Starting phenix.real_space_refine
on Fri Aug 22 14:05:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sdy_40354/08_2025/8sdy_40354.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sdy_40354/08_2025/8sdy_40354.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sdy_40354/08_2025/8sdy_40354.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sdy_40354/08_2025/8sdy_40354.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sdy_40354/08_2025/8sdy_40354.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sdy_40354/08_2025/8sdy_40354.map"
  }
  resolution = 2.79
  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=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    2528      2.51       5
     N     653      2.21       5
     O     683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3894
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3840
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 494, 3831
          Classifications: {'peptide': 494}
          Link IDs: {'PTRANS': 25, 'TRANS': 468}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 494, 3831
          Classifications: {'peptide': 494}
          Link IDs: {'PTRANS': 25, 'TRANS': 468}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 3912
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 13, 26
          Unusual residues: {'ZWD': 1}
          Classifications: {'undetermined': 1, 'water': 12}
          Link IDs: {None: 12}
      Conformer: "B"
        Number of residues, atoms: 13, 26
          Unusual residues: {'ZWD': 1}
          Classifications: {'undetermined': 1, 'water': 12}
          Link IDs: {None: 12}
      Conformer: "C"
        Number of residues, atoms: 13, 26
          Unusual residues: {'ZWD': 1}
          Classifications: {'undetermined': 1, 'water': 12}
          Link IDs: {None: 12}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ALYS A 382 " occ=0.52
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 382 " occ=0.48
    residue:
      pdb=" C01AZWD A 601 " occ=0.85
      ... (40 atoms not shown)
      pdb=" O13CZWD A 601 " occ=0.14
  Time building chain proxies: 1.54, per 1000 atoms: 0.40
  Number of scatterers: 3894
  At special positions: 0
  Unit cell: (85.49, 68.89, 94.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     683      8.00
     N     653      7.00
     C    2528      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 128 " distance=2.02

  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: 0.35
  Conformation dependent library (CDL) restraints added in 201.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  918

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      82.0% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
      removed outlier: 3.786A  pdb=" N   GLY A  11 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 26
    Processing helix  chain 'A' and resid 27 through 36
      removed outlier: 4.003A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   SER A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 119 through 125
    Processing helix  chain 'A' and resid 127 through 130
    Processing helix  chain 'A' and resid 131 through 160
      removed outlier: 4.204A  pdb=" N   GLN A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLN A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASP A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ARG A 158 " --> pdb=" O   TYR A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 181
    Processing helix  chain 'A' and resid 184 through 213
      removed outlier: 3.844A  pdb=" N   MET A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 218 through 244
      removed outlier: 3.563A  pdb=" N   PHE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 238 " --> pdb=" O   GLN A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
    Processing helix  chain 'A' and resid 256 through 266
      removed outlier: 3.966A  pdb=" N   ILE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   TRP A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 280 through 296
    Processing helix  chain 'A' and resid 297 through 304
      removed outlier: 3.786A  pdb=" N   LYS A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU A 304 " --> pdb=" O   GLU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 314
    Processing helix  chain 'A' and resid 327 through 332
      removed outlier: 3.623A  pdb=" N   ARG A 331 " --> pdb=" O   MET A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 358
      removed outlier: 3.861A  pdb=" N   LEU A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 364
      removed outlier: 4.128A  pdb=" N   PHE A 363 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLY A 364 " --> pdb=" O   GLN A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 377
    Processing helix  chain 'A' and resid 377 through 392
    Processing helix  chain 'A' and resid 393 through 415
      removed outlier: 3.500A  pdb=" N   ALA A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 449
      removed outlier: 3.684A  pdb=" N   TYR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 477
      Proline residue:  A 473  - end of helix
    Processing helix  chain 'A' and resid 478 through 481
    Processing helix  chain 'A' and resid 484 through 502
      Proline residue:  A 494  - end of helix
      removed outlier: 3.813A  pdb=" N   ALA A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 524
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81

    274 hydrogen bonds defined for protein.
    811 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: 0.55

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 586
        1.31 -     1.44: 1105
        1.44 -     1.56: 2236
        1.56 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 3974
  Sorted by residual:
  bond pdb=" C07AZWD A 601 "
       pdb=" N09AZWD A 601 "
    ideal  model  delta    sigma   weight residual
    1.350  1.453 -0.103 2.00e-02 2.50e+03 2.65e+01
  bond pdb=" C07BZWD A 601 "
       pdb=" N09BZWD A 601 "
    ideal  model  delta    sigma   weight residual
    1.350  1.451 -0.101 2.00e-02 2.50e+03 2.57e+01
  bond pdb=" C07CZWD A 601 "
       pdb=" N09CZWD A 601 "
    ideal  model  delta    sigma   weight residual
    1.350  1.450 -0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" C03AZWD A 601 "
       pdb=" N14AZWD A 601 "
    ideal  model  delta    sigma   weight residual
    1.379  1.451 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C03BZWD A 601 "
       pdb=" N14BZWD A 601 "
    ideal  model  delta    sigma   weight residual
    1.379  1.450 -0.071 2.00e-02 2.50e+03 1.25e+01
  ... (remaining 3969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 5217
        1.46 -     2.91: 121
        2.91 -     4.37: 50
        4.37 -     5.82: 10
        5.82 -     7.28: 4
  Bond angle restraints: 5402
  Sorted by residual:
  angle pdb=" CA  GLN A 289 "
        pdb=" CB  GLN A 289 "
        pdb=" CG  GLN A 289 "
      ideal   model   delta    sigma   weight residual
     114.10  120.60   -6.50 2.00e+00 2.50e-01 1.06e+01
  angle pdb=" CA  TYR A 264 "
        pdb=" CB  TYR A 264 "
        pdb=" CG  TYR A 264 "
      ideal   model   delta    sigma   weight residual
     113.90  119.00   -5.10 1.80e+00 3.09e-01 8.02e+00
  angle pdb=" CG  ARG A 290 "
        pdb=" CD  ARG A 290 "
        pdb=" NE  ARG A 290 "
      ideal   model   delta    sigma   weight residual
     112.00  117.66   -5.66 2.20e+00 2.07e-01 6.62e+00
  angle pdb=" O12AZWD A 601 "
        pdb=" C11AZWD A 601 "
        pdb=" O13AZWD A 601 "
      ideal   model   delta    sigma   weight residual
     127.09  119.81    7.28 3.00e+00 1.11e-01 5.89e+00
  angle pdb=" O12BZWD A 601 "
        pdb=" C11BZWD A 601 "
        pdb=" O13BZWD A 601 "
      ideal   model   delta    sigma   weight residual
     127.09  120.13    6.96 3.00e+00 1.11e-01 5.39e+00
  ... (remaining 5397 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 2001
       17.59 -    35.18: 255
       35.18 -    52.77: 80
       52.77 -    70.36: 9
       70.36 -    87.95: 4
  Dihedral angle restraints: 2349
    sinusoidal: 920
      harmonic: 1429
  Sorted by residual:
  dihedral pdb=" CG  ARG A 290 "
           pdb=" CD  ARG A 290 "
           pdb=" NE  ARG A 290 "
           pdb=" CZ  ARG A 290 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.14   48.86     2      1.50e+01 4.44e-03 1.21e+01
  dihedral pdb=" CG  ARG A 280 "
           pdb=" CD  ARG A 280 "
           pdb=" NE  ARG A 280 "
           pdb=" CZ  ARG A 280 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.55   43.45     2      1.50e+01 4.44e-03 1.01e+01
  dihedral pdb=" CG  ARG A  80 "
           pdb=" CD  ARG A  80 "
           pdb=" NE  ARG A  80 "
           pdb=" CZ  ARG A  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.22  -43.22     2      1.50e+01 4.44e-03 1.00e+01
  ... (remaining 2346 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 390
       0.027 -    0.055: 149
       0.055 -    0.082: 58
       0.082 -    0.110: 20
       0.110 -    0.137: 8
  Chirality restraints: 625
  Sorted by residual:
  chirality pdb=" CA  ILE A  44 "
            pdb=" N   ILE A  44 "
            pdb=" C   ILE A  44 "
            pdb=" CB  ILE A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.70e-01
  chirality pdb=" CA  ILE A 269 "
            pdb=" N   ILE A 269 "
            pdb=" C   ILE A 269 "
            pdb=" CB  ILE A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CA  ILE A 415 "
            pdb=" N   ILE A 415 "
            pdb=" C   ILE A 415 "
            pdb=" CB  ILE A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 622 not shown)

  Planarity restraints: 673
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 290 "   -0.202 9.50e-02 1.11e+02   9.10e-02 5.88e+00
        pdb=" NE  ARG A 290 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 290 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 290 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 290 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 395 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.89e+00
        pdb=" N   PRO A 396 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 396 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 396 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 332 "   -0.018 5.00e-02 4.00e+02   2.73e-02 1.19e+00
        pdb=" N   PRO A 333 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 333 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 333 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 670 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 40
        2.59 -     3.17: 3437
        3.17 -     3.75: 6386
        3.75 -     4.32: 8807
        4.32 -     4.90: 14720
  Nonbonded interactions: 33390
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 444 "
            pdb=" O   PRO A 505 "
     model   vdw
     2.018 3.040
  nonbonded pdb=" OG  SER A  33 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.066 3.040
  nonbonded pdb=" OD1 ASN A 168 "
            pdb=" OG  SER A 201 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" NH2 ARG A  80 "
            pdb=" OE2 GLU A 103 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OG1 THR A 172 "
            pdb=" OG  SER A 198 "
     model   vdw
     2.226 3.040
  ... (remaining 33385 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.01 max=1.00 mean=0.99
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:             0.300
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     5.850
  Find NCS groups from input model:        0.010
  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:8.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.103   3976  Z= 0.249
  Angle     :  0.660   7.279   5406  Z= 0.319
  Chirality :  0.037   0.137    625
  Planarity :  0.005   0.091    673
  Dihedral  : 16.845  87.947   1425
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 23.50 %
    Favored  : 75.78 %
  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:  2.03 (0.38), residues: 489
  helix:  1.62 (0.27), residues: 374
  sheet: -2.13 (1.49), residues: 10
  loop :  1.03 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 290 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 442 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 3974)
  covalent geometry    : angle       0.65976 ( 5402)
  SS BOND              : bond        0.00660 (    2)
  SS BOND              : angle       1.12290 (    4)
  hydrogen bonds       : bond        0.10762 (  274)
  hydrogen bonds       : angle       5.41264 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  290 ARG cc_start: 0.6347 (mtp85) cc_final: 0.6129 (mmm-85)
REVERT: A  389 ILE cc_start: 0.7839 (mt) cc_final: 0.7617 (mp)
REVERT: A  437 SER cc_start: 0.8553 (t) cc_final: 0.8204 (p)
REVERT: A  460 MET cc_start: 0.7089 (mmm) cc_final: 0.6785 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 52
  average time/residue: 0.5365
  time to fit residues: 28.8741
Evaluate side-chains
  52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 SER
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  462 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A  17 GLN
A 289 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.181291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.137344 restraints weight = 16630.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 3.25
r_work: 0.3473 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3440
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3976  Z= 0.145
  Angle     :  0.571   6.212   5406  Z= 0.290
  Chirality :  0.039   0.138    625
  Planarity :  0.004   0.033    673
  Dihedral  :  6.575  54.800    563
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 21.34 %
    Favored  : 76.74 %
  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:  2.22 (0.39), residues: 489
  helix:  1.79 (0.27), residues: 375
  sheet: -1.65 (1.44), residues: 10
  loop :  0.89 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 290 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.012   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3974)
  covalent geometry    : angle       0.57057 ( 5402)
  SS BOND              : bond        0.00689 (    2)
  SS BOND              : angle       0.79143 (    4)
  hydrogen bonds       : bond        0.05136 (  274)
  hydrogen bonds       : angle       4.44202 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  289 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7728 (tp-100)
REVERT: A  313 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6683 (mm)
REVERT: A  437 SER cc_start: 0.8588 (t) cc_final: 0.8174 (p)
REVERT: A  460 MET cc_start: 0.6901 (mmm) cc_final: 0.6635 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 55
  average time/residue: 0.5653
  time to fit residues: 32.1476
Evaluate side-chains
  55 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  289 GLN
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  429 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0030
   chunk 5 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A 217 HIS
A 289 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.183472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.139009 restraints weight = 13172.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 3.01
r_work: 0.3515 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3976  Z= 0.126
  Angle     :  0.539   7.195   5406  Z= 0.273
  Chirality :  0.038   0.131    625
  Planarity :  0.004   0.031    673
  Dihedral  :  6.029  53.669    561
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.86 %
    Favored  : 76.26 %
  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:  2.42 (0.39), residues: 489
  helix:  1.93 (0.27), residues: 374
  sheet: -1.43 (1.47), residues: 10
  loop :  0.92 (0.69), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 290 
 TYR   0.015   0.001   TYR A 264 
 PHE   0.015   0.001   PHE A 351 
 TRP   0.015   0.001   TRP A 274 
 HIS   0.003   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3974)
  covalent geometry    : angle       0.53853 ( 5402)
  SS BOND              : bond        0.00508 (    2)
  SS BOND              : angle       0.73346 (    4)
  hydrogen bonds       : bond        0.04595 (  274)
  hydrogen bonds       : angle       4.23108 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  225 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6956 (tm)
REVERT: A  313 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6642 (mm)
REVERT: A  437 SER cc_start: 0.8605 (t) cc_final: 0.8193 (p)
REVERT: A  460 MET cc_start: 0.6729 (mmt) cc_final: 0.6458 (mmm)
  outliers start: 12
  outliers final: 3
  residues processed: 59
  average time/residue: 0.5407
  time to fit residues: 33.0193
Evaluate side-chains
  55 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  429 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 32 optimal weight:    0.0270
   chunk 17 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0470
   chunk 2 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 13 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.186598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.142510 restraints weight = 11543.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.87
r_work: 0.3560 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3543
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3543 r_free = 0.3543    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3543 r_free = 0.3543    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3543
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3976  Z= 0.114
  Angle     :  0.516   7.323   5406  Z= 0.261
  Chirality :  0.037   0.156    625
  Planarity :  0.004   0.037    673
  Dihedral  :  5.516  51.970    561
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.38 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.39), residues: 489
  helix:  2.02 (0.27), residues: 373
  sheet: -1.33 (1.44), residues: 10
  loop :  0.85 (0.68), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 290 
 TYR   0.015   0.001   TYR A 264 
 PHE   0.015   0.001   PHE A 351 
 TRP   0.015   0.002   TRP A 274 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3974)
  covalent geometry    : angle       0.51628 ( 5402)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       0.64886 (    4)
  hydrogen bonds       : bond        0.04106 (  274)
  hydrogen bonds       : angle       4.03640 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.6608 (pt0) cc_final: 0.5593 (pm20)
REVERT: A  289 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7647 (tp-100)
REVERT: A  437 SER cc_start: 0.8596 (t) cc_final: 0.8205 (p)
REVERT: A  460 MET cc_start: 0.6675 (mmt) cc_final: 0.6413 (mmm)
  outliers start: 15
  outliers final: 3
  residues processed: 62
  average time/residue: 0.4385
  time to fit residues: 28.2554
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  289 GLN
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  429 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 15 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.183931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.139996 restraints weight = 16167.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.14
r_work: 0.3522 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3492
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3976  Z= 0.129
  Angle     :  0.540   7.162   5406  Z= 0.272
  Chirality :  0.038   0.161    625
  Planarity :  0.004   0.027    673
  Dihedral  :  5.340  51.311    561
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.58 %
    Favored  : 75.78 %
  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:  2.41 (0.39), residues: 489
  helix:  1.94 (0.27), residues: 373
  sheet: -1.38 (1.43), residues: 10
  loop :  0.87 (0.68), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 290 
 TYR   0.018   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.011   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3974)
  covalent geometry    : angle       0.53988 ( 5402)
  SS BOND              : bond        0.00530 (    2)
  SS BOND              : angle       0.64309 (    4)
  hydrogen bonds       : bond        0.04488 (  274)
  hydrogen bonds       : angle       4.08492 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.6717 (pt0) cc_final: 0.5733 (pm20)
REVERT: A  225 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6922 (tm)
REVERT: A  286 ARG cc_start: 0.6247 (ttp-170) cc_final: 0.6016 (ttp-170)
REVERT: A  313 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6654 (mm)
REVERT: A  437 SER cc_start: 0.8603 (t) cc_final: 0.8218 (p)
REVERT: A  460 MET cc_start: 0.6858 (mmt) cc_final: 0.6602 (mmm)
  outliers start: 11
  outliers final: 4
  residues processed: 56
  average time/residue: 0.5122
  time to fit residues: 29.6841
Evaluate side-chains
  52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  429 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.184289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.140755 restraints weight = 9181.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.56
r_work: 0.3554 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3976  Z= 0.122
  Angle     :  0.532   7.234   5406  Z= 0.268
  Chirality :  0.038   0.183    625
  Planarity :  0.004   0.030    673
  Dihedral  :  5.084  50.172    561
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.34 %
    Favored  : 76.26 %
  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:  2.39 (0.38), residues: 489
  helix:  1.92 (0.26), residues: 373
  sheet: -1.15 (1.48), residues: 10
  loop :  0.85 (0.68), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 290 
 TYR   0.017   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3974)
  covalent geometry    : angle       0.53161 ( 5402)
  SS BOND              : bond        0.00478 (    2)
  SS BOND              : angle       0.63854 (    4)
  hydrogen bonds       : bond        0.04426 (  274)
  hydrogen bonds       : angle       4.07886 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.6697 (pt0) cc_final: 0.5760 (pm20)
REVERT: A  286 ARG cc_start: 0.6268 (ttp-170) cc_final: 0.6036 (ttp-170)
REVERT: A  313 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6578 (mm)
REVERT: A  437 SER cc_start: 0.8670 (t) cc_final: 0.8269 (p)
REVERT: A  460 MET cc_start: 0.6826 (mmt) cc_final: 0.6579 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 54
  average time/residue: 0.4901
  time to fit residues: 27.4951
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  429 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   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 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.183972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.140931 restraints weight = 8197.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.42
r_work: 0.3575 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3976  Z= 0.125
  Angle     :  0.543   7.356   5406  Z= 0.273
  Chirality :  0.038   0.177    625
  Planarity :  0.004   0.032    673
  Dihedral  :  5.069  49.269    561
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.58 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.38), residues: 489
  helix:  1.86 (0.26), residues: 374
  sheet: -1.10 (1.49), residues: 10
  loop :  0.90 (0.69), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 290 
 TYR   0.017   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3974)
  covalent geometry    : angle       0.54302 ( 5402)
  SS BOND              : bond        0.00504 (    2)
  SS BOND              : angle       0.62481 (    4)
  hydrogen bonds       : bond        0.04453 (  274)
  hydrogen bonds       : angle       4.15721 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.6771 (pt0) cc_final: 0.5800 (pm20)
REVERT: A  313 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6587 (mm)
REVERT: A  437 SER cc_start: 0.8697 (t) cc_final: 0.8296 (p)
REVERT: A  458 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7835 (mp)
REVERT: A  460 MET cc_start: 0.6818 (mmt) cc_final: 0.6559 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 55
  average time/residue: 0.4952
  time to fit residues: 28.2370
Evaluate side-chains
  53 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  458 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4132 r_free = 0.4132 target = 0.184558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.139121 restraints weight = 16454.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 3.40
r_work: 0.3522 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3514
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3514 r_free = 0.3514    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3514 r_free = 0.3514    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3514
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   3976  Z= 0.122
  Angle     :  0.541   7.402   5406  Z= 0.273
  Chirality :  0.038   0.168    625
  Planarity :  0.004   0.032    673
  Dihedral  :  4.922  48.309    561
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.82 %
    Favored  : 75.78 %
  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:  2.31 (0.39), residues: 489
  helix:  1.85 (0.27), residues: 374
  sheet: -1.05 (1.51), residues: 10
  loop :  0.88 (0.69), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 290 
 TYR   0.017   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 213 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3974)
  covalent geometry    : angle       0.54101 ( 5402)
  SS BOND              : bond        0.00448 (    2)
  SS BOND              : angle       0.61303 (    4)
  hydrogen bonds       : bond        0.04317 (  274)
  hydrogen bonds       : angle       4.15808 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.6749 (pt0) cc_final: 0.5780 (pm20)
REVERT: A  313 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6560 (mm)
REVERT: A  437 SER cc_start: 0.8645 (t) cc_final: 0.8255 (p)
REVERT: A  458 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7765 (mp)
REVERT: A  460 MET cc_start: 0.6793 (mmt) cc_final: 0.6520 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 51
  average time/residue: 0.4402
  time to fit residues: 23.3840
Evaluate side-chains
  51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  458 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0980
   chunk 20 optimal weight:    7.9990
   chunk 46 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.185209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.141727 restraints weight = 9481.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.62
r_work: 0.3572 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3561
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3976  Z= 0.118
  Angle     :  0.539   7.482   5406  Z= 0.272
  Chirality :  0.038   0.159    625
  Planarity :  0.004   0.033    673
  Dihedral  :  4.836  47.406    561
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 22.54 %
    Favored  : 75.54 %
  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:  2.33 (0.39), residues: 489
  helix:  1.86 (0.27), residues: 375
  sheet: -1.01 (1.53), residues: 10
  loop :  0.86 (0.69), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 290 
 TYR   0.017   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.011   0.001   TRP A 213 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3974)
  covalent geometry    : angle       0.53887 ( 5402)
  SS BOND              : bond        0.00419 (    2)
  SS BOND              : angle       0.60847 (    4)
  hydrogen bonds       : bond        0.04211 (  274)
  hydrogen bonds       : angle       4.13439 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.6725 (pt0) cc_final: 0.5756 (pm20)
REVERT: A  313 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6586 (mm)
REVERT: A  394 ARG cc_start: 0.6018 (mpt180) cc_final: 0.5753 (mtm-85)
REVERT: A  437 SER cc_start: 0.8620 (t) cc_final: 0.8215 (p)
REVERT: A  458 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7673 (mp)
REVERT: A  460 MET cc_start: 0.6681 (mmt) cc_final: 0.6413 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 52
  average time/residue: 0.5591
  time to fit residues: 30.1626
Evaluate side-chains
  52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  458 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 10 optimal weight:    0.0970
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0570
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.3594

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.188536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.144453 restraints weight = 12241.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.97
r_work: 0.3599 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   3976  Z= 0.112
  Angle     :  0.534   7.404   5406  Z= 0.268
  Chirality :  0.037   0.156    625
  Planarity :  0.004   0.035    673
  Dihedral  :  4.634  45.812    561
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 22.54 %
    Favored  : 75.78 %
  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:  2.38 (0.39), residues: 489
  helix:  1.87 (0.27), residues: 378
  sheet: -1.00 (1.53), residues: 10
  loop :  0.98 (0.70), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 290 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.014   0.001   TRP A 274 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3974)
  covalent geometry    : angle       0.53432 ( 5402)
  SS BOND              : bond        0.00283 (    2)
  SS BOND              : angle       0.61723 (    4)
  hydrogen bonds       : bond        0.03814 (  274)
  hydrogen bonds       : angle       4.04409 (  811)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.6731 (pt0) cc_final: 0.5746 (pm20)
REVERT: A  289 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7605 (tp-100)
REVERT: A  313 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6523 (mm)
REVERT: A  437 SER cc_start: 0.8659 (t) cc_final: 0.8280 (p)
REVERT: A  458 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7684 (mp)
REVERT: A  460 MET cc_start: 0.6662 (mmt) cc_final: 0.6398 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 57
  average time/residue: 0.4748
  time to fit residues: 28.0928
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  289 GLN
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  458 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.188017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.143497 restraints weight = 14133.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 3.18
r_work: 0.3583 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.452   3976  Z= 0.359
  Angle     :  1.195  59.149   5406  Z= 0.708
  Chirality :  0.041   0.356    625
  Planarity :  0.004   0.043    673
  Dihedral  :  4.763  45.848    561
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  1.65 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 23.50 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.22 %
  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:  2.30 (0.39), residues: 489
  helix:  1.84 (0.27), residues: 375
  sheet: -1.02 (1.53), residues: 10
  loop :  0.83 (0.69), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 286 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.013   0.002   TRP A 274 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00863 ( 3974)
  covalent geometry    : angle       1.19501 ( 5402)
  SS BOND              : bond        0.00418 (    2)
  SS BOND              : angle       0.62894 (    4)
  hydrogen bonds       : bond        0.03903 (  274)
  hydrogen bonds       : angle       4.06798 (  811)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1593.91 seconds
wall clock time: 28 minutes 6.04 seconds (1686.04 seconds total)