Starting phenix.real_space_refine
on Mon Apr 28 08:13:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ky5_62640/04_2025/9ky5_62640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ky5_62640/04_2025/9ky5_62640.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ky5_62640/04_2025/9ky5_62640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ky5_62640/04_2025/9ky5_62640.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ky5_62640/04_2025/9ky5_62640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ky5_62640/04_2025/9ky5_62640.cif"
  }
  resolution = 3.6
  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=   0.004 sd=   0.067
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      30      5.16       5
     C    4743      2.51       5
     N    1193      2.21       5
     O    1311      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7277
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3595
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 21, 'TRANS': 441}
    Chain: "B"
      Number of atoms: 3670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3670
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 22, 'TRANS': 448}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 4.87, per 1000 atoms: 0.67
  Number of scatterers: 7277
  At special positions: 0
  Unit cell: (105.029, 103.375, 84.354, 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      30     16.00
     O    1311      8.00
     N    1193      7.00
     C    4743      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 159 " - pdb=" SG  CYS B 211 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      58.6% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 59
    Processing helix  chain 'A' and resid 70 through 74
    Processing helix  chain 'A' and resid 77 through 105
    Processing helix  chain 'A' and resid 115 through 120
      removed outlier: 3.611A  pdb=" N   PHE A 119 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 134
      removed outlier: 3.808A  pdb=" N   ALA A 124 " --> pdb=" O   GLY A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 152
      removed outlier: 3.563A  pdb=" N   ILE A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 156
    Processing helix  chain 'A' and resid 162 through 184
      removed outlier: 3.579A  pdb=" N   TYR A 184 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 218
      removed outlier: 4.318A  pdb=" N   GLY A 217 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   HIS A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
      removed outlier: 3.523A  pdb=" N   LEU A 236 " --> pdb=" O   ASP A 232 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   LEU A 238 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE A 245 " --> pdb=" O   TYR A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 255
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 265 through 293
      Proline residue:  A 276  - end of helix
    Processing helix  chain 'A' and resid 294 through 301
    Processing helix  chain 'A' and resid 303 through 313
    Processing helix  chain 'A' and resid 318 through 331
      removed outlier: 3.740A  pdb=" N   ILE A 322 " --> pdb=" O   TRP A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 350
      removed outlier: 3.635A  pdb=" N   PHE A 344 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY A 350 " --> pdb=" O   GLY A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 358
    Processing helix  chain 'A' and resid 366 through 380
    Processing helix  chain 'A' and resid 385 through 392
      removed outlier: 3.659A  pdb=" N   GLN A 388 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE A 390 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 415
    Processing helix  chain 'A' and resid 426 through 446
      Proline residue:  A 443  - end of helix
    Processing helix  chain 'A' and resid 447 through 460
    Processing helix  chain 'A' and resid 461 through 469
    Processing helix  chain 'A' and resid 477 through 495
    Processing helix  chain 'B' and resid 166 through 173
    Processing helix  chain 'B' and resid 176 through 206
      removed outlier: 3.597A  pdb=" N   VAL B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 222
      removed outlier: 3.759A  pdb=" N   HIS B 221 " --> pdb=" O   LYS B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 3.967A  pdb=" N   GLN B 235 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 246
    Processing helix  chain 'B' and resid 248 through 253
      removed outlier: 3.727A  pdb=" N   SER B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 301
      removed outlier: 3.780A  pdb=" N   PHE B 291 " --> pdb=" O   SER B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 342
      removed outlier: 3.656A  pdb=" N   GLU B 336 " --> pdb=" O   LYS B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 354
    Processing helix  chain 'B' and resid 356 through 372
      removed outlier: 3.515A  pdb=" N   SER B 372 " --> pdb=" O   THR B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 393
      removed outlier: 3.518A  pdb=" N   ILE B 389 " --> pdb=" O   ASP B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 428
    Processing helix  chain 'B' and resid 447 through 449
      No H-bonds generated for 'chain 'B' and resid 447 through 449'
    Processing helix  chain 'B' and resid 450 through 459
      removed outlier: 3.763A  pdb=" N   PHE B 459 " --> pdb=" O   GLN B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 515
      removed outlier: 4.181A  pdb=" N   GLU B 515 " --> pdb=" O   LYS B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 532
    Processing helix  chain 'B' and resid 534 through 539
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.596A  pdb=" N   SER B 589 " --> pdb=" O   ALA B 586 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 360
    Processing sheet with id=AA2, first strand: chain 'B' and resid 225 through 226
      removed outlier: 3.877A  pdb=" N   PHE B 467 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   CYS B 432 " --> pdb=" O   THR B 464 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   VAL B 466 " --> pdb=" O   CYS B 432 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   TRP B 434 " --> pdb=" O   VAL B 466 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 261 through 262
      removed outlier: 3.586A  pdb=" N   LEU B 262 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 349
      removed outlier: 3.987A  pdb=" N   LEU B 400 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 541 through 544
    Processing sheet with id=AA6, first strand: chain 'B' and resid 575 through 576
    Processing sheet with id=AA7, first strand: chain 'B' and resid 593 through 594

    384 hydrogen bonds defined for protein.
    1086 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: 2.10

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1155
        1.32 -     1.44: 2052
        1.44 -     1.56: 4205
        1.56 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 7457
  Sorted by residual:
  bond pdb=" CA  ARG A 601 "
       pdb=" C   ARG A 601 "
    ideal  model  delta    sigma   weight residual
    1.525  1.460  0.065 2.10e-02 2.27e+03 9.68e+00
  bond pdb=" CA  SER A 335 "
       pdb=" C   SER A 335 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.026 1.34e-02 5.57e+03 3.76e+00
  bond pdb=" C   ARG A 601 "
       pdb=" OXT ARG A 601 "
    ideal  model  delta    sigma   weight residual
    1.231  1.193  0.038 2.00e-02 2.50e+03 3.65e+00
  bond pdb=" CA  ALA A 303 "
       pdb=" C   ALA A 303 "
    ideal  model  delta    sigma   weight residual
    1.531  1.505  0.027 1.46e-02 4.69e+03 3.33e+00
  bond pdb=" C   VAL A 442 "
       pdb=" N   PRO A 443 "
    ideal  model  delta    sigma   weight residual
    1.334  1.346 -0.012 8.40e-03 1.42e+04 2.18e+00
  ... (remaining 7452 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 9670
        1.48 -     2.97: 390
        2.97 -     4.45: 71
        4.45 -     5.94: 11
        5.94 -     7.42: 2
  Bond angle restraints: 10144
  Sorted by residual:
  angle pdb=" C   VAL A 134 "
        pdb=" N   VAL A 135 "
        pdb=" CA  VAL A 135 "
      ideal   model   delta    sigma   weight residual
     123.16  119.09    4.07 1.06e+00 8.90e-01 1.47e+01
  angle pdb=" N   ASP A 302 "
        pdb=" CA  ASP A 302 "
        pdb=" C   ASP A 302 "
      ideal   model   delta    sigma   weight residual
     112.54  108.24    4.30 1.22e+00 6.72e-01 1.24e+01
  angle pdb=" N   ALA A 303 "
        pdb=" CA  ALA A 303 "
        pdb=" C   ALA A 303 "
      ideal   model   delta    sigma   weight residual
     108.49  103.47    5.02 1.65e+00 3.67e-01 9.25e+00
  angle pdb=" N   GLU B 169 "
        pdb=" CA  GLU B 169 "
        pdb=" C   GLU B 169 "
      ideal   model   delta    sigma   weight residual
     111.36  108.22    3.14 1.09e+00 8.42e-01 8.32e+00
  angle pdb=" N   LEU B 170 "
        pdb=" CA  LEU B 170 "
        pdb=" C   LEU B 170 "
      ideal   model   delta    sigma   weight residual
     112.87  109.55    3.32 1.20e+00 6.94e-01 7.64e+00
  ... (remaining 10139 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 3868
       17.56 -    35.12: 401
       35.12 -    52.68: 86
       52.68 -    70.24: 11
       70.24 -    87.80: 5
  Dihedral angle restraints: 4371
    sinusoidal: 1687
      harmonic: 2684
  Sorted by residual:
  dihedral pdb=" CB  CYS A 159 "
           pdb=" SG  CYS A 159 "
           pdb=" SG  CYS B 211 "
           pdb=" CB  CYS B 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.35   82.35     1      1.00e+01 1.00e-02 8.32e+01
  dihedral pdb=" CA  SER A 219 "
           pdb=" C   SER A 219 "
           pdb=" N   GLU A 220 "
           pdb=" CA  GLU A 220 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  SER A  66 "
           pdb=" C   SER A  66 "
           pdb=" N   PRO A  67 "
           pdb=" CA  PRO A  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.68   19.32     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 4368 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 597
       0.028 -    0.056: 384
       0.056 -    0.085: 127
       0.085 -    0.113: 46
       0.113 -    0.141: 9
  Chirality restraints: 1163
  Sorted by residual:
  chirality pdb=" CA  VAL A 298 "
            pdb=" N   VAL A 298 "
            pdb=" C   VAL A 298 "
            pdb=" CB  VAL A 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CA  ILE B 228 "
            pdb=" N   ILE B 228 "
            pdb=" C   ILE B 228 "
            pdb=" CB  ILE B 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.88e-01
  chirality pdb=" CB  VAL A 134 "
            pdb=" CA  VAL A 134 "
            pdb=" CG1 VAL A 134 "
            pdb=" CG2 VAL A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 1160 not shown)

  Planarity restraints: 1274
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 442 "   -0.035 5.00e-02 4.00e+02   5.26e-02 4.42e+00
        pdb=" N   PRO A 443 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 443 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 443 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 320 "   -0.030 5.00e-02 4.00e+02   4.56e-02 3.32e+00
        pdb=" N   PRO A 321 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 462 "   -0.030 5.00e-02 4.00e+02   4.51e-02 3.26e+00
        pdb=" N   PRO A 463 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1271 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 998
        2.74 -     3.28: 7772
        3.28 -     3.82: 12568
        3.82 -     4.36: 14506
        4.36 -     4.90: 24785
  Nonbonded interactions: 60629
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 463 "
            pdb=" NH2 ARG B 531 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NH1 ARG B 227 "
            pdb=" O   GLN B 438 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   VAL B 510 "
            pdb=" OG  SER B 514 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   SER B 302 "
            pdb=" OG  SER B 302 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OH  TYR B 251 "
            pdb=" OE2 GLU B 472 "
     model   vdw
     2.268 3.040
  ... (remaining 60624 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:          0.340
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     20.950
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:3.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
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      :  0.005   0.065   7458  Z= 0.212
  Angle     :  0.708   7.421  10146  Z= 0.408
  Chirality :  0.041   0.141   1163
  Planarity :  0.004   0.053   1274
  Dihedral  : 14.695  87.797   2644
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  6.08 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.42 (0.23), residues: 930
  helix: -1.62 (0.20), residues: 487
  sheet: -2.30 (0.51), residues: 65
  loop : -3.07 (0.26), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 398 
 HIS   0.002   0.000   HIS B 221 
 PHE   0.017   0.002   PHE A 400 
 TYR   0.015   0.002   TYR A 163 
 ARG   0.003   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13467 (  384)
  hydrogen bonds       : angle       6.47629 ( 1086)
  SS BOND              : bond        0.00102 (    1)
  SS BOND              : angle       0.87237 (    2)
  covalent geometry    : bond        0.00455 ( 7457)
  covalent geometry    : angle       0.70789 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 SER cc_start: 0.5843 (OUTLIER) cc_final: 0.5194 (t)
REVERT: A  360 HIS cc_start: 0.7327 (t-90) cc_final: 0.7101 (t70)
REVERT: A  489 ARG cc_start: 0.7910 (tmm-80) cc_final: 0.7621 (mpt-90)
REVERT: B  204 ILE cc_start: 0.8832 (mm) cc_final: 0.8523 (tt)
REVERT: B  285 PHE cc_start: 0.8095 (m-80) cc_final: 0.7801 (m-80)
REVERT: B  307 LEU cc_start: 0.9099 (tt) cc_final: 0.8898 (tt)
REVERT: B  360 PHE cc_start: 0.9058 (m-80) cc_final: 0.8431 (m-80)
REVERT: B  364 TRP cc_start: 0.8562 (m-10) cc_final: 0.8092 (m-10)
REVERT: B  392 LEU cc_start: 0.8765 (mt) cc_final: 0.8170 (tt)
REVERT: B  562 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6925 (mm-30)
REVERT: B  621 GLU cc_start: 0.6626 (tt0) cc_final: 0.6420 (tt0)
REVERT: A  601 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.5720 (mtt90)
  outliers start: 10
  outliers final: 2
  residues processed: 172
  average time/residue: 0.2056
  time to fit residues: 46.4302
Evaluate side-chains
  127 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  601 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 70 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 GLN
A 262 ASN
A 391 ASN
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 GLN
** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 GLN
** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 366 ASN
B 388 GLN
B 422 GLN
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.196559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.140792 restraints weight = 8725.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.141234 restraints weight = 5102.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.144169 restraints weight = 4091.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7458  Z= 0.140
  Angle     :  0.616   6.494  10146  Z= 0.312
  Chirality :  0.041   0.176   1163
  Planarity :  0.005   0.055   1274
  Dihedral  :  5.755  61.660   1007
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.08 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.60 (0.26), residues: 930
  helix: -0.07 (0.23), residues: 488
  sheet: -1.71 (0.57), residues: 64
  loop : -2.25 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 319 
 HIS   0.002   0.001   HIS B 539 
 PHE   0.021   0.002   PHE B 291 
 TYR   0.014   0.002   TYR A 163 
 ARG   0.005   0.001   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 (  384)
  hydrogen bonds       : angle       4.82732 ( 1086)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.21865 (    2)
  covalent geometry    : bond        0.00321 ( 7457)
  covalent geometry    : angle       0.61646 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  224 ASP cc_start: 0.8035 (t70) cc_final: 0.7815 (t70)
REVERT: A  254 ASN cc_start: 0.8383 (t0) cc_final: 0.7727 (t0)
REVERT: A  489 ARG cc_start: 0.7885 (tmm-80) cc_final: 0.7627 (mpt-90)
REVERT: B  204 ILE cc_start: 0.8725 (mm) cc_final: 0.8425 (tt)
REVERT: B  210 ARG cc_start: 0.8241 (mmt180) cc_final: 0.7952 (tpt90)
REVERT: B  278 LEU cc_start: 0.9081 (tp) cc_final: 0.8811 (tt)
REVERT: B  307 LEU cc_start: 0.9086 (tt) cc_final: 0.8828 (tt)
REVERT: B  360 PHE cc_start: 0.9164 (m-80) cc_final: 0.8612 (m-80)
REVERT: B  392 LEU cc_start: 0.8834 (mt) cc_final: 0.8294 (tt)
REVERT: B  471 ASP cc_start: 0.7581 (m-30) cc_final: 0.7306 (m-30)
REVERT: B  562 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6838 (mm-30)
REVERT: B  606 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5828 (mt-10)
REVERT: B  620 HIS cc_start: 0.7948 (m170) cc_final: 0.7621 (m-70)
REVERT: B  621 GLU cc_start: 0.6466 (tt0) cc_final: 0.6187 (tt0)
  outliers start: 15
  outliers final: 11
  residues processed: 148
  average time/residue: 0.1737
  time to fit residues: 35.4512
Evaluate side-chains
  129 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  433 SER
Chi-restraints excluded: chain B residue  597 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   chunk 64 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 235 ASN
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 235 GLN
** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 530 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.183877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.122113 restraints weight = 8857.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.126747 restraints weight = 5236.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.129781 restraints weight = 3820.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7458  Z= 0.198
  Angle     :  0.643   6.983  10146  Z= 0.325
  Chirality :  0.042   0.151   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  5.134  55.540   1002
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.11 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.22 (0.27), residues: 930
  helix:  0.26 (0.23), residues: 488
  sheet: -1.43 (0.58), residues: 64
  loop : -2.12 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 319 
 HIS   0.006   0.001   HIS B 415 
 PHE   0.018   0.002   PHE B 162 
 TYR   0.016   0.002   TYR A 163 
 ARG   0.005   0.001   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  384)
  hydrogen bonds       : angle       4.74501 ( 1086)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.38502 (    2)
  covalent geometry    : bond        0.00477 ( 7457)
  covalent geometry    : angle       0.64327 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 TYR cc_start: 0.8110 (m-80) cc_final: 0.7595 (m-80)
REVERT: A  254 ASN cc_start: 0.8571 (t0) cc_final: 0.7771 (t0)
REVERT: B  204 ILE cc_start: 0.8724 (mm) cc_final: 0.8347 (tt)
REVERT: B  210 ARG cc_start: 0.8326 (mmt180) cc_final: 0.7968 (tpt90)
REVERT: B  278 LEU cc_start: 0.9020 (tp) cc_final: 0.8702 (tt)
REVERT: B  307 LEU cc_start: 0.8991 (tt) cc_final: 0.8748 (tt)
REVERT: B  335 LEU cc_start: 0.8679 (mt) cc_final: 0.8208 (mt)
REVERT: B  360 PHE cc_start: 0.9256 (m-80) cc_final: 0.8497 (m-80)
REVERT: B  364 TRP cc_start: 0.7772 (m-10) cc_final: 0.7140 (m-10)
REVERT: B  392 LEU cc_start: 0.8784 (mt) cc_final: 0.8247 (tt)
REVERT: B  471 ASP cc_start: 0.7568 (m-30) cc_final: 0.7347 (m-30)
REVERT: B  562 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6834 (mm-30)
REVERT: B  606 GLU cc_start: 0.6321 (mt-10) cc_final: 0.6043 (mt-10)
REVERT: B  621 GLU cc_start: 0.6667 (tt0) cc_final: 0.6063 (tt0)
  outliers start: 27
  outliers final: 21
  residues processed: 154
  average time/residue: 0.1905
  time to fit residues: 39.7829
Evaluate side-chains
  144 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  186 LYS
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  424 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  597 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 6 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0010
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 317 ASN
B 353 ASN
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.198831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.147086 restraints weight = 8759.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145459 restraints weight = 5071.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.146848 restraints weight = 4407.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7458  Z= 0.115
  Angle     :  0.576   7.361  10146  Z= 0.292
  Chirality :  0.039   0.160   1163
  Planarity :  0.004   0.038   1274
  Dihedral  :  4.572  50.217   1001
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.14 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.62 (0.27), residues: 930
  helix:  0.74 (0.23), residues: 496
  sheet: -1.12 (0.61), residues: 64
  loop : -1.88 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 191 
 HIS   0.010   0.001   HIS B 415 
 PHE   0.024   0.001   PHE B 162 
 TYR   0.015   0.001   TYR B 405 
 ARG   0.004   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03466 (  384)
  hydrogen bonds       : angle       4.32536 ( 1086)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.19086 (    2)
  covalent geometry    : bond        0.00257 ( 7457)
  covalent geometry    : angle       0.57592 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A  254 ASN cc_start: 0.8318 (t0) cc_final: 0.7714 (t0)
REVERT: A  489 ARG cc_start: 0.7826 (mpt-90) cc_final: 0.7444 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8222 (mmt180) cc_final: 0.7930 (tpt90)
REVERT: B  278 LEU cc_start: 0.9014 (tp) cc_final: 0.8678 (tt)
REVERT: B  292 ASP cc_start: 0.8769 (m-30) cc_final: 0.8027 (t70)
REVERT: B  307 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8816 (tt)
REVERT: B  349 ARG cc_start: 0.8512 (mtm110) cc_final: 0.7906 (ptp-110)
REVERT: B  360 PHE cc_start: 0.9162 (m-80) cc_final: 0.8619 (m-80)
REVERT: B  392 LEU cc_start: 0.8841 (mt) cc_final: 0.8293 (tt)
REVERT: B  471 ASP cc_start: 0.7367 (m-30) cc_final: 0.7121 (m-30)
REVERT: B  562 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6784 (mm-30)
REVERT: B  606 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6245 (mt-10)
REVERT: B  621 GLU cc_start: 0.6366 (tt0) cc_final: 0.5969 (tt0)
  outliers start: 25
  outliers final: 17
  residues processed: 149
  average time/residue: 0.1955
  time to fit residues: 39.4619
Evaluate side-chains
  135 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  597 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 232 GLN
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.181522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121686 restraints weight = 8922.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.123752 restraints weight = 5399.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.125376 restraints weight = 4306.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7458  Z= 0.265
  Angle     :  0.708  11.304  10146  Z= 0.356
  Chirality :  0.045   0.168   1163
  Planarity :  0.005   0.048   1274
  Dihedral  :  4.827  46.129    999
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.05 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.80 (0.27), residues: 930
  helix:  0.53 (0.23), residues: 489
  sheet: -1.18 (0.61), residues: 64
  loop : -1.82 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 413 
 HIS   0.006   0.001   HIS A 360 
 PHE   0.019   0.002   PHE B 542 
 TYR   0.019   0.002   TYR A 163 
 ARG   0.006   0.001   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04190 (  384)
  hydrogen bonds       : angle       4.73367 ( 1086)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       0.43323 (    2)
  covalent geometry    : bond        0.00643 ( 7457)
  covalent geometry    : angle       0.70835 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: A  489 ARG cc_start: 0.7806 (mpt-90) cc_final: 0.7372 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8325 (mmt180) cc_final: 0.7917 (tpt90)
REVERT: B  278 LEU cc_start: 0.9105 (tp) cc_final: 0.8721 (tt)
REVERT: B  292 ASP cc_start: 0.8844 (m-30) cc_final: 0.8129 (t70)
REVERT: B  307 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8784 (tt)
REVERT: B  360 PHE cc_start: 0.9298 (m-80) cc_final: 0.8709 (m-80)
REVERT: B  471 ASP cc_start: 0.7559 (m-30) cc_final: 0.7137 (m-30)
REVERT: B  562 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6933 (mm-30)
REVERT: B  606 GLU cc_start: 0.6434 (mt-10) cc_final: 0.6218 (mt-10)
REVERT: B  621 GLU cc_start: 0.6543 (tt0) cc_final: 0.6059 (tt0)
  outliers start: 32
  outliers final: 24
  residues processed: 140
  average time/residue: 0.1870
  time to fit residues: 36.1418
Evaluate side-chains
  142 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  424 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  597 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 1 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 43 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 69 optimal weight:    9.9990
   chunk 79 optimal weight:    0.0670
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.184765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.133135 restraints weight = 8484.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132501 restraints weight = 5071.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.134030 restraints weight = 4681.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7458  Z= 0.127
  Angle     :  0.601  13.370  10146  Z= 0.299
  Chirality :  0.040   0.314   1163
  Planarity :  0.004   0.039   1274
  Dihedral  :  4.467  41.946    999
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.18 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.26 (0.28), residues: 930
  helix:  0.99 (0.24), residues: 490
  sheet: -0.87 (0.64), residues: 64
  loop : -1.63 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 398 
 HIS   0.007   0.001   HIS A 360 
 PHE   0.016   0.001   PHE A 400 
 TYR   0.013   0.001   TYR A 163 
 ARG   0.004   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  384)
  hydrogen bonds       : angle       4.31634 ( 1086)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.31502 (    2)
  covalent geometry    : bond        0.00294 ( 7457)
  covalent geometry    : angle       0.60144 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A  254 ASN cc_start: 0.8406 (t0) cc_final: 0.7756 (t0)
REVERT: A  489 ARG cc_start: 0.7749 (mpt-90) cc_final: 0.7330 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8324 (mmt180) cc_final: 0.7936 (tpt90)
REVERT: B  278 LEU cc_start: 0.9083 (tp) cc_final: 0.8759 (tt)
REVERT: B  292 ASP cc_start: 0.8894 (m-30) cc_final: 0.8170 (t70)
REVERT: B  307 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8590 (tt)
REVERT: B  360 PHE cc_start: 0.9328 (m-80) cc_final: 0.8699 (m-80)
REVERT: B  392 LEU cc_start: 0.8891 (mt) cc_final: 0.8358 (tt)
REVERT: B  427 THR cc_start: 0.8681 (m) cc_final: 0.8460 (t)
REVERT: B  562 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6641 (mm-30)
REVERT: B  606 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6244 (mt-10)
REVERT: B  621 GLU cc_start: 0.6413 (tt0) cc_final: 0.5895 (tt0)
REVERT: B  623 LEU cc_start: 0.7761 (mt) cc_final: 0.7342 (mt)
  outliers start: 28
  outliers final: 20
  residues processed: 141
  average time/residue: 0.1950
  time to fit residues: 38.2836
Evaluate side-chains
  135 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  597 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 48 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.181996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.130024 restraints weight = 8486.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.129732 restraints weight = 5242.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.131470 restraints weight = 4576.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7458  Z= 0.161
  Angle     :  0.625  12.763  10146  Z= 0.307
  Chirality :  0.041   0.283   1163
  Planarity :  0.004   0.046   1274
  Dihedral  :  4.430  38.464    999
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 21.93 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.17 (0.28), residues: 930
  helix:  0.99 (0.24), residues: 492
  sheet: -0.86 (0.64), residues: 64
  loop : -1.48 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 364 
 HIS   0.009   0.001   HIS B 266 
 PHE   0.020   0.002   PHE B 291 
 TYR   0.014   0.001   TYR A 163 
 ARG   0.003   0.000   ARG B 452 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03582 (  384)
  hydrogen bonds       : angle       4.33243 ( 1086)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.38218 (    2)
  covalent geometry    : bond        0.00386 ( 7457)
  covalent geometry    : angle       0.62523 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A  254 ASN cc_start: 0.8435 (t0) cc_final: 0.7803 (t0)
REVERT: A  489 ARG cc_start: 0.7767 (mpt-90) cc_final: 0.7345 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8304 (mmt180) cc_final: 0.7928 (tpt90)
REVERT: B  278 LEU cc_start: 0.9102 (tp) cc_final: 0.8645 (tt)
REVERT: B  292 ASP cc_start: 0.8861 (m-30) cc_final: 0.8102 (t70)
REVERT: B  307 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8579 (tt)
REVERT: B  360 PHE cc_start: 0.9319 (m-80) cc_final: 0.8668 (m-80)
REVERT: B  365 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6015 (tp-100)
REVERT: B  392 LEU cc_start: 0.8903 (mt) cc_final: 0.8381 (tt)
REVERT: B  562 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6756 (mm-30)
REVERT: B  606 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6240 (mt-10)
REVERT: B  621 GLU cc_start: 0.6412 (tt0) cc_final: 0.5910 (tt0)
  outliers start: 33
  outliers final: 24
  residues processed: 143
  average time/residue: 0.1758
  time to fit residues: 35.0933
Evaluate side-chains
  136 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  424 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  597 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 91 optimal weight:    0.0980
   chunk 77 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0050
   chunk 88 optimal weight:    0.0770
   chunk 80 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 32 optimal weight:    0.4980
   chunk 78 optimal weight:    0.6980
   chunk 66 optimal weight:    9.9990
   overall best weight:    0.2752

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.187944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.136254 restraints weight = 8505.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136907 restraints weight = 5195.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.137933 restraints weight = 4618.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7458  Z= 0.113
  Angle     :  0.622  12.342  10146  Z= 0.301
  Chirality :  0.040   0.253   1163
  Planarity :  0.004   0.052   1274
  Dihedral  :  4.170  27.764    999
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 23.45 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.03 (0.28), residues: 930
  helix:  1.15 (0.24), residues: 498
  sheet: -0.94 (0.63), residues: 69
  loop : -1.49 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 364 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.016   0.001   PHE B 542 
 TYR   0.011   0.001   TYR B 405 
 ARG   0.005   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  384)
  hydrogen bonds       : angle       4.19826 ( 1086)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.35555 (    2)
  covalent geometry    : bond        0.00253 ( 7457)
  covalent geometry    : angle       0.62250 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 ASP cc_start: 0.8045 (t70) cc_final: 0.7826 (t70)
REVERT: A  233 MET cc_start: 0.7412 (mmp) cc_final: 0.7189 (mmp)
REVERT: A  254 ASN cc_start: 0.8202 (t0) cc_final: 0.7740 (t0)
REVERT: A  489 ARG cc_start: 0.7818 (mpt-90) cc_final: 0.7449 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8242 (mmt180) cc_final: 0.7889 (tpt90)
REVERT: B  278 LEU cc_start: 0.9081 (tp) cc_final: 0.8696 (tt)
REVERT: B  285 PHE cc_start: 0.7768 (m-80) cc_final: 0.7408 (m-80)
REVERT: B  292 ASP cc_start: 0.8795 (m-30) cc_final: 0.8134 (t70)
REVERT: B  307 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8483 (tt)
REVERT: B  360 PHE cc_start: 0.9318 (m-80) cc_final: 0.8665 (m-80)
REVERT: B  392 LEU cc_start: 0.8903 (mt) cc_final: 0.8400 (tt)
REVERT: B  562 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6676 (mm-30)
REVERT: B  605 GLU cc_start: 0.8342 (pm20) cc_final: 0.8008 (pt0)
REVERT: B  606 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6055 (mt-10)
REVERT: B  621 GLU cc_start: 0.6351 (tt0) cc_final: 0.5938 (tt0)
  outliers start: 25
  outliers final: 17
  residues processed: 140
  average time/residue: 0.2289
  time to fit residues: 45.5704
Evaluate side-chains
  134 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  597 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 78 optimal weight:    0.4980
   chunk 87 optimal weight:    7.9990
   chunk 84 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0870
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.186000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131978 restraints weight = 8738.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.132690 restraints weight = 4887.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.134260 restraints weight = 4197.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7458  Z= 0.122
  Angle     :  0.629  12.848  10146  Z= 0.302
  Chirality :  0.040   0.255   1163
  Planarity :  0.004   0.049   1274
  Dihedral  :  4.131  23.795    999
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 24.21 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.11 (0.28), residues: 930
  helix:  1.29 (0.24), residues: 490
  sheet: -0.93 (0.63), residues: 69
  loop : -1.39 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 364 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.024   0.001   PHE B 291 
 TYR   0.012   0.001   TYR A 163 
 ARG   0.005   0.000   ARG B 452 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03334 (  384)
  hydrogen bonds       : angle       4.18783 ( 1086)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.42014 (    2)
  covalent geometry    : bond        0.00283 ( 7457)
  covalent geometry    : angle       0.62884 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 ASP cc_start: 0.8064 (t70) cc_final: 0.7750 (t70)
REVERT: A  233 MET cc_start: 0.7331 (mmp) cc_final: 0.7131 (mmp)
REVERT: A  254 ASN cc_start: 0.8158 (t0) cc_final: 0.7760 (t0)
REVERT: A  489 ARG cc_start: 0.7731 (mpt-90) cc_final: 0.7359 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8231 (mmt180) cc_final: 0.7873 (tpt90)
REVERT: B  278 LEU cc_start: 0.9180 (tp) cc_final: 0.8758 (tt)
REVERT: B  292 ASP cc_start: 0.8929 (m-30) cc_final: 0.8155 (t70)
REVERT: B  307 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8361 (tt)
REVERT: B  360 PHE cc_start: 0.9384 (m-80) cc_final: 0.8737 (m-80)
REVERT: B  392 LEU cc_start: 0.8975 (mt) cc_final: 0.8511 (tt)
REVERT: B  457 MET cc_start: 0.6847 (tmm) cc_final: 0.6491 (tmm)
REVERT: B  562 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6632 (mm-30)
REVERT: B  606 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6035 (mt-10)
REVERT: B  621 GLU cc_start: 0.6378 (tt0) cc_final: 0.5889 (tt0)
  outliers start: 19
  outliers final: 13
  residues processed: 143
  average time/residue: 0.1824
  time to fit residues: 36.1020
Evaluate side-chains
  134 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  597 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 37 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 68 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.186705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.136014 restraints weight = 8629.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.138922 restraints weight = 6255.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.139903 restraints weight = 5867.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7458  Z= 0.134
  Angle     :  0.634  11.401  10146  Z= 0.310
  Chirality :  0.040   0.262   1163
  Planarity :  0.004   0.056   1274
  Dihedral  :  4.142  21.794    999
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 24.46 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.14 (0.28), residues: 930
  helix:  1.27 (0.24), residues: 490
  sheet: -0.78 (0.65), residues: 69
  loop : -1.34 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 364 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.016   0.001   PHE B 545 
 TYR   0.013   0.001   TYR A 163 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  384)
  hydrogen bonds       : angle       4.19173 ( 1086)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.42089 (    2)
  covalent geometry    : bond        0.00318 ( 7457)
  covalent geometry    : angle       0.63419 (10144)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.8035 (tt0) cc_final: 0.7470 (tm-30)
REVERT: A  224 ASP cc_start: 0.8026 (t70) cc_final: 0.7783 (t70)
REVERT: A  233 MET cc_start: 0.7416 (mmp) cc_final: 0.7186 (mmp)
REVERT: A  254 ASN cc_start: 0.8209 (t0) cc_final: 0.7769 (t0)
REVERT: A  489 ARG cc_start: 0.7844 (mpt-90) cc_final: 0.7478 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8240 (mmt180) cc_final: 0.7883 (tpt90)
REVERT: B  278 LEU cc_start: 0.9017 (tp) cc_final: 0.8659 (tt)
REVERT: B  285 PHE cc_start: 0.7517 (m-80) cc_final: 0.7218 (m-80)
REVERT: B  292 ASP cc_start: 0.8748 (m-30) cc_final: 0.8078 (t70)
REVERT: B  307 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8505 (tt)
REVERT: B  360 PHE cc_start: 0.9283 (m-80) cc_final: 0.8609 (m-80)
REVERT: B  392 LEU cc_start: 0.8848 (mt) cc_final: 0.8371 (tt)
REVERT: B  454 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6520 (t80)
REVERT: B  457 MET cc_start: 0.7130 (tmm) cc_final: 0.6799 (tmm)
REVERT: B  562 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6810 (mm-30)
REVERT: B  606 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6177 (mt-10)
REVERT: B  621 GLU cc_start: 0.6311 (tt0) cc_final: 0.5930 (tt0)
  outliers start: 20
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1998
  time to fit residues: 36.9360
Evaluate side-chains
  133 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  454 TYR
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  605 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 91 optimal weight:    0.0570
   chunk 70 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0970
   chunk 82 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 77 optimal weight:    0.1980
   chunk 69 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.2096

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 317 ASN
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.189703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136201 restraints weight = 8474.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137582 restraints weight = 5280.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.139388 restraints weight = 3947.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   7458  Z= 0.112
  Angle     :  0.629  10.876  10146  Z= 0.308
  Chirality :  0.039   0.201   1163
  Planarity :  0.004   0.054   1274
  Dihedral  :  4.037  18.627    999
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 24.71 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.34 (0.29), residues: 930
  helix:  1.46 (0.24), residues: 490
  sheet: -0.76 (0.64), residues: 70
  loop : -1.28 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 364 
 HIS   0.004   0.001   HIS B 266 
 PHE   0.015   0.001   PHE B 542 
 TYR   0.011   0.001   TYR B 405 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  384)
  hydrogen bonds       : angle       4.09841 ( 1086)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.39731 (    2)
  covalent geometry    : bond        0.00249 ( 7457)
  covalent geometry    : angle       0.62872 (10144)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3058.61 seconds
wall clock time: 55 minutes 0.04 seconds (3300.04 seconds total)