Starting phenix.real_space_refine
on Wed Mar 12 05:43:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qlo_18486/03_2025/8qlo_18486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qlo_18486/03_2025/8qlo_18486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qlo_18486/03_2025/8qlo_18486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qlo_18486/03_2025/8qlo_18486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qlo_18486/03_2025/8qlo_18486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qlo_18486/03_2025/8qlo_18486.cif"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4726      2.51       5
     N    1203      2.21       5
     O    1331      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7282
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3657
          Classifications: {'peptide': 455}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 431}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3625
          Classifications: {'peptide': 437}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 419}
  Time building chain proxies: 5.49, per 1000 atoms: 0.75
  Number of scatterers: 7282
  At special positions: 0
  Unit cell: (80.6, 81.25, 124.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O    1331      8.00
     N    1203      7.00
     C    4726      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 993.8 milliseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 12 sheets defined
      41.9% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 22 through 30
    Processing helix  chain 'B' and resid 46 through 60
    Processing helix  chain 'B' and resid 77 through 82
    Processing helix  chain 'B' and resid 97 through 106
      removed outlier: 3.580A  pdb=" N   ILE B 101 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 132
      removed outlier: 3.731A  pdb=" N   GLU B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 151
      removed outlier: 3.694A  pdb=" N   TYR B 148 " --> pdb=" O   PRO B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 216
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 248 through 264
      removed outlier: 3.688A  pdb=" N   ALA B 253 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TRP B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 351
    Processing helix  chain 'B' and resid 366 through 377
      removed outlier: 3.612A  pdb=" N   TRP B 370 " --> pdb=" O   ASN B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 465
      removed outlier: 3.731A  pdb=" N   LEU B 465 " --> pdb=" O   ALA B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 482
      removed outlier: 4.258A  pdb=" N   PHE B 482 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 493
      removed outlier: 3.706A  pdb=" N   SER B 493 " --> pdb=" O   ILE B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 506
      No H-bonds generated for 'chain 'B' and resid 504 through 506'
    Processing helix  chain 'A' and resid 14 through 28
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 65 through 71
    Processing helix  chain 'A' and resid 71 through 89
    Processing helix  chain 'A' and resid 104 through 108
    Processing helix  chain 'A' and resid 109 through 113
      removed outlier: 3.743A  pdb=" N   ILE A 113 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 138
    Processing helix  chain 'A' and resid 146 through 159
      removed outlier: 3.721A  pdb=" N   SER A 150 " --> pdb=" O   ASP A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 222 through 226
      removed outlier: 4.330A  pdb=" N   HIS A 225 " --> pdb=" O   ASP A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 233
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 243 through 248
    Processing helix  chain 'A' and resid 257 through 280
    Processing helix  chain 'A' and resid 300 through 302
      No H-bonds generated for 'chain 'A' and resid 300 through 302'
    Processing helix  chain 'A' and resid 353 through 368
    Processing helix  chain 'A' and resid 369 through 385
    Processing helix  chain 'A' and resid 423 through 436
    Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3
      removed outlier: 6.430A  pdb=" N   LYS B   2 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6
      removed outlier: 6.607A  pdb=" N   SER B 417 " --> pdb=" O   VAL B 413 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   ILE B 443 " --> pdb=" O   THR B 389 " (cutoff:3.500A)
      removed outlier: 7.404A  pdb=" N   THR B 389 " --> pdb=" O   ILE B 443 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   ILE B 445 " --> pdb=" O   THR B 387 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   THR B 387 " --> pdb=" O   ILE B 445 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   VAL B 386 " --> pdb=" O   ILE B 359 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 20
    Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 95
      removed outlier: 6.116A  pdb=" N   SER B  41 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   LYS B  94 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   VAL B  43 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 5.862A  pdb=" N   GLY B  42 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   VAL B 142 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   VAL B  44 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287
    Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 322
    Processing sheet with id=AA7, first strand: chain 'B' and resid 425 through 426
    Processing sheet with id=AA8, first strand: chain 'A' and resid 31 through 33
      removed outlier: 8.307A  pdb=" N   LEU A  61 " --> pdb=" O   LYS A   4 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   PHE A   6 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   ALA A  63 " --> pdb=" O   PHE A   6 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   SER A   8 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   PHE A  60 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   LEU A  97 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU A  62 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   VAL A 118 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 283 through 285
    Processing sheet with id=AB1, first strand: chain 'A' and resid 283 through 285
      removed outlier: 7.438A  pdb=" N   TRP A 175 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   GLU A 406 " --> pdb=" O   TRP A 175 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   SER A 177 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   TYR A 402 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AB3, first strand: chain 'A' and resid 304 through 305

    338 hydrogen bonds defined for protein.
    912 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: 3.74

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1216
        1.30 -     1.43: 1942
        1.43 -     1.55: 4274
        1.55 -     1.68: 0
        1.68 -     1.81: 34
  Bond restraints: 7466
  Sorted by residual:
  bond pdb=" C   PRO B 404 "
       pdb=" O   PRO B 404 "
    ideal  model  delta    sigma   weight residual
    1.235  1.169  0.066 1.30e-02 5.92e+03 2.55e+01
  bond pdb=" C   PRO B 268 "
       pdb=" O   PRO B 268 "
    ideal  model  delta    sigma   weight residual
    1.235  1.173  0.062 1.30e-02 5.92e+03 2.25e+01
  bond pdb=" C   PRO B  76 "
       pdb=" O   PRO B  76 "
    ideal  model  delta    sigma   weight residual
    1.238  1.174  0.064 1.35e-02 5.49e+03 2.24e+01
  bond pdb=" CA  TYR B 425 "
       pdb=" C   TYR B 425 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.051 1.19e-02 7.06e+03 1.81e+01
  bond pdb=" C   PRO B 499 "
       pdb=" O   PRO B 499 "
    ideal  model  delta    sigma   weight residual
    1.240  1.193  0.047 1.12e-02 7.97e+03 1.78e+01
  ... (remaining 7461 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 8839
        1.83 -     3.66: 1100
        3.66 -     5.49: 119
        5.49 -     7.32: 26
        7.32 -     9.15: 6
  Bond angle restraints: 10090
  Sorted by residual:
  angle pdb=" N   LEU A  37 "
        pdb=" CA  LEU A  37 "
        pdb=" C   LEU A  37 "
      ideal   model   delta    sigma   weight residual
     113.15  104.98    8.17 1.19e+00 7.06e-01 4.72e+01
  angle pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
        pdb=" C   PRO B 499 "
      ideal   model   delta    sigma   weight residual
     110.70  103.30    7.40 1.22e+00 6.72e-01 3.68e+01
  angle pdb=" N   ILE A  58 "
        pdb=" CA  ILE A  58 "
        pdb=" C   ILE A  58 "
      ideal   model   delta    sigma   weight residual
     113.07  105.02    8.05 1.36e+00 5.41e-01 3.51e+01
  angle pdb=" N   TYR B 472 "
        pdb=" CA  TYR B 472 "
        pdb=" C   TYR B 472 "
      ideal   model   delta    sigma   weight residual
     111.33  104.31    7.02 1.21e+00 6.83e-01 3.37e+01
  angle pdb=" N   ILE B  70 "
        pdb=" CA  ILE B  70 "
        pdb=" C   ILE B  70 "
      ideal   model   delta    sigma   weight residual
     111.56  106.68    4.88 8.60e-01 1.35e+00 3.22e+01
  ... (remaining 10085 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.89: 3833
       14.89 -    29.79: 441
       29.79 -    44.68: 141
       44.68 -    59.57: 37
       59.57 -    74.47: 21
  Dihedral angle restraints: 4473
    sinusoidal: 1858
      harmonic: 2615
  Sorted by residual:
  dihedral pdb=" C   TYR B 425 "
           pdb=" N   TYR B 425 "
           pdb=" CA  TYR B 425 "
           pdb=" CB  TYR B 425 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.27  -11.33     0      2.50e+00 1.60e-01 2.06e+01
  dihedral pdb=" CA  ARG B 213 "
           pdb=" C   ARG B 213 "
           pdb=" N   LEU B 214 "
           pdb=" CA  LEU B 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.03   16.97     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" N   ALA A  63 "
           pdb=" C   ALA A  63 "
           pdb=" CA  ALA A  63 "
           pdb=" CB  ALA A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  114.66    8.24     0      2.50e+00 1.60e-01 1.09e+01
  ... (remaining 4470 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 633
       0.051 -    0.103: 238
       0.103 -    0.154: 137
       0.154 -    0.205: 58
       0.205 -    0.257: 10
  Chirality restraints: 1076
  Sorted by residual:
  chirality pdb=" CA  VAL B 423 "
            pdb=" N   VAL B 423 "
            pdb=" C   VAL B 423 "
            pdb=" CB  VAL B 423 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  VAL A 334 "
            pdb=" CA  VAL A 334 "
            pdb=" CG1 VAL A 334 "
            pdb=" CG2 VAL A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  ILE B 122 "
            pdb=" N   ILE B 122 "
            pdb=" C   ILE B 122 "
            pdb=" CB  ILE B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 1073 not shown)

  Planarity restraints: 1288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  40 "    0.016 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   LYS B  40 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   LYS B  40 "    0.022 2.00e-02 2.50e+03
        pdb=" N   SER B  41 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  24 "   -0.272 9.50e-02 1.11e+02   1.22e-01 9.09e+00
        pdb=" NE  ARG B  24 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  24 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  24 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  24 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 315 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.55e+00
        pdb=" C   GLY B 315 "    0.041 2.00e-02 2.50e+03
        pdb=" O   GLY B 315 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLU B 316 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1285 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 742
        2.75 -     3.29: 7331
        3.29 -     3.82: 12272
        3.82 -     4.36: 15855
        4.36 -     4.90: 25514
  Nonbonded interactions: 61714
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 284 "
            pdb=" OE1 GLU A 284 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   LEU A 227 "
            pdb=" OG1 THR A 230 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OD1 ASN B 307 "
            pdb=" N   ASP B 309 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" N   GLU B 132 "
            pdb=" OE1 GLU B 132 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OG  SER A 173 "
            pdb=" O   VAL A 408 "
     model   vdw
     2.321 3.040
  ... (remaining 61709 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.190
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:20.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
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      :  0.009   0.069   7466  Z= 0.572
  Angle     :  1.180   9.151  10090  Z= 0.854
  Chirality :  0.076   0.257   1076
  Planarity :  0.007   0.122   1288
  Dihedral  : 15.285  74.466   2785
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.51 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.15 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.27), residues: 886
  helix: -0.42 (0.28), residues: 307
  sheet: -1.11 (0.39), residues: 171
  loop : -1.14 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 370 
 HIS   0.003   0.001   HIS B 326 
 PHE   0.022   0.002   PHE B 373 
 TYR   0.021   0.002   TYR B 472 
 ARG   0.008   0.001   ARG A 209 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8138 (m-10) cc_final: 0.7779 (p90)
REVERT: B   87 ASP cc_start: 0.8225 (t0) cc_final: 0.7190 (t70)
REVERT: B   89 ASP cc_start: 0.7473 (m-30) cc_final: 0.6974 (m-30)
REVERT: B  135 LYS cc_start: 0.7348 (mttt) cc_final: 0.7081 (pptt)
REVERT: B  225 ARG cc_start: 0.7472 (mtp180) cc_final: 0.7137 (mtp180)
REVERT: A   44 ASP cc_start: 0.6514 (OUTLIER) cc_final: 0.6240 (p0)
REVERT: A   54 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7428 (ptp-110)
REVERT: A   84 VAL cc_start: 0.8370 (t) cc_final: 0.8097 (p)
REVERT: A   90 ASP cc_start: 0.7941 (t0) cc_final: 0.7270 (t0)
REVERT: A   91 ASP cc_start: 0.8109 (m-30) cc_final: 0.7782 (t70)
REVERT: A  263 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7117 (tmm-80)
REVERT: A  267 GLN cc_start: 0.8385 (mm110) cc_final: 0.7828 (mp10)
  outliers start: 17
  outliers final: 8
  residues processed: 157
  average time/residue: 1.5743
  time to fit residues: 262.9519
Evaluate side-chains
  101 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   44 ASP
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  255 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0170
   chunk 37 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
B 251 HIS
B 439 ASN
A  15 ASN
A 155 GLN
A 234 ASN
A 434 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.123998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.095204 restraints weight = 12137.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 3.35
r_work: 0.3323 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7466  Z= 0.205
  Angle     :  0.602   7.234  10090  Z= 0.312
  Chirality :  0.043   0.227   1076
  Planarity :  0.004   0.038   1288
  Dihedral  :  5.488  50.198    971
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.44 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.28), residues: 886
  helix:  0.87 (0.28), residues: 325
  sheet: -0.87 (0.40), residues: 163
  loop : -0.57 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 370 
 HIS   0.002   0.001   HIS A   9 
 PHE   0.016   0.002   PHE A 259 
 TYR   0.013   0.001   TYR B 262 
 ARG   0.006   0.001   ARG A 209 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8511 (m-10) cc_final: 0.7837 (p90)
REVERT: B   87 ASP cc_start: 0.8583 (t0) cc_final: 0.7939 (t70)
REVERT: B  135 LYS cc_start: 0.7546 (mttt) cc_final: 0.7220 (pptt)
REVERT: B  148 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.6126 (m-80)
REVERT: B  400 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6632 (mp0)
REVERT: A   41 LYS cc_start: 0.5628 (OUTLIER) cc_final: 0.5376 (ptmm)
REVERT: A   54 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7684 (ptp-110)
REVERT: A   88 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8412 (mm)
REVERT: A   91 ASP cc_start: 0.8667 (m-30) cc_final: 0.8250 (t0)
REVERT: A  398 GLU cc_start: 0.8727 (mp0) cc_final: 0.8019 (tm-30)
  outliers start: 26
  outliers final: 7
  residues processed: 120
  average time/residue: 1.0645
  time to fit residues: 136.2418
Evaluate side-chains
  95 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue  148 TYR
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0570
   chunk 42 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.123668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.094643 restraints weight = 12338.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 3.39
r_work: 0.3304 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7466  Z= 0.185
  Angle     :  0.551   6.285  10090  Z= 0.285
  Chirality :  0.042   0.233   1076
  Planarity :  0.004   0.048   1288
  Dihedral  :  4.644  35.774    960
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.71 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.28), residues: 886
  helix:  1.27 (0.28), residues: 325
  sheet: -0.88 (0.39), residues: 163
  loop : -0.33 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 370 
 HIS   0.003   0.001   HIS A   9 
 PHE   0.013   0.001   PHE A 158 
 TYR   0.012   0.001   TYR B 285 
 ARG   0.009   0.001   ARG A 263 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8567 (m-10) cc_final: 0.7879 (p90)
REVERT: B   87 ASP cc_start: 0.8630 (t0) cc_final: 0.8021 (t70)
REVERT: B  135 LYS cc_start: 0.7634 (mttt) cc_final: 0.7055 (pptt)
REVERT: B  400 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6830 (mp0)
REVERT: B  471 ILE cc_start: 0.8328 (mt) cc_final: 0.7992 (mp)
REVERT: A   41 LYS cc_start: 0.5651 (OUTLIER) cc_final: 0.5375 (ptmm)
REVERT: A   54 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7679 (ptp-110)
REVERT: A   77 GLU cc_start: 0.7404 (mp0) cc_final: 0.6920 (mm-30)
REVERT: A   88 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8377 (mm)
REVERT: A  101 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8139 (mt-10)
REVERT: A  345 LYS cc_start: 0.8405 (mptt) cc_final: 0.7930 (mmtm)
REVERT: A  398 GLU cc_start: 0.8723 (mp0) cc_final: 0.7942 (tm-30)
  outliers start: 24
  outliers final: 10
  residues processed: 110
  average time/residue: 1.0472
  time to fit residues: 122.9202
Evaluate side-chains
  97 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** B 302 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 = 0.3885 r_free = 0.3885 target = 0.123690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.094395 restraints weight = 12331.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 3.38
r_work: 0.3302 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7466  Z= 0.189
  Angle     :  0.542   6.546  10090  Z= 0.277
  Chirality :  0.042   0.239   1076
  Planarity :  0.004   0.037   1288
  Dihedral  :  4.405  18.268    957
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.60 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.28), residues: 886
  helix:  1.49 (0.28), residues: 324
  sheet: -0.71 (0.39), residues: 163
  loop : -0.26 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 370 
 HIS   0.008   0.001   HIS B  59 
 PHE   0.011   0.001   PHE A 158 
 TYR   0.011   0.001   TYR A 293 
 ARG   0.008   0.001   ARG A 263 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8596 (m-10) cc_final: 0.7907 (p90)
REVERT: B   87 ASP cc_start: 0.8678 (t0) cc_final: 0.8064 (t70)
REVERT: B  350 ASN cc_start: 0.8675 (m-40) cc_final: 0.8248 (m110)
REVERT: B  400 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6816 (mp0)
REVERT: B  471 ILE cc_start: 0.8367 (mt) cc_final: 0.8043 (mp)
REVERT: A   41 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.4931 (mtmm)
REVERT: A   54 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7608 (ptp-110)
REVERT: A   77 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6928 (mm-30)
REVERT: A   88 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8379 (mm)
REVERT: A  226 GLN cc_start: 0.8044 (mt0) cc_final: 0.7824 (mt0)
REVERT: A  240 ARG cc_start: 0.8532 (ptp90) cc_final: 0.7974 (mtp85)
REVERT: A  349 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6811 (pm20)
REVERT: A  398 GLU cc_start: 0.8734 (mp0) cc_final: 0.7935 (tm-30)
  outliers start: 27
  outliers final: 12
  residues processed: 109
  average time/residue: 0.9710
  time to fit residues: 113.3679
Evaluate side-chains
  97 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 55 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0270
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.8640

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

Flipped N/Q/H residues before XYZ refinement:
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.121613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.092462 restraints weight = 12278.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 3.39
r_work: 0.3274 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7466  Z= 0.221
  Angle     :  0.555   8.098  10090  Z= 0.284
  Chirality :  0.042   0.235   1076
  Planarity :  0.004   0.061   1288
  Dihedral  :  4.386  17.111    955
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.98 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.28), residues: 886
  helix:  1.43 (0.28), residues: 324
  sheet: -0.54 (0.40), residues: 163
  loop : -0.19 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 370 
 HIS   0.007   0.001   HIS B  59 
 PHE   0.012   0.001   PHE A 158 
 TYR   0.011   0.001   TYR B 285 
 ARG   0.004   0.000   ARG B  72 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8627 (m-10) cc_final: 0.7889 (p90)
REVERT: B   87 ASP cc_start: 0.8714 (t0) cc_final: 0.8091 (t70)
REVERT: B  350 ASN cc_start: 0.8689 (m-40) cc_final: 0.8254 (m-40)
REVERT: B  400 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6935 (mp0)
REVERT: A   54 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7559 (ptp-110)
REVERT: A   77 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6958 (mm-30)
REVERT: A   88 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8405 (mm)
REVERT: A  212 ASN cc_start: 0.8849 (t0) cc_final: 0.8314 (t0)
REVERT: A  267 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8153 (mm-40)
REVERT: A  362 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8271 (tpp-160)
REVERT: A  398 GLU cc_start: 0.8745 (mp0) cc_final: 0.7896 (tm-30)
  outliers start: 27
  outliers final: 11
  residues processed: 105
  average time/residue: 0.9545
  time to fit residues: 107.4393
Evaluate side-chains
  97 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  267 GLN
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 302 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 = 0.3862 r_free = 0.3862 target = 0.121467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.092132 restraints weight = 12313.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 3.41
r_work: 0.3269 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7466  Z= 0.218
  Angle     :  0.558   7.633  10090  Z= 0.286
  Chirality :  0.042   0.238   1076
  Planarity :  0.004   0.043   1288
  Dihedral  :  4.360  16.374    955
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 22.62 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.28), residues: 886
  helix:  1.41 (0.28), residues: 324
  sheet: -0.52 (0.39), residues: 163
  loop : -0.10 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 370 
 HIS   0.007   0.001   HIS B  59 
 PHE   0.019   0.002   PHE A 259 
 TYR   0.011   0.001   TYR B 285 
 ARG   0.004   0.000   ARG B  72 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8615 (m-10) cc_final: 0.7892 (p90)
REVERT: B   87 ASP cc_start: 0.8753 (t0) cc_final: 0.8129 (t70)
REVERT: B  350 ASN cc_start: 0.8725 (m-40) cc_final: 0.8285 (m-40)
REVERT: B  400 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7043 (mp0)
REVERT: A   41 LYS cc_start: 0.5611 (OUTLIER) cc_final: 0.4981 (mtmm)
REVERT: A   54 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7446 (ptp-110)
REVERT: A   77 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6956 (mm-30)
REVERT: A   88 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8405 (mm)
REVERT: A  184 GLU cc_start: 0.8360 (pt0) cc_final: 0.8095 (pp20)
REVERT: A  212 ASN cc_start: 0.8854 (t0) cc_final: 0.8306 (t0)
REVERT: A  267 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7824 (mp10)
REVERT: A  362 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8274 (tpp-160)
REVERT: A  398 GLU cc_start: 0.8757 (mp0) cc_final: 0.7924 (tm-30)
  outliers start: 32
  outliers final: 14
  residues processed: 112
  average time/residue: 1.0136
  time to fit residues: 121.3898
Evaluate side-chains
  102 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  348 GLU
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  267 GLN
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 37 optimal weight:    0.2980
   chunk 11 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN
A   9 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.120614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.092030 restraints weight = 12304.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 3.35
r_work: 0.3269 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7466  Z= 0.236
  Angle     :  0.573   8.057  10090  Z= 0.293
  Chirality :  0.042   0.237   1076
  Planarity :  0.004   0.055   1288
  Dihedral  :  4.384  16.916    955
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 23.00 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 886
  helix:  1.43 (0.28), residues: 324
  sheet: -0.54 (0.40), residues: 164
  loop : -0.08 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 370 
 HIS   0.007   0.001   HIS B  59 
 PHE   0.011   0.001   PHE A 158 
 TYR   0.011   0.001   TYR B 285 
 ARG   0.004   0.000   ARG B  72 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 90
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8577 (m-10) cc_final: 0.7925 (p90)
REVERT: B   87 ASP cc_start: 0.8751 (t0) cc_final: 0.8158 (t70)
REVERT: B  330 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7042 (pp)
REVERT: B  350 ASN cc_start: 0.8678 (m-40) cc_final: 0.8234 (m110)
REVERT: B  400 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7164 (mp0)
REVERT: A   41 LYS cc_start: 0.5738 (OUTLIER) cc_final: 0.5148 (mtmm)
REVERT: A   54 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7415 (ptp-110)
REVERT: A   77 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6962 (mm-30)
REVERT: A   88 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8378 (mm)
REVERT: A  184 GLU cc_start: 0.8349 (pt0) cc_final: 0.8075 (pp20)
REVERT: A  212 ASN cc_start: 0.8878 (t0) cc_final: 0.8327 (t0)
REVERT: A  267 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8165 (mm-40)
REVERT: A  349 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6931 (pm20)
REVERT: A  398 GLU cc_start: 0.8737 (mp0) cc_final: 0.7919 (tm-30)
  outliers start: 31
  outliers final: 12
  residues processed: 112
  average time/residue: 0.9243
  time to fit residues: 111.9781
Evaluate side-chains
  102 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  267 GLN
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0000
   chunk 74 optimal weight:    3.9990
   chunk 68 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A   9 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.121970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.093334 restraints weight = 12401.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 3.38
r_work: 0.3282 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7466  Z= 0.194
  Angle     :  0.578   8.867  10090  Z= 0.291
  Chirality :  0.042   0.245   1076
  Planarity :  0.004   0.053   1288
  Dihedral  :  4.339  17.685    955
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 24.27 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.29), residues: 886
  helix:  1.61 (0.28), residues: 318
  sheet: -0.53 (0.40), residues: 169
  loop : -0.10 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 370 
 HIS   0.007   0.001   HIS B  59 
 PHE   0.022   0.001   PHE A 223 
 TYR   0.016   0.001   TYR B  48 
 ARG   0.004   0.000   ARG B  72 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8586 (m-10) cc_final: 0.7919 (p90)
REVERT: B   87 ASP cc_start: 0.8773 (t0) cc_final: 0.8167 (t70)
REVERT: B  330 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7040 (pp)
REVERT: B  400 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7165 (mp0)
REVERT: A   41 LYS cc_start: 0.5716 (OUTLIER) cc_final: 0.5167 (mtmm)
REVERT: A   54 ARG cc_start: 0.7805 (mtm110) cc_final: 0.7395 (ptp-110)
REVERT: A   77 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6969 (mm-30)
REVERT: A   86 LYS cc_start: 0.9010 (tptp) cc_final: 0.8796 (tppp)
REVERT: A   88 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8333 (mm)
REVERT: A  184 GLU cc_start: 0.8251 (pt0) cc_final: 0.8016 (pp20)
REVERT: A  212 ASN cc_start: 0.8890 (t0) cc_final: 0.8344 (t0)
REVERT: A  267 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7860 (mp10)
REVERT: A  349 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6951 (pm20)
REVERT: A  398 GLU cc_start: 0.8736 (mp0) cc_final: 0.7929 (tm-30)
  outliers start: 28
  outliers final: 13
  residues processed: 111
  average time/residue: 0.9749
  time to fit residues: 115.9022
Evaluate side-chains
  107 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  267 GLN
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 87 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A   9 HIS
A 129 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.121147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.092351 restraints weight = 12549.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 3.39
r_work: 0.3269 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7466  Z= 0.225
  Angle     :  0.615   9.084  10090  Z= 0.308
  Chirality :  0.043   0.243   1076
  Planarity :  0.004   0.053   1288
  Dihedral  :  4.381  18.764    955
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 25.54 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.28), residues: 886
  helix:  1.63 (0.28), residues: 312
  sheet: -0.54 (0.40), residues: 169
  loop : -0.14 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  33 
 HIS   0.007   0.001   HIS B  59 
 PHE   0.011   0.001   PHE A 176 
 TYR   0.010   0.001   TYR B 285 
 ARG   0.004   0.000   ARG B  72 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8602 (m-10) cc_final: 0.7927 (p90)
REVERT: B   87 ASP cc_start: 0.8789 (t0) cc_final: 0.8187 (t70)
REVERT: B  330 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7117 (pp)
REVERT: B  400 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7220 (mp0)
REVERT: B  497 LYS cc_start: 0.9250 (tppt) cc_final: 0.8890 (tmmt)
REVERT: A   41 LYS cc_start: 0.5652 (OUTLIER) cc_final: 0.5141 (mtmm)
REVERT: A   54 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7408 (ptp-110)
REVERT: A   77 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6935 (mm-30)
REVERT: A   87 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8886 (tm-30)
REVERT: A  212 ASN cc_start: 0.8913 (t0) cc_final: 0.8374 (t0)
REVERT: A  223 PHE cc_start: 0.6187 (m-80) cc_final: 0.5833 (m-80)
REVERT: A  267 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8183 (mm-40)
REVERT: A  349 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6960 (pm20)
REVERT: A  398 GLU cc_start: 0.8752 (mp0) cc_final: 0.7930 (tm-30)
  outliers start: 23
  outliers final: 15
  residues processed: 105
  average time/residue: 0.9768
  time to fit residues: 109.9878
Evaluate side-chains
  105 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  348 GLU
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  267 GLN
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 85 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A   9 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.121513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.092634 restraints weight = 12712.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 3.44
r_work: 0.3271 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7466  Z= 0.217
  Angle     :  0.625   9.647  10090  Z= 0.313
  Chirality :  0.043   0.243   1076
  Planarity :  0.004   0.048   1288
  Dihedral  :  4.380  18.601    955
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 26.30 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.28), residues: 886
  helix:  1.68 (0.28), residues: 312
  sheet: -0.60 (0.39), residues: 169
  loop : -0.14 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 370 
 HIS   0.007   0.001   HIS A   9 
 PHE   0.019   0.001   PHE A 259 
 TYR   0.025   0.001   TYR B  48 
 ARG   0.004   0.000   ARG B  72 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 TYR cc_start: 0.8603 (m-10) cc_final: 0.7930 (p90)
REVERT: B   87 ASP cc_start: 0.8801 (t0) cc_final: 0.8207 (t70)
REVERT: B  330 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7098 (pp)
REVERT: B  400 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7215 (mp0)
REVERT: B  497 LYS cc_start: 0.9229 (tppt) cc_final: 0.8883 (tmmt)
REVERT: A   41 LYS cc_start: 0.5632 (OUTLIER) cc_final: 0.5050 (mtmm)
REVERT: A   54 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7461 (ptp-110)
REVERT: A   77 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6940 (mm-30)
REVERT: A   86 LYS cc_start: 0.8771 (tppp) cc_final: 0.8390 (mptt)
REVERT: A   87 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8810 (tm-30)
REVERT: A  212 ASN cc_start: 0.8915 (t0) cc_final: 0.8356 (t0)
REVERT: A  267 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7889 (mp10)
REVERT: A  349 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6975 (pm20)
REVERT: A  398 GLU cc_start: 0.8760 (mp0) cc_final: 0.7925 (tm-30)
  outliers start: 21
  outliers final: 12
  residues processed: 101
  average time/residue: 0.9873
  time to fit residues: 107.0046
Evaluate side-chains
  104 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  267 GLN
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  423 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0170
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 73 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 371 ASN
A   9 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.121690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.092874 restraints weight = 12426.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 3.40
r_work: 0.3278 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7466  Z= 0.217
  Angle     :  0.626   9.652  10090  Z= 0.313
  Chirality :  0.043   0.241   1076
  Planarity :  0.004   0.045   1288
  Dihedral  :  4.353  18.390    955
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 26.30 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.29), residues: 886
  helix:  1.69 (0.28), residues: 312
  sheet: -0.62 (0.39), residues: 169
  loop : -0.13 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 370 
 HIS   0.007   0.001   HIS A   9 
 PHE   0.011   0.001   PHE A 176 
 TYR   0.011   0.001   TYR A 293 
 ARG   0.004   0.000   ARG A 186 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6217.65 seconds
wall clock time: 107 minutes 30.68 seconds (6450.68 seconds total)