Starting phenix.real_space_refine
on Tue Mar 11 18:21:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y6m_38991/03_2025/8y6m_38991_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y6m_38991/03_2025/8y6m_38991.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y6m_38991/03_2025/8y6m_38991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y6m_38991/03_2025/8y6m_38991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y6m_38991/03_2025/8y6m_38991_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y6m_38991/03_2025/8y6m_38991_neut.cif"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.052
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      32      5.16       5
     C    4352      2.51       5
     N    1010      2.21       5
     O    1108      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6502
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 413, 3251
          Classifications: {'peptide': 413}
          Link IDs: {'PTRANS': 16, 'TRANS': 396}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 413, 3251
          Classifications: {'peptide': 413}
          Link IDs: {'PTRANS': 16, 'TRANS': 396}
          Chain breaks: 3
  Time building chain proxies: 4.52, per 1000 atoms: 0.70
  Number of scatterers: 6502
  At special positions: 0
  Unit cell: (69.68, 96.72, 83.2, 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      32     16.00
     O    1108      8.00
     N    1010      7.00
     C    4352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 476 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 476 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 801.9 milliseconds
  

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 2 sheets defined
      76.9% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 62
    Processing helix  chain 'A' and resid 72 through 85
      removed outlier: 3.508A  pdb=" N   MET A  76 " --> pdb=" O   GLY A  72 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 112
      removed outlier: 3.769A  pdb=" N   VAL A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 124
    Processing helix  chain 'A' and resid 187 through 214
    Processing helix  chain 'A' and resid 214 through 223
      Proline residue:  A 220  - end of helix
      removed outlier: 3.582A  pdb=" N   LYS A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 241
    Processing helix  chain 'A' and resid 250 through 256
      removed outlier: 4.137A  pdb=" N   ILE A 254 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER A 256 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 273
    Processing helix  chain 'A' and resid 275 through 292
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 303 through 307
      removed outlier: 3.547A  pdb=" N   LEU A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 339
    Processing helix  chain 'A' and resid 342 through 346
      removed outlier: 3.968A  pdb=" N   ASP A 346 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 365
      removed outlier: 3.840A  pdb=" N   ARG A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 391
      removed outlier: 3.522A  pdb=" N   LEU A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 423
    Processing helix  chain 'A' and resid 425 through 441
    Processing helix  chain 'A' and resid 441 through 448
    Processing helix  chain 'A' and resid 453 through 466
    Processing helix  chain 'A' and resid 475 through 481
    Processing helix  chain 'A' and resid 494 through 499
    Processing helix  chain 'A' and resid 500 through 516
    Processing helix  chain 'A' and resid 517 through 519
      No H-bonds generated for 'chain 'A' and resid 517 through 519'
    Processing helix  chain 'B' and resid 39 through 62
    Processing helix  chain 'B' and resid 72 through 85
      removed outlier: 3.554A  pdb=" N   MET B  76 " --> pdb=" O   GLY B  72 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LEU B  79 " --> pdb=" O   ASP B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 97
      removed outlier: 3.612A  pdb=" N   LEU B  97 " --> pdb=" O   MET B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 112
      removed outlier: 4.239A  pdb=" N   VAL B 104 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE B 105 " --> pdb=" O   GLN B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 123
    Processing helix  chain 'B' and resid 187 through 214
    Processing helix  chain 'B' and resid 214 through 225
      Proline residue:  B 220  - end of helix
      removed outlier: 4.123A  pdb=" N   LYS B 224 " --> pdb=" O   PRO B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 241
    Processing helix  chain 'B' and resid 250 through 256
      removed outlier: 4.086A  pdb=" N   ILE B 254 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   SER B 256 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 273
      removed outlier: 3.573A  pdb=" N   LEU B 262 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 292
    Processing helix  chain 'B' and resid 293 through 302
    Processing helix  chain 'B' and resid 303 through 307
    Processing helix  chain 'B' and resid 313 through 339
    Processing helix  chain 'B' and resid 342 through 346
      removed outlier: 3.915A  pdb=" N   ASP B 346 " --> pdb=" O   SER B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 365
      removed outlier: 3.845A  pdb=" N   ARG B 365 " --> pdb=" O   ALA B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 391
      removed outlier: 3.529A  pdb=" N   LEU B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 423
    Processing helix  chain 'B' and resid 425 through 441
    Processing helix  chain 'B' and resid 441 through 448
    Processing helix  chain 'B' and resid 453 through 466
    Processing helix  chain 'B' and resid 475 through 481
    Processing helix  chain 'B' and resid 494 through 499
    Processing helix  chain 'B' and resid 500 through 516
      removed outlier: 3.697A  pdb=" N   LEU B 516 " --> pdb=" O   LEU B 512 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397
    Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528

    428 hydrogen bonds defined for protein.
    1230 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1910
        1.34 -     1.46: 1551
        1.46 -     1.58: 3145
        1.58 -     1.70: 0
        1.70 -     1.82: 56
  Bond restraints: 6662
  Sorted by residual:
  bond pdb=" CG  PRO A 316 "
       pdb=" CD  PRO A 316 "
    ideal  model  delta    sigma   weight residual
    1.503  1.457  0.046 3.40e-02 8.65e+02 1.81e+00
  bond pdb=" CG1 ILE A  43 "
       pdb=" CD1 ILE A  43 "
    ideal  model  delta    sigma   weight residual
    1.513  1.466  0.047 3.90e-02 6.57e+02 1.42e+00
  bond pdb=" CG  LEU B  84 "
       pdb=" CD2 LEU B  84 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.17e+00
  bond pdb=" CG1 ILE B  43 "
       pdb=" CD1 ILE B  43 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.15e+00
  bond pdb=" CB  ILE B 105 "
       pdb=" CG2 ILE B 105 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.10e+00
  ... (remaining 6657 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 8746
        1.63 -     3.26: 236
        3.26 -     4.88: 50
        4.88 -     6.51: 13
        6.51 -     8.14: 7
  Bond angle restraints: 9052
  Sorted by residual:
  angle pdb=" CA  PRO A 316 "
        pdb=" N   PRO A 316 "
        pdb=" CD  PRO A 316 "
      ideal   model   delta    sigma   weight residual
     112.00  105.43    6.57 1.40e+00 5.10e-01 2.21e+01
  angle pdb=" CA  MET B  76 "
        pdb=" CB  MET B  76 "
        pdb=" CG  MET B  76 "
      ideal   model   delta    sigma   weight residual
     114.10  122.24   -8.14 2.00e+00 2.50e-01 1.66e+01
  angle pdb=" N   PRO A 316 "
        pdb=" CD  PRO A 316 "
        pdb=" CG  PRO A 316 "
      ideal   model   delta    sigma   weight residual
     103.20   98.50    4.70 1.50e+00 4.44e-01 9.81e+00
  angle pdb=" N   MET B  76 "
        pdb=" CA  MET B  76 "
        pdb=" C   MET B  76 "
      ideal   model   delta    sigma   weight residual
     113.88  110.44    3.44 1.23e+00 6.61e-01 7.84e+00
  angle pdb=" CG  MET B  76 "
        pdb=" SD  MET B  76 "
        pdb=" CE  MET B  76 "
      ideal   model   delta    sigma   weight residual
     100.90  106.87   -5.97 2.20e+00 2.07e-01 7.37e+00
  ... (remaining 9047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 3196
       17.38 -    34.75: 495
       34.75 -    52.13: 167
       52.13 -    69.50: 19
       69.50 -    86.88: 5
  Dihedral angle restraints: 3882
    sinusoidal: 1492
      harmonic: 2390
  Sorted by residual:
  dihedral pdb=" CB  CYS A 476 "
           pdb=" SG  CYS A 476 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -53.16  -32.84     1      1.00e+01 1.00e-02 1.53e+01
  dihedral pdb=" CB  CYS B 476 "
           pdb=" SG  CYS B 476 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -53.17  -32.83     1      1.00e+01 1.00e-02 1.53e+01
  dihedral pdb=" CA  ASN B 273 "
           pdb=" C   ASN B 273 "
           pdb=" N   THR B 274 "
           pdb=" CA  THR B 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.14  -18.86     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 3879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 787
       0.047 -    0.094: 238
       0.094 -    0.141: 50
       0.141 -    0.187: 5
       0.187 -    0.234: 2
  Chirality restraints: 1082
  Sorted by residual:
  chirality pdb=" CG  LEU A  54 "
            pdb=" CB  LEU A  54 "
            pdb=" CD1 LEU A  54 "
            pdb=" CD2 LEU A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CG  LEU B  54 "
            pdb=" CB  LEU B  54 "
            pdb=" CD1 LEU B  54 "
            pdb=" CD2 LEU B  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.09e-01
  chirality pdb=" CB  ILE B 199 "
            pdb=" CA  ILE B 199 "
            pdb=" CG1 ILE B 199 "
            pdb=" CG2 ILE B 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 1079 not shown)

  Planarity restraints: 1084
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 315 "   -0.062 5.00e-02 4.00e+02   9.02e-02 1.30e+01
        pdb=" N   PRO A 316 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO A 316 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 316 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 315 "    0.036 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO B 316 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B 316 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 316 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 246 "   -0.027 5.00e-02 4.00e+02   4.17e-02 2.79e+00
        pdb=" N   PRO B 247 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 247 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 247 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1081 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 78
        2.63 -     3.20: 6053
        3.20 -     3.77: 11072
        3.77 -     4.33: 15185
        4.33 -     4.90: 24941
  Nonbonded interactions: 57329
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 235 "
            pdb=" OG  SER A 239 "
     model   vdw
     2.065 3.040
  nonbonded pdb=" O   VAL B 235 "
            pdb=" OG  SER B 239 "
     model   vdw
     2.066 3.040
  nonbonded pdb=" O   SER A 234 "
            pdb=" OG  SER A 238 "
     model   vdw
     2.104 3.040
  nonbonded pdb=" O   SER B 234 "
            pdb=" OG  SER B 238 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" O   SER A  88 "
            pdb=" OG  SER A  88 "
     model   vdw
     2.183 3.040
  ... (remaining 57324 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.920
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.590
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
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      :  0.006   0.047   6662  Z= 0.367
  Angle     :  0.699   8.140   9052  Z= 0.357
  Chirality :  0.046   0.234   1082
  Planarity :  0.006   0.090   1084
  Dihedral  : 18.430  86.877   2332
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 28.59 %
    Favored  : 64.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.29), residues: 810
  helix:  1.12 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.18 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 499 
 HIS   0.010   0.003   HIS A 200 
 PHE   0.012   0.002   PHE B 204 
 TYR   0.021   0.003   TYR B  47 
 ARG   0.006   0.001   ARG A 213 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 73
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A   38 ILE cc_start: 0.5869 (OUTLIER) cc_final: 0.5108 (mt)
REVERT: B   38 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5338 (mp)
  outliers start: 53
  outliers final: 43
  residues processed: 123
  average time/residue: 0.7250
  time to fit residues: 96.7638
Evaluate side-chains
  118 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 73
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   47 TYR
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   75 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  475 SER
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  508 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0870
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 ASN
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4090 r_free = 0.4090 target = 0.196520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.182520 restraints weight = 7692.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 1.39
r_work: 0.3887 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3804 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6683
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6662  Z= 0.212
  Angle     :  0.559   7.516   9052  Z= 0.286
  Chirality :  0.041   0.134   1082
  Planarity :  0.004   0.053   1084
  Dihedral  :  7.898  51.624    934
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 28.45 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 810
  helix:  1.59 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.37 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 499 
 HIS   0.006   0.002   HIS B 200 
 PHE   0.008   0.001   PHE A  78 
 TYR   0.017   0.002   TYR B  47 
 ARG   0.004   0.001   ARG B 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 78
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A   60 MET cc_start: 0.5525 (mpp) cc_final: 0.5262 (mmm)
REVERT: A   76 MET cc_start: 0.5652 (tpt) cc_final: 0.5283 (mmm)
REVERT: A  314 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7569 (tmmm)
REVERT: B  509 PHE cc_start: 0.6206 (m-10) cc_final: 0.5388 (t80)
  outliers start: 39
  outliers final: 18
  residues processed: 105
  average time/residue: 0.8229
  time to fit residues: 93.2955
Evaluate side-chains
  97 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  424 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4056 r_free = 0.4056 target = 0.193492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.179338 restraints weight = 7795.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 1.40
r_work: 0.3856 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3773 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.0908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6662  Z= 0.240
  Angle     :  0.572   7.886   9052  Z= 0.292
  Chirality :  0.042   0.143   1082
  Planarity :  0.004   0.040   1084
  Dihedral  :  6.584  51.375    885
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 28.04 %
    Favored  : 65.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 810
  helix:  1.61 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.41 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 499 
 HIS   0.007   0.002   HIS A 200 
 PHE   0.010   0.001   PHE B  41 
 TYR   0.020   0.002   TYR B  47 
 ARG   0.005   0.001   ARG B 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 78
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A   60 MET cc_start: 0.5603 (mpp) cc_final: 0.5310 (mmm)
REVERT: A  240 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.4654 (m-80)
REVERT: A  360 MET cc_start: 0.8245 (mmm) cc_final: 0.7924 (mmp)
REVERT: A  424 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7780 (OUTLIER)
REVERT: A  528 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7354 (mtt90)
REVERT: B   38 ILE cc_start: 0.6017 (OUTLIER) cc_final: 0.5573 (mp)
REVERT: B  424 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7773 (OUTLIER)
REVERT: B  509 PHE cc_start: 0.6303 (m-10) cc_final: 0.5539 (t80)
  outliers start: 44
  outliers final: 19
  residues processed: 113
  average time/residue: 0.8538
  time to fit residues: 103.9341
Evaluate side-chains
  101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  528 ARG
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  424 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 37 optimal weight:    0.0870
   chunk 75 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0020
   chunk 10 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 29 optimal weight:    0.1980
   chunk 22 optimal weight:    0.1980
   chunk 52 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.2366

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
A 366 HIS
B  44 GLN
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4137 r_free = 0.4137 target = 0.201866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.188038 restraints weight = 7778.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3988 rms_B_bonded: 1.39
r_work: 0.3930 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3847 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   6662  Z= 0.164
  Angle     :  0.516   6.237   9052  Z= 0.264
  Chirality :  0.040   0.155   1082
  Planarity :  0.004   0.035   1084
  Dihedral  :  6.041  49.790    883
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 27.76 %
    Favored  : 65.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.29), residues: 810
  helix:  2.00 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.38 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 499 
 HIS   0.005   0.001   HIS B 366 
 PHE   0.006   0.001   PHE B 116 
 TYR   0.017   0.001   TYR B  47 
 ARG   0.003   0.000   ARG B 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 86
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A  424 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7574 (m-10)
REVERT: B   60 MET cc_start: 0.5249 (mpp) cc_final: 0.5045 (mmm)
REVERT: B  424 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7569 (m-10)
REVERT: B  509 PHE cc_start: 0.6235 (m-10) cc_final: 0.5444 (t80)
  outliers start: 47
  outliers final: 19
  residues processed: 124
  average time/residue: 0.8145
  time to fit residues: 109.1705
Evaluate side-chains
  100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  502 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0000
   chunk 25 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4122 r_free = 0.4122 target = 0.200221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.186182 restraints weight = 7700.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 1.38
r_work: 0.3923 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3841 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6662  Z= 0.186
  Angle     :  0.541   6.857   9052  Z= 0.274
  Chirality :  0.041   0.151   1082
  Planarity :  0.004   0.033   1084
  Dihedral  :  6.073  49.908    883
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 28.18 %
    Favored  : 65.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.29), residues: 810
  helix:  2.01 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.46 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 499 
 HIS   0.005   0.002   HIS B 366 
 PHE   0.008   0.001   PHE B 119 
 TYR   0.017   0.002   TYR B  47 
 ARG   0.005   0.000   ARG A 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 81
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A  424 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7670 (m-10)
REVERT: B   76 MET cc_start: 0.6075 (tpt) cc_final: 0.5467 (tpt)
REVERT: B  240 PHE cc_start: 0.4980 (OUTLIER) cc_final: 0.4508 (m-80)
REVERT: B  424 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7656 (m-10)
REVERT: B  509 PHE cc_start: 0.6261 (m-10) cc_final: 0.5451 (t80)
  outliers start: 47
  outliers final: 19
  residues processed: 121
  average time/residue: 0.7836
  time to fit residues: 102.3024
Evaluate side-chains
  102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  512 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 24 optimal weight:    0.0570
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4115 r_free = 0.4115 target = 0.199406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.185421 restraints weight = 7661.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.38
r_work: 0.3915 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3832 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6705
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6662  Z= 0.204
  Angle     :  0.562   6.625   9052  Z= 0.285
  Chirality :  0.042   0.164   1082
  Planarity :  0.004   0.032   1084
  Dihedral  :  5.759  50.986    879
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 28.45 %
    Favored  : 65.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.29), residues: 810
  helix:  1.97 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.52 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 499 
 HIS   0.005   0.002   HIS A 200 
 PHE   0.007   0.001   PHE B 204 
 TYR   0.018   0.002   TYR B  47 
 ARG   0.005   0.000   ARG A 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 77
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A   38 ILE cc_start: 0.6339 (OUTLIER) cc_final: 0.5791 (mt)
REVERT: A   60 MET cc_start: 0.5630 (mpp) cc_final: 0.5358 (mmm)
REVERT: A  360 MET cc_start: 0.8139 (mmm) cc_final: 0.7843 (mmp)
REVERT: A  424 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7684 (m-10)
REVERT: B   60 MET cc_start: 0.5539 (mpp) cc_final: 0.5335 (mmm)
REVERT: B  240 PHE cc_start: 0.5136 (OUTLIER) cc_final: 0.4751 (m-80)
REVERT: B  424 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7706 (m-10)
REVERT: B  509 PHE cc_start: 0.6295 (m-10) cc_final: 0.5470 (t80)
  outliers start: 42
  outliers final: 19
  residues processed: 112
  average time/residue: 0.8263
  time to fit residues: 99.6153
Evaluate side-chains
  101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  512 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4110 r_free = 0.4110 target = 0.198915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.184875 restraints weight = 7719.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 1.38
r_work: 0.3923 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3841 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6662  Z= 0.212
  Angle     :  0.573   6.627   9052  Z= 0.289
  Chirality :  0.042   0.184   1082
  Planarity :  0.004   0.032   1084
  Dihedral  :  5.546  53.083    877
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 27.62 %
    Favored  : 65.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.29), residues: 810
  helix:  1.90 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.54 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 499 
 HIS   0.005   0.002   HIS B 366 
 PHE   0.011   0.001   PHE A 116 
 TYR   0.017   0.002   TYR B  47 
 ARG   0.006   0.000   ARG A 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 77
  time to evaluate  : 1.882 
Fit side-chains
REVERT: A   38 ILE cc_start: 0.6125 (OUTLIER) cc_final: 0.5546 (mt)
REVERT: A  360 MET cc_start: 0.8213 (mmm) cc_final: 0.7918 (mmp)
REVERT: A  424 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7725 (m-10)
REVERT: B   38 ILE cc_start: 0.5989 (OUTLIER) cc_final: 0.5431 (mt)
REVERT: B   76 MET cc_start: 0.5877 (tpt) cc_final: 0.5300 (tpt)
REVERT: B  240 PHE cc_start: 0.5165 (OUTLIER) cc_final: 0.4777 (m-80)
REVERT: B  424 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7742 (m-10)
REVERT: B  491 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6403 (mmtm)
REVERT: B  509 PHE cc_start: 0.6323 (m-10) cc_final: 0.5495 (t80)
  outliers start: 49
  outliers final: 19
  residues processed: 118
  average time/residue: 1.0512
  time to fit residues: 135.5656
Evaluate side-chains
  102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  491 LYS
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  512 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 12 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0270
   chunk 18 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4118 r_free = 0.4118 target = 0.199925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.185892 restraints weight = 7708.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 1.38
r_work: 0.3924 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3842 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6662  Z= 0.197
  Angle     :  0.585   9.077   9052  Z= 0.294
  Chirality :  0.042   0.200   1082
  Planarity :  0.004   0.032   1084
  Dihedral  :  5.544  54.534    877
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 30.39 %
    Favored  : 65.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.29), residues: 810
  helix:  1.95 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.56 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 499 
 HIS   0.005   0.002   HIS A 200 
 PHE   0.010   0.001   PHE A 116 
 TYR   0.017   0.002   TYR B  47 
 ARG   0.006   0.000   ARG A 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.645 
Fit side-chains
REVERT: A   38 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.5663 (mt)
REVERT: A   60 MET cc_start: 0.5695 (mpp) cc_final: 0.5377 (mmm)
REVERT: A   76 MET cc_start: 0.5851 (tpt) cc_final: 0.5360 (mmm)
REVERT: A  424 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7707 (m-10)
REVERT: B   38 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5496 (mt)
REVERT: B   76 MET cc_start: 0.5583 (tpt) cc_final: 0.5308 (mmm)
REVERT: B  240 PHE cc_start: 0.4956 (OUTLIER) cc_final: 0.4539 (m-80)
REVERT: B  245 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6924 (mp)
REVERT: B  360 MET cc_start: 0.8052 (mmm) cc_final: 0.7731 (mmp)
REVERT: B  424 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7713 (m-10)
REVERT: B  491 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6429 (mmtm)
REVERT: B  509 PHE cc_start: 0.6307 (m-10) cc_final: 0.5495 (t80)
  outliers start: 33
  outliers final: 18
  residues processed: 105
  average time/residue: 0.8462
  time to fit residues: 95.3968
Evaluate side-chains
  103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  491 LYS
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  512 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0570
   chunk 3 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 78 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4126 r_free = 0.4126 target = 0.200866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.186778 restraints weight = 7844.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 1.39
r_work: 0.3934 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3852 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6662  Z= 0.183
  Angle     :  0.570   6.684   9052  Z= 0.287
  Chirality :  0.042   0.230   1082
  Planarity :  0.004   0.031   1084
  Dihedral  :  5.517  57.160    877
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 29.70 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.29), residues: 810
  helix:  2.01 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.57 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 499 
 HIS   0.005   0.002   HIS B 366 
 PHE   0.010   0.001   PHE A 116 
 TYR   0.016   0.002   TYR A  47 
 ARG   0.006   0.001   ARG A 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 78
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A   60 MET cc_start: 0.5575 (mpp) cc_final: 0.5342 (mmm)
REVERT: A   76 MET cc_start: 0.5623 (tpt) cc_final: 0.5353 (mmm)
REVERT: A  109 MET cc_start: 0.6427 (mtm) cc_final: 0.6176 (mtm)
REVERT: A  424 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7682 (m-10)
REVERT: B   76 MET cc_start: 0.5543 (tpt) cc_final: 0.5245 (mmm)
REVERT: B  424 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7708 (m-10)
REVERT: B  491 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6395 (mmtm)
REVERT: B  509 PHE cc_start: 0.6325 (m-10) cc_final: 0.5521 (t80)
  outliers start: 37
  outliers final: 18
  residues processed: 105
  average time/residue: 0.9217
  time to fit residues: 103.8269
Evaluate side-chains
  98 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  491 LYS
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  512 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   chunk 26 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 81 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
** B 273 ASN ** 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 = 0.4096 r_free = 0.4096 target = 0.197453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.183335 restraints weight = 7831.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 1.40
r_work: 0.3904 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3821 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6662  Z= 0.249
  Angle     :  0.627  10.872   9052  Z= 0.314
  Chirality :  0.044   0.228   1082
  Planarity :  0.004   0.032   1084
  Dihedral  :  5.658  59.284    876
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 31.22 %
    Favored  : 64.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.29), residues: 810
  helix:  1.78 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.59 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 499 
 HIS   0.006   0.002   HIS A 366 
 PHE   0.010   0.001   PHE B  41 
 TYR   0.017   0.002   TYR B  47 
 ARG   0.006   0.001   ARG A 528 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A   60 MET cc_start: 0.5778 (mpp) cc_final: 0.5442 (mmm)
REVERT: A   76 MET cc_start: 0.5732 (tpt) cc_final: 0.5296 (mmm)
REVERT: A  424 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7847 (m-10)
REVERT: B   38 ILE cc_start: 0.5893 (OUTLIER) cc_final: 0.5326 (mt)
REVERT: B   60 MET cc_start: 0.5789 (mmm) cc_final: 0.5586 (mpp)
REVERT: B   76 MET cc_start: 0.5570 (tpt) cc_final: 0.5356 (mmm)
REVERT: B  424 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7880 (m-10)
REVERT: B  491 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6398 (mmtm)
REVERT: B  509 PHE cc_start: 0.6384 (m-10) cc_final: 0.5531 (t80)
  outliers start: 28
  outliers final: 15
  residues processed: 100
  average time/residue: 0.9589
  time to fit residues: 102.4788
Evaluate side-chains
  96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  491 LYS
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  512 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
** B 273 ASN ** 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 = 0.4094 r_free = 0.4094 target = 0.197280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.183137 restraints weight = 7873.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 1.39
r_work: 0.3887 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3804 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6662  Z= 0.242
  Angle     :  0.621  10.332   9052  Z= 0.311
  Chirality :  0.043   0.215   1082
  Planarity :  0.004   0.032   1084
  Dihedral  :  5.680  57.842    876
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 31.49 %
    Favored  : 64.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.29), residues: 810
  helix:  1.69 (0.21), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.49 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 499 
 HIS   0.005   0.002   HIS B 366 
 PHE   0.010   0.001   PHE B  48 
 TYR   0.018   0.002   TYR B  47 
 ARG   0.006   0.001   ARG A 528 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4300.40 seconds
wall clock time: 74 minutes 15.06 seconds (4455.06 seconds total)