Starting phenix.real_space_refine
on Sat Apr 26 23:28:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sdy_40354/04_2025/8sdy_40354.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sdy_40354/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sdy_40354/04_2025/8sdy_40354.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sdy_40354/04_2025/8sdy_40354.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sdy_40354/04_2025/8sdy_40354.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sdy_40354/04_2025/8sdy_40354.cif"
  }
  resolution = 2.79
  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=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.87, per 1000 atoms: 1.25
  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: 1.25
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.52
  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: 1.17

  Time building geometry restraints manager: 1.43 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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     17.700
  Find NCS groups from input model:        0.040
  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:14.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.680
-------------------------------------------------------------------------------
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 (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:  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
 TRP   0.009   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 217 
 PHE   0.013   0.001   PHE A 442 
 TYR   0.016   0.001   TYR A 264 
 ARG   0.016   0.001   ARG A 290 

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

*********************** 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  : 0.439 
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: 1.1504
  time to fit residues: 62.1344
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  : 0.403 
-------------------------------------------------------------------------------
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 41 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    0.2980
   chunk 38 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4106 r_free = 0.4106 target = 0.181144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.138324 restraints weight = 12521.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.90
r_work: 0.3489 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3468 r_free = 0.3468    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3468
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.0835

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= 0.144
  Angle     :  0.570   6.190   5406  Z= 0.289
  Chirality :  0.039   0.137    625
  Planarity :  0.004   0.033    673
  Dihedral  :  6.595  54.834    563
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 22.06 %
    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 (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:  2.21 (0.39), residues: 489
  helix:  1.78 (0.27), residues: 375
  sheet: -1.65 (1.45), residues: 10
  loop :  0.88 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 346 
 HIS   0.003   0.001   HIS A  48 
 PHE   0.014   0.001   PHE A 351 
 TYR   0.016   0.001   TYR A 264 
 ARG   0.009   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05153 (  274)
  hydrogen bonds       : angle       4.44640 (  811)
  SS BOND              : bond        0.00675 (    2)
  SS BOND              : angle       0.80429 (    4)
  covalent geometry    : bond        0.00317 ( 3974)
  covalent geometry    : angle       0.57001 ( 5402)

*********************** 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
  58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A  313 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6675 (mm)
REVERT: A  437 SER cc_start: 0.8571 (t) cc_final: 0.8149 (p)
REVERT: A  460 MET cc_start: 0.6848 (mmm) cc_final: 0.6578 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 54
  average time/residue: 1.1370
  time to fit residues: 63.7994
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  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ILE
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 6 optimal weight:   20.0000
   chunk 47 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.183598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.139781 restraints weight = 10853.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.75
r_work: 0.3535 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1173

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     :  0.529   7.002   5406  Z= 0.268
  Chirality :  0.038   0.130    625
  Planarity :  0.004   0.031    673
  Dihedral  :  5.931  53.444    561
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.10 %
    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 (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:  2.44 (0.39), residues: 489
  helix:  1.96 (0.27), residues: 374
  sheet: -1.44 (1.47), residues: 10
  loop :  0.91 (0.69), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 274 
 HIS   0.003   0.001   HIS A 217 
 PHE   0.015   0.001   PHE A 351 
 TYR   0.016   0.001   TYR A 264 
 ARG   0.008   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04597 (  274)
  hydrogen bonds       : angle       4.21005 (  811)
  SS BOND              : bond        0.00499 (    2)
  SS BOND              : angle       0.70881 (    4)
  covalent geometry    : bond        0.00265 ( 3974)
  covalent geometry    : angle       0.52917 ( 5402)

*********************** 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
  63 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6300 (pm20)
REVERT: A  225 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6976 (tm)
REVERT: A  437 SER cc_start: 0.8593 (t) cc_final: 0.8185 (p)
REVERT: A  460 MET cc_start: 0.6727 (mmt) cc_final: 0.6448 (mmm)
  outliers start: 12
  outliers final: 3
  residues processed: 57
  average time/residue: 1.0786
  time to fit residues: 63.9746
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  225 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 14 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    0.1980
   chunk 34 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0170
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.5020

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.185795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.142001 restraints weight = 18372.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 3.28
r_work: 0.3523 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
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 = 0.24   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 = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3976  Z= 0.115
  Angle     :  0.513   7.346   5406  Z= 0.258
  Chirality :  0.037   0.160    625
  Planarity :  0.004   0.037    673
  Dihedral  :  5.559  52.127    561
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.86 %
    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 (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:  2.48 (0.39), residues: 489
  helix:  2.00 (0.27), residues: 373
  sheet: -1.36 (1.47), residues: 10
  loop :  0.87 (0.68), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 213 
 HIS   0.001   0.000   HIS A  48 
 PHE   0.015   0.001   PHE A 351 
 TYR   0.015   0.001   TYR A 264 
 ARG   0.008   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04220 (  274)
  hydrogen bonds       : angle       4.06033 (  811)
  SS BOND              : bond        0.00387 (    2)
  SS BOND              : angle       0.68808 (    4)
  covalent geometry    : bond        0.00234 ( 3974)
  covalent geometry    : angle       0.51241 ( 5402)

*********************** 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
  65 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.7053 (pt0) cc_final: 0.6026 (pm20)
REVERT: A  313 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6662 (mm)
REVERT: A  437 SER cc_start: 0.8588 (t) cc_final: 0.8204 (p)
REVERT: A  460 MET cc_start: 0.6808 (mmt) cc_final: 0.6555 (mmm)
  outliers start: 14
  outliers final: 3
  residues processed: 61
  average time/residue: 1.3587
  time to fit residues: 86.2599
Evaluate side-chains
  52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 MET
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.182950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138429 restraints weight = 12013.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.91
r_work: 0.3519 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3511
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3511
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1434

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= 0.131
  Angle     :  0.536   6.984   5406  Z= 0.270
  Chirality :  0.039   0.159    625
  Planarity :  0.004   0.031    673
  Dihedral  :  5.316  51.219    561
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.10 %
    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 (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:  2.40 (0.39), residues: 489
  helix:  1.90 (0.26), residues: 375
  sheet: -1.28 (1.45), residues: 10
  loop :  0.99 (0.69), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A  48 
 PHE   0.012   0.001   PHE A 351 
 TYR   0.018   0.001   TYR A 264 
 ARG   0.009   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  274)
  hydrogen bonds       : angle       4.11859 (  811)
  SS BOND              : bond        0.00600 (    2)
  SS BOND              : angle       0.66187 (    4)
  covalent geometry    : bond        0.00288 ( 3974)
  covalent geometry    : angle       0.53543 ( 5402)

*********************** 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
  57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.5966 (pm20)
REVERT: A  225 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6856 (tm)
REVERT: A  286 ARG cc_start: 0.6205 (ttp-170) cc_final: 0.5983 (ttp-170)
REVERT: A  313 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6555 (mm)
REVERT: A  437 SER cc_start: 0.8595 (t) cc_final: 0.8178 (p)
REVERT: A  460 MET cc_start: 0.6692 (mmt) cc_final: 0.6419 (mmm)
  outliers start: 11
  outliers final: 3
  residues processed: 53
  average time/residue: 1.0546
  time to fit residues: 58.2427
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  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
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 1 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 = 0.4081 r_free = 0.4081 target = 0.178910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.134424 restraints weight = 12530.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.94
r_work: 0.3445 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3446
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3976  Z= 0.171
  Angle     :  0.578   7.022   5406  Z= 0.294
  Chirality :  0.041   0.195    625
  Planarity :  0.004   0.031    673
  Dihedral  :  5.459  50.989    561
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.34 %
    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 (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:  1.95 (0.38), residues: 489
  helix:  1.57 (0.26), residues: 382
  sheet: -1.45 (1.39), residues: 10
  loop :  0.79 (0.69), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 213 
 HIS   0.003   0.001   HIS A  48 
 PHE   0.011   0.002   PHE A 235 
 TYR   0.021   0.002   TYR A 264 
 ARG   0.007   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05517 (  274)
  hydrogen bonds       : angle       4.30853 (  811)
  SS BOND              : bond        0.00929 (    2)
  SS BOND              : angle       0.73203 (    4)
  covalent geometry    : bond        0.00403 ( 3974)
  covalent geometry    : angle       0.57827 ( 5402)

*********************** 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
  60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6380 (pm20)
REVERT: A  313 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6539 (mm)
REVERT: A  437 SER cc_start: 0.8602 (t) cc_final: 0.8167 (p)
REVERT: A  460 MET cc_start: 0.6804 (mmt) cc_final: 0.6506 (mmm)
  outliers start: 12
  outliers final: 5
  residues processed: 56
  average time/residue: 1.1471
  time to fit residues: 66.6112
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
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 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0020
   chunk 16 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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 = 0.4131 r_free = 0.4131 target = 0.183910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.140358 restraints weight = 15520.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 3.15
r_work: 0.3518 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3495
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3976  Z= 0.121
  Angle     :  0.544   7.744   5406  Z= 0.272
  Chirality :  0.038   0.174    625
  Planarity :  0.004   0.032    673
  Dihedral  :  5.199  49.745    561
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 22.78 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.29 (0.38), residues: 489
  helix:  1.84 (0.26), residues: 373
  sheet: -1.15 (1.49), residues: 10
  loop :  0.88 (0.68), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A  48 
 PHE   0.016   0.001   PHE A 351 
 TYR   0.016   0.001   TYR A 264 
 ARG   0.008   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04533 (  274)
  hydrogen bonds       : angle       4.16321 (  811)
  SS BOND              : bond        0.00416 (    2)
  SS BOND              : angle       0.67251 (    4)
  covalent geometry    : bond        0.00252 ( 3974)
  covalent geometry    : angle       0.54425 ( 5402)

*********************** 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
  55 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6409 (pm20)
REVERT: A  289 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7757 (tp-100)
REVERT: A  313 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6580 (mm)
REVERT: A  437 SER cc_start: 0.8629 (t) cc_final: 0.8244 (p)
REVERT: A  458 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7829 (mp)
REVERT: A  460 MET cc_start: 0.6804 (mmt) cc_final: 0.6508 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 53
  average time/residue: 1.1615
  time to fit residues: 64.0200
Evaluate side-chains
  52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
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 22 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.182639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.138455 restraints weight = 13009.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 3.00
r_work: 0.3514 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1522

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= 0.133
  Angle     :  0.554   7.461   5406  Z= 0.280
  Chirality :  0.039   0.172    625
  Planarity :  0.004   0.033    673
  Dihedral  :  5.211  49.263    561
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.30 %
    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 (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:  2.17 (0.38), residues: 489
  helix:  1.74 (0.26), residues: 374
  sheet: -1.17 (1.47), residues: 10
  loop :  0.87 (0.69), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 213 
 HIS   0.002   0.001   HIS A  48 
 PHE   0.013   0.001   PHE A 351 
 TYR   0.017   0.001   TYR A 264 
 ARG   0.008   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04707 (  274)
  hydrogen bonds       : angle       4.23911 (  811)
  SS BOND              : bond        0.00591 (    2)
  SS BOND              : angle       0.65812 (    4)
  covalent geometry    : bond        0.00298 ( 3974)
  covalent geometry    : angle       0.55427 ( 5402)

*********************** 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
  56 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6079 (pm20)
REVERT: A  289 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7595 (tp-100)
REVERT: A  313 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6552 (mm)
REVERT: A  437 SER cc_start: 0.8630 (t) cc_final: 0.8209 (p)
REVERT: A  458 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7757 (mp)
REVERT: A  460 MET cc_start: 0.6726 (mmt) cc_final: 0.6426 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 53
  average time/residue: 1.1492
  time to fit residues: 63.2882
Evaluate side-chains
  56 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
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 15 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.184340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.141192 restraints weight = 9528.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.58
r_work: 0.3564 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    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 = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   3976  Z= 0.124
  Angle     :  0.547   7.566   5406  Z= 0.277
  Chirality :  0.038   0.165    625
  Planarity :  0.004   0.033    673
  Dihedral  :  5.069  49.988    561
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.54 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.22 (0.39), residues: 489
  helix:  1.74 (0.26), residues: 377
  sheet: -1.07 (1.51), residues: 10
  loop :  1.01 (0.70), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 346 
 HIS   0.001   0.000   HIS A  48 
 PHE   0.015   0.001   PHE A 351 
 TYR   0.016   0.001   TYR A 264 
 ARG   0.008   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04370 (  274)
  hydrogen bonds       : angle       4.18671 (  811)
  SS BOND              : bond        0.00455 (    2)
  SS BOND              : angle       0.64340 (    4)
  covalent geometry    : bond        0.00275 ( 3974)
  covalent geometry    : angle       0.54694 ( 5402)

*********************** 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
  57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6094 (pm20)
REVERT: A  313 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6537 (mm)
REVERT: A  437 SER cc_start: 0.8601 (t) cc_final: 0.8214 (p)
REVERT: A  458 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7734 (mp)
REVERT: A  460 MET cc_start: 0.6753 (mmt) cc_final: 0.6450 (mmm)
  outliers start: 9
  outliers final: 6
  residues processed: 53
  average time/residue: 1.2019
  time to fit residues: 66.0863
Evaluate side-chains
  57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  214 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 18 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   chunk 26 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0270
   chunk 34 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7238

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.184927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140732 restraints weight = 12780.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.99
r_work: 0.3548 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3511
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3511
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3976  Z= 0.122
  Angle     :  0.557   7.984   5406  Z= 0.283
  Chirality :  0.038   0.164    625
  Planarity :  0.004   0.032    673
  Dihedral  :  5.022  51.081    561
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.30 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.22 (0.39), residues: 489
  helix:  1.75 (0.26), residues: 377
  sheet: -1.11 (1.50), residues: 10
  loop :  0.97 (0.70), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 346 
 HIS   0.001   0.000   HIS A  48 
 PHE   0.014   0.001   PHE A 351 
 TYR   0.016   0.001   TYR A 264 
 ARG   0.009   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04311 (  274)
  hydrogen bonds       : angle       4.17444 (  811)
  SS BOND              : bond        0.00453 (    2)
  SS BOND              : angle       0.63561 (    4)
  covalent geometry    : bond        0.00265 ( 3974)
  covalent geometry    : angle       0.55697 ( 5402)

********************** 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: 10
    poor density    : 48
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6093 (pm20)
REVERT: A  289 GLN cc_start: 0.7862 (tp-100) cc_final: 0.6941 (tm-30)
REVERT: A  313 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6529 (mm)
REVERT: A  437 SER cc_start: 0.8611 (t) cc_final: 0.8225 (p)
REVERT: A  458 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7737 (mp)
REVERT: A  460 MET cc_start: 0.6789 (mmt) cc_final: 0.6509 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 54
  average time/residue: 1.2089
  time to fit residues: 67.8079
Evaluate side-chains
  56 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  214 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 18 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.9362

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.184195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.141071 restraints weight = 9520.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.59
r_work: 0.3557 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1719

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= 0.127
  Angle     :  0.561   7.420   5406  Z= 0.285
  Chirality :  0.039   0.164    625
  Planarity :  0.004   0.033    673
  Dihedral  :  5.073  53.607    561
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.30 %
    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 (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:  2.17 (0.38), residues: 489
  helix:  1.69 (0.26), residues: 377
  sheet: -1.12 (1.50), residues: 10
  loop :  1.03 (0.70), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 213 
 HIS   0.002   0.001   HIS A  48 
 PHE   0.014   0.001   PHE A 351 
 TYR   0.017   0.001   TYR A 264 
 ARG   0.008   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04453 (  274)
  hydrogen bonds       : angle       4.19359 (  811)
  SS BOND              : bond        0.00511 (    2)
  SS BOND              : angle       0.62113 (    4)
  covalent geometry    : bond        0.00282 ( 3974)
  covalent geometry    : angle       0.56051 ( 5402)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3369.35 seconds
wall clock time: 58 minutes 11.94 seconds (3491.94 seconds total)