Starting phenix.real_space_refine
on Wed Sep 17 08:37:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ky5_62640/09_2025/9ky5_62640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ky5_62640/09_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_62640/09_2025/9ky5_62640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ky5_62640/09_2025/9ky5_62640.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ky5_62640/09_2025/9ky5_62640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ky5_62640/09_2025/9ky5_62640.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.68, per 1000 atoms: 0.23
  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: 0.56
  Conformation dependent library (CDL) restraints added in 406.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.25
  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: 1.17

  Time building geometry restraints manager: 0.77 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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.250
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.800
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG B 227 
 TYR   0.015   0.002   TYR A 163 
 PHE   0.017   0.002   PHE A 400 
 TRP   0.018   0.001   TRP A 398 
 HIS   0.002   0.000   HIS B 221 

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

*********************** 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  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 SER cc_start: 0.5843 (OUTLIER) cc_final: 0.5193 (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: 0.6419 (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: 0.0953
  time to fit residues: 21.5691
Evaluate side-chains
  126 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.0870
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.9764

-------------------------------------------------------------------------------
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 235 ASN
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 530 GLN
B 620 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.191089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.136905 restraints weight = 8905.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.137505 restraints weight = 7122.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.140013 restraints weight = 5280.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.140228 restraints weight = 3968.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.140710 restraints weight = 3557.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7458  Z= 0.221
  Angle     :  0.683   7.076  10146  Z= 0.345
  Chirality :  0.044   0.190   1163
  Planarity :  0.005   0.061   1274
  Dihedral  :  6.069  59.722   1007
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.84 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.26), residues: 930
  helix: -0.31 (0.22), residues: 486
  sheet: -1.81 (0.56), residues: 64
  loop : -2.37 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 227 
 TYR   0.017   0.002   TYR A 163 
 PHE   0.020   0.002   PHE B 291 
 TRP   0.017   0.001   TRP A 398 
 HIS   0.003   0.001   HIS B 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 7457)
  covalent geometry    : angle       0.68346 (10144)
  SS BOND              : bond        0.00302 (    1)
  SS BOND              : angle       0.37378 (    2)
  hydrogen bonds       : bond        0.04205 (  384)
  hydrogen bonds       : angle       5.05541 ( 1086)

*********************** 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
  159 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 TYR cc_start: 0.8170 (m-80) cc_final: 0.7621 (m-80)
REVERT: A  233 MET cc_start: 0.7727 (mmp) cc_final: 0.7420 (mmm)
REVERT: A  254 ASN cc_start: 0.8644 (t0) cc_final: 0.7963 (t0)
REVERT: A  376 MET cc_start: 0.7923 (mmm) cc_final: 0.7691 (mmt)
REVERT: B  204 ILE cc_start: 0.8818 (mm) cc_final: 0.8507 (tt)
REVERT: B  210 ARG cc_start: 0.8269 (mmt180) cc_final: 0.7947 (tpt90)
REVERT: B  360 PHE cc_start: 0.8917 (m-80) cc_final: 0.8346 (m-80)
REVERT: B  392 LEU cc_start: 0.8598 (mt) cc_final: 0.8018 (tt)
REVERT: B  455 GLN cc_start: 0.8065 (mt0) cc_final: 0.7851 (tt0)
REVERT: B  471 ASP cc_start: 0.7674 (m-30) cc_final: 0.7431 (m-30)
REVERT: B  562 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7046 (mm-30)
REVERT: B  606 GLU cc_start: 0.6384 (mt-10) cc_final: 0.6021 (mt-10)
REVERT: B  621 GLU cc_start: 0.6454 (tt0) cc_final: 0.6031 (tt0)
  outliers start: 21
  outliers final: 17
  residues processed: 150
  average time/residue: 0.0830
  time to fit residues: 17.2266
Evaluate side-chains
  141 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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  178 THR
Chi-restraints excluded: chain A residue  204 ILE
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  198 LEU
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  281 ILE
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  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 45 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.3980
   chunk 40 optimal weight:    0.0050
   overall best weight:    0.5794

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.188656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.135153 restraints weight = 8751.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138770 restraints weight = 6033.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.139284 restraints weight = 4900.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.139525 restraints weight = 3834.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.139710 restraints weight = 3777.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7458  Z= 0.125
  Angle     :  0.603   9.396  10146  Z= 0.303
  Chirality :  0.040   0.153   1163
  Planarity :  0.004   0.039   1274
  Dihedral  :  4.809  55.106   1001
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.60 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.27), residues: 930
  helix:  0.41 (0.23), residues: 494
  sheet: -1.33 (0.60), residues: 64
  loop : -2.18 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 227 
 TYR   0.012   0.001   TYR A 163 
 PHE   0.023   0.001   PHE B 162 
 TRP   0.016   0.001   TRP B 319 
 HIS   0.004   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7457)
  covalent geometry    : angle       0.60324 (10144)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.19541 (    2)
  hydrogen bonds       : bond        0.03615 (  384)
  hydrogen bonds       : angle       4.55533 ( 1086)

*********************** 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
  158 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 ASN cc_start: 0.8383 (t0) cc_final: 0.7730 (t0)
REVERT: A  489 ARG cc_start: 0.7810 (mpt-90) cc_final: 0.7439 (mpt-90)
REVERT: B  204 ILE cc_start: 0.8731 (mm) cc_final: 0.8359 (tt)
REVERT: B  210 ARG cc_start: 0.8279 (mmt180) cc_final: 0.7952 (tpt90)
REVERT: B  278 LEU cc_start: 0.8818 (tp) cc_final: 0.8599 (tt)
REVERT: B  335 LEU cc_start: 0.8692 (mt) cc_final: 0.8289 (mt)
REVERT: B  360 PHE cc_start: 0.9066 (m-80) cc_final: 0.8362 (m-80)
REVERT: B  364 TRP cc_start: 0.7831 (m-10) cc_final: 0.7219 (m-10)
REVERT: B  392 LEU cc_start: 0.8691 (mt) cc_final: 0.8138 (tt)
REVERT: B  471 ASP cc_start: 0.7493 (m-30) cc_final: 0.7160 (m-30)
REVERT: B  562 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6820 (mm-30)
REVERT: B  606 GLU cc_start: 0.6364 (mt-10) cc_final: 0.6111 (mt-10)
REVERT: B  621 GLU cc_start: 0.6480 (tt0) cc_final: 0.6167 (tt0)
  outliers start: 26
  outliers final: 15
  residues processed: 151
  average time/residue: 0.0875
  time to fit residues: 17.9062
Evaluate side-chains
  128 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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  271 ILE
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  351 ILE
Chi-restraints excluded: chain B residue  412 THR
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 88 optimal weight:    7.9990
   chunk 43 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 13 optimal weight:    0.5980
   chunk 90 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 71 optimal weight:   20.0000
   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 232 GLN
B 235 GLN
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.186437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124565 restraints weight = 8862.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.129459 restraints weight = 5150.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.132662 restraints weight = 3709.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.134517 restraints weight = 3047.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.135786 restraints weight = 2709.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7458  Z= 0.162
  Angle     :  0.611   8.440  10146  Z= 0.307
  Chirality :  0.041   0.144   1163
  Planarity :  0.004   0.040   1274
  Dihedral  :  4.647  49.184    999
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.41 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.27), residues: 930
  helix:  0.65 (0.23), residues: 488
  sheet: -1.19 (0.60), residues: 64
  loop : -1.94 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 525 
 TYR   0.014   0.001   TYR A 163 
 PHE   0.018   0.002   PHE B 162 
 TRP   0.014   0.001   TRP B 319 
 HIS   0.007   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 7457)
  covalent geometry    : angle       0.61152 (10144)
  SS BOND              : bond        0.00129 (    1)
  SS BOND              : angle       0.25550 (    2)
  hydrogen bonds       : bond        0.03665 (  384)
  hydrogen bonds       : angle       4.52558 ( 1086)

*********************** 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
  148 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  254 ASN cc_start: 0.8444 (t0) cc_final: 0.7725 (t0)
REVERT: A  489 ARG cc_start: 0.7863 (mpt-90) cc_final: 0.7441 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7959 (tpt90)
REVERT: B  278 LEU cc_start: 0.9029 (tp) cc_final: 0.8706 (tt)
REVERT: B  360 PHE cc_start: 0.9163 (m-80) cc_final: 0.8619 (m-80)
REVERT: B  392 LEU cc_start: 0.8804 (mt) cc_final: 0.8216 (tt)
REVERT: B  562 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6864 (mm-30)
REVERT: B  579 LEU cc_start: 0.7859 (tp) cc_final: 0.7585 (tp)
REVERT: B  606 GLU cc_start: 0.6426 (mt-10) cc_final: 0.6211 (mt-10)
REVERT: B  621 GLU cc_start: 0.6604 (tt0) cc_final: 0.6150 (tt0)
  outliers start: 24
  outliers final: 20
  residues processed: 142
  average time/residue: 0.0918
  time to fit residues: 17.6447
Evaluate side-chains
  130 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  105 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  271 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  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  262 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  510 VAL
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 84 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   chunk 76 optimal weight:    0.5980
   chunk 72 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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**
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** 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 = 0.4171 r_free = 0.4171 target = 0.188060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134238 restraints weight = 8749.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.136972 restraints weight = 5992.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137672 restraints weight = 5293.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.138069 restraints weight = 4014.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.138227 restraints weight = 3984.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7458  Z= 0.147
  Angle     :  0.619  14.188  10146  Z= 0.306
  Chirality :  0.040   0.188   1163
  Planarity :  0.004   0.048   1274
  Dihedral  :  4.481  41.493    999
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 21.67 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.27), residues: 930
  helix:  0.78 (0.24), residues: 490
  sheet: -1.01 (0.62), residues: 64
  loop : -1.77 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 525 
 TYR   0.014   0.001   TYR A 163 
 PHE   0.020   0.001   PHE B 162 
 TRP   0.015   0.001   TRP B 364 
 HIS   0.007   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7457)
  covalent geometry    : angle       0.61942 (10144)
  SS BOND              : bond        0.00055 (    1)
  SS BOND              : angle       0.23562 (    2)
  hydrogen bonds       : bond        0.03571 (  384)
  hydrogen bonds       : angle       4.39907 ( 1086)

*********************** 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: 30
    poor density    : 120
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 ASP cc_start: 0.8085 (t70) cc_final: 0.7813 (t70)
REVERT: A  254 ASN cc_start: 0.8414 (t0) cc_final: 0.7748 (t0)
REVERT: A  489 ARG cc_start: 0.7925 (mpt-90) cc_final: 0.7502 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8294 (mmt180) cc_final: 0.7942 (tpt90)
REVERT: B  278 LEU cc_start: 0.8819 (tp) cc_final: 0.8548 (tt)
REVERT: B  292 ASP cc_start: 0.8606 (m-30) cc_final: 0.8003 (t70)
REVERT: B  299 LYS cc_start: 0.7951 (mmmm) cc_final: 0.7734 (mmmm)
REVERT: B  360 PHE cc_start: 0.9098 (m-80) cc_final: 0.8524 (m-80)
REVERT: B  427 THR cc_start: 0.8583 (m) cc_final: 0.8368 (t)
REVERT: B  562 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6878 (mm-30)
REVERT: B  606 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6319 (mt-10)
REVERT: B  621 GLU cc_start: 0.6455 (tt0) cc_final: 0.6085 (tt0)
  outliers start: 30
  outliers final: 25
  residues processed: 144
  average time/residue: 0.0827
  time to fit residues: 16.3174
Evaluate side-chains
  140 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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  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  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  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  351 ILE
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
Chi-restraints excluded: chain B residue  612 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4084 r_free = 0.4084 target = 0.183898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.123972 restraints weight = 8759.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.124159 restraints weight = 5322.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.127321 restraints weight = 3803.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.127309 restraints weight = 3014.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.129153 restraints weight = 2907.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7458  Z= 0.149
  Angle     :  0.623  13.084  10146  Z= 0.306
  Chirality :  0.042   0.341   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.421  37.585    999
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.94 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.28), residues: 930
  helix:  0.93 (0.24), residues: 490
  sheet: -0.94 (0.63), residues: 64
  loop : -1.68 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 525 
 TYR   0.014   0.001   TYR A 163 
 PHE   0.022   0.001   PHE B 162 
 TRP   0.015   0.001   TRP A 398 
 HIS   0.007   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7457)
  covalent geometry    : angle       0.62310 (10144)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.28771 (    2)
  hydrogen bonds       : bond        0.03569 (  384)
  hydrogen bonds       : angle       4.36096 ( 1086)

*********************** 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
  146 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.8035 (tp30) cc_final: 0.7276 (tm-30)
REVERT: A  224 ASP cc_start: 0.8170 (t70) cc_final: 0.7824 (t70)
REVERT: A  254 ASN cc_start: 0.8316 (t0) cc_final: 0.7605 (t0)
REVERT: A  367 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8228 (mt)
REVERT: A  489 ARG cc_start: 0.7771 (mpt-90) cc_final: 0.7344 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8344 (mmt180) cc_final: 0.7956 (tpt90)
REVERT: B  278 LEU cc_start: 0.9154 (tp) cc_final: 0.8777 (tt)
REVERT: B  292 ASP cc_start: 0.8924 (m-30) cc_final: 0.8115 (t70)
REVERT: B  299 LYS cc_start: 0.8030 (mmmm) cc_final: 0.7818 (mmmm)
REVERT: B  360 PHE cc_start: 0.9341 (m-80) cc_final: 0.8756 (m-80)
REVERT: B  392 LEU cc_start: 0.8908 (mt) cc_final: 0.8379 (tt)
REVERT: B  562 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6727 (mm-30)
REVERT: B  606 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6212 (mt-10)
REVERT: B  621 GLU cc_start: 0.6485 (tt0) cc_final: 0.5957 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 143
  average time/residue: 0.0909
  time to fit residues: 17.4122
Evaluate side-chains
  134 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   98 TYR
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  204 ILE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  367 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   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 = 0.4099 r_free = 0.4099 target = 0.185504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.121607 restraints weight = 8708.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.127220 restraints weight = 4765.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.130927 restraints weight = 3311.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.133154 restraints weight = 2654.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.134117 restraints weight = 2331.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7458  Z= 0.130
  Angle     :  0.608  12.491  10146  Z= 0.298
  Chirality :  0.041   0.302   1163
  Planarity :  0.004   0.047   1274
  Dihedral  :  4.302  33.875    999
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.19 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.28), residues: 930
  helix:  1.09 (0.24), residues: 488
  sheet: -0.84 (0.65), residues: 64
  loop : -1.60 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 525 
 TYR   0.013   0.001   TYR A 163 
 PHE   0.021   0.001   PHE B 162 
 TRP   0.016   0.001   TRP B 364 
 HIS   0.009   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7457)
  covalent geometry    : angle       0.60794 (10144)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.28582 (    2)
  hydrogen bonds       : bond        0.03449 (  384)
  hydrogen bonds       : angle       4.26449 ( 1086)

*********************** 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
  150 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.8090 (tp30) cc_final: 0.7295 (tm-30)
REVERT: A  254 ASN cc_start: 0.8280 (t0) cc_final: 0.7587 (t0)
REVERT: A  489 ARG cc_start: 0.7808 (mpt-90) cc_final: 0.7389 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8300 (mmt180) cc_final: 0.7916 (tpt90)
REVERT: B  278 LEU cc_start: 0.9116 (tp) cc_final: 0.8783 (tt)
REVERT: B  292 ASP cc_start: 0.8855 (m-30) cc_final: 0.8161 (t70)
REVERT: B  299 LYS cc_start: 0.8018 (mmmm) cc_final: 0.7807 (mmmm)
REVERT: B  349 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7516 (ptp-110)
REVERT: B  360 PHE cc_start: 0.9342 (m-80) cc_final: 0.8736 (m-80)
REVERT: B  392 LEU cc_start: 0.8869 (mt) cc_final: 0.8283 (tt)
REVERT: B  562 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6694 (mm-30)
REVERT: B  606 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6261 (mt-10)
REVERT: B  621 GLU cc_start: 0.6413 (tt0) cc_final: 0.5932 (tt0)
  outliers start: 26
  outliers final: 22
  residues processed: 147
  average time/residue: 0.0932
  time to fit residues: 18.6766
Evaluate side-chains
  136 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  108 SER
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  204 ILE
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  271 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  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  250 ASP
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 75 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0970
   chunk 53 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    2.1984

-------------------------------------------------------------------------------
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 = 0.4050 r_free = 0.4050 target = 0.179998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.120029 restraints weight = 8830.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.120636 restraints weight = 5303.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.123049 restraints weight = 4114.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.124080 restraints weight = 3296.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.124341 restraints weight = 3145.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   7458  Z= 0.232
  Angle     :  0.708  11.632  10146  Z= 0.344
  Chirality :  0.045   0.328   1163
  Planarity :  0.004   0.049   1274
  Dihedral  :  4.593  34.949    999
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 23.70 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.28), residues: 930
  helix:  0.79 (0.24), residues: 490
  sheet: -0.92 (0.64), residues: 64
  loop : -1.58 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 452 
 TYR   0.018   0.002   TYR A 163 
 PHE   0.019   0.002   PHE B 291 
 TRP   0.023   0.002   TRP B 364 
 HIS   0.008   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 7457)
  covalent geometry    : angle       0.70794 (10144)
  SS BOND              : bond        0.00202 (    1)
  SS BOND              : angle       0.41905 (    2)
  hydrogen bonds       : bond        0.03982 (  384)
  hydrogen bonds       : angle       4.56249 ( 1086)

*********************** 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
  149 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.8171 (tp30) cc_final: 0.7703 (tp30)
REVERT: A  413 TRP cc_start: 0.7936 (t60) cc_final: 0.7464 (t60)
REVERT: A  489 ARG cc_start: 0.7813 (mpt-90) cc_final: 0.7408 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8316 (mmt180) cc_final: 0.7899 (tpt90)
REVERT: B  278 LEU cc_start: 0.9237 (tp) cc_final: 0.8728 (tt)
REVERT: B  292 ASP cc_start: 0.8900 (m-30) cc_final: 0.8132 (t70)
REVERT: B  299 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7801 (mmmm)
REVERT: B  360 PHE cc_start: 0.9348 (m-80) cc_final: 0.8723 (m-80)
REVERT: B  392 LEU cc_start: 0.8928 (mt) cc_final: 0.8393 (tt)
REVERT: B  562 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6903 (mm-30)
REVERT: B  606 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6205 (mt-10)
REVERT: B  621 GLU cc_start: 0.6568 (tt0) cc_final: 0.5910 (tt0)
  outliers start: 28
  outliers final: 23
  residues processed: 143
  average time/residue: 0.0881
  time to fit residues: 17.0379
Evaluate side-chains
  141 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  108 SER
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  271 ILE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  449 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  204 ILE
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  390 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
Chi-restraints excluded: chain B residue  605 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 81 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.184612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.121065 restraints weight = 8703.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.126574 restraints weight = 4769.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.130185 restraints weight = 3325.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.132318 restraints weight = 2676.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.133730 restraints weight = 2352.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7458  Z= 0.132
  Angle     :  0.654  13.900  10146  Z= 0.314
  Chirality :  0.041   0.316   1163
  Planarity :  0.004   0.049   1274
  Dihedral  :  4.385  32.003    999
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 24.71 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.28), residues: 930
  helix:  1.05 (0.24), residues: 489
  sheet: -0.86 (0.65), residues: 64
  loop : -1.46 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 452 
 TYR   0.013   0.001   TYR A 163 
 PHE   0.016   0.001   PHE B 542 
 TRP   0.025   0.001   TRP B 364 
 HIS   0.012   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7457)
  covalent geometry    : angle       0.65423 (10144)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       0.27971 (    2)
  hydrogen bonds       : bond        0.03585 (  384)
  hydrogen bonds       : angle       4.33079 ( 1086)

*********************** 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
  143 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 MET cc_start: 0.7428 (mmp) cc_final: 0.7219 (mmp)
REVERT: A  254 ASN cc_start: 0.8301 (t0) cc_final: 0.7691 (t0)
REVERT: A  489 ARG cc_start: 0.7789 (mpt-90) cc_final: 0.7405 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8271 (mmt180) cc_final: 0.7882 (tpt90)
REVERT: B  278 LEU cc_start: 0.9163 (tp) cc_final: 0.8706 (tt)
REVERT: B  285 PHE cc_start: 0.7709 (m-80) cc_final: 0.7369 (m-80)
REVERT: B  292 ASP cc_start: 0.8874 (m-30) cc_final: 0.8136 (t70)
REVERT: B  360 PHE cc_start: 0.9352 (m-80) cc_final: 0.8694 (m-80)
REVERT: B  392 LEU cc_start: 0.8883 (mt) cc_final: 0.8356 (tt)
REVERT: B  562 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6715 (mm-30)
REVERT: B  606 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6042 (mt-10)
REVERT: B  621 GLU cc_start: 0.6491 (tt0) cc_final: 0.5981 (tt0)
  outliers start: 25
  outliers final: 23
  residues processed: 138
  average time/residue: 0.0851
  time to fit residues: 15.8310
Evaluate side-chains
  133 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  108 SER
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  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  484 LEU
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  250 ASP
Chi-restraints excluded: chain B residue  390 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
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 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0020
   chunk 10 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0670
   chunk 58 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.7730

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.185037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.121599 restraints weight = 8819.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.127223 restraints weight = 4808.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.130845 restraints weight = 3331.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.133105 restraints weight = 2672.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.134316 restraints weight = 2338.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3062

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= 0.133
  Angle     :  0.651  13.214  10146  Z= 0.316
  Chirality :  0.041   0.313   1163
  Planarity :  0.004   0.049   1274
  Dihedral  :  4.283  28.299    999
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 25.35 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.28), residues: 930
  helix:  1.07 (0.24), residues: 493
  sheet: -1.02 (0.61), residues: 69
  loop : -1.40 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 227 
 TYR   0.013   0.001   TYR A 163 
 PHE   0.037   0.002   PHE B 291 
 TRP   0.029   0.001   TRP B 364 
 HIS   0.010   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7457)
  covalent geometry    : angle       0.65138 (10144)
  SS BOND              : bond        0.00031 (    1)
  SS BOND              : angle       0.30267 (    2)
  hydrogen bonds       : bond        0.03483 (  384)
  hydrogen bonds       : angle       4.28574 ( 1086)

********************** 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
  147 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.6800 (pmm) cc_final: 0.6235 (pmm)
REVERT: A  233 MET cc_start: 0.7448 (mmp) cc_final: 0.7228 (mmp)
REVERT: A  254 ASN cc_start: 0.8281 (t0) cc_final: 0.7692 (t0)
REVERT: A  489 ARG cc_start: 0.7819 (mpt-90) cc_final: 0.7443 (mpt-90)
REVERT: B  210 ARG cc_start: 0.8249 (mmt180) cc_final: 0.7870 (tpt90)
REVERT: B  278 LEU cc_start: 0.9205 (tp) cc_final: 0.8773 (tt)
REVERT: B  285 PHE cc_start: 0.7739 (m-80) cc_final: 0.7390 (m-80)
REVERT: B  292 ASP cc_start: 0.8868 (m-30) cc_final: 0.8157 (t70)
REVERT: B  360 PHE cc_start: 0.9358 (m-80) cc_final: 0.8690 (m-80)
REVERT: B  392 LEU cc_start: 0.8880 (mt) cc_final: 0.8416 (tt)
REVERT: B  562 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6698 (mm-30)
REVERT: B  606 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6082 (mt-10)
REVERT: B  621 GLU cc_start: 0.6415 (tt0) cc_final: 0.5948 (tt0)
  outliers start: 24
  outliers final: 23
  residues processed: 141
  average time/residue: 0.0847
  time to fit residues: 16.2212
Evaluate side-chains
  138 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  108 SER
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  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  484 LEU
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  250 ASP
Chi-restraints excluded: chain B residue  390 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
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 39 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 50 optimal weight:    0.3980
   chunk 37 optimal weight:    0.1980
   chunk 82 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0670
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.4115 r_free = 0.4115 target = 0.186705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.124446 restraints weight = 8645.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.129925 restraints weight = 4780.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.133461 restraints weight = 3339.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.135655 restraints weight = 2688.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.136729 restraints weight = 2356.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.3201

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= 0.121
  Angle     :  0.636  12.482  10146  Z= 0.308
  Chirality :  0.040   0.315   1163
  Planarity :  0.004   0.051   1274
  Dihedral  :  4.183  24.819    999
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 26.62 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.29), residues: 930
  helix:  1.21 (0.24), residues: 492
  sheet: -0.96 (0.62), residues: 69
  loop : -1.33 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 227 
 TYR   0.012   0.001   TYR A 163 
 PHE   0.016   0.001   PHE B 545 
 TRP   0.022   0.001   TRP B 364 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7457)
  covalent geometry    : angle       0.63611 (10144)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.30888 (    2)
  hydrogen bonds       : bond        0.03383 (  384)
  hydrogen bonds       : angle       4.19099 ( 1086)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1516.07 seconds
wall clock time: 26 minutes 51.91 seconds (1611.91 seconds total)