Starting phenix.real_space_refine
on Thu Mar  6 02:45:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bvt_16271/03_2025/8bvt_16271.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bvt_16271/03_2025/8bvt_16271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bvt_16271/03_2025/8bvt_16271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bvt_16271/03_2025/8bvt_16271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bvt_16271/03_2025/8bvt_16271.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bvt_16271/03_2025/8bvt_16271.cif"
  }
  resolution = 3.94
  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=   0.002 sd=   0.042
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      33      5.16       5
     C    2907      2.51       5
     N     776      2.21       5
     O     801      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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4517
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 3933
          Classifications: {'peptide': 508}
          Link IDs: {'PTRANS': 28, 'TRANS': 479}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 565
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 353
          Unresolved non-hydrogen angles: 462
          Unresolved non-hydrogen dihedrals: 309
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 216
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'RTO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.78, per 1000 atoms: 0.84
  Number of scatterers: 4517
  At special positions: 0
  Unit cell: (115.648, 70.72, 82.368, 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      33     16.00
     O     801      8.00
     N     776      7.00
     C    2907      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=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 558.8 milliseconds
  

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1146

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      64.0% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.611A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 26
      removed outlier: 4.283A  pdb=" N   VAL A  21 " --> pdb=" O   GLN A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 37
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 119 through 125
    Processing helix  chain 'A' and resid 132 through 160
      removed outlier: 3.687A  pdb=" N   GLN A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLY A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 181
    Processing helix  chain 'A' and resid 184 through 214
      removed outlier: 3.746A  pdb=" N   SER A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   MET A 207 " --> pdb=" O   ALA A 203 " (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
    Processing helix  chain 'A' and resid 246 through 266
      Proline residue:  A 257  - end of helix
      removed outlier: 4.009A  pdb=" N   ILE A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   TYR A 264 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 279
    Processing helix  chain 'A' and resid 281 through 296
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 4.255A  pdb=" N   LYS A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 311
      removed outlier: 3.508A  pdb=" N   LEU A 309 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 332
      removed outlier: 3.531A  pdb=" N   CYS A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 359
      removed outlier: 3.981A  pdb=" N   ASP A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 364
      removed outlier: 3.974A  pdb=" N   GLY A 364 " --> pdb=" O   GLN A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 392
      removed outlier: 3.733A  pdb=" N   ASP A 378 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LEU A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'A' and resid 420 through 449
    Processing helix  chain 'A' and resid 453 through 478
      Proline residue:  A 473  - end of helix
      removed outlier: 4.010A  pdb=" N   THR A 478 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 502
      Proline residue:  A 494  - end of helix
    Processing helix  chain 'A' and resid 515 through 517
      No H-bonds generated for 'chain 'A' and resid 515 through 517'
    Processing helix  chain 'A' and resid 518 through 523
    Processing helix  chain 'B' and resid 53 through 56
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 4.101A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81
    Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.802A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  83 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   MET B  83 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS B  22 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 59
      removed outlier: 3.607A  pdb=" N   ARG B  59 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    843 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: 1.45

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.01 -     1.17: 1
        1.17 -     1.33: 1150
        1.33 -     1.49: 1534
        1.49 -     1.66: 1875
        1.66 -     1.82: 53
  Bond restraints: 4613
  Sorted by residual:
  bond pdb=" CB  PRO A  88 "
       pdb=" CG  PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.492  1.011  0.481 5.00e-02 4.00e+02 9.25e+01
  bond pdb=" CG  PRO A  88 "
       pdb=" CD  PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.503  1.217  0.286 3.40e-02 8.65e+02 7.06e+01
  bond pdb=" N   PRO A  88 "
       pdb=" CA  PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.465  1.566 -0.101 2.03e-02 2.43e+03 2.49e+01
  bond pdb=" N04 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.625  1.711 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C11 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.776  1.817 -0.041 2.00e-02 2.50e+03 4.10e+00
  ... (remaining 4608 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.67: 6278
        8.67 -    17.35: 10
       17.35 -    26.02: 1
       26.02 -    34.69: 1
       34.69 -    43.37: 2
  Bond angle restraints: 6292
  Sorted by residual:
  angle pdb=" CA  PRO A  88 "
        pdb=" CB  PRO A  88 "
        pdb=" CG  PRO A  88 "
      ideal   model   delta    sigma   weight residual
     104.50   66.53   37.97 1.90e+00 2.77e-01 3.99e+02
  angle pdb=" N   PRO A  88 "
        pdb=" CD  PRO A  88 "
        pdb=" CG  PRO A  88 "
      ideal   model   delta    sigma   weight residual
     103.20   74.08   29.12 1.50e+00 4.44e-01 3.77e+02
  angle pdb=" CB  PRO A  88 "
        pdb=" CG  PRO A  88 "
        pdb=" CD  PRO A  88 "
      ideal   model   delta    sigma   weight residual
     106.10  149.47  -43.37 3.20e+00 9.77e-02 1.84e+02
  angle pdb=" CA  PRO A  88 "
        pdb=" N   PRO A  88 "
        pdb=" CD  PRO A  88 "
      ideal   model   delta    sigma   weight residual
     112.00   99.99   12.01 1.40e+00 5.10e-01 7.36e+01
  angle pdb=" CA  PRO A 494 "
        pdb=" N   PRO A 494 "
        pdb=" CD  PRO A 494 "
      ideal   model   delta    sigma   weight residual
     112.00  102.70    9.30 1.40e+00 5.10e-01 4.41e+01
  ... (remaining 6287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 2318
       17.69 -    35.37: 314
       35.37 -    53.06: 74
       53.06 -    70.75: 12
       70.75 -    88.44: 10
  Dihedral angle restraints: 2728
    sinusoidal: 944
      harmonic: 1784
  Sorted by residual:
  dihedral pdb=" CB  CYS A  78 "
           pdb=" SG  CYS A  78 "
           pdb=" SG  CYS A 128 "
           pdb=" CB  CYS A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.55   65.45     1      1.00e+01 1.00e-02 5.61e+01
  dihedral pdb=" N   PRO A  88 "
           pdb=" CG  PRO A  88 "
           pdb=" CD  PRO A  88 "
           pdb=" CB  PRO A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00  107.54  -77.54     1      1.50e+01 4.44e-03 3.35e+01
  dihedral pdb=" CA  PRO A  88 "
           pdb=" CB  PRO A  88 "
           pdb=" CG  PRO A  88 "
           pdb=" CD  PRO A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      38.00  123.96  -85.96     1      2.00e+01 2.50e-03 2.23e+01
  ... (remaining 2725 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 564
       0.048 -    0.095: 138
       0.095 -    0.143: 31
       0.143 -    0.190: 6
       0.190 -    0.238: 3
  Chirality restraints: 742
  Sorted by residual:
  chirality pdb=" CA  PRO A 494 "
            pdb=" N   PRO A 494 "
            pdb=" C   PRO A 494 "
            pdb=" CB  PRO A 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  PRO A  88 "
            pdb=" N   PRO A  88 "
            pdb=" C   PRO A  88 "
            pdb=" CB  PRO A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.93   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  PRO A 257 "
            pdb=" N   PRO A 257 "
            pdb=" C   PRO A 257 "
            pdb=" CB  PRO A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.11e-01
  ... (remaining 739 not shown)

  Planarity restraints: 799
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 114 "    0.052 2.00e-02 2.50e+03   9.66e-02 9.34e+01
        pdb=" C   SER B 114 "   -0.167 2.00e-02 2.50e+03
        pdb=" O   SER B 114 "    0.061 2.00e-02 2.50e+03
        pdb=" N   ALA B 115 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 493 "    0.070 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO A 494 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO A 494 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 494 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  87 "    0.046 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO A  88 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.035 5.00e-02 4.00e+02
  ... (remaining 796 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 164
        2.71 -     3.25: 4839
        3.25 -     3.80: 7722
        3.80 -     4.35: 8493
        4.35 -     4.90: 14395
  Nonbonded interactions: 35613
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 172 "
            pdb=" OG  SER A 198 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OD1 ASP A  70 "
            pdb=" N   GLN A  74 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" OG  SER A 401 "
            pdb=" O   CYS A 433 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NH1 ARG A 394 "
            pdb=" OG1 THR A 507 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" ND2 ASN A  39 "
            pdb=" O   MET A 358 "
     model   vdw
     2.285 3.120
  ... (remaining 35608 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.170
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.040
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:5.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
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      :  0.009   0.481   4613  Z= 0.522
  Angle     :  1.221  43.365   6292  Z= 0.576
  Chirality :  0.046   0.238    742
  Planarity :  0.007   0.100    799
  Dihedral  : 17.639  88.436   1576
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 44.99 %
    Favored  : 54.78 %
  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:  0.33 (0.34), residues: 615
  helix:  1.09 (0.27), residues: 357
  sheet:  0.48 (0.82), residues: 48
  loop : -1.34 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 109 
 HIS   0.002   0.001   HIS A  47 
 PHE   0.025   0.002   PHE A 262 
 TYR   0.016   0.001   TYR A 482 
 ARG   0.008   0.000   ARG A 273 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A  482 TYR cc_start: 0.7709 (t80) cc_final: 0.7377 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1106
  time to fit residues: 14.5847
Evaluate side-chains
  92 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:   50.0000
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    9.9990
   chunk 35 optimal weight:    0.6980
   chunk 55 optimal weight:   20.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.126964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.106152 restraints weight = 12205.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.109132 restraints weight = 6208.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.110996 restraints weight = 3960.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.0716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4613  Z= 0.193
  Angle     :  0.747  13.987   6292  Z= 0.350
  Chirality :  0.041   0.149    742
  Planarity :  0.004   0.036    799
  Dihedral  :  5.035  29.273    686
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 39.86 %
    Favored  : 57.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.35), residues: 615
  helix:  1.27 (0.27), residues: 362
  sheet:  0.86 (0.81), residues: 49
  loop : -1.29 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 109 
 HIS   0.002   0.000   HIS A  47 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.017   0.001   TYR A 354 
 ARG   0.005   0.000   ARG A 273 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8705 (tpt) cc_final: 0.8261 (tpt)
REVERT: A  122 THR cc_start: 0.9381 (p) cc_final: 0.9077 (t)
REVERT: A  142 MET cc_start: 0.9578 (tpp) cc_final: 0.9257 (tpp)
REVERT: A  168 ASN cc_start: 0.7960 (m-40) cc_final: 0.7547 (m110)
REVERT: A  482 TYR cc_start: 0.7562 (t80) cc_final: 0.7146 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1043
  time to fit residues: 16.0898
Evaluate side-chains
  103 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 50 optimal weight:   40.0000
   chunk 41 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.125149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.103513 restraints weight = 12447.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.106512 restraints weight = 6342.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.108514 restraints weight = 4076.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4613  Z= 0.244
  Angle     :  0.704  10.074   6292  Z= 0.330
  Chirality :  0.041   0.156    742
  Planarity :  0.005   0.045    799
  Dihedral  :  5.006  30.253    686
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 38.93 %
    Favored  : 56.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.35), residues: 615
  helix:  1.38 (0.27), residues: 359
  sheet:  0.86 (0.81), residues: 49
  loop : -1.30 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A  47 
 PHE   0.014   0.001   PHE A 262 
 TYR   0.013   0.001   TYR A 354 
 ARG   0.003   0.000   ARG A 273 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8806 (tpt) cc_final: 0.8392 (tpt)
REVERT: A   76 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7934 (mm-30)
REVERT: A  122 THR cc_start: 0.9434 (p) cc_final: 0.9135 (t)
REVERT: A  361 GLN cc_start: 0.7680 (mm110) cc_final: 0.7476 (mm110)
REVERT: A  394 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7015 (mtm180)
REVERT: A  482 TYR cc_start: 0.7556 (t80) cc_final: 0.6998 (t80)
REVERT: A  485 MET cc_start: 0.9198 (tmm) cc_final: 0.8736 (tpt)
  outliers start: 21
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1131
  time to fit residues: 17.7405
Evaluate side-chains
  115 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  339 PHE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.126583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.105016 restraints weight = 12473.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.108038 restraints weight = 6315.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.110133 restraints weight = 4047.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4613  Z= 0.193
  Angle     :  0.696  11.063   6292  Z= 0.319
  Chirality :  0.041   0.165    742
  Planarity :  0.004   0.046    799
  Dihedral  :  4.818  30.606    686
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 39.86 %
    Favored  : 54.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.35), residues: 615
  helix:  1.40 (0.27), residues: 362
  sheet:  0.96 (0.81), residues: 49
  loop : -1.31 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 274 
 HIS   0.002   0.000   HIS A  47 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.010   0.001   TYR A 354 
 ARG   0.002   0.000   ARG A 273 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   76 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7893 (mm-30)
REVERT: A  122 THR cc_start: 0.9434 (p) cc_final: 0.9136 (t)
REVERT: A  394 ARG cc_start: 0.7728 (mtm180) cc_final: 0.6963 (mtm180)
REVERT: A  482 TYR cc_start: 0.7591 (t80) cc_final: 0.6962 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 112
  average time/residue: 0.1091
  time to fit residues: 17.0654
Evaluate side-chains
  112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 59 optimal weight:   40.0000
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.125587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.103765 restraints weight = 12549.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.106776 restraints weight = 6426.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.108833 restraints weight = 4164.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4613  Z= 0.194
  Angle     :  0.717  15.568   6292  Z= 0.324
  Chirality :  0.041   0.169    742
  Planarity :  0.004   0.050    799
  Dihedral  :  4.723  31.353    686
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 38.69 %
    Favored  : 55.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.35), residues: 615
  helix:  1.44 (0.27), residues: 359
  sheet:  0.84 (0.83), residues: 50
  loop : -1.28 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 274 
 HIS   0.002   0.000   HIS A  47 
 PHE   0.013   0.001   PHE A 347 
 TYR   0.009   0.001   TYR A 354 
 ARG   0.002   0.000   ARG A 273 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A   76 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7914 (mm-30)
REVERT: A  122 THR cc_start: 0.9422 (p) cc_final: 0.9120 (t)
REVERT: A  361 GLN cc_start: 0.7534 (mm110) cc_final: 0.7293 (mm110)
REVERT: A  399 MET cc_start: 0.7981 (mpp) cc_final: 0.7747 (mpp)
REVERT: A  482 TYR cc_start: 0.7588 (t80) cc_final: 0.6930 (t80)
REVERT: A  485 MET cc_start: 0.9156 (tmm) cc_final: 0.8703 (tpt)
  outliers start: 26
  outliers final: 20
  residues processed: 111
  average time/residue: 0.1033
  time to fit residues: 16.5727
Evaluate side-chains
  113 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 54 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 51 optimal weight:   50.0000
   chunk 60 optimal weight:   20.0000
   chunk 15 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.125726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.104059 restraints weight = 12485.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.107069 restraints weight = 6348.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.108980 restraints weight = 4077.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4613  Z= 0.217
  Angle     :  0.730  15.314   6292  Z= 0.328
  Chirality :  0.041   0.168    742
  Planarity :  0.004   0.049    799
  Dihedral  :  4.675  32.438    686
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 38.46 %
    Favored  : 54.78 %
  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:  0.77 (0.35), residues: 615
  helix:  1.46 (0.27), residues: 359
  sheet:  0.91 (0.83), residues: 50
  loop : -1.32 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 274 
 HIS   0.003   0.001   HIS A  47 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.009   0.001   TYR A 354 
 ARG   0.002   0.000   ARG A 273 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   76 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7912 (mm-30)
REVERT: A  122 THR cc_start: 0.9444 (p) cc_final: 0.9171 (t)
REVERT: A  361 GLN cc_start: 0.7696 (mm110) cc_final: 0.7412 (mm110)
REVERT: A  482 TYR cc_start: 0.7583 (t80) cc_final: 0.6921 (t80)
  outliers start: 29
  outliers final: 24
  residues processed: 114
  average time/residue: 0.0947
  time to fit residues: 15.4161
Evaluate side-chains
  117 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 GLN
A 371 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.125363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.103627 restraints weight = 12369.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.106596 restraints weight = 6376.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.108640 restraints weight = 4143.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4613  Z= 0.204
  Angle     :  0.761  15.704   6292  Z= 0.337
  Chirality :  0.041   0.178    742
  Planarity :  0.004   0.049    799
  Dihedral  :  4.644  32.970    686
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 38.93 %
    Favored  : 54.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.35), residues: 615
  helix:  1.45 (0.27), residues: 359
  sheet:  1.12 (0.84), residues: 49
  loop : -1.34 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.000   HIS A  47 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.010   0.001   TYR A 354 
 ARG   0.002   0.000   ARG A 273 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A   76 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7926 (mm-30)
REVERT: A  122 THR cc_start: 0.9435 (p) cc_final: 0.9149 (t)
REVERT: A  361 GLN cc_start: 0.7678 (mm110) cc_final: 0.7439 (mm110)
REVERT: A  464 MET cc_start: 0.7951 (ttt) cc_final: 0.7556 (ttp)
REVERT: A  482 TYR cc_start: 0.7602 (t80) cc_final: 0.6946 (t80)
REVERT: A  485 MET cc_start: 0.9146 (tmm) cc_final: 0.8641 (tpt)
  outliers start: 29
  outliers final: 22
  residues processed: 117
  average time/residue: 0.1004
  time to fit residues: 16.7762
Evaluate side-chains
  117 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 55 optimal weight:   20.0000
   chunk 58 optimal weight:   20.0000
   chunk 45 optimal weight:    0.9980
   chunk 51 optimal weight:   40.0000
   chunk 43 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 57 optimal weight:   30.0000
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.125317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.103473 restraints weight = 12449.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.106403 restraints weight = 6468.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.108475 restraints weight = 4231.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4613  Z= 0.217
  Angle     :  0.807  16.128   6292  Z= 0.353
  Chirality :  0.042   0.163    742
  Planarity :  0.004   0.048    799
  Dihedral  :  4.605  33.260    686
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 38.23 %
    Favored  : 55.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.35), residues: 615
  helix:  1.33 (0.27), residues: 359
  sheet:  1.12 (0.84), residues: 49
  loop : -1.35 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.000   HIS A  47 
 PHE   0.016   0.001   PHE A 347 
 TYR   0.017   0.001   TYR A 354 
 ARG   0.001   0.000   ARG A 394 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A   76 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7915 (mm-30)
REVERT: A  122 THR cc_start: 0.9437 (p) cc_final: 0.9141 (t)
REVERT: A  361 GLN cc_start: 0.7644 (mm110) cc_final: 0.7434 (mm110)
REVERT: A  367 MET cc_start: 0.8334 (mmt) cc_final: 0.8107 (mmt)
REVERT: A  482 TYR cc_start: 0.7595 (t80) cc_final: 0.6931 (t80)
REVERT: A  485 MET cc_start: 0.9131 (tmm) cc_final: 0.8679 (tpt)
  outliers start: 26
  outliers final: 24
  residues processed: 110
  average time/residue: 0.1101
  time to fit residues: 17.0409
Evaluate side-chains
  114 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 60 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 52 optimal weight:   20.0000
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.125918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.104073 restraints weight = 12481.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.107045 restraints weight = 6524.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.108939 restraints weight = 4250.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4613  Z= 0.226
  Angle     :  0.822  16.384   6292  Z= 0.359
  Chirality :  0.043   0.208    742
  Planarity :  0.004   0.048    799
  Dihedral  :  4.574  33.951    686
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 37.53 %
    Favored  : 56.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.35), residues: 615
  helix:  1.31 (0.27), residues: 359
  sheet:  1.14 (0.85), residues: 49
  loop : -1.36 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 109 
 HIS   0.002   0.000   HIS A  47 
 PHE   0.013   0.001   PHE A 347 
 TYR   0.008   0.001   TYR A 354 
 ARG   0.001   0.000   ARG A 394 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8835 (tpt) cc_final: 0.8421 (tpt)
REVERT: A   76 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8021 (mm-30)
REVERT: A  122 THR cc_start: 0.9454 (p) cc_final: 0.9182 (t)
REVERT: A  464 MET cc_start: 0.8003 (ttt) cc_final: 0.7654 (ttp)
REVERT: A  482 TYR cc_start: 0.7607 (t80) cc_final: 0.6918 (t80)
REVERT: A  485 MET cc_start: 0.9175 (tmm) cc_final: 0.8706 (tpt)
  outliers start: 26
  outliers final: 26
  residues processed: 110
  average time/residue: 0.1111
  time to fit residues: 17.1087
Evaluate side-chains
  116 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0060
   chunk 56 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 51 optimal weight:   40.0000
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.127004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.105374 restraints weight = 12490.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.108314 restraints weight = 6488.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.110362 restraints weight = 4209.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4613  Z= 0.201
  Angle     :  0.826  16.338   6292  Z= 0.359
  Chirality :  0.042   0.189    742
  Planarity :  0.005   0.048    799
  Dihedral  :  4.513  33.531    686
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 37.06 %
    Favored  : 56.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.35), residues: 615
  helix:  1.32 (0.27), residues: 359
  sheet:  1.11 (0.85), residues: 50
  loop : -1.42 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  86 
 HIS   0.002   0.000   HIS A  47 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.010   0.001   TYR A 444 
 ARG   0.008   0.000   ARG A 273 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8841 (tpt) cc_final: 0.8431 (tpt)
REVERT: A   76 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8088 (mm-30)
REVERT: A  464 MET cc_start: 0.8011 (ttt) cc_final: 0.7641 (ttp)
REVERT: A  482 TYR cc_start: 0.7646 (t80) cc_final: 0.6931 (t80)
REVERT: A  485 MET cc_start: 0.9136 (tmm) cc_final: 0.8686 (tpt)
  outliers start: 27
  outliers final: 21
  residues processed: 114
  average time/residue: 0.1088
  time to fit residues: 17.3494
Evaluate side-chains
  109 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:   30.0000
   chunk 32 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 4 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.130635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.105728 restraints weight = 12733.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.108764 restraints weight = 6458.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.110949 restraints weight = 4186.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4613  Z= 0.216
  Angle     :  0.837  16.166   6292  Z= 0.365
  Chirality :  0.043   0.196    742
  Planarity :  0.005   0.047    799
  Dihedral  :  4.530  33.485    686
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 37.76 %
    Favored  : 56.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.35), residues: 615
  helix:  1.21 (0.27), residues: 365
  sheet:  1.13 (0.84), residues: 50
  loop : -1.47 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 274 
 HIS   0.003   0.001   HIS A  47 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.007   0.001   TYR A 169 
 ARG   0.006   0.000   ARG A 273 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1631.73 seconds
wall clock time: 29 minutes 25.29 seconds (1765.29 seconds total)