Starting phenix.real_space_refine
on Wed Sep 17 05:39:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o9t_70262/09_2025/9o9t_70262.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o9t_70262/09_2025/9o9t_70262.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o9t_70262/09_2025/9o9t_70262.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o9t_70262/09_2025/9o9t_70262.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o9t_70262/09_2025/9o9t_70262.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o9t_70262/09_2025/9o9t_70262.map"
  }
  resolution = 3.31
  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=  -0.030 sd=   0.905
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      18      5.16       5
     C    3374      2.51       5
     N     865      2.21       5
     O     965      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5222
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1862
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
    Chain: "A"
      Number of atoms: 3360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3360
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 25, 'TRANS': 406}
          Chain breaks: 1
  Time building chain proxies: 1.47, per 1000 atoms: 0.28
  Number of scatterers: 5222
  At special positions: 0
  Unit cell: (67.158, 98.892, 116.604, 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      18     16.00
     O     965      8.00
     N     865      7.00
     C    3374      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 141.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1246

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      65.1% alpha, 9.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 43 through 61
      removed outlier: 3.701A  pdb=" N   ILE B  47 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ALA B  58 " --> pdb=" O   CYS B  54 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   ASP B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 67
      removed outlier: 5.986A  pdb=" N   GLU B  65 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 85
    Processing helix  chain 'B' and resid 93 through 137
    Processing helix  chain 'B' and resid 138 through 149
    Processing helix  chain 'B' and resid 161 through 170
      removed outlier: 3.518A  pdb=" N   LEU B 165 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 181
    Processing helix  chain 'B' and resid 194 through 202
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 227 through 236
      removed outlier: 3.937A  pdb=" N   TRP B 235 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 247
    Processing helix  chain 'B' and resid 260 through 269
    Processing helix  chain 'B' and resid 270 through 281
    Processing helix  chain 'A' and resid 25 through 45
      Proline residue:  A  30  - end of helix
      Proline residue:  A  37  - end of helix
      removed outlier: 4.163A  pdb=" N   LYS A  45 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 73
    Processing helix  chain 'A' and resid 77 through 94
    Processing helix  chain 'A' and resid 138 through 153
    Processing helix  chain 'A' and resid 164 through 174
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 3.570A  pdb=" N   TYR A 192 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 211
      removed outlier: 3.550A  pdb=" N   LEU A 211 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 218
    Processing helix  chain 'A' and resid 252 through 263
      removed outlier: 4.758A  pdb=" N   ALA A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 287
      removed outlier: 3.779A  pdb=" N   THR A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      Proline residue:  A 281  - end of helix
      removed outlier: 4.475A  pdb=" N   ASP A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLY A 287 " --> pdb=" O   ILE A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
      removed outlier: 4.419A  pdb=" N   ASP A 306 " --> pdb=" O   VAL A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 303 through 306'
    Processing helix  chain 'A' and resid 307 through 323
    Processing helix  chain 'A' and resid 331 through 341
    Processing helix  chain 'A' and resid 350 through 352
      No H-bonds generated for 'chain 'A' and resid 350 through 352'
    Processing helix  chain 'A' and resid 353 through 360
      removed outlier: 3.532A  pdb=" N   ILE A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 405
    Processing helix  chain 'A' and resid 408 through 419
    Processing helix  chain 'A' and resid 426 through 435
      removed outlier: 4.066A  pdb=" N   LYS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
    Processing helix  chain 'A' and resid 457 through 474
    Processing helix  chain 'A' and resid 478 through 487
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 160
      removed outlier: 6.173A  pdb=" N   LEU A 129 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   GLU A 160 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   ILE A 131 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   GLY A 382 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   VAL A 232 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LEU A 384 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160
      removed outlier: 6.173A  pdb=" N   LEU A 129 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   GLU A 160 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   ILE A 131 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221
    Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 269
      removed outlier: 6.037A  pdb=" N   ALA A 268 " --> pdb=" O   MET A 346 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   ILE A 348 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ALA A 345 " --> pdb=" O   ASN A 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294

    311 hydrogen bonds defined for protein.
    906 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: 0.80

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1677
        1.34 -     1.46: 1014
        1.46 -     1.58: 2627
        1.58 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 5350
  Sorted by residual:
  bond pdb=" C   LEU A  36 "
       pdb=" N   PRO A  37 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 1.51e-02 4.39e+03 6.06e+00
  bond pdb=" CA  LEU A  36 "
       pdb=" C   LEU A  36 "
    ideal  model  delta    sigma   weight residual
    1.521  1.535 -0.013 1.08e-02 8.57e+03 1.52e+00
  bond pdb=" CB  ASP A 302 "
       pdb=" CG  ASP A 302 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.35e+00
  bond pdb=" CB  PHE B 102 "
       pdb=" CG  PHE B 102 "
    ideal  model  delta    sigma   weight residual
    1.502  1.526 -0.024 2.30e-02 1.89e+03 1.05e+00
  bond pdb=" CB  VAL B 175 "
       pdb=" CG1 VAL B 175 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 9.84e-01
  ... (remaining 5345 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 7131
        1.50 -     3.00: 111
        3.00 -     4.49: 19
        4.49 -     5.99: 8
        5.99 -     7.49: 1
  Bond angle restraints: 7270
  Sorted by residual:
  angle pdb=" C   ASP A 302 "
        pdb=" CA  ASP A 302 "
        pdb=" CB  ASP A 302 "
      ideal   model   delta    sigma   weight residual
     109.75  115.71   -5.96 1.65e+00 3.67e-01 1.30e+01
  angle pdb=" CA  ASP A 302 "
        pdb=" CB  ASP A 302 "
        pdb=" CG  ASP A 302 "
      ideal   model   delta    sigma   weight residual
     112.60  115.84   -3.24 1.00e+00 1.00e+00 1.05e+01
  angle pdb=" CA  PRO A  37 "
        pdb=" N   PRO A  37 "
        pdb=" CD  PRO A  37 "
      ideal   model   delta    sigma   weight residual
     112.00  107.48    4.52 1.40e+00 5.10e-01 1.04e+01
  angle pdb=" C   GLU A 294 "
        pdb=" N   ASN A 295 "
        pdb=" CA  ASN A 295 "
      ideal   model   delta    sigma   weight residual
     121.54  126.82   -5.28 1.91e+00 2.74e-01 7.63e+00
  angle pdb=" CB  ASP A 302 "
        pdb=" CG  ASP A 302 "
        pdb=" OD1 ASP A 302 "
      ideal   model   delta    sigma   weight residual
     118.40  124.15   -5.75 2.30e+00 1.89e-01 6.26e+00
  ... (remaining 7265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 2717
       17.84 -    35.69: 333
       35.69 -    53.53: 75
       53.53 -    71.38: 20
       71.38 -    89.22: 8
  Dihedral angle restraints: 3153
    sinusoidal: 1213
      harmonic: 1940
  Sorted by residual:
  dihedral pdb=" CA  PHE A  66 "
           pdb=" C   PHE A  66 "
           pdb=" N   MET A  67 "
           pdb=" CA  MET A  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.28   17.72     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CB  GLU A 396 "
           pdb=" CG  GLU A 396 "
           pdb=" CD  GLU A 396 "
           pdb=" OE1 GLU A 396 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.22   89.22     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU A 167 "
           pdb=" CG  GLU A 167 "
           pdb=" CD  GLU A 167 "
           pdb=" OE1 GLU A 167 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.23   88.23     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 3150 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 497
       0.028 -    0.057: 205
       0.057 -    0.085: 53
       0.085 -    0.114: 35
       0.114 -    0.142: 12
  Chirality restraints: 802
  Sorted by residual:
  chirality pdb=" CA  PRO A  37 "
            pdb=" N   PRO A  37 "
            pdb=" C   PRO A  37 "
            pdb=" CB  PRO A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.04e-01
  chirality pdb=" CA  LEU A  36 "
            pdb=" N   LEU A  36 "
            pdb=" C   LEU A  36 "
            pdb=" CB  LEU A  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CA  PRO A  30 "
            pdb=" N   PRO A  30 "
            pdb=" C   PRO A  30 "
            pdb=" CB  PRO A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 799 not shown)

  Planarity restraints: 933
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  36 "    0.058 5.00e-02 4.00e+02   8.70e-02 1.21e+01
        pdb=" N   PRO A  37 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A  37 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A  37 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  29 "    0.048 5.00e-02 4.00e+02   7.23e-02 8.36e+00
        pdb=" N   PRO A  30 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A  30 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A  30 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 302 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.98e+00
        pdb=" C   ASP A 302 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ASP A 302 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL A 303 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 930 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 70
        2.65 -     3.21: 4950
        3.21 -     3.78: 8233
        3.78 -     4.34: 11235
        4.34 -     4.90: 18481
  Nonbonded interactions: 42969
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  85 "
            pdb=" OD1 ASN A  77 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OH  TYR A 192 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OE1 GLN A 194 "
            pdb=" OH  TYR A 221 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   TYR A 212 "
            pdb=" OG1 THR A 215 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OD1 ASP A 217 "
            pdb=" NH2 ARG A 220 "
     model   vdw
     2.302 3.120
  ... (remaining 42964 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.440
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
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      :  0.003   0.037   5350  Z= 0.137
  Angle     :  0.512   7.490   7270  Z= 0.275
  Chirality :  0.039   0.142    802
  Planarity :  0.005   0.087    933
  Dihedral  : 17.172  89.222   1907
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 24.30 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.33), residues: 668
  helix:  1.17 (0.25), residues: 405
  sheet: -0.27 (1.06), residues: 25
  loop : -0.07 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 128 
 TYR   0.011   0.001   TYR B 168 
 PHE   0.012   0.001   PHE A 149 
 TRP   0.009   0.001   TRP A 184 
 HIS   0.002   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5350)
  covalent geometry    : angle       0.51161 ( 7270)
  hydrogen bonds       : bond        0.13181 (  304)
  hydrogen bonds       : angle       6.15037 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: B  117 TYR cc_start: 0.8301 (t80) cc_final: 0.8055 (t80)
REVERT: B  168 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8455 (t80)
REVERT: B  193 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8557 (m-10)
REVERT: B  212 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7518 (pt)
REVERT: B  221 MET cc_start: 0.8533 (mtt) cc_final: 0.8260 (mtm)
REVERT: A   55 MET cc_start: 0.7729 (tpp) cc_final: 0.7159 (tpp)
REVERT: A   88 GLU cc_start: 0.6195 (tm-30) cc_final: 0.5879 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 77
  average time/residue: 0.0618
  time to fit residues: 6.3835
Evaluate side-chains
  76 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  380 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0670
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.162000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.131706 restraints weight = 6068.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.55
r_work: 0.3259 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.0754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5350  Z= 0.124
  Angle     :  0.506   8.673   7270  Z= 0.268
  Chirality :  0.040   0.144    802
  Planarity :  0.005   0.091    933
  Dihedral  :  6.948  51.250    738
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 24.49 %
    Favored  : 71.78 %
  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:  1.44 (0.33), residues: 668
  helix:  1.66 (0.25), residues: 406
  sheet: -0.18 (1.04), residues: 25
  loop : -0.04 (0.43), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 438 
 TYR   0.012   0.001   TYR B 168 
 PHE   0.012   0.001   PHE A 149 
 TRP   0.007   0.001   TRP A 354 
 HIS   0.003   0.000   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5350)
  covalent geometry    : angle       0.50594 ( 7270)
  hydrogen bonds       : bond        0.03941 (  304)
  hydrogen bonds       : angle       4.50965 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.132 
Fit side-chains
REVERT: B   89 ILE cc_start: 0.3990 (OUTLIER) cc_final: 0.3788 (pt)
REVERT: B  112 PHE cc_start: 0.8183 (t80) cc_final: 0.7656 (t80)
REVERT: B  117 TYR cc_start: 0.8323 (t80) cc_final: 0.7996 (t80)
REVERT: B  140 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7751 (p0)
REVERT: B  157 ASN cc_start: 0.7866 (m110) cc_final: 0.7645 (t0)
REVERT: B  168 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8505 (t80)
REVERT: B  212 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7441 (pt)
REVERT: B  221 MET cc_start: 0.8469 (mtt) cc_final: 0.8199 (mtm)
REVERT: A   55 MET cc_start: 0.7695 (tpp) cc_final: 0.7247 (tpp)
  outliers start: 20
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0728
  time to fit residues: 7.6260
Evaluate side-chains
  75 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  140 ASP
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   33 ASN
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue  168 LYS
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 46 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0980
   chunk 27 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.158771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127972 restraints weight = 6002.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 1.63
r_work: 0.3271 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5350  Z= 0.111
  Angle     :  0.495   9.397   7270  Z= 0.255
  Chirality :  0.039   0.139    802
  Planarity :  0.005   0.094    933
  Dihedral  :  5.770  54.321    721
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 22.99 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.33), residues: 668
  helix:  1.83 (0.25), residues: 406
  sheet: -0.15 (1.04), residues: 25
  loop :  0.01 (0.43), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 438 
 TYR   0.011   0.001   TYR B 168 
 PHE   0.018   0.001   PHE B  97 
 TRP   0.006   0.001   TRP A  34 
 HIS   0.001   0.000   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5350)
  covalent geometry    : angle       0.49511 ( 7270)
  hydrogen bonds       : bond        0.03694 (  304)
  hydrogen bonds       : angle       4.18340 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.194 
Fit side-chains
REVERT: B  112 PHE cc_start: 0.8160 (t80) cc_final: 0.7660 (t80)
REVERT: B  117 TYR cc_start: 0.8376 (t80) cc_final: 0.8134 (t80)
REVERT: B  157 ASN cc_start: 0.7999 (m110) cc_final: 0.7708 (t0)
REVERT: B  168 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8535 (t80)
REVERT: B  193 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8538 (m-10)
REVERT: B  212 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7488 (pt)
REVERT: A   55 MET cc_start: 0.7774 (tpp) cc_final: 0.7249 (tpp)
  outliers start: 24
  outliers final: 10
  residues processed: 91
  average time/residue: 0.0810
  time to fit residues: 9.5842
Evaluate side-chains
  75 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 445 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.151631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.121179 restraints weight = 6170.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.47
r_work: 0.3143 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   5350  Z= 0.249
  Angle     :  0.601   9.001   7270  Z= 0.315
  Chirality :  0.046   0.180    802
  Planarity :  0.006   0.094    933
  Dihedral  :  5.832  51.260    719
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 23.55 %
    Favored  : 71.78 %
  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:  1.18 (0.32), residues: 668
  helix:  1.37 (0.25), residues: 413
  sheet: -0.86 (0.93), residues: 25
  loop :  0.05 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 188 
 TYR   0.018   0.002   TYR B 168 
 PHE   0.018   0.002   PHE A 149 
 TRP   0.009   0.001   TRP A 280 
 HIS   0.004   0.001   HIS B 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 5350)
  covalent geometry    : angle       0.60094 ( 7270)
  hydrogen bonds       : bond        0.04663 (  304)
  hydrogen bonds       : angle       4.56816 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.235 
Fit side-chains
REVERT: B  112 PHE cc_start: 0.8183 (t80) cc_final: 0.7723 (t80)
REVERT: B  117 TYR cc_start: 0.8464 (t80) cc_final: 0.8065 (t80)
REVERT: B  168 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8507 (t80)
REVERT: B  212 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7524 (pt)
REVERT: A   55 MET cc_start: 0.7834 (tpp) cc_final: 0.7442 (tpt)
REVERT: A   78 TRP cc_start: 0.7053 (m-10) cc_final: 0.6693 (m100)
REVERT: A  417 LYS cc_start: 0.7406 (mptm) cc_final: 0.6948 (mtpt)
  outliers start: 25
  outliers final: 17
  residues processed: 87
  average time/residue: 0.0755
  time to fit residues: 8.7253
Evaluate side-chains
  82 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 15 optimal weight:    0.3980
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.154363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.124311 restraints weight = 6215.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.54
r_work: 0.3214 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5350  Z= 0.141
  Angle     :  0.513   8.883   7270  Z= 0.271
  Chirality :  0.041   0.148    802
  Planarity :  0.005   0.096    933
  Dihedral  :  5.208  51.352    717
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 22.43 %
    Favored  : 72.71 %
  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:  1.39 (0.32), residues: 668
  helix:  1.58 (0.25), residues: 408
  sheet: -0.83 (0.92), residues: 25
  loop :  0.06 (0.43), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 128 
 TYR   0.032   0.002   TYR B  85 
 PHE   0.018   0.001   PHE B  97 
 TRP   0.010   0.001   TRP A  78 
 HIS   0.002   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5350)
  covalent geometry    : angle       0.51296 ( 7270)
  hydrogen bonds       : bond        0.03939 (  304)
  hydrogen bonds       : angle       4.32799 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 64
  time to evaluate  : 0.173 
Fit side-chains
REVERT: B   44 TRP cc_start: 0.7525 (m100) cc_final: 0.7137 (m100)
REVERT: B  112 PHE cc_start: 0.8212 (t80) cc_final: 0.7727 (t80)
REVERT: B  117 TYR cc_start: 0.8394 (t80) cc_final: 0.8073 (t80)
REVERT: B  168 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8545 (t80)
REVERT: B  212 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7505 (pt)
REVERT: A   55 MET cc_start: 0.7869 (tpp) cc_final: 0.7451 (tpt)
  outliers start: 26
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0747
  time to fit residues: 8.2969
Evaluate side-chains
  79 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   chunk 64 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 278 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.154816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.123252 restraints weight = 6194.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.55
r_work: 0.3258 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5350  Z= 0.136
  Angle     :  0.517   8.835   7270  Z= 0.268
  Chirality :  0.040   0.143    802
  Planarity :  0.005   0.096    933
  Dihedral  :  5.132  51.212    717
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 23.36 %
    Favored  : 72.71 %
  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:  1.54 (0.33), residues: 668
  helix:  1.69 (0.25), residues: 409
  sheet: -0.83 (0.91), residues: 25
  loop :  0.18 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 188 
 TYR   0.027   0.001   TYR B  85 
 PHE   0.017   0.001   PHE B 102 
 TRP   0.007   0.001   TRP A 280 
 HIS   0.002   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5350)
  covalent geometry    : angle       0.51725 ( 7270)
  hydrogen bonds       : bond        0.03807 (  304)
  hydrogen bonds       : angle       4.22831 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B  112 PHE cc_start: 0.8203 (t80) cc_final: 0.7719 (t80)
REVERT: B  117 TYR cc_start: 0.8384 (t80) cc_final: 0.8106 (t80)
REVERT: B  168 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8555 (t80)
REVERT: B  212 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7445 (pt)
REVERT: B  262 PHE cc_start: 0.8810 (t80) cc_final: 0.8025 (t80)
REVERT: A   55 MET cc_start: 0.7815 (tpp) cc_final: 0.7334 (tpp)
  outliers start: 21
  outliers final: 17
  residues processed: 80
  average time/residue: 0.0800
  time to fit residues: 8.4350
Evaluate side-chains
  82 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.154230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.122773 restraints weight = 6151.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.58
r_work: 0.3180 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5350  Z= 0.147
  Angle     :  0.511   8.843   7270  Z= 0.269
  Chirality :  0.041   0.141    802
  Planarity :  0.005   0.096    933
  Dihedral  :  5.138  51.059    717
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 21.68 %
    Favored  : 73.64 %
  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:  1.54 (0.33), residues: 668
  helix:  1.69 (0.25), residues: 409
  sheet: -0.93 (0.88), residues: 25
  loop :  0.16 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 128 
 TYR   0.033   0.002   TYR B  85 
 PHE   0.021   0.001   PHE B 262 
 TRP   0.006   0.001   TRP A 280 
 HIS   0.002   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5350)
  covalent geometry    : angle       0.51091 ( 7270)
  hydrogen bonds       : bond        0.03826 (  304)
  hydrogen bonds       : angle       4.23234 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.205 
Fit side-chains
REVERT: B  112 PHE cc_start: 0.8216 (t80) cc_final: 0.7734 (t80)
REVERT: B  117 TYR cc_start: 0.8397 (t80) cc_final: 0.8112 (t80)
REVERT: B  168 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8548 (t80)
REVERT: B  212 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7487 (pt)
REVERT: A   55 MET cc_start: 0.7784 (tpp) cc_final: 0.7343 (tpp)
  outliers start: 25
  outliers final: 19
  residues processed: 86
  average time/residue: 0.0755
  time to fit residues: 8.6473
Evaluate side-chains
  82 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0970
   chunk 20 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.156438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.125907 restraints weight = 6077.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.43
r_work: 0.3168 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5350  Z= 0.116
  Angle     :  0.498   8.864   7270  Z= 0.260
  Chirality :  0.040   0.140    802
  Planarity :  0.005   0.097    933
  Dihedral  :  5.086  50.912    717
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 22.24 %
    Favored  : 73.64 %
  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:  1.69 (0.33), residues: 668
  helix:  1.81 (0.25), residues: 409
  sheet: -0.55 (0.95), residues: 24
  loop :  0.19 (0.44), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 128 
 TYR   0.033   0.001   TYR B  85 
 PHE   0.022   0.002   PHE B  97 
 TRP   0.007   0.001   TRP B  50 
 HIS   0.002   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5350)
  covalent geometry    : angle       0.49807 ( 7270)
  hydrogen bonds       : bond        0.03531 (  304)
  hydrogen bonds       : angle       4.12902 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.192 
Fit side-chains
REVERT: B  112 PHE cc_start: 0.8107 (t80) cc_final: 0.7661 (t80)
REVERT: B  117 TYR cc_start: 0.8344 (t80) cc_final: 0.8074 (t80)
REVERT: B  168 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8526 (t80)
REVERT: B  212 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7462 (pt)
REVERT: A   55 MET cc_start: 0.7766 (tpp) cc_final: 0.7359 (tpp)
  outliers start: 22
  outliers final: 17
  residues processed: 88
  average time/residue: 0.0727
  time to fit residues: 8.5759
Evaluate side-chains
  85 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   33 ASN
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0980
   chunk 31 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.155829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.125627 restraints weight = 6094.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.47
r_work: 0.3191 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5350  Z= 0.124
  Angle     :  0.502   8.864   7270  Z= 0.261
  Chirality :  0.040   0.139    802
  Planarity :  0.005   0.097    933
  Dihedral  :  5.096  50.671    717
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 22.99 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.33), residues: 668
  helix:  1.85 (0.25), residues: 407
  sheet: -0.90 (0.96), residues: 23
  loop :  0.28 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 188 
 TYR   0.037   0.002   TYR B  85 
 PHE   0.016   0.001   PHE B 102 
 TRP   0.006   0.001   TRP A 280 
 HIS   0.003   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5350)
  covalent geometry    : angle       0.50187 ( 7270)
  hydrogen bonds       : bond        0.03559 (  304)
  hydrogen bonds       : angle       4.11160 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.206 
Fit side-chains
REVERT: B  112 PHE cc_start: 0.8089 (t80) cc_final: 0.7667 (t80)
REVERT: B  117 TYR cc_start: 0.8345 (t80) cc_final: 0.8098 (t80)
REVERT: B  168 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8589 (t80)
REVERT: B  212 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7429 (pt)
REVERT: B  250 ASP cc_start: 0.8145 (t0) cc_final: 0.7920 (t0)
REVERT: A   55 MET cc_start: 0.7668 (tpp) cc_final: 0.7352 (tpp)
  outliers start: 20
  outliers final: 18
  residues processed: 84
  average time/residue: 0.0759
  time to fit residues: 8.4639
Evaluate side-chains
  85 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   33 ASN
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 65 optimal weight:    0.2980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.156264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.127740 restraints weight = 6141.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.51
r_work: 0.3210 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5350  Z= 0.122
  Angle     :  0.503   8.933   7270  Z= 0.263
  Chirality :  0.040   0.139    802
  Planarity :  0.005   0.098    933
  Dihedral  :  5.067  50.547    717
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 23.36 %
    Favored  : 72.71 %
  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:  1.78 (0.33), residues: 668
  helix:  1.87 (0.25), residues: 407
  sheet: -0.77 (0.98), residues: 23
  loop :  0.31 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 128 
 TYR   0.023   0.002   TYR B  85 
 PHE   0.012   0.001   PHE A  81 
 TRP   0.006   0.001   TRP A 280 
 HIS   0.002   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5350)
  covalent geometry    : angle       0.50338 ( 7270)
  hydrogen bonds       : bond        0.03513 (  304)
  hydrogen bonds       : angle       4.09397 (  906)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.225 
Fit side-chains
REVERT: B  112 PHE cc_start: 0.8172 (t80) cc_final: 0.7713 (t80)
REVERT: B  117 TYR cc_start: 0.8379 (t80) cc_final: 0.8116 (t80)
REVERT: B  168 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8612 (t80)
REVERT: B  212 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7501 (pt)
REVERT: B  250 ASP cc_start: 0.8233 (t0) cc_final: 0.7954 (t0)
REVERT: B  270 ASN cc_start: 0.7651 (m110) cc_final: 0.7343 (m110)
REVERT: A   55 MET cc_start: 0.7758 (tpp) cc_final: 0.7349 (tpp)
REVERT: A  331 ASP cc_start: 0.9089 (p0) cc_final: 0.8831 (p0)
  outliers start: 21
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0764
  time to fit residues: 8.5876
Evaluate side-chains
  86 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   33 ASN
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0020
   overall best weight:    0.6988

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.155805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.127363 restraints weight = 6159.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.52
r_work: 0.3249 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5350  Z= 0.129
  Angle     :  0.507   8.932   7270  Z= 0.263
  Chirality :  0.040   0.139    802
  Planarity :  0.005   0.098    933
  Dihedral  :  5.073  50.444    717
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.80 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.76 (0.33), residues: 668
  helix:  1.85 (0.25), residues: 407
  sheet: -0.90 (0.95), residues: 24
  loop :  0.30 (0.44), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 188 
 TYR   0.025   0.002   TYR B  85 
 PHE   0.011   0.001   PHE A 149 
 TRP   0.006   0.001   TRP A 280 
 HIS   0.003   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5350)
  covalent geometry    : angle       0.50746 ( 7270)
  hydrogen bonds       : bond        0.03558 (  304)
  hydrogen bonds       : angle       4.10362 (  906)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1809.74 seconds
wall clock time: 31 minutes 37.07 seconds (1897.07 seconds total)