Starting phenix.real_space_refine
on Tue Mar  3 13:30:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s8u_24922/03_2026/7s8u_24922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s8u_24922/03_2026/7s8u_24922.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s8u_24922/03_2026/7s8u_24922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s8u_24922/03_2026/7s8u_24922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s8u_24922/03_2026/7s8u_24922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s8u_24922/03_2026/7s8u_24922.cif"
  }
  resolution = 3.7
  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=   0.073
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      35      5.16       5
     C    3390      2.51       5
     N     854      2.21       5
     O     931      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5210
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 667, 5210
          Classifications: {'peptide': 667}
          Link IDs: {'PTRANS': 30, 'TRANS': 636}
  Time building chain proxies: 1.30, per 1000 atoms: 0.25
  Number of scatterers: 5210
  At special positions: 0
  Unit cell: (99.146, 100.26, 99.146, 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      35     16.00
     O     931      8.00
     N     854      7.00
     C    3390      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 539 " - pdb=" SG  CYS A 565 " 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: 0.41
  Conformation dependent library (CDL) restraints added in 388.7 milliseconds
  

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1236

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 4 sheets defined
      55.6% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 45
    Processing helix  chain 'A' and resid 49 through 78
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 80 through 104
    Processing helix  chain 'A' and resid 120 through 153
      Proline residue:  A 142  - end of helix
      removed outlier: 5.023A  pdb=" N   SER A 145 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA A 146 " --> pdb=" O   PRO A 142 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   PHE A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 187
      removed outlier: 3.535A  pdb=" N   SER A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
      Proline residue:  A 183  - end of helix
      removed outlier: 3.622A  pdb=" N   VAL A 187 " --> pdb=" O   PRO A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 217
      removed outlier: 4.033A  pdb=" N   ALA A 202 " --> pdb=" O   CYS A 198 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.643A  pdb=" N   LEU A 209 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 249
      removed outlier: 4.391A  pdb=" N   CYS A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 269
    Processing helix  chain 'A' and resid 272 through 289
    Processing helix  chain 'A' and resid 291 through 311
      removed outlier: 3.948A  pdb=" N   THR A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 344
      Proline residue:  A 339  - end of helix
      removed outlier: 3.857A  pdb=" N   ASP A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ALA A 343 " --> pdb=" O   PRO A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 384
      removed outlier: 3.556A  pdb=" N   ASP A 384 " --> pdb=" O   GLN A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 582
      No H-bonds generated for 'chain 'A' and resid 580 through 582'
    Processing helix  chain 'A' and resid 583 through 609
    Processing helix  chain 'A' and resid 611 through 613
      No H-bonds generated for 'chain 'A' and resid 611 through 613'
    Processing helix  chain 'A' and resid 614 through 638
    Processing helix  chain 'A' and resid 644 through 669
      removed outlier: 4.047A  pdb=" N   GLU A 648 " --> pdb=" O   LYS A 644 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 669 " --> pdb=" O   ILE A 665 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 432
      removed outlier: 8.225A  pdb=" N   HIS A 460 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   GLN A 397 " --> pdb=" O   HIS A 460 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   ILE A 462 " --> pdb=" O   GLN A 397 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   LYS A 399 " --> pdb=" O   ILE A 462 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   VAL A 464 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   LEU A 401 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   ALA A 466 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TRP A 465 " --> pdb=" O   HIS A 469 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   HIS A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 419
    Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521
      removed outlier: 3.904A  pdb=" N   GLN A 519 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ILE A 488 " --> pdb=" O   GLN A 519 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ASN A 486 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TYR A 554 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE A 574 " --> pdb=" O   ALA A 553 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   THR A 555 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   GLY A 572 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   VAL A 557 " --> pdb=" O   VAL A 570 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL A 570 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 510
      removed outlier: 3.667A  pdb=" N   ASN A 509 " --> pdb=" O   PHE A 498 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   PHE A 498 " --> pdb=" O   ASN A 509 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    915 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: 1.02

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 823
        1.31 -     1.44: 1465
        1.44 -     1.56: 2991
        1.56 -     1.69: 0
        1.69 -     1.82: 59
  Bond restraints: 5338
  Sorted by residual:
  bond pdb=" C   TRP A 295 "
       pdb=" O   TRP A 295 "
    ideal  model  delta    sigma   weight residual
    1.237  1.301 -0.064 1.17e-02 7.31e+03 3.04e+01
  bond pdb=" C   LEU A 176 "
       pdb=" O   LEU A 176 "
    ideal  model  delta    sigma   weight residual
    1.236  1.296 -0.060 1.15e-02 7.56e+03 2.73e+01
  bond pdb=" C   VAL A 596 "
       pdb=" O   VAL A 596 "
    ideal  model  delta    sigma   weight residual
    1.236  1.293 -0.057 1.19e-02 7.06e+03 2.31e+01
  bond pdb=" C   GLY A 302 "
       pdb=" O   GLY A 302 "
    ideal  model  delta    sigma   weight residual
    1.235  1.297 -0.062 1.35e-02 5.49e+03 2.10e+01
  bond pdb=" C   PHE A 298 "
       pdb=" O   PHE A 298 "
    ideal  model  delta    sigma   weight residual
    1.236  1.288 -0.052 1.15e-02 7.56e+03 2.01e+01
  ... (remaining 5333 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 6769
        2.41 -     4.82: 422
        4.82 -     7.23: 52
        7.23 -     9.64: 7
        9.64 -    12.05: 1
  Bond angle restraints: 7251
  Sorted by residual:
  angle pdb=" CA  PRO A 183 "
        pdb=" N   PRO A 183 "
        pdb=" CD  PRO A 183 "
      ideal   model   delta    sigma   weight residual
     112.00   99.95   12.05 1.40e+00 5.10e-01 7.40e+01
  angle pdb=" C   PHE A 294 "
        pdb=" N   TRP A 295 "
        pdb=" CA  TRP A 295 "
      ideal   model   delta    sigma   weight residual
     120.28  111.61    8.67 1.34e+00 5.57e-01 4.19e+01
  angle pdb=" N   GLN A 300 "
        pdb=" CA  GLN A 300 "
        pdb=" C   GLN A 300 "
      ideal   model   delta    sigma   weight residual
     111.28  104.30    6.98 1.09e+00 8.42e-01 4.10e+01
  angle pdb=" C   LEU A  38 "
        pdb=" N   ILE A  39 "
        pdb=" CA  ILE A  39 "
      ideal   model   delta    sigma   weight residual
     120.56  113.27    7.29 1.26e+00 6.30e-01 3.35e+01
  angle pdb=" N   GLN A 327 "
        pdb=" CA  GLN A 327 "
        pdb=" C   GLN A 327 "
      ideal   model   delta    sigma   weight residual
     112.54  105.50    7.04 1.22e+00 6.72e-01 3.33e+01
  ... (remaining 7246 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 2834
       16.07 -    32.14: 223
       32.14 -    48.21: 57
       48.21 -    64.28: 21
       64.28 -    80.35: 8
  Dihedral angle restraints: 3143
    sinusoidal: 1218
      harmonic: 1925
  Sorted by residual:
  dihedral pdb=" C   ILE A 585 "
           pdb=" N   ILE A 585 "
           pdb=" CA  ILE A 585 "
           pdb=" CB  ILE A 585 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.18   13.18     0      2.50e+00 1.60e-01 2.78e+01
  dihedral pdb=" N   ILE A 585 "
           pdb=" C   ILE A 585 "
           pdb=" CA  ILE A 585 "
           pdb=" CB  ILE A 585 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.00  -11.60     0      2.50e+00 1.60e-01 2.15e+01
  dihedral pdb=" C   ILE A 289 "
           pdb=" N   ILE A 289 "
           pdb=" CA  ILE A 289 "
           pdb=" CB  ILE A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.07    9.07     0      2.50e+00 1.60e-01 1.32e+01
  ... (remaining 3140 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 573
       0.060 -    0.120: 180
       0.120 -    0.181: 54
       0.181 -    0.241: 18
       0.241 -    0.301: 2
  Chirality restraints: 827
  Sorted by residual:
  chirality pdb=" CA  ILE A 585 "
            pdb=" N   ILE A 585 "
            pdb=" C   ILE A 585 "
            pdb=" CB  ILE A 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.13    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CB  ILE A 585 "
            pdb=" CA  ILE A 585 "
            pdb=" CG1 ILE A 585 "
            pdb=" CG2 ILE A 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CA  ILE A 319 "
            pdb=" N   ILE A 319 "
            pdb=" C   ILE A 319 "
            pdb=" CB  ILE A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 824 not shown)

  Planarity restraints: 917
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 182 "   -0.082 5.00e-02 4.00e+02   1.17e-01 2.18e+01
        pdb=" N   PRO A 183 "    0.201 5.00e-02 4.00e+02
        pdb=" CA  PRO A 183 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 183 "   -0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 302 "   -0.016 2.00e-02 2.50e+03   3.29e-02 1.08e+01
        pdb=" C   GLY A 302 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLY A 302 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   SER A 303 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  39 "    0.011 2.00e-02 2.50e+03   2.32e-02 5.37e+00
        pdb=" C   ILE A  39 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A  39 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A  40 "    0.014 2.00e-02 2.50e+03
  ... (remaining 914 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 983
        2.77 -     3.31: 5547
        3.31 -     3.84: 8613
        3.84 -     4.37: 9757
        4.37 -     4.90: 16386
  Nonbonded interactions: 41286
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 555 "
            pdb=" O   PHE A 571 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   VAL A 123 "
            pdb=" OG  SER A 126 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   GLN A 301 "
            pdb=" C   GLY A 302 "
     model   vdw
     2.354 3.270
  nonbonded pdb=" OG  SER A 536 "
            pdb=" OE1 GLN A 538 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   ILE A  56 "
            pdb=" OG1 THR A  59 "
     model   vdw
     2.382 3.040
  ... (remaining 41281 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.680
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.280
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5918
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      :  0.008   0.064   5339  Z= 0.582
  Angle     :  1.189  12.046   7253  Z= 0.848
  Chirality :  0.070   0.301    827
  Planarity :  0.007   0.117    917
  Dihedral  : 14.003  80.348   1904
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  1.20 %
    Allowed  :  8.27 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  :  3.68 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.33), residues: 665
  helix:  0.16 (0.28), residues: 339
  sheet:  1.49 (0.72), residues: 54
  loop : -2.48 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 252 
 TYR   0.025   0.002   TYR A  41 
 PHE   0.015   0.002   PHE A 356 
 TRP   0.020   0.002   TRP A 622 
 HIS   0.004   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00764 ( 5338)
  covalent geometry    : angle       1.18844 ( 7251)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       1.41029 (    2)
  hydrogen bonds       : bond        0.17257 (  312)
  hydrogen bonds       : angle       7.27829 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   76 ASP cc_start: 0.6653 (t70) cc_final: 0.6325 (m-30)
REVERT: A  183 PRO cc_start: 0.8466 (OUTLIER) cc_final: 0.7871 (Cg_endo)
REVERT: A  286 PHE cc_start: 0.7024 (m-10) cc_final: 0.6651 (t80)
REVERT: A  458 HIS cc_start: 0.4926 (m90) cc_final: 0.4465 (m90)
REVERT: A  465 TRP cc_start: 0.3603 (p90) cc_final: 0.2985 (p90)
REVERT: A  541 ARG cc_start: 0.6430 (ptt180) cc_final: 0.6164 (ptt180)
REVERT: A  632 ILE cc_start: 0.8696 (mt) cc_final: 0.8402 (mt)
  outliers start: 26
  outliers final: 7
  residues processed: 211
  average time/residue: 0.0674
  time to fit residues: 18.7140
Evaluate side-chains
  158 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue  183 PRO
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  292 PRO
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  586 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 193 HIS
A 315 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.222948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.200962 restraints weight = 11200.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.203899 restraints weight = 6746.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.206475 restraints weight = 4668.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.208385 restraints weight = 3293.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.208320 restraints weight = 3061.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.4454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6140
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5339  Z= 0.193
  Angle     :  0.763   8.653   7253  Z= 0.407
  Chirality :  0.049   0.226    827
  Planarity :  0.006   0.066    917
  Dihedral  :  6.765  59.395    729
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  8.87 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 14.21 %
    Favored  : 81.75 %
  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 are not related in a simple way.
  whole: -0.76 (0.32), residues: 665
  helix:  0.67 (0.27), residues: 353
  sheet:  1.57 (0.66), residues: 52
  loop : -2.70 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 186 
 TYR   0.020   0.002   TYR A 588 
 PHE   0.034   0.002   PHE A 243 
 TRP   0.009   0.001   TRP A 622 
 HIS   0.007   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 5338)
  covalent geometry    : angle       0.76102 ( 7251)
  SS BOND              : bond        0.01727 (    1)
  SS BOND              : angle       3.05426 (    2)
  hydrogen bonds       : bond        0.06927 (  312)
  hydrogen bonds       : angle       5.13653 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  285 MET cc_start: 0.7698 (ttp) cc_final: 0.7265 (mtp)
REVERT: A  286 PHE cc_start: 0.6849 (m-10) cc_final: 0.6377 (t80)
REVERT: A  301 GLN cc_start: 0.6098 (OUTLIER) cc_final: 0.4314 (tm130)
REVERT: A  541 ARG cc_start: 0.6452 (ptt180) cc_final: 0.6219 (ptt180)
REVERT: A  595 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: A  632 ILE cc_start: 0.8844 (mt) cc_final: 0.8580 (mt)
REVERT: A  644 LYS cc_start: 0.7375 (pttm) cc_final: 0.6929 (pttm)
  outliers start: 23
  outliers final: 15
  residues processed: 159
  average time/residue: 0.0645
  time to fit residues: 13.8131
Evaluate side-chains
  144 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 193 HIS
A 277 GLN
A 458 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.222566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.201334 restraints weight = 10975.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.205079 restraints weight = 6165.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.207430 restraints weight = 4081.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.208288 restraints weight = 2897.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.208919 restraints weight = 2806.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6124
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5339  Z= 0.165
  Angle     :  0.727   9.810   7253  Z= 0.380
  Chirality :  0.046   0.216    827
  Planarity :  0.005   0.062    917
  Dihedral  :  6.454  58.756    719
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.87 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.12 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.33), residues: 665
  helix:  0.82 (0.27), residues: 354
  sheet:  1.65 (0.66), residues: 52
  loop : -2.40 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 186 
 TYR   0.017   0.002   TYR A 224 
 PHE   0.027   0.002   PHE A 243 
 TRP   0.010   0.001   TRP A 622 
 HIS   0.007   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5338)
  covalent geometry    : angle       0.72651 ( 7251)
  SS BOND              : bond        0.00436 (    1)
  SS BOND              : angle       2.04931 (    2)
  hydrogen bonds       : bond        0.06275 (  312)
  hydrogen bonds       : angle       4.89715 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8669 (p) cc_final: 0.8446 (p)
REVERT: A  223 MET cc_start: 0.5332 (ppp) cc_final: 0.5129 (ppp)
REVERT: A  285 MET cc_start: 0.7529 (ttp) cc_final: 0.7105 (mtp)
REVERT: A  286 PHE cc_start: 0.6799 (m-10) cc_final: 0.6302 (t80)
REVERT: A  301 GLN cc_start: 0.5908 (OUTLIER) cc_final: 0.4279 (tm130)
REVERT: A  595 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: A  632 ILE cc_start: 0.8830 (mt) cc_final: 0.8550 (mt)
REVERT: A  644 LYS cc_start: 0.7326 (pttm) cc_final: 0.6977 (pttm)
  outliers start: 22
  outliers final: 16
  residues processed: 151
  average time/residue: 0.0569
  time to fit residues: 11.7096
Evaluate side-chains
  148 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  585 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0030
   chunk 6 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 277 GLN
A 458 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.222219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.201146 restraints weight = 11132.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.204965 restraints weight = 6364.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.206457 restraints weight = 4082.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.207317 restraints weight = 3461.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.209207 restraints weight = 2838.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6122
moved from start:          0.3866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5339  Z= 0.159
  Angle     :  0.720   8.752   7253  Z= 0.372
  Chirality :  0.045   0.226    827
  Planarity :  0.006   0.085    917
  Dihedral  :  6.098  55.117    717
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.87 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 20.70 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.33), residues: 665
  helix:  0.93 (0.27), residues: 353
  sheet:  1.72 (0.68), residues: 52
  loop : -2.38 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  28 
 TYR   0.015   0.002   TYR A  41 
 PHE   0.021   0.002   PHE A 243 
 TRP   0.010   0.001   TRP A 622 
 HIS   0.007   0.002   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5338)
  covalent geometry    : angle       0.72016 ( 7251)
  SS BOND              : bond        0.00186 (    1)
  SS BOND              : angle       0.70865 (    2)
  hydrogen bonds       : bond        0.05980 (  312)
  hydrogen bonds       : angle       4.87420 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8676 (p) cc_final: 0.8454 (p)
REVERT: A  285 MET cc_start: 0.7512 (ttp) cc_final: 0.7114 (mtp)
REVERT: A  286 PHE cc_start: 0.6788 (m-10) cc_final: 0.6305 (t80)
REVERT: A  301 GLN cc_start: 0.5934 (OUTLIER) cc_final: 0.4306 (tm130)
REVERT: A  558 MET cc_start: 0.5297 (mmp) cc_final: 0.5056 (mmp)
REVERT: A  595 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7588 (tm-30)
REVERT: A  632 ILE cc_start: 0.8835 (mt) cc_final: 0.8598 (mt)
REVERT: A  644 LYS cc_start: 0.7364 (pttm) cc_final: 0.6995 (pttm)
  outliers start: 25
  outliers final: 21
  residues processed: 152
  average time/residue: 0.0608
  time to fit residues: 12.4964
Evaluate side-chains
  152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    8.9990
   chunk 24 optimal weight:    0.1980
   chunk 64 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 458 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.223008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.201389 restraints weight = 11543.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.206326 restraints weight = 7103.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.207568 restraints weight = 4148.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.208485 restraints weight = 3917.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.210174 restraints weight = 2918.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.4465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6131
moved from start:          0.4141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5339  Z= 0.153
  Angle     :  0.731  10.313   7253  Z= 0.373
  Chirality :  0.045   0.170    827
  Planarity :  0.006   0.087    917
  Dihedral  :  6.032  55.037    717
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.02 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 21.75 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.33), residues: 665
  helix:  1.01 (0.27), residues: 356
  sheet:  1.62 (0.69), residues: 52
  loop : -2.45 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 250 
 TYR   0.018   0.002   TYR A 224 
 PHE   0.024   0.002   PHE A 356 
 TRP   0.010   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5338)
  covalent geometry    : angle       0.73036 ( 7251)
  SS BOND              : bond        0.00346 (    1)
  SS BOND              : angle       2.35525 (    2)
  hydrogen bonds       : bond        0.05784 (  312)
  hydrogen bonds       : angle       4.85843 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8685 (p) cc_final: 0.8442 (p)
REVERT: A  225 LYS cc_start: 0.7688 (tppt) cc_final: 0.7483 (tppt)
REVERT: A  285 MET cc_start: 0.7404 (ttp) cc_final: 0.7059 (mtp)
REVERT: A  286 PHE cc_start: 0.6925 (m-10) cc_final: 0.6459 (t80)
REVERT: A  301 GLN cc_start: 0.5847 (OUTLIER) cc_final: 0.4396 (tm130)
REVERT: A  541 ARG cc_start: 0.6356 (ptt180) cc_final: 0.5417 (mtm180)
REVERT: A  558 MET cc_start: 0.5352 (mmp) cc_final: 0.5057 (mmp)
REVERT: A  595 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7714 (tm-30)
REVERT: A  632 ILE cc_start: 0.8828 (mt) cc_final: 0.8587 (mt)
REVERT: A  644 LYS cc_start: 0.7391 (pttm) cc_final: 0.7062 (pttm)
  outliers start: 28
  outliers final: 21
  residues processed: 151
  average time/residue: 0.0522
  time to fit residues: 10.8413
Evaluate side-chains
  151 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  608 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   chunk 11 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 6 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 458 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.223228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.201660 restraints weight = 11414.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.206866 restraints weight = 6902.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.208857 restraints weight = 4039.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.209553 restraints weight = 3185.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.211685 restraints weight = 2663.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6085
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5339  Z= 0.151
  Angle     :  0.721   9.494   7253  Z= 0.368
  Chirality :  0.044   0.161    827
  Planarity :  0.005   0.083    917
  Dihedral  :  5.988  55.623    717
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.02 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 21.93 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.33), residues: 665
  helix:  1.03 (0.27), residues: 356
  sheet:  1.56 (0.69), residues: 52
  loop : -2.61 (0.36), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 250 
 TYR   0.016   0.002   TYR A  41 
 PHE   0.023   0.002   PHE A 356 
 TRP   0.010   0.001   TRP A 622 
 HIS   0.010   0.002   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5338)
  covalent geometry    : angle       0.72025 ( 7251)
  SS BOND              : bond        0.00909 (    1)
  SS BOND              : angle       2.22432 (    2)
  hydrogen bonds       : bond        0.05614 (  312)
  hydrogen bonds       : angle       4.83200 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8701 (p) cc_final: 0.8463 (p)
REVERT: A  285 MET cc_start: 0.7438 (ttp) cc_final: 0.7092 (mtp)
REVERT: A  286 PHE cc_start: 0.6859 (m-10) cc_final: 0.6421 (t80)
REVERT: A  301 GLN cc_start: 0.5915 (OUTLIER) cc_final: 0.4424 (tm130)
REVERT: A  558 MET cc_start: 0.5340 (mmp) cc_final: 0.5098 (mmp)
REVERT: A  595 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7853 (tm-30)
REVERT: A  632 ILE cc_start: 0.8795 (mt) cc_final: 0.8541 (mt)
REVERT: A  644 LYS cc_start: 0.7444 (pttm) cc_final: 0.7110 (pttm)
  outliers start: 34
  outliers final: 27
  residues processed: 153
  average time/residue: 0.0565
  time to fit residues: 11.8663
Evaluate side-chains
  154 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  666 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 458 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.221759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.200348 restraints weight = 11339.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.205558 restraints weight = 7032.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.205786 restraints weight = 4316.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.206957 restraints weight = 3784.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.208979 restraints weight = 3019.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.4450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6157
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5339  Z= 0.160
  Angle     :  0.728   8.569   7253  Z= 0.372
  Chirality :  0.045   0.197    827
  Planarity :  0.006   0.081    917
  Dihedral  :  5.996  59.178    717
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.87 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 22.63 %
    Favored  : 70.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.33), residues: 665
  helix:  1.04 (0.27), residues: 356
  sheet:  1.42 (0.69), residues: 52
  loop : -2.53 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 250 
 TYR   0.014   0.002   TYR A  41 
 PHE   0.022   0.002   PHE A 356 
 TRP   0.009   0.001   TRP A 622 
 HIS   0.007   0.002   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5338)
  covalent geometry    : angle       0.72757 ( 7251)
  SS BOND              : bond        0.00331 (    1)
  SS BOND              : angle       0.96392 (    2)
  hydrogen bonds       : bond        0.05691 (  312)
  hydrogen bonds       : angle       4.84488 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 132
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  285 MET cc_start: 0.7525 (ttp) cc_final: 0.7189 (mtp)
REVERT: A  286 PHE cc_start: 0.6858 (m-10) cc_final: 0.6532 (t80)
REVERT: A  301 GLN cc_start: 0.5434 (OUTLIER) cc_final: 0.3929 (tm130)
REVERT: A  499 ASP cc_start: 0.2550 (p0) cc_final: 0.2287 (p0)
REVERT: A  632 ILE cc_start: 0.8842 (mt) cc_final: 0.8594 (mt)
REVERT: A  644 LYS cc_start: 0.7470 (pttm) cc_final: 0.7120 (pttm)
REVERT: A  657 LEU cc_start: 0.7516 (tp) cc_final: 0.7213 (mt)
  outliers start: 37
  outliers final: 31
  residues processed: 151
  average time/residue: 0.0537
  time to fit residues: 11.2183
Evaluate side-chains
  156 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  666 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 54 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 458 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.220615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.198505 restraints weight = 11378.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.203704 restraints weight = 7373.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.206008 restraints weight = 4089.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.206883 restraints weight = 2904.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.207272 restraints weight = 2806.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.4438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6191
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5339  Z= 0.171
  Angle     :  0.765   9.537   7253  Z= 0.389
  Chirality :  0.046   0.171    827
  Planarity :  0.006   0.078    917
  Dihedral  :  6.089  57.854    717
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.77 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 22.98 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.33), residues: 665
  helix:  1.04 (0.27), residues: 356
  sheet:  1.26 (0.67), residues: 52
  loop : -2.51 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 250 
 TYR   0.014   0.002   TYR A  41 
 PHE   0.024   0.002   PHE A  18 
 TRP   0.009   0.002   TRP A  48 
 HIS   0.008   0.002   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5338)
  covalent geometry    : angle       0.76410 ( 7251)
  SS BOND              : bond        0.00714 (    1)
  SS BOND              : angle       1.91018 (    2)
  hydrogen bonds       : bond        0.05859 (  312)
  hydrogen bonds       : angle       4.88119 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 134
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 PHE cc_start: 0.3778 (OUTLIER) cc_final: 0.3439 (m-80)
REVERT: A  285 MET cc_start: 0.7522 (ttp) cc_final: 0.7204 (mtp)
REVERT: A  286 PHE cc_start: 0.6855 (m-10) cc_final: 0.6514 (t80)
REVERT: A  301 GLN cc_start: 0.5658 (OUTLIER) cc_final: 0.4119 (tm130)
REVERT: A  499 ASP cc_start: 0.2712 (p0) cc_final: 0.2450 (p0)
REVERT: A  560 ARG cc_start: 0.6333 (mtt90) cc_final: 0.5938 (ptm160)
REVERT: A  632 ILE cc_start: 0.8866 (mt) cc_final: 0.8621 (mt)
REVERT: A  644 LYS cc_start: 0.7527 (pttm) cc_final: 0.7149 (pttm)
REVERT: A  657 LEU cc_start: 0.7564 (tp) cc_final: 0.7314 (mt)
  outliers start: 37
  outliers final: 31
  residues processed: 150
  average time/residue: 0.0598
  time to fit residues: 12.2483
Evaluate side-chains
  163 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  666 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 458 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.221911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.199963 restraints weight = 11278.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.205128 restraints weight = 7298.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.207956 restraints weight = 4005.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.208577 restraints weight = 2735.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.209062 restraints weight = 2553.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.4456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6141
moved from start:          0.4962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5339  Z= 0.155
  Angle     :  0.766  10.610   7253  Z= 0.384
  Chirality :  0.046   0.176    827
  Planarity :  0.005   0.077    917
  Dihedral  :  6.093  56.565    717
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.47 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 25.26 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.33), residues: 665
  helix:  1.13 (0.27), residues: 353
  sheet:  1.43 (0.69), residues: 52
  loop : -2.58 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 250 
 TYR   0.015   0.002   TYR A 507 
 PHE   0.026   0.002   PHE A 356 
 TRP   0.010   0.002   TRP A 622 
 HIS   0.006   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5338)
  covalent geometry    : angle       0.76495 ( 7251)
  SS BOND              : bond        0.01392 (    1)
  SS BOND              : angle       2.83521 (    2)
  hydrogen bonds       : bond        0.05621 (  312)
  hydrogen bonds       : angle       4.81314 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 PHE cc_start: 0.3664 (OUTLIER) cc_final: 0.3331 (m-80)
REVERT: A  285 MET cc_start: 0.7443 (ttp) cc_final: 0.7115 (mtp)
REVERT: A  286 PHE cc_start: 0.6854 (m-10) cc_final: 0.6238 (t80)
REVERT: A  301 GLN cc_start: 0.5828 (OUTLIER) cc_final: 0.4301 (tm130)
REVERT: A  560 ARG cc_start: 0.6180 (mtt90) cc_final: 0.5906 (ptm160)
REVERT: A  632 ILE cc_start: 0.8784 (mt) cc_final: 0.8508 (mt)
REVERT: A  644 LYS cc_start: 0.7464 (pttm) cc_final: 0.7123 (pttm)
REVERT: A  657 LEU cc_start: 0.7573 (tp) cc_final: 0.7259 (mt)
  outliers start: 31
  outliers final: 26
  residues processed: 151
  average time/residue: 0.0569
  time to fit residues: 11.8661
Evaluate side-chains
  162 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  666 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0050
   chunk 13 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.223165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.201222 restraints weight = 11307.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.206862 restraints weight = 7400.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.208947 restraints weight = 4027.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.209827 restraints weight = 2820.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.210220 restraints weight = 2739.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.4469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6111
moved from start:          0.5168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5339  Z= 0.153
  Angle     :  0.761  11.146   7253  Z= 0.381
  Chirality :  0.046   0.177    827
  Planarity :  0.005   0.076    917
  Dihedral  :  6.030  56.039    717
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.32 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 25.61 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.33), residues: 665
  helix:  1.10 (0.27), residues: 353
  sheet:  1.32 (0.70), residues: 54
  loop : -2.45 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 186 
 TYR   0.014   0.002   TYR A 470 
 PHE   0.016   0.001   PHE A 298 
 TRP   0.012   0.001   TRP A 622 
 HIS   0.005   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5338)
  covalent geometry    : angle       0.76129 ( 7251)
  SS BOND              : bond        0.00432 (    1)
  SS BOND              : angle       1.08293 (    2)
  hydrogen bonds       : bond        0.05353 (  312)
  hydrogen bonds       : angle       4.81299 (  915)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.4546 (OUTLIER) cc_final: 0.4261 (m-80)
REVERT: A  285 MET cc_start: 0.7465 (ttp) cc_final: 0.7211 (mtp)
REVERT: A  286 PHE cc_start: 0.6747 (m-10) cc_final: 0.6358 (t80)
REVERT: A  301 GLN cc_start: 0.5650 (OUTLIER) cc_final: 0.4288 (tm130)
REVERT: A  632 ILE cc_start: 0.8746 (mt) cc_final: 0.8478 (mt)
REVERT: A  644 LYS cc_start: 0.7464 (pttm) cc_final: 0.6574 (pttm)
REVERT: A  657 LEU cc_start: 0.7573 (tp) cc_final: 0.7300 (mt)
  outliers start: 29
  outliers final: 22
  residues processed: 154
  average time/residue: 0.0570
  time to fit residues: 12.1138
Evaluate side-chains
  154 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  625 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0770
   chunk 62 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0970
   chunk 58 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
** A 587 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 = 0.4613 r_free = 0.4613 target = 0.224242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.202182 restraints weight = 11440.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.207499 restraints weight = 7380.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.210069 restraints weight = 4109.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.210839 restraints weight = 2869.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.211146 restraints weight = 2660.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6101
moved from start:          0.5334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5339  Z= 0.151
  Angle     :  0.762  10.013   7253  Z= 0.387
  Chirality :  0.046   0.178    827
  Planarity :  0.005   0.071    917
  Dihedral  :  6.086  55.941    717
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.47 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 27.19 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.33), residues: 665
  helix:  1.07 (0.27), residues: 353
  sheet:  1.25 (0.68), residues: 54
  loop : -2.44 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 186 
 TYR   0.016   0.002   TYR A 507 
 PHE   0.024   0.001   PHE A 356 
 TRP   0.013   0.001   TRP A 622 
 HIS   0.005   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5338)
  covalent geometry    : angle       0.76115 ( 7251)
  SS BOND              : bond        0.00717 (    1)
  SS BOND              : angle       2.38901 (    2)
  hydrogen bonds       : bond        0.05247 (  312)
  hydrogen bonds       : angle       4.79197 (  915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1045.10 seconds
wall clock time: 18 minutes 41.71 seconds (1121.71 seconds total)