarity :  0.004   0.065   1381
  Dihedral  : 16.966 141.516   1437
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.44 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 24.46 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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 (0.28), residues: 931
  helix:  1.82 (0.30), residues: 319
  sheet: -0.49 (0.36), residues: 171
  loop : -0.16 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 358 
 TYR   0.021   0.002   TYR A 457 
 PHE   0.009   0.001   PHE A 160 
 TRP   0.031   0.001   TRP A 406 
 HIS   0.006   0.002   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 ( 8715)
  covalent geometry    : angle       0.56808 /  0.31 (12018)
  hydrogen bonds       : bond        0.03741 /  2.53 (  361)
  hydrogen bonds       : angle       4.34732 /  3.08 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 73
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8573 (mppt)
REVERT: A   64 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7963 (mtpp)
REVERT: A  431 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8591 (mtpp)
REVERT: A  454 LYS cc_start: 0.7225 (mtmm) cc_final: 0.6365 (ttpt)
REVERT: A  461 LYS cc_start: 0.8691 (mptt) cc_final: 0.8458 (mptt)
REVERT: A  500 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7734 (mp10)
REVERT: A  542 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4689 (mp)
REVERT: B  242 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6918 (mt0)
REVERT: B  277 ARG cc_start: 0.8623 (ttp-110) cc_final: 0.8394 (ttp80)
REVERT: B  326 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8485 (mt)
REVERT: B  356 ARG cc_start: 0.7510 (tpm-80) cc_final: 0.7004 (tpp80)
REVERT: B  425 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7430 (pp)
  outliers start: 32
  outliers final: 12
  residues processed: 97
  average time/residue: 0.5224
  time to fit residues: 53.8152
Evaluate side-chains
  85 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LYS
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue  211 ARG
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0970
   chunk 76 optimal weight:    0.4980
   chunk 89 optimal weight:    0.1980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 93 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  91 GLN
A 367 GLN
B 265 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.135566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.102061 restraints weight = 15316.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.45
r_work: 0.3251 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8715  Z= 0.148
  Angle     :  0.560   9.239  12018  Z= 0.300
  Chirality :  0.043   0.286   1316
  Planarity :  0.005   0.088   1381
  Dihedral  : 16.596 142.102   1425
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.76 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 25.30 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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:  0.69 (0.28), residues: 931
  helix:  1.91 (0.30), residues: 319
  sheet: -0.51 (0.36), residues: 171
  loop : -0.13 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 358 
 TYR   0.021   0.001   TYR A 457 
 PHE   0.010   0.001   PHE B  61 
 TRP   0.038   0.001   TRP A 406 
 HIS   0.006   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 8715)
  covalent geometry    : angle       0.55961 /  0.30 (12018)
  hydrogen bonds       : bond        0.03557 /  2.40 (  361)
  hydrogen bonds       : angle       4.26515 /  3.03 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7601 (mtt)
REVERT: A   64 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7849 (tttp)
REVERT: A  431 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8584 (mtpp)
REVERT: A  454 LYS cc_start: 0.7236 (mtmm) cc_final: 0.6398 (ttpt)
REVERT: A  500 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7705 (mp10)
REVERT: A  530 LYS cc_start: 0.8560 (mttm) cc_final: 0.8207 (mtpm)
REVERT: A  542 ILE cc_start: 0.4974 (OUTLIER) cc_final: 0.4744 (mp)
REVERT: B  242 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6938 (mt0)
REVERT: B  277 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8363 (ttp80)
REVERT: B  326 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8471 (mt)
REVERT: B  356 ARG cc_start: 0.7485 (tpm-80) cc_final: 0.6985 (tpp80)
REVERT: B  425 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7432 (pp)
  outliers start: 24
  outliers final: 10
  residues processed: 88
  average time/residue: 0.4734
  time to fit residues: 44.3354
Evaluate side-chains
  81 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue  211 ARG
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0040
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0870
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.4770

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.136312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.103222 restraints weight = 14621.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.39
r_work: 0.3270 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8715  Z= 0.128
  Angle     :  0.536   7.226  12018  Z= 0.288
  Chirality :  0.042   0.292   1316
  Planarity :  0.004   0.080   1381
  Dihedral  : 16.407 141.686   1424
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.94 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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:  0.91 (0.28), residues: 931
  helix:  2.20 (0.30), residues: 314
  sheet: -0.45 (0.37), residues: 171
  loop : -0.04 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 358 
 TYR   0.021   0.001   TYR A 457 
 PHE   0.009   0.001   PHE B  61 
 TRP   0.036   0.001   TRP A 406 
 HIS   0.005   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.13 ( 8715)
  covalent geometry    : angle       0.53617 /  0.29 (12018)
  hydrogen bonds       : bond        0.03336 /  2.27 (  361)
  hydrogen bonds       : angle       4.16378 /  2.96 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7509 (mtt)
REVERT: A  431 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8580 (mtpp)
REVERT: A  454 LYS cc_start: 0.7191 (mtmm) cc_final: 0.6368 (ttpt)
REVERT: A  461 LYS cc_start: 0.8678 (mptt) cc_final: 0.8432 (mptt)
REVERT: A  500 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7676 (mp10)
REVERT: A  530 LYS cc_start: 0.8522 (mttm) cc_final: 0.8169 (mtpm)
REVERT: B  242 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6889 (mt0)
REVERT: B  277 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8352 (ttp80)
REVERT: B  326 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8466 (mt)
REVERT: B  356 ARG cc_start: 0.7443 (tpm-80) cc_final: 0.6985 (tpp80)
REVERT: B  425 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7428 (pp)
  outliers start: 25
  outliers final: 10
  residues processed: 91
  average time/residue: 0.4340
  time to fit residues: 42.2144
Evaluate side-chains
  79 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  361 HIS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain B residue  211 ARG
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  91 GLN
A 494 ASN
A 498 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.135325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.101815 restraints weight = 15900.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.48
r_work: 0.3243 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8715  Z= 0.153
  Angle     :  0.543   7.235  12018  Z= 0.293
  Chirality :  0.043   0.287   1316
  Planarity :  0.005   0.086   1381
  Dihedral  : 16.373 142.594   1422
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 24.82 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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 (0.28), residues: 931
  helix:  2.25 (0.30), residues: 314
  sheet: -0.45 (0.36), residues: 171
  loop : -0.04 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 358 
 TYR   0.021   0.001   TYR A 457 
 PHE   0.010   0.001   PHE A 160 
 TRP   0.037   0.001   TRP A 406 
 HIS   0.005   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 8715)
  covalent geometry    : angle       0.54327 /  0.29 (12018)
  hydrogen bonds       : bond        0.03485 /  2.36 (  361)
  hydrogen bonds       : angle       4.16719 /  2.97 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  431 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8597 (mtpp)
REVERT: A  454 LYS cc_start: 0.7216 (mtmm) cc_final: 0.6367 (ttpt)
REVERT: A  500 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7682 (mp10)
REVERT: A  530 LYS cc_start: 0.8546 (mttm) cc_final: 0.8200 (mtpm)
REVERT: B  242 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.7077 (mt0)
REVERT: B  250 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5921 (p0)
REVERT: B  277 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8366 (ttp80)
REVERT: B  326 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8473 (mt)
REVERT: B  356 ARG cc_start: 0.7429 (tpm-80) cc_final: 0.6967 (tpp80)
REVERT: B  425 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7447 (pp)
  outliers start: 22
  outliers final: 9
  residues processed: 85
  average time/residue: 0.4437
  time to fit residues: 40.2774
Evaluate side-chains
  76 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  361 HIS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 73 optimal weight:    8.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 498 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.134877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.100474 restraints weight = 20528.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.82
r_work: 0.3220 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8715  Z= 0.160
  Angle     :  0.559  11.123  12018  Z= 0.299
  Chirality :  0.043   0.286   1316
  Planarity :  0.005   0.093   1381
  Dihedral  : 16.304 142.698   1418
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 25.06 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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:  0.96 (0.28), residues: 931
  helix:  2.25 (0.30), residues: 314
  sheet: -0.44 (0.36), residues: 171
  loop : -0.02 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 358 
 TYR   0.021   0.001   TYR A 457 
 PHE   0.010   0.001   PHE A 160 
 TRP   0.053   0.001   TRP A 406 
 HIS   0.005   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 ( 8715)
  covalent geometry    : angle       0.55924 /  0.30 (12018)
  hydrogen bonds       : bond        0.03514 /  2.39 (  361)
  hydrogen bonds       : angle       4.18637 /  2.98 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  431 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8618 (mtpt)
REVERT: A  454 LYS cc_start: 0.7272 (mtmm) cc_final: 0.6400 (ttpt)
REVERT: A  461 LYS cc_start: 0.8653 (mptt) cc_final: 0.8423 (mptt)
REVERT: A  500 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7609 (mp10)
REVERT: A  530 LYS cc_start: 0.8484 (mttm) cc_final: 0.8120 (mtpm)
REVERT: B  242 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7149 (mt0)
REVERT: B  277 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8393 (ttp80)
REVERT: B  326 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8442 (mt)
REVERT: B  356 ARG cc_start: 0.7311 (tpm-80) cc_final: 0.6910 (tpp80)
REVERT: B  425 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7496 (pp)
  outliers start: 20
  outliers final: 7
  residues processed: 87
  average time/residue: 0.5166
  time to fit residues: 48.0177
Evaluate side-chains
  76 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  361 HIS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  91 GLN
A 494 ASN
A 507 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.135337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.101080 restraints weight = 22912.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.93
r_work: 0.3224 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3217
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8715  Z= 0.146
  Angle     :  0.547   9.494  12018  Z= 0.294
  Chirality :  0.043   0.290   1316
  Planarity :  0.005   0.089   1381
  Dihedral  : 16.225 142.311   1416
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.44 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 26.15 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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:  1.03 (0.28), residues: 931
  helix:  2.32 (0.30), residues: 314
  sheet: -0.41 (0.36), residues: 171
  loop :  0.02 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 358 
 TYR   0.022   0.001   TYR A 457 
 PHE   0.010   0.001   PHE A 160 
 TRP   0.053   0.001   TRP A 406 
 HIS   0.004   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 ( 8715)
  covalent geometry    : angle       0.54693 /  0.29 (12018)
  hydrogen bonds       : bond        0.03424 /  2.32 (  361)
  hydrogen bonds       : angle       4.16698 /  2.97 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  431 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8562 (mtpp)
REVERT: A  454 LYS cc_start: 0.7271 (mtmm) cc_final: 0.6365 (ttpt)
REVERT: A  461 LYS cc_start: 0.8677 (mptt) cc_final: 0.8439 (mptt)
REVERT: A  500 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7539 (mp10)
REVERT: B  277 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8391 (ttp80)
REVERT: B  326 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8450 (mt)
REVERT: B  356 ARG cc_start: 0.7293 (tpm-80) cc_final: 0.6908 (tpp80)
REVERT: B  425 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7507 (pp)
  outliers start: 14
  outliers final: 7
  residues processed: 79
  average time/residue: 0.4758
  time to fit residues: 40.1634
Evaluate side-chains
  74 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  361 HIS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 72 optimal weight:    3.9990
   chunk 42 optimal weight:    0.1980
   chunk 14 optimal weight:    0.5980
   chunk 81 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0270
   chunk 0 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4838

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 498 ASN
B 265 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.136085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.103047 restraints weight = 16160.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.49
r_work: 0.3267 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8715  Z= 0.130
  Angle     :  0.542   8.939  12018  Z= 0.291
  Chirality :  0.042   0.296   1316
  Planarity :  0.005   0.102   1381
  Dihedral  : 15.967 141.977   1411
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.44 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 27.12 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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:  1.14 (0.28), residues: 931
  helix:  2.44 (0.30), residues: 314
  sheet: -0.33 (0.37), residues: 171
  loop :  0.05 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 358 
 TYR   0.023   0.001   TYR A 457 
 PHE   0.009   0.001   PHE B  61 
 TRP   0.058   0.001   TRP A 406 
 HIS   0.004   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 ( 8715)
  covalent geometry    : angle       0.54194 /  0.29 (12018)
  hydrogen bonds       : bond        0.03267 /  2.22 (  361)
  hydrogen bonds       : angle       4.13561 /  2.97 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  431 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8618 (mtpt)
REVERT: A  454 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6316 (ttpt)
REVERT: A  461 LYS cc_start: 0.8676 (mptt) cc_final: 0.8427 (mptt)
REVERT: B  207 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7342 (mm-40)
REVERT: B  277 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8383 (ttp80)
REVERT: B  284 ARG cc_start: 0.6954 (mtt-85) cc_final: 0.6736 (mtp85)
REVERT: B  326 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8464 (mt)
REVERT: B  356 ARG cc_start: 0.7346 (tpm-80) cc_final: 0.6853 (tpp80)
REVERT: B  425 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7498 (pp)
  outliers start: 8
  outliers final: 5
  residues processed: 78
  average time/residue: 0.5269
  time to fit residues: 44.0616
Evaluate side-chains
  77 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0010
   chunk 12 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 80 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0570
   chunk 82 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.4104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  91 GLN
A 494 ASN
A 498 ASN
** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.133946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.097053 restraints weight = 23122.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 3.21
r_work: 0.3118 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8715  Z= 0.124
  Angle     :  0.538   8.474  12018  Z= 0.290
  Chirality :  0.042   0.298   1316
  Planarity :  0.005   0.092   1381
  Dihedral  : 15.904 142.017   1411
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.23 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 27.24 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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:  1.19 (0.28), residues: 931
  helix:  2.50 (0.30), residues: 314
  sheet: -0.27 (0.38), residues: 165
  loop :  0.05 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 358 
 TYR   0.024   0.001   TYR A 457 
 PHE   0.009   0.001   PHE B  61 
 TRP   0.047   0.001   TRP A 406 
 HIS   0.004   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 8715)
  covalent geometry    : angle       0.53761 /  0.29 (12018)
  hydrogen bonds       : bond        0.03200 /  2.18 (  361)
  hydrogen bonds       : angle       4.09917 /  2.94 (  969)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  431 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8553 (mtpt)
REVERT: A  454 LYS cc_start: 0.7136 (mtmm) cc_final: 0.6213 (ttpt)
REVERT: A  461 LYS cc_start: 0.8606 (mptt) cc_final: 0.8358 (mptt)
REVERT: B  277 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8390 (ttp80)
REVERT: B  284 ARG cc_start: 0.6851 (mtt-85) cc_final: 0.6633 (mtp85)
REVERT: B  356 ARG cc_start: 0.7251 (tpm-80) cc_final: 0.6779 (tpp80)
REVERT: B  425 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7415 (pp)
  outliers start: 9
  outliers final: 5
  residues processed: 78
  average time/residue: 0.4972
  time to fit residues: 41.5863
Evaluate side-chains
  74 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  425 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 81 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 498 ASN
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.132361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.097726 restraints weight = 11733.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.32
r_work: 0.3097 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8715  Z= 0.162
  Angle     :  0.562   8.705  12018  Z= 0.302
  Chirality :  0.043   0.291   1316
  Planarity :  0.005   0.098   1381
  Dihedral  : 15.987 142.958   1411
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.33 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 27.12 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    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:  1.12 (0.28), residues: 931
  helix:  2.43 (0.30), residues: 314
  sheet: -0.34 (0.37), residues: 171
  loop :  0.04 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 358 
 TYR   0.023   0.001   TYR A 457 
 PHE   0.011   0.001   PHE A 160 
 TRP   0.049   0.001   TRP A 406 
 HIS   0.004   0.001   HIS B 198 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 ( 8715)
  covalent geometry    : angle       0.56204 /  0.30 (12018)
  hydrogen bonds       : bond        0.03443 /  2.34 (  361)
  hydrogen bonds       : angle       4.13769 /  2.97 (  969)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3362.63 seconds
wall clock time: 57 minutes 51.45 seconds (3471.45 seconds total)