Starting phenix.real_space_refine
on Fri Aug 22 14:07:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdp_37142/08_2025/8kdp_37142.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdp_37142/08_2025/8kdp_37142.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdp_37142/08_2025/8kdp_37142.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdp_37142/08_2025/8kdp_37142.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdp_37142/08_2025/8kdp_37142.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdp_37142/08_2025/8kdp_37142.cif"
  }
  resolution = 4.12
  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=   0.002 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    2626      2.51       5
     N     614      2.21       5
     O     656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3918
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 409
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 2, 'TRANS': 49}
    Chain: "B"
      Number of atoms: 3509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3509
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 23, 'TRANS': 430}
          Chain breaks: 1
  Time building chain proxies: 0.97, per 1000 atoms: 0.25
  Number of scatterers: 3918
  At special positions: 0
  Unit cell: (78.2595, 85.932, 79.794, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O     656      8.00
     N     614      7.00
     C    2626      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.14

  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: 0.27
  Conformation dependent library (CDL) restraints added in 125.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      85.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 174
      removed outlier: 3.618A  pdb=" N   LEU A 170 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 207
    Processing helix  chain 'B' and resid 51 through 65
      removed outlier: 4.322A  pdb=" N   GLY B  65 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 72 through 77
      removed outlier: 4.101A  pdb=" N   LEU B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 4.198A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 125
      removed outlier: 3.737A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.549A  pdb=" N   ALA B 129 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.874A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 222
    Processing helix  chain 'B' and resid 239 through 255
      removed outlier: 4.674A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 264
      removed outlier: 3.860A  pdb=" N   LEU B 260 " --> pdb=" O   TRP B 257 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASN B 261 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE B 262 " --> pdb=" O   TYR B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 298
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 310 through 321
      removed outlier: 3.544A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.579A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN B 340 " --> pdb=" O   PHE B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 393 through 399
      removed outlier: 3.802A  pdb=" N   ILE B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASN B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   PHE B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 393 through 399'
    Processing helix  chain 'B' and resid 400 through 422
      removed outlier: 3.942A  pdb=" N   ASN B 404 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS B 420 " --> pdb=" O   ILE B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 454
      removed outlier: 4.888A  pdb=" N   SER B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 466
      removed outlier: 4.053A  pdb=" N   LEU B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 3.869A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.833A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    849 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: 0.58

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 704
        1.33 -     1.47: 1446
        1.47 -     1.60: 1840
        1.60 -     1.74: 0
        1.74 -     1.87: 31
  Bond restraints: 4021
  Sorted by residual:
  bond pdb=" C   ALA B 310 "
       pdb=" O   ALA B 310 "
    ideal  model  delta    sigma   weight residual
    1.235  1.196  0.039 1.26e-02 6.30e+03 9.79e+00
  bond pdb=" C   ARG B 141 "
       pdb=" O   ARG B 141 "
    ideal  model  delta    sigma   weight residual
    1.244  1.213  0.031 1.00e-02 1.00e+04 9.53e+00
  bond pdb=" C   VAL B 166 "
       pdb=" N   PRO B 167 "
    ideal  model  delta    sigma   weight residual
    1.332  1.366 -0.034 1.12e-02 7.97e+03 8.98e+00
  bond pdb=" C   GLY B 114 "
       pdb=" O   GLY B 114 "
    ideal  model  delta    sigma   weight residual
    1.235  1.199  0.036 1.23e-02 6.61e+03 8.45e+00
  bond pdb=" CG  MET A 196 "
       pdb=" SD  MET A 196 "
    ideal  model  delta    sigma   weight residual
    1.803  1.870 -0.067 2.50e-02 1.60e+03 7.25e+00
  ... (remaining 4016 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 4197
        1.85 -     3.69: 1081
        3.69 -     5.54: 188
        5.54 -     7.39: 21
        7.39 -     9.23: 3
  Bond angle restraints: 5490
  Sorted by residual:
  angle pdb=" CA  PHE B 399 "
        pdb=" CB  PHE B 399 "
        pdb=" CG  PHE B 399 "
      ideal   model   delta    sigma   weight residual
     113.80  123.03   -9.23 1.00e+00 1.00e+00 8.52e+01
  angle pdb=" CA  HIS B 319 "
        pdb=" CB  HIS B 319 "
        pdb=" CG  HIS B 319 "
      ideal   model   delta    sigma   weight residual
     113.80  107.02    6.78 1.00e+00 1.00e+00 4.60e+01
  angle pdb=" CA  HIS B 367 "
        pdb=" CB  HIS B 367 "
        pdb=" CG  HIS B 367 "
      ideal   model   delta    sigma   weight residual
     113.80  107.47    6.33 1.00e+00 1.00e+00 4.01e+01
  angle pdb=" CA  ASP B 198 "
        pdb=" CB  ASP B 198 "
        pdb=" CG  ASP B 198 "
      ideal   model   delta    sigma   weight residual
     112.60  118.88   -6.28 1.00e+00 1.00e+00 3.95e+01
  angle pdb=" CA  ASN B  49 "
        pdb=" CB  ASN B  49 "
        pdb=" CG  ASN B  49 "
      ideal   model   delta    sigma   weight residual
     112.60  118.08   -5.48 1.00e+00 1.00e+00 3.00e+01
  ... (remaining 5485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.62: 2147
       17.62 -    35.23: 153
       35.23 -    52.84: 19
       52.84 -    70.45: 4
       70.45 -    88.06: 1
  Dihedral angle restraints: 2324
    sinusoidal: 873
      harmonic: 1451
  Sorted by residual:
  dihedral pdb=" CA  ALA B 310 "
           pdb=" C   ALA B 310 "
           pdb=" N   VAL B 311 "
           pdb=" CA  VAL B 311 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.35  -34.65     0      5.00e+00 4.00e-02 4.80e+01
  dihedral pdb=" CA  PHE B 389 "
           pdb=" C   PHE B 389 "
           pdb=" N   SER B 390 "
           pdb=" CA  SER B 390 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.89  -30.11     0      5.00e+00 4.00e-02 3.63e+01
  dihedral pdb=" CA  VAL B 476 "
           pdb=" C   VAL B 476 "
           pdb=" N   TRP B 477 "
           pdb=" CA  TRP B 477 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.84  -27.16     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 2321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 344
       0.058 -    0.115: 208
       0.115 -    0.173: 88
       0.173 -    0.230: 18
       0.230 -    0.288: 6
  Chirality restraints: 664
  Sorted by residual:
  chirality pdb=" CA  ASP B 116 "
            pdb=" N   ASP B 116 "
            pdb=" C   ASP B 116 "
            pdb=" CB  ASP B 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  TYR B 155 "
            pdb=" N   TYR B 155 "
            pdb=" C   TYR B 155 "
            pdb=" CB  TYR B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  TYR B 387 "
            pdb=" N   TYR B 387 "
            pdb=" C   TYR B 387 "
            pdb=" CB  TYR B 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 661 not shown)

  Planarity restraints: 658
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 399 "    0.034 2.00e-02 2.50e+03   2.05e-02 7.38e+00
        pdb=" CG  PHE B 399 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 399 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 399 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 399 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 399 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 399 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 427 "    0.215 9.50e-02 1.11e+02   9.65e-02 5.85e+00
        pdb=" NE  ARG B 427 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 427 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 427 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 427 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 419 "    0.208 9.50e-02 1.11e+02   9.35e-02 5.46e+00
        pdb=" NE  ARG B 419 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 419 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 419 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 419 "    0.009 2.00e-02 2.50e+03
  ... (remaining 655 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 2206
        3.03 -     3.49: 4342
        3.49 -     3.96: 6262
        3.96 -     4.43: 7198
        4.43 -     4.90: 11259
  Nonbonded interactions: 31267
  Sorted by model distance:
  nonbonded pdb=" O   GLN B 304 "
            pdb=" OG  SER B 308 "
     model   vdw
     2.557 3.040
  nonbonded pdb=" O   VAL B 331 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.575 3.040
  nonbonded pdb=" O   SER B 347 "
            pdb=" OG  SER B 376 "
     model   vdw
     2.613 3.040
  nonbonded pdb=" O   PHE B 233 "
            pdb=" OG1 THR B 236 "
     model   vdw
     2.618 3.040
  nonbonded pdb=" O   SER B 113 "
            pdb=" OG  SER B 113 "
     model   vdw
     2.628 3.040
  ... (remaining 31262 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.030
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.910
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
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      :  0.011   0.106   4022  Z= 0.695
  Angle     :  1.674   9.231   5492  Z= 1.136
  Chirality :  0.083   0.288    664
  Planarity :  0.010   0.097    658
  Dihedral  : 12.569  88.063   1389
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 0.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  6.57 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.32), residues: 500
  helix: -1.28 (0.22), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.69 (0.53), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 427 
 TYR   0.028   0.006   TYR B 146 
 PHE   0.034   0.005   PHE B 399 
 TRP   0.026   0.005   TRP A 193 
 HIS   0.007   0.002   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.01079 ( 4021)
  covalent geometry    : angle       1.67049 ( 5490)
  SS BOND              : bond        0.10559 (    1)
  SS BOND              : angle       5.75406 (    2)
  hydrogen bonds       : bond        0.18447 (  290)
  hydrogen bonds       : angle       7.21159 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.7064 (mtm110) cc_final: 0.6407 (ttt-90)
REVERT: A  206 ARG cc_start: 0.9104 (ttm170) cc_final: 0.8677 (mpt180)
REVERT: B   95 PHE cc_start: 0.7162 (t80) cc_final: 0.6764 (t80)
REVERT: B  112 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7811 (mmmt)
REVERT: B  116 ASP cc_start: 0.8746 (p0) cc_final: 0.8462 (p0)
REVERT: B  120 MET cc_start: 0.9011 (ttm) cc_final: 0.8767 (ttm)
REVERT: B  146 TYR cc_start: 0.8646 (t80) cc_final: 0.8401 (t80)
REVERT: B  293 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8367 (t0)
REVERT: B  297 PHE cc_start: 0.8713 (m-10) cc_final: 0.7923 (m-80)
REVERT: B  309 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8755 (tp30)
REVERT: B  365 MET cc_start: 0.8812 (mmt) cc_final: 0.8497 (mmm)
REVERT: B  472 TYR cc_start: 0.8156 (t80) cc_final: 0.7762 (t80)
REVERT: B  501 GLN cc_start: 0.8554 (tt0) cc_final: 0.7502 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0518
  time to fit residues: 11.4062
Evaluate side-chains
  126 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
B 145 GLN
** B 197 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 = 0.3250 r_free = 0.3250 target = 0.096402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.078139 restraints weight = 8959.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.081091 restraints weight = 4750.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.083161 restraints weight = 3066.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.084503 restraints weight = 2268.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.085274 restraints weight = 1850.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4022  Z= 0.159
  Angle     :  0.657   5.909   5492  Z= 0.340
  Chirality :  0.045   0.208    664
  Planarity :  0.004   0.027    658
  Dihedral  :  5.346  22.923    533
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  3.52 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.38), residues: 500
  helix:  1.21 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.25 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 195 
 TYR   0.016   0.002   TYR B 155 
 PHE   0.027   0.002   PHE B 399 
 TRP   0.018   0.002   TRP B 477 
 HIS   0.008   0.002   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4021)
  covalent geometry    : angle       0.65645 ( 5490)
  SS BOND              : bond        0.00296 (    1)
  SS BOND              : angle       1.26328 (    2)
  hydrogen bonds       : bond        0.05151 (  290)
  hydrogen bonds       : angle       4.50553 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 145
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.8463 (mp0) cc_final: 0.8159 (mp0)
REVERT: A  182 ARG cc_start: 0.7980 (mtm110) cc_final: 0.6666 (ttt-90)
REVERT: B  120 MET cc_start: 0.8862 (ttm) cc_final: 0.8517 (ttm)
REVERT: B  146 TYR cc_start: 0.8538 (t80) cc_final: 0.8262 (t80)
REVERT: B  249 SER cc_start: 0.8810 (m) cc_final: 0.8543 (t)
REVERT: B  365 MET cc_start: 0.8669 (mmt) cc_final: 0.7755 (mmm)
REVERT: B  410 LEU cc_start: 0.8518 (mt) cc_final: 0.8275 (mp)
REVERT: B  474 PHE cc_start: 0.8453 (t80) cc_final: 0.8211 (t80)
REVERT: B  501 GLN cc_start: 0.7870 (tt0) cc_final: 0.7359 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0522
  time to fit residues: 9.6739
Evaluate side-chains
  114 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0070
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.9202

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

Flipped N/Q/H residues before XYZ refinement:
B 186 ASN
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN
B 304 GLN
** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.099255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.081589 restraints weight = 8463.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.084486 restraints weight = 4395.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.086523 restraints weight = 2797.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.087813 restraints weight = 2058.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.088878 restraints weight = 1671.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.4083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4022  Z= 0.137
  Angle     :  0.629   7.078   5492  Z= 0.316
  Chirality :  0.043   0.166    664
  Planarity :  0.004   0.031    658
  Dihedral  :  4.776  17.861    533
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.05 %
    Favored  : 96.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.39), residues: 500
  helix:  1.91 (0.28), residues: 368
  sheet:  None (None), residues: 0
  loop : -0.38 (0.56), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 348 
 TYR   0.022   0.001   TYR B 103 
 PHE   0.021   0.002   PHE A 189 
 TRP   0.011   0.001   TRP B 477 
 HIS   0.003   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4021)
  covalent geometry    : angle       0.62869 ( 5490)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       1.04641 (    2)
  hydrogen bonds       : bond        0.04449 (  290)
  hydrogen bonds       : angle       4.13341 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.7989 (mtm110) cc_final: 0.6737 (ttt-90)
REVERT: A  187 LEU cc_start: 0.7821 (mm) cc_final: 0.7425 (mm)
REVERT: B  120 MET cc_start: 0.8793 (ttm) cc_final: 0.8506 (ttm)
REVERT: B  146 TYR cc_start: 0.8449 (t80) cc_final: 0.8234 (t80)
REVERT: B  168 GLU cc_start: 0.7764 (pm20) cc_final: 0.7394 (pm20)
REVERT: B  362 ILE cc_start: 0.8868 (tp) cc_final: 0.8549 (tp)
REVERT: B  365 MET cc_start: 0.8582 (mmt) cc_final: 0.7621 (mmm)
REVERT: B  410 LEU cc_start: 0.8663 (mt) cc_final: 0.8450 (mp)
REVERT: B  501 GLN cc_start: 0.7594 (tt0) cc_final: 0.7328 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0519
  time to fit residues: 9.0081
Evaluate side-chains
  105 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B  49 ASN
** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 497 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 = 0.3312 r_free = 0.3312 target = 0.100072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.082417 restraints weight = 8504.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.085285 restraints weight = 4404.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.087300 restraints weight = 2805.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.088259 restraints weight = 2053.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.089305 restraints weight = 1720.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4022  Z= 0.134
  Angle     :  0.606   6.904   5492  Z= 0.302
  Chirality :  0.042   0.172    664
  Planarity :  0.004   0.030    658
  Dihedral  :  4.635  18.371    533
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  2.11 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.39), residues: 500
  helix:  1.86 (0.28), residues: 368
  sheet:  None (None), residues: 0
  loop : -0.23 (0.59), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 427 
 TYR   0.011   0.001   TYR B 103 
 PHE   0.024   0.002   PHE B 451 
 TRP   0.009   0.001   TRP B 477 
 HIS   0.005   0.002   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4021)
  covalent geometry    : angle       0.60605 ( 5490)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.98541 (    2)
  hydrogen bonds       : bond        0.04127 (  290)
  hydrogen bonds       : angle       4.08370 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.8023 (mtm110) cc_final: 0.6757 (ttt-90)
REVERT: A  187 LEU cc_start: 0.7911 (mm) cc_final: 0.7397 (mm)
REVERT: B  120 MET cc_start: 0.8699 (ttm) cc_final: 0.8306 (ttm)
REVERT: B  146 TYR cc_start: 0.8508 (t80) cc_final: 0.8270 (t80)
REVERT: B  173 LEU cc_start: 0.9056 (tp) cc_final: 0.8778 (tp)
REVERT: B  178 CYS cc_start: 0.8651 (t) cc_final: 0.8432 (t)
REVERT: B  365 MET cc_start: 0.8580 (mmt) cc_final: 0.7803 (mmm)
REVERT: B  407 CYS cc_start: 0.8147 (m) cc_final: 0.7806 (t)
REVERT: B  410 LEU cc_start: 0.8660 (mt) cc_final: 0.8453 (mp)
REVERT: B  501 GLN cc_start: 0.7752 (tt0) cc_final: 0.7256 (mp10)
  outliers start: 2
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0511
  time to fit residues: 8.8332
Evaluate side-chains
  108 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:   20.0000
   chunk 42 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
B  49 ASN
** B 197 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 = 0.3295 r_free = 0.3295 target = 0.099354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.081565 restraints weight = 8606.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.084460 restraints weight = 4488.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.086386 restraints weight = 2876.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.087853 restraints weight = 2126.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.088846 restraints weight = 1715.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4022  Z= 0.139
  Angle     :  0.604   7.297   5492  Z= 0.301
  Chirality :  0.043   0.173    664
  Planarity :  0.004   0.030    658
  Dihedral  :  4.611  18.462    533
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.17 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.39), residues: 500
  helix:  1.86 (0.28), residues: 368
  sheet:  None (None), residues: 0
  loop : -0.27 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.011   0.001   TYR B 289 
 PHE   0.023   0.002   PHE B 451 
 TRP   0.024   0.001   TRP B 477 
 HIS   0.005   0.002   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4021)
  covalent geometry    : angle       0.60390 ( 5490)
  SS BOND              : bond        0.00504 (    1)
  SS BOND              : angle       1.10439 (    2)
  hydrogen bonds       : bond        0.04150 (  290)
  hydrogen bonds       : angle       4.01599 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.8135 (mtm110) cc_final: 0.6734 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8083 (mm) cc_final: 0.7612 (mm)
REVERT: B  120 MET cc_start: 0.8400 (ttm) cc_final: 0.8063 (ttm)
REVERT: B  249 SER cc_start: 0.8829 (m) cc_final: 0.8541 (t)
REVERT: B  254 TYR cc_start: 0.7487 (m-80) cc_final: 0.7001 (m-80)
REVERT: B  365 MET cc_start: 0.8519 (mmt) cc_final: 0.7796 (mmm)
REVERT: B  407 CYS cc_start: 0.8154 (m) cc_final: 0.7752 (t)
REVERT: B  415 MET cc_start: 0.8084 (ttt) cc_final: 0.7370 (ttt)
REVERT: B  501 GLN cc_start: 0.7772 (tt0) cc_final: 0.7278 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0553
  time to fit residues: 9.1088
Evaluate side-chains
  104 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0980
   chunk 2 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B  49 ASN
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 HIS
** B 497 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 = 0.3314 r_free = 0.3314 target = 0.100706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.083310 restraints weight = 8409.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.086079 restraints weight = 4326.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.088157 restraints weight = 2773.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.089444 restraints weight = 2034.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.090553 restraints weight = 1649.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4022  Z= 0.121
  Angle     :  0.598   8.705   5492  Z= 0.293
  Chirality :  0.042   0.155    664
  Planarity :  0.004   0.030    658
  Dihedral  :  4.443  17.798    533
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.41 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.39), residues: 500
  helix:  1.86 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop : -0.29 (0.57), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 348 
 TYR   0.010   0.001   TYR B 103 
 PHE   0.022   0.001   PHE B 451 
 TRP   0.019   0.001   TRP B 477 
 HIS   0.003   0.001   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4021)
  covalent geometry    : angle       0.59811 ( 5490)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       1.02358 (    2)
  hydrogen bonds       : bond        0.03803 (  290)
  hydrogen bonds       : angle       3.96080 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.8115 (mtm110) cc_final: 0.6898 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8262 (mm) cc_final: 0.7894 (mm)
REVERT: B  120 MET cc_start: 0.8350 (ttm) cc_final: 0.7942 (ttm)
REVERT: B  178 CYS cc_start: 0.8752 (t) cc_final: 0.8533 (t)
REVERT: B  213 LEU cc_start: 0.8534 (pp) cc_final: 0.8190 (mt)
REVERT: B  249 SER cc_start: 0.8856 (m) cc_final: 0.8536 (t)
REVERT: B  254 TYR cc_start: 0.7788 (m-80) cc_final: 0.7363 (m-80)
REVERT: B  305 MET cc_start: 0.8137 (mmm) cc_final: 0.7795 (mmt)
REVERT: B  365 MET cc_start: 0.8498 (mmt) cc_final: 0.7802 (mmm)
REVERT: B  417 TRP cc_start: 0.7114 (t60) cc_final: 0.6892 (t60)
REVERT: B  501 GLN cc_start: 0.7913 (tt0) cc_final: 0.7276 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0556
  time to fit residues: 9.1654
Evaluate side-chains
  104 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0570
   chunk 19 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
B  49 ASN
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 HIS
** B 497 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 = 0.3334 r_free = 0.3334 target = 0.101505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.084084 restraints weight = 8721.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.086924 restraints weight = 4409.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.088982 restraints weight = 2782.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.090315 restraints weight = 2034.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.091403 restraints weight = 1642.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4022  Z= 0.125
  Angle     :  0.621   7.717   5492  Z= 0.307
  Chirality :  0.042   0.145    664
  Planarity :  0.004   0.031    658
  Dihedral  :  4.571  18.824    533
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.70 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.38), residues: 500
  helix:  1.87 (0.28), residues: 369
  sheet:  None (None), residues: 0
  loop : -0.40 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 209 
 TYR   0.016   0.001   TYR B 146 
 PHE   0.022   0.001   PHE A 189 
 TRP   0.016   0.001   TRP B 477 
 HIS   0.002   0.001   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4021)
  covalent geometry    : angle       0.61625 ( 5490)
  SS BOND              : bond        0.00395 (    1)
  SS BOND              : angle       3.91229 (    2)
  hydrogen bonds       : bond        0.03699 (  290)
  hydrogen bonds       : angle       3.92656 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.8018 (mtm110) cc_final: 0.6832 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8309 (mm) cc_final: 0.7868 (mm)
REVERT: B  120 MET cc_start: 0.8464 (ttm) cc_final: 0.8120 (ttm)
REVERT: B  146 TYR cc_start: 0.8556 (t80) cc_final: 0.8355 (t80)
REVERT: B  213 LEU cc_start: 0.8497 (pp) cc_final: 0.8205 (mt)
REVERT: B  249 SER cc_start: 0.8853 (m) cc_final: 0.8533 (t)
REVERT: B  254 TYR cc_start: 0.7723 (m-80) cc_final: 0.7306 (m-80)
REVERT: B  305 MET cc_start: 0.8200 (mmm) cc_final: 0.7785 (mmt)
REVERT: B  365 MET cc_start: 0.8517 (mmt) cc_final: 0.7784 (mmm)
REVERT: B  407 CYS cc_start: 0.7757 (t) cc_final: 0.7529 (t)
REVERT: B  417 TRP cc_start: 0.6744 (t60) cc_final: 0.6521 (t60)
REVERT: B  501 GLN cc_start: 0.8055 (tt0) cc_final: 0.7286 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0516
  time to fit residues: 8.5850
Evaluate side-chains
  103 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0870
   chunk 23 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
B  49 ASN
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 HIS
** B 497 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 = 0.3324 r_free = 0.3324 target = 0.101342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.084406 restraints weight = 8622.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.087212 restraints weight = 4440.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.089059 restraints weight = 2813.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.090567 restraints weight = 2074.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.091329 restraints weight = 1656.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.5606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4022  Z= 0.119
  Angle     :  0.605   7.416   5492  Z= 0.294
  Chirality :  0.042   0.136    664
  Planarity :  0.004   0.032    658
  Dihedral  :  4.414  17.294    533
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.70 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.39), residues: 500
  helix:  1.83 (0.28), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.56 (0.55), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 209 
 TYR   0.013   0.001   TYR B 146 
 PHE   0.022   0.001   PHE A 189 
 TRP   0.015   0.001   TRP B 477 
 HIS   0.002   0.001   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4021)
  covalent geometry    : angle       0.60403 ( 5490)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       1.79457 (    2)
  hydrogen bonds       : bond        0.03499 (  290)
  hydrogen bonds       : angle       3.88288 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  165 SER cc_start: 0.7721 (m) cc_final: 0.7494 (m)
REVERT: A  182 ARG cc_start: 0.7831 (mtm110) cc_final: 0.6867 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8182 (mm) cc_final: 0.7726 (mm)
REVERT: A  209 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7494 (mtt180)
REVERT: B  146 TYR cc_start: 0.8596 (t80) cc_final: 0.8379 (t80)
REVERT: B  173 LEU cc_start: 0.9038 (tp) cc_final: 0.8793 (tp)
REVERT: B  213 LEU cc_start: 0.8551 (pp) cc_final: 0.8244 (mt)
REVERT: B  249 SER cc_start: 0.8852 (m) cc_final: 0.8543 (t)
REVERT: B  254 TYR cc_start: 0.7774 (m-80) cc_final: 0.7479 (m-80)
REVERT: B  305 MET cc_start: 0.8182 (mmm) cc_final: 0.7804 (mmt)
REVERT: B  365 MET cc_start: 0.8480 (mmt) cc_final: 0.7765 (mmm)
REVERT: B  384 THR cc_start: 0.8943 (m) cc_final: 0.8471 (p)
REVERT: B  407 CYS cc_start: 0.7725 (t) cc_final: 0.7482 (t)
REVERT: B  417 TRP cc_start: 0.6455 (t60) cc_final: 0.6240 (t60)
REVERT: B  501 GLN cc_start: 0.8115 (tt0) cc_final: 0.7332 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0542
  time to fit residues: 9.2811
Evaluate side-chains
  108 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 42 optimal weight:   30.0000
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  49 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.084204 restraints weight = 8831.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.087064 restraints weight = 4557.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.088930 restraints weight = 2905.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.090469 restraints weight = 2140.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.091273 restraints weight = 1700.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.5655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4022  Z= 0.124
  Angle     :  0.618   7.415   5492  Z= 0.306
  Chirality :  0.042   0.141    664
  Planarity :  0.004   0.035    658
  Dihedral  :  4.446  17.083    533
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.00 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.38), residues: 500
  helix:  1.83 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.60 (0.55), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 209 
 TYR   0.015   0.001   TYR B 103 
 PHE   0.019   0.001   PHE A 189 
 TRP   0.033   0.001   TRP B 477 
 HIS   0.006   0.002   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4021)
  covalent geometry    : angle       0.61733 ( 5490)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       1.66634 (    2)
  hydrogen bonds       : bond        0.03509 (  290)
  hydrogen bonds       : angle       3.85039 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.7819 (mtm110) cc_final: 0.6694 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8127 (mm) cc_final: 0.7646 (mm)
REVERT: A  209 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7894 (mmm160)
REVERT: B  173 LEU cc_start: 0.9069 (tp) cc_final: 0.8778 (tp)
REVERT: B  197 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7545 (tm-30)
REVERT: B  213 LEU cc_start: 0.8511 (pp) cc_final: 0.8238 (mt)
REVERT: B  249 SER cc_start: 0.8861 (m) cc_final: 0.8530 (t)
REVERT: B  254 TYR cc_start: 0.7750 (m-80) cc_final: 0.7471 (m-80)
REVERT: B  305 MET cc_start: 0.8179 (mmm) cc_final: 0.7797 (mmt)
REVERT: B  365 MET cc_start: 0.8358 (mmt) cc_final: 0.7562 (mmm)
REVERT: B  384 THR cc_start: 0.8940 (m) cc_final: 0.8472 (p)
REVERT: B  407 CYS cc_start: 0.7796 (t) cc_final: 0.7565 (t)
REVERT: B  501 GLN cc_start: 0.8140 (tt0) cc_final: 0.7218 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0468
  time to fit residues: 7.9793
Evaluate side-chains
  106 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0770
   chunk 4 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7942

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.101920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.084998 restraints weight = 8821.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.087872 restraints weight = 4524.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.089932 restraints weight = 2872.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.091302 restraints weight = 2087.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.091982 restraints weight = 1673.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.5748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4022  Z= 0.121
  Angle     :  0.611   7.393   5492  Z= 0.300
  Chirality :  0.042   0.149    664
  Planarity :  0.004   0.034    658
  Dihedral  :  4.322  17.086    533
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.38), residues: 500
  helix:  1.82 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.73 (0.54), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 209 
 TYR   0.017   0.001   TYR B 103 
 PHE   0.019   0.001   PHE A 189 
 TRP   0.034   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4021)
  covalent geometry    : angle       0.61047 ( 5490)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       1.45787 (    2)
  hydrogen bonds       : bond        0.03463 (  290)
  hydrogen bonds       : angle       3.81840 (  849)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  182 ARG cc_start: 0.7824 (mtm110) cc_final: 0.6694 (ttt-90)
REVERT: A  187 LEU cc_start: 0.8252 (mm) cc_final: 0.7817 (mm)
REVERT: B  197 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: B  213 LEU cc_start: 0.8501 (pp) cc_final: 0.8222 (mt)
REVERT: B  218 GLN cc_start: 0.8578 (tp40) cc_final: 0.8293 (tp40)
REVERT: B  249 SER cc_start: 0.8863 (m) cc_final: 0.8520 (t)
REVERT: B  254 TYR cc_start: 0.7784 (m-80) cc_final: 0.7510 (m-80)
REVERT: B  305 MET cc_start: 0.8165 (mmm) cc_final: 0.7908 (mmm)
REVERT: B  365 MET cc_start: 0.8382 (mmt) cc_final: 0.7655 (mmm)
REVERT: B  384 THR cc_start: 0.8898 (m) cc_final: 0.8464 (p)
REVERT: B  407 CYS cc_start: 0.7822 (t) cc_final: 0.7588 (t)
REVERT: B  501 GLN cc_start: 0.8162 (tt0) cc_final: 0.7198 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0464
  time to fit residues: 7.3095
Evaluate side-chains
  105 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.099729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.083612 restraints weight = 8680.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.086225 restraints weight = 4510.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.088217 restraints weight = 2881.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.089594 restraints weight = 2102.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.090410 restraints weight = 1681.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.5755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4022  Z= 0.136
  Angle     :  0.625   7.342   5492  Z= 0.312
  Chirality :  0.043   0.178    664
  Planarity :  0.004   0.034    658
  Dihedral  :  4.445  18.007    533
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.38), residues: 500
  helix:  1.77 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -0.93 (0.53), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 209 
 TYR   0.020   0.001   TYR B 103 
 PHE   0.020   0.002   PHE A 189 
 TRP   0.033   0.002   TRP B 477 
 HIS   0.005   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4021)
  covalent geometry    : angle       0.62422 ( 5490)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       1.64941 (    2)
  hydrogen bonds       : bond        0.03691 (  290)
  hydrogen bonds       : angle       3.84948 (  849)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 654.35 seconds
wall clock time: 11 minutes 58.91 seconds (718.91 seconds total)