Starting phenix.real_space_refine
on Thu Jul  2 06:33:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gqu_34202/07_2026/8gqu_34202_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gqu_34202/07_2026/8gqu_34202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gqu_34202/07_2026/8gqu_34202_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gqu_34202/07_2026/8gqu_34202_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gqu_34202/07_2026/8gqu_34202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gqu_34202/07_2026/8gqu_34202.map"
  }
  resolution = 3.5
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     Cl      4      4.86       5
     C    4846      2.51       5
     N    1188      2.21       5
     O    1246      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 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: 7328
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3638
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
    Chain: "B"
      Number of atoms: 3638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3638
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'GH6': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'GH6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.02, per 1000 atoms: 0.28
  Number of scatterers: 7328
  At special positions: 0
  Unit cell: (77.097, 116.06, 81.242, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      4     17.00
     S      44     16.00
     O    1246      8.00
     N    1188      7.00
     C    4846      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
      
  Atom "HETATM 7326  O17 GH6 B 901 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 422.9 milliseconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 1 sheets defined
      80.0% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 126
      removed outlier: 3.563A  pdb=" N   LEU A 126 " --> pdb=" O   MET A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 156
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 163 through 172
      removed outlier: 3.566A  pdb=" N   MET A 167 " --> pdb=" O   GLY A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 197
    Processing helix  chain 'A' and resid 206 through 226
      removed outlier: 3.821A  pdb=" N   PHE A 226 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 231
      removed outlier: 3.692A  pdb=" N   TYR A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU A 231 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 227 through 231'
    Processing helix  chain 'A' and resid 232 through 235
      removed outlier: 3.972A  pdb=" N   ARG A 235 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 232 through 235'
    Processing helix  chain 'A' and resid 236 through 253
      removed outlier: 3.799A  pdb=" N   PHE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 267
      removed outlier: 3.621A  pdb=" N   SER A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 296
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 320 through 352
    Processing helix  chain 'A' and resid 352 through 363
    Processing helix  chain 'A' and resid 364 through 378
      removed outlier: 3.767A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 392 through 401
    Processing helix  chain 'A' and resid 419 through 425
    Processing helix  chain 'A' and resid 430 through 450
      removed outlier: 4.541A  pdb=" N   TRP A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 481
      removed outlier: 3.783A  pdb=" N   VAL A 462 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 3.988A  pdb=" N   TYR A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 526
    Processing helix  chain 'A' and resid 530 through 549
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'B' and resid 90 through 126
    Processing helix  chain 'B' and resid 129 through 156
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 157 through 160
    Processing helix  chain 'B' and resid 163 through 173
      removed outlier: 3.507A  pdb=" N   MET B 167 " --> pdb=" O   GLY B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 180
      removed outlier: 3.600A  pdb=" N   LEU B 180 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 197
    Processing helix  chain 'B' and resid 204 through 225
      removed outlier: 3.840A  pdb=" N   LEU B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 7.008A  pdb=" N   ILE B 229 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   TYR B 230 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 253
      removed outlier: 3.701A  pdb=" N   PHE B 252 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 267
      removed outlier: 3.652A  pdb=" N   SER B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 297
      removed outlier: 3.539A  pdb=" N   ARG B 297 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 319
      No H-bonds generated for 'chain 'B' and resid 317 through 319'
    Processing helix  chain 'B' and resid 320 through 352
    Processing helix  chain 'B' and resid 352 through 361
    Processing helix  chain 'B' and resid 364 through 378
      removed outlier: 3.731A  pdb=" N   ALA B 368 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 392 through 401
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 430 through 451
      removed outlier: 4.440A  pdb=" N   TRP B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   THR B 451 " --> pdb=" O   ALA B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 481
      removed outlier: 3.840A  pdb=" N   VAL B 462 " --> pdb=" O   ALA B 458 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B 481 " --> pdb=" O   MET B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 3.944A  pdb=" N   TYR B 499 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 526
      removed outlier: 3.510A  pdb=" N   PHE B 522 " --> pdb=" O   ALA B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 549
    Processing helix  chain 'B' and resid 551 through 560
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271
      removed outlier: 3.705A  pdb=" N   PHE A 270 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE B 270 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1

    542 hydrogen bonds defined for protein.
    1578 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2235
        1.34 -     1.46: 1269
        1.46 -     1.57: 3933
        1.57 -     1.69: 1
        1.69 -     1.81: 78
  Bond restraints: 7516
  Sorted by residual:
  bond pdb=" C25 GH6 A 901 "
       pdb="CL2  GH6 A 901 "
    ideal  model  delta    sigma   weight residual
    1.695  1.785 -0.090 2.00e-02 2.50e+03 2.01e+01
  bond pdb=" C25 GH6 B 901 "
       pdb="CL2  GH6 B 901 "
    ideal  model  delta    sigma   weight residual
    1.695  1.784 -0.089 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" C12 GH6 B 901 "
       pdb="CL1  GH6 B 901 "
    ideal  model  delta    sigma   weight residual
    1.708  1.782 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C12 GH6 A 901 "
       pdb="CL1  GH6 A 901 "
    ideal  model  delta    sigma   weight residual
    1.708  1.782 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" C09 GH6 A 901 "
       pdb=" N08 GH6 A 901 "
    ideal  model  delta    sigma   weight residual
    1.393  1.320  0.073 2.00e-02 2.50e+03 1.32e+01
  ... (remaining 7511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9973
        1.78 -     3.57: 203
        3.57 -     5.35: 48
        5.35 -     7.13: 7
        7.13 -     8.92: 5
  Bond angle restraints: 10236
  Sorted by residual:
  angle pdb=" CA  PRO A 381 "
        pdb=" N   PRO A 381 "
        pdb=" CD  PRO A 381 "
      ideal   model   delta    sigma   weight residual
     112.00  103.08    8.92 1.40e+00 5.10e-01 4.06e+01
  angle pdb=" CA  PRO B 315 "
        pdb=" N   PRO B 315 "
        pdb=" CD  PRO B 315 "
      ideal   model   delta    sigma   weight residual
     112.00  104.75    7.25 1.40e+00 5.10e-01 2.68e+01
  angle pdb=" N   PRO B 315 "
        pdb=" CD  PRO B 315 "
        pdb=" CG  PRO B 315 "
      ideal   model   delta    sigma   weight residual
     103.20   96.09    7.11 1.50e+00 4.44e-01 2.25e+01
  angle pdb=" N   ILE B 528 "
        pdb=" CA  ILE B 528 "
        pdb=" C   ILE B 528 "
      ideal   model   delta    sigma   weight residual
     111.77  108.17    3.60 1.04e+00 9.25e-01 1.20e+01
  angle pdb=" CA  PRO B 381 "
        pdb=" N   PRO B 381 "
        pdb=" CD  PRO B 381 "
      ideal   model   delta    sigma   weight residual
     112.00  107.38    4.62 1.40e+00 5.10e-01 1.09e+01
  ... (remaining 10231 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3947
       17.92 -    35.83: 319
       35.83 -    53.75: 78
       53.75 -    71.67: 14
       71.67 -    89.58: 10
  Dihedral angle restraints: 4368
    sinusoidal: 1662
      harmonic: 2706
  Sorted by residual:
  dihedral pdb=" CA  LEU B 548 "
           pdb=" C   LEU B 548 "
           pdb=" N   GLN B 549 "
           pdb=" CA  GLN B 549 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.33  -18.67     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  PHE B 269 "
           pdb=" C   PHE B 269 "
           pdb=" N   PHE B 270 "
           pdb=" CA  PHE B 270 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.76  -16.24     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  LEU A 548 "
           pdb=" C   LEU A 548 "
           pdb=" N   GLN A 549 "
           pdb=" CA  GLN A 549 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.87  -16.13     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 4365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 994
       0.054 -    0.109: 188
       0.109 -    0.163: 17
       0.163 -    0.218: 0
       0.218 -    0.272: 1
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" CA  ASP B 109 "
            pdb=" N   ASP B 109 "
            pdb=" C   ASP B 109 "
            pdb=" CB  ASP B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CA  PRO A 381 "
            pdb=" N   PRO A 381 "
            pdb=" C   PRO A 381 "
            pdb=" CB  PRO A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.41e-01
  chirality pdb=" CB  ILE A 539 "
            pdb=" CA  ILE A 539 "
            pdb=" CG1 ILE A 539 "
            pdb=" CG2 ILE A 539 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 1197 not shown)

  Planarity restraints: 1264
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 380 "    0.053 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO A 381 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 381 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 381 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 314 "   -0.050 5.00e-02 4.00e+02   7.19e-02 8.28e+00
        pdb=" N   PRO B 315 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B 315 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 315 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 314 "   -0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO A 315 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 315 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 315 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1261 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 138
        2.70 -     3.25: 7788
        3.25 -     3.80: 12139
        3.80 -     4.35: 14696
        4.35 -     4.90: 24721
  Nonbonded interactions: 59482
  Sorted by model distance:
  nonbonded pdb=" CE  LYS B 204 "
            pdb=" O17 GH6 B 901 "
     model   vdw
     2.151 3.440
  nonbonded pdb=" OE1 GLU B 238 "
            pdb=" ND2 ASN B 274 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" O   GLU B 166 "
            pdb=" OG1 THR B 169 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OG1 THR A 169 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OD1 ASN A 274 "
            pdb=" NH1 ARG A 277 "
     model   vdw
     2.271 3.120
  ... (remaining 59477 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.460
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
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      :  0.006   0.330   7517  Z= 0.444
  Angle     :  0.681   8.917  10236  Z= 0.374
  Chirality :  0.041   0.272   1200
  Planarity :  0.005   0.075   1264
  Dihedral  : 14.751  89.584   2624
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.28), residues: 940
  helix:  2.13 (0.20), residues: 678
  sheet:  None (None), residues: 0
  loop : -0.68 (0.40), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 493 
 TYR   0.015   0.001   TYR A 134 
 PHE   0.017   0.001   PHE A 279 
 TRP   0.013   0.001   TRP A 444 
 HIS   0.011   0.002   HIS B 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00491 /  0.23 ( 7516)
  covalent geometry    : angle       0.68100 /  0.37 (10236)
  hydrogen bonds       : bond        0.11114 /  7.23 (  542)
  hydrogen bonds       : angle       4.48648 /  3.25 ( 1578)
  Misc. bond           : bond        0.32971 / 17.35 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6685 (tt0)
REVERT: A  140 TYR cc_start: 0.7840 (t80) cc_final: 0.7495 (t80)
REVERT: A  190 ILE cc_start: 0.8795 (mm) cc_final: 0.8430 (mm)
REVERT: A  200 MET cc_start: 0.5763 (mmm) cc_final: 0.5297 (mmp)
REVERT: A  270 PHE cc_start: 0.5169 (t80) cc_final: 0.4405 (t80)
REVERT: A  309 ARG cc_start: 0.5749 (ttp-170) cc_final: 0.5140 (mtp-110)
REVERT: A  377 LEU cc_start: 0.7974 (mt) cc_final: 0.7768 (tp)
REVERT: B  190 ILE cc_start: 0.8730 (mm) cc_final: 0.8458 (mm)
REVERT: B  490 SER cc_start: 0.6061 (t) cc_final: 0.5381 (p)
REVERT: B  531 ILE cc_start: 0.8422 (tt) cc_final: 0.8216 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.0746
  time to fit residues: 28.0763
Evaluate side-chains
  178 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0270
   overall best weight:    0.7038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 133 GLN
A 347 GLN
A 425 ASN
B 133 GLN
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 486 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.159128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.131558 restraints weight = 10805.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.135179 restraints weight = 6578.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.137546 restraints weight = 4903.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.138921 restraints weight = 4093.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.138921 restraints weight = 3679.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7517  Z= 0.148
  Angle     :  0.642  18.000  10236  Z= 0.317
  Chirality :  0.041   0.165   1200
  Planarity :  0.005   0.048   1264
  Dihedral  :  5.181  46.914   1028
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.10 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.28), residues: 940
  helix:  2.16 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.71 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 235 
 TYR   0.018   0.001   TYR A 134 
 PHE   0.013   0.002   PHE B 279 
 TRP   0.019   0.001   TRP A 106 
 HIS   0.011   0.002   HIS B 486 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 ( 7516)
  covalent geometry    : angle       0.64231 /  0.32 (10236)
  hydrogen bonds       : bond        0.04394 /  2.91 (  542)
  hydrogen bonds       : angle       3.91065 /  2.83 ( 1578)
  Misc. bond           : bond        0.01085 /  0.57 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6952 (tt0)
REVERT: A  395 GLU cc_start: 0.6571 (tp30) cc_final: 0.6015 (tp30)
REVERT: A  442 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8254 (mmtm)
REVERT: A  556 ILE cc_start: 0.8687 (mm) cc_final: 0.8211 (mt)
REVERT: B  205 GLU cc_start: 0.7591 (pm20) cc_final: 0.6668 (pt0)
REVERT: B  490 SER cc_start: 0.6041 (t) cc_final: 0.5348 (p)
  outliers start: 20
  outliers final: 10
  residues processed: 207
  average time/residue: 0.0669
  time to fit residues: 19.6603
Evaluate side-chains
  168 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  377 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0470
   overall best weight:    0.5678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 ASN
** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 GLN
** B 393 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 = 0.3810 r_free = 0.3810 target = 0.156246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.129205 restraints weight = 10766.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.132798 restraints weight = 6530.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.135124 restraints weight = 4853.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.136474 restraints weight = 4048.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137404 restraints weight = 3639.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7517  Z= 0.129
  Angle     :  0.577  13.222  10236  Z= 0.284
  Chirality :  0.039   0.156   1200
  Planarity :  0.004   0.045   1264
  Dihedral  :  5.079  49.898   1028
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.32 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.26 (0.28), residues: 940
  helix:  2.24 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.72 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 493 
 TYR   0.009   0.001   TYR B 340 
 PHE   0.014   0.001   PHE B 280 
 TRP   0.014   0.001   TRP A 106 
 HIS   0.002   0.001   HIS A 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 7516)
  covalent geometry    : angle       0.57744 /  0.28 (10236)
  hydrogen bonds       : bond        0.04113 /  2.74 (  542)
  hydrogen bonds       : angle       3.79556 /  2.73 ( 1578)
  Misc. bond           : bond        0.00952 /  0.50 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6708 (tt0)
REVERT: A  200 MET cc_start: 0.6000 (mmp) cc_final: 0.5658 (mmm)
REVERT: A  274 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6843 (t0)
REVERT: A  395 GLU cc_start: 0.6618 (tp30) cc_final: 0.6010 (tp30)
REVERT: A  442 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8242 (mmtm)
REVERT: B  239 MET cc_start: 0.6441 (mmp) cc_final: 0.6198 (mmp)
REVERT: B  442 LYS cc_start: 0.8521 (mmtp) cc_final: 0.8264 (mmtm)
  outliers start: 23
  outliers final: 11
  residues processed: 194
  average time/residue: 0.0647
  time to fit residues: 18.3369
Evaluate side-chains
  164 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  348 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 87 optimal weight:    0.0060
   chunk 55 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 91 optimal weight:    0.1980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.4396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 GLN
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.155650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.128250 restraints weight = 10971.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.131931 restraints weight = 6582.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.134331 restraints weight = 4847.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.135767 restraints weight = 4018.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.136498 restraints weight = 3595.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7517  Z= 0.121
  Angle     :  0.552  12.605  10236  Z= 0.272
  Chirality :  0.039   0.152   1200
  Planarity :  0.004   0.046   1264
  Dihedral  :  4.936  48.893   1028
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.45 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.31 (0.28), residues: 940
  helix:  2.28 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.69 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 273 
 TYR   0.014   0.001   TYR B 134 
 PHE   0.022   0.001   PHE A 280 
 TRP   0.015   0.001   TRP B 106 
 HIS   0.001   0.001   HIS A 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 7516)
  covalent geometry    : angle       0.55183 /  0.27 (10236)
  hydrogen bonds       : bond        0.03957 /  2.65 (  542)
  hydrogen bonds       : angle       3.73808 /  2.68 ( 1578)
  Misc. bond           : bond        0.00845 /  0.44 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.7125 (tm-30) cc_final: 0.6680 (tt0)
REVERT: A  239 MET cc_start: 0.6770 (mmp) cc_final: 0.6463 (mmp)
REVERT: A  395 GLU cc_start: 0.6619 (tp30) cc_final: 0.5997 (tp30)
REVERT: A  442 LYS cc_start: 0.8588 (mmtp) cc_final: 0.8210 (mmtm)
REVERT: B  279 PHE cc_start: 0.7808 (t80) cc_final: 0.7274 (t80)
REVERT: B  283 THR cc_start: 0.8699 (m) cc_final: 0.8469 (p)
REVERT: B  442 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8295 (mmtm)
REVERT: B  490 SER cc_start: 0.6038 (t) cc_final: 0.5317 (p)
REVERT: B  492 TYR cc_start: 0.7424 (m-80) cc_final: 0.7120 (m-80)
  outliers start: 19
  outliers final: 10
  residues processed: 179
  average time/residue: 0.0708
  time to fit residues: 18.0903
Evaluate side-chains
  160 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  208 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 ASN
** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 GLN
B 232 ASN
** B 393 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 = 0.3800 r_free = 0.3800 target = 0.155141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127995 restraints weight = 10905.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.131546 restraints weight = 6616.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.133802 restraints weight = 4933.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.135204 restraints weight = 4136.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.136023 restraints weight = 3711.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7517  Z= 0.133
  Angle     :  0.559  12.311  10236  Z= 0.277
  Chirality :  0.040   0.157   1200
  Planarity :  0.004   0.043   1264
  Dihedral  :  4.913  49.573   1028
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.62 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.28), residues: 940
  helix:  2.28 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.84 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 235 
 TYR   0.020   0.002   TYR A 134 
 PHE   0.021   0.002   PHE A 280 
 TRP   0.013   0.001   TRP B 106 
 HIS   0.002   0.001   HIS A 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 7516)
  covalent geometry    : angle       0.55901 /  0.28 (10236)
  hydrogen bonds       : bond        0.04054 /  2.70 (  542)
  hydrogen bonds       : angle       3.78852 /  2.71 ( 1578)
  Misc. bond           : bond        0.00856 /  0.45 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 MET cc_start: 0.6060 (mmp) cc_final: 0.5724 (mmm)
REVERT: A  239 MET cc_start: 0.6753 (mmp) cc_final: 0.6234 (mmp)
REVERT: A  274 ASN cc_start: 0.7178 (t0) cc_final: 0.6618 (t0)
REVERT: A  279 PHE cc_start: 0.7634 (t80) cc_final: 0.7301 (t80)
REVERT: A  395 GLU cc_start: 0.6769 (tp30) cc_final: 0.6493 (tp30)
REVERT: A  442 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8103 (mmtm)
REVERT: B  239 MET cc_start: 0.6567 (mmp) cc_final: 0.6353 (mmp)
REVERT: B  279 PHE cc_start: 0.7741 (t80) cc_final: 0.7536 (t80)
REVERT: B  280 PHE cc_start: 0.7527 (t80) cc_final: 0.7262 (t80)
REVERT: B  442 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8210 (mmtm)
REVERT: B  490 SER cc_start: 0.6132 (t) cc_final: 0.5427 (p)
  outliers start: 18
  outliers final: 10
  residues processed: 173
  average time/residue: 0.0679
  time to fit residues: 16.7974
Evaluate side-chains
  157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 147
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  208 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0570
   chunk 5 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.5898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.154960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.127736 restraints weight = 10953.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131335 restraints weight = 6564.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.133631 restraints weight = 4854.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.135075 restraints weight = 4046.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.135741 restraints weight = 3613.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7517  Z= 0.124
  Angle     :  0.544  11.766  10236  Z= 0.270
  Chirality :  0.039   0.141   1200
  Planarity :  0.004   0.042   1264
  Dihedral  :  4.817  48.622   1028
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.58 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.26 (0.28), residues: 940
  helix:  2.29 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.87 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 235 
 TYR   0.020   0.001   TYR A 134 
 PHE   0.026   0.001   PHE B 270 
 TRP   0.011   0.001   TRP B 106 
 HIS   0.002   0.001   HIS A 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 7516)
  covalent geometry    : angle       0.54381 /  0.27 (10236)
  hydrogen bonds       : bond        0.03913 /  2.62 (  542)
  hydrogen bonds       : angle       3.75919 /  2.69 ( 1578)
  Misc. bond           : bond        0.00827 /  0.44 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 PHE cc_start: 0.7628 (t80) cc_final: 0.7304 (t80)
REVERT: A  395 GLU cc_start: 0.6852 (tp30) cc_final: 0.6586 (tp30)
REVERT: A  442 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8122 (mmtm)
REVERT: B   89 GLU cc_start: 0.4874 (mp0) cc_final: 0.4464 (mm-30)
REVERT: B  239 MET cc_start: 0.6595 (mmp) cc_final: 0.6346 (mmp)
REVERT: B  279 PHE cc_start: 0.7800 (t80) cc_final: 0.7565 (t80)
REVERT: B  280 PHE cc_start: 0.7468 (t80) cc_final: 0.7249 (t80)
REVERT: B  442 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8140 (mmtm)
REVERT: B  490 SER cc_start: 0.6199 (t) cc_final: 0.5432 (p)
  outliers start: 18
  outliers final: 12
  residues processed: 168
  average time/residue: 0.0717
  time to fit residues: 17.3005
Evaluate side-chains
  156 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  208 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 80 optimal weight:    0.0980
   chunk 91 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 133 GLN
A 274 ASN
** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 GLN
** B 393 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 = 0.3780 r_free = 0.3780 target = 0.153525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.126693 restraints weight = 10995.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.130252 restraints weight = 6599.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132514 restraints weight = 4875.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.133898 restraints weight = 4056.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.134625 restraints weight = 3634.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7517  Z= 0.120
  Angle     :  0.537  11.397  10236  Z= 0.268
  Chirality :  0.039   0.181   1200
  Planarity :  0.004   0.041   1264
  Dihedral  :  4.748  47.293   1028
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.89 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.28), residues: 940
  helix:  2.32 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.76 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 350 
 TYR   0.019   0.001   TYR A 134 
 PHE   0.025   0.001   PHE B 270 
 TRP   0.011   0.001   TRP B 106 
 HIS   0.002   0.001   HIS A 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 7516)
  covalent geometry    : angle       0.53670 /  0.27 (10236)
  hydrogen bonds       : bond        0.03838 /  2.56 (  542)
  hydrogen bonds       : angle       3.72214 /  2.66 ( 1578)
  Misc. bond           : bond        0.00787 /  0.41 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 PHE cc_start: 0.7639 (t80) cc_final: 0.7353 (t80)
REVERT: A  239 MET cc_start: 0.6789 (mmp) cc_final: 0.6324 (mmp)
REVERT: A  274 ASN cc_start: 0.7208 (t0) cc_final: 0.6621 (t0)
REVERT: A  280 PHE cc_start: 0.7606 (t80) cc_final: 0.7295 (t80)
REVERT: A  395 GLU cc_start: 0.6937 (tp30) cc_final: 0.6325 (tp30)
REVERT: A  442 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8029 (mmtm)
REVERT: A  445 MET cc_start: 0.8330 (mtm) cc_final: 0.7912 (mtp)
REVERT: B   89 GLU cc_start: 0.4838 (mp0) cc_final: 0.4269 (mm-30)
REVERT: B  151 PHE cc_start: 0.7555 (t80) cc_final: 0.7266 (t80)
REVERT: B  239 MET cc_start: 0.6570 (mmp) cc_final: 0.6331 (mmp)
REVERT: B  279 PHE cc_start: 0.7780 (t80) cc_final: 0.7567 (t80)
REVERT: B  280 PHE cc_start: 0.7464 (t80) cc_final: 0.7248 (t80)
REVERT: B  442 LYS cc_start: 0.8593 (mmtp) cc_final: 0.8063 (mmtm)
REVERT: B  445 MET cc_start: 0.8304 (mtm) cc_final: 0.7915 (mtp)
REVERT: B  490 SER cc_start: 0.6134 (t) cc_final: 0.5368 (p)
  outliers start: 20
  outliers final: 15
  residues processed: 165
  average time/residue: 0.0662
  time to fit residues: 15.6456
Evaluate side-chains
  159 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  477 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 GLN
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.124912 restraints weight = 11118.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.128457 restraints weight = 6742.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.130722 restraints weight = 5018.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.132092 restraints weight = 4198.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.132669 restraints weight = 3767.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7517  Z= 0.143
  Angle     :  0.575  11.530  10236  Z= 0.289
  Chirality :  0.041   0.196   1200
  Planarity :  0.004   0.039   1264
  Dihedral  :  4.878  49.803   1028
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.37 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.28), residues: 940
  helix:  2.24 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.92 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 290 
 TYR   0.020   0.002   TYR A 134 
 PHE   0.028   0.002   PHE B 270 
 TRP   0.011   0.001   TRP A 480 
 HIS   0.004   0.001   HIS A 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 7516)
  covalent geometry    : angle       0.57476 /  0.29 (10236)
  hydrogen bonds       : bond        0.04161 /  2.79 (  542)
  hydrogen bonds       : angle       3.83422 /  2.76 ( 1578)
  Misc. bond           : bond        0.00826 /  0.43 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 PHE cc_start: 0.7648 (t80) cc_final: 0.7401 (t80)
REVERT: A  274 ASN cc_start: 0.7465 (t0) cc_final: 0.6845 (t0)
REVERT: A  280 PHE cc_start: 0.7663 (t80) cc_final: 0.7406 (t80)
REVERT: A  309 ARG cc_start: 0.5903 (ttp-170) cc_final: 0.4926 (mtm110)
REVERT: A  395 GLU cc_start: 0.6951 (tp30) cc_final: 0.6366 (tp30)
REVERT: A  442 LYS cc_start: 0.8650 (mmtp) cc_final: 0.8092 (mmtm)
REVERT: A  445 MET cc_start: 0.8340 (mtm) cc_final: 0.7970 (mtp)
REVERT: B   89 GLU cc_start: 0.4932 (mp0) cc_final: 0.4274 (mm-30)
REVERT: B  119 GLN cc_start: 0.7539 (tm-30) cc_final: 0.6434 (tt0)
REVERT: B  151 PHE cc_start: 0.7532 (t80) cc_final: 0.7238 (t80)
REVERT: B  279 PHE cc_start: 0.7836 (t80) cc_final: 0.7578 (t80)
REVERT: B  280 PHE cc_start: 0.7538 (t80) cc_final: 0.7322 (t80)
REVERT: B  442 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8120 (mmtm)
REVERT: B  445 MET cc_start: 0.8313 (mtm) cc_final: 0.7964 (mtp)
REVERT: B  490 SER cc_start: 0.6165 (t) cc_final: 0.5504 (p)
  outliers start: 24
  outliers final: 19
  residues processed: 166
  average time/residue: 0.0531
  time to fit residues: 12.6086
Evaluate side-chains
  163 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  477 MET
Chi-restraints excluded: chain B residue  542 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 64 optimal weight:    0.3980
   chunk 1 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 86 optimal weight:    0.3980
   chunk 78 optimal weight:    0.1980
   chunk 63 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 133 GLN
** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.153586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.126463 restraints weight = 11044.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.129925 restraints weight = 6732.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.132186 restraints weight = 5026.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.133589 restraints weight = 4204.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.134377 restraints weight = 3765.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7517  Z= 0.123
  Angle     :  0.559  11.279  10236  Z= 0.280
  Chirality :  0.041   0.349   1200
  Planarity :  0.004   0.040   1264
  Dihedral  :  4.829  48.620   1028
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.41 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.28 (0.28), residues: 940
  helix:  2.31 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.83 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 235 
 TYR   0.022   0.001   TYR A 134 
 PHE   0.027   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 480 
 HIS   0.001   0.000   HIS A 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 7516)
  covalent geometry    : angle       0.55891 /  0.28 (10236)
  hydrogen bonds       : bond        0.03831 /  2.55 (  542)
  hydrogen bonds       : angle       3.76560 /  2.70 ( 1578)
  Misc. bond           : bond        0.00757 /  0.40 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 PHE cc_start: 0.7637 (t80) cc_final: 0.7401 (t80)
REVERT: A  205 GLU cc_start: 0.7246 (pm20) cc_final: 0.6687 (pt0)
REVERT: A  239 MET cc_start: 0.6749 (mmp) cc_final: 0.6355 (mmp)
REVERT: A  280 PHE cc_start: 0.7620 (t80) cc_final: 0.7396 (t80)
REVERT: A  395 GLU cc_start: 0.6945 (tp30) cc_final: 0.6373 (tp30)
REVERT: A  442 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8077 (mmtm)
REVERT: A  556 ILE cc_start: 0.8743 (mm) cc_final: 0.8363 (mt)
REVERT: B   89 GLU cc_start: 0.4937 (mp0) cc_final: 0.4288 (mm-30)
REVERT: B  151 PHE cc_start: 0.7546 (t80) cc_final: 0.7236 (t80)
REVERT: B  239 MET cc_start: 0.6446 (mmp) cc_final: 0.6232 (mmp)
REVERT: B  279 PHE cc_start: 0.7698 (t80) cc_final: 0.7285 (t80)
REVERT: B  280 PHE cc_start: 0.7428 (t80) cc_final: 0.6973 (t80)
REVERT: B  442 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8143 (mmtm)
REVERT: B  490 SER cc_start: 0.6146 (t) cc_final: 0.5511 (p)
  outliers start: 18
  outliers final: 17
  residues processed: 164
  average time/residue: 0.0540
  time to fit residues: 12.8150
Evaluate side-chains
  158 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  477 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.0170
   chunk 50 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 61 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.9422

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 ASN
** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.150793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123712 restraints weight = 11059.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.127151 restraints weight = 6824.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.129354 restraints weight = 5107.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.130707 restraints weight = 4275.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.131425 restraints weight = 3837.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7517  Z= 0.149
  Angle     :  0.585  11.120  10236  Z= 0.297
  Chirality :  0.041   0.201   1200
  Planarity :  0.004   0.038   1264
  Dihedral  :  4.950  50.643   1028
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.41 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.29), residues: 940
  helix:  2.20 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.03 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 235 
 TYR   0.021   0.002   TYR A 134 
 PHE   0.025   0.002   PHE B 270 
 TRP   0.015   0.001   TRP A 480 
 HIS   0.003   0.001   HIS A 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 7516)
  covalent geometry    : angle       0.58533 /  0.30 (10236)
  hydrogen bonds       : bond        0.04169 /  2.79 (  542)
  hydrogen bonds       : angle       3.85644 /  2.78 ( 1578)
  Misc. bond           : bond        0.00810 /  0.43 (    1)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 GLN cc_start: 0.6963 (pt0) cc_final: 0.6667 (pt0)
REVERT: A  151 PHE cc_start: 0.7639 (t80) cc_final: 0.7405 (t80)
REVERT: A  205 GLU cc_start: 0.7375 (pm20) cc_final: 0.6731 (pt0)
REVERT: A  239 MET cc_start: 0.6932 (mmp) cc_final: 0.6484 (mmp)
REVERT: A  270 PHE cc_start: 0.5920 (t80) cc_final: 0.5427 (t80)
REVERT: A  280 PHE cc_start: 0.7680 (t80) cc_final: 0.7464 (t80)
REVERT: A  309 ARG cc_start: 0.5958 (ttp-170) cc_final: 0.4749 (mtp-110)
REVERT: A  395 GLU cc_start: 0.6969 (tp30) cc_final: 0.6479 (tp30)
REVERT: A  445 MET cc_start: 0.8323 (mtm) cc_final: 0.8050 (mtp)
REVERT: B   89 GLU cc_start: 0.4991 (mp0) cc_final: 0.4414 (mm-30)
REVERT: B  119 GLN cc_start: 0.7644 (tm-30) cc_final: 0.6460 (tt0)
REVERT: B  151 PHE cc_start: 0.7560 (t80) cc_final: 0.7239 (t80)
REVERT: B  239 MET cc_start: 0.6533 (mmp) cc_final: 0.6283 (mmp)
REVERT: B  280 PHE cc_start: 0.7343 (t80) cc_final: 0.7141 (t80)
REVERT: B  442 LYS cc_start: 0.8606 (mmtp) cc_final: 0.8136 (mmtm)
REVERT: B  445 MET cc_start: 0.8349 (mtm) cc_final: 0.8115 (mtp)
REVERT: B  490 SER cc_start: 0.6236 (t) cc_final: 0.5676 (p)
  outliers start: 22
  outliers final: 18
  residues processed: 154
  average time/residue: 0.0517
  time to fit residues: 11.5367
Evaluate side-chains
  156 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  477 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0170
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.5218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 ASN
** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.149340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.123137 restraints weight = 11041.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.126724 restraints weight = 6397.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.129125 restraints weight = 4623.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.130555 restraints weight = 3765.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.131491 restraints weight = 3330.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.4995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7517  Z= 0.126
  Angle     :  0.565  10.848  10236  Z= 0.286
  Chirality :  0.040   0.204   1200
  Planarity :  0.004   0.040   1264
  Dihedral  :  4.900  49.783   1028
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.93 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.29), residues: 940
  helix:  2.27 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.98 (0.43), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 235 
 TYR   0.021   0.001   TYR A 134 
 PHE   0.032   0.001   PHE A 469 
 TRP   0.014   0.001   TRP B 444 
 HIS   0.001   0.000   HIS A 513 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 7516)
  covalent geometry    : angle       0.56460 /  0.29 (10236)
  hydrogen bonds       : bond        0.03878 /  2.58 (  542)
  hydrogen bonds       : angle       3.78548 /  2.72 ( 1578)
  Misc. bond           : bond        0.00795 /  0.42 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1165.20 seconds
wall clock time: 20 minutes 45.00 seconds (1245.00 seconds total)