Starting phenix.real_space_refine
on Sat Apr  4 23:11:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dmf_27535/04_2026/8dmf_27535.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dmf_27535/04_2026/8dmf_27535.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dmf_27535/04_2026/8dmf_27535.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dmf_27535/04_2026/8dmf_27535.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dmf_27535/04_2026/8dmf_27535.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dmf_27535/04_2026/8dmf_27535.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      33      5.16       5
     C    3589      2.51       5
     N     951      2.21       5
     O    1093      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5670
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 718, 5637
          Classifications: {'peptide': 718}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 685}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.28, per 1000 atoms: 0.23
  Number of scatterers: 5670
  At special positions: 0
  Unit cell: (75.828, 72.624, 127.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      33     16.00
     P       3     15.00
     Mg      1     11.99
     O    1093      8.00
     N     951      7.00
     C    3589      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 163.3 milliseconds
  

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1312

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 9 sheets defined
      31.5% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 7
      No H-bonds generated for 'chain 'A' and resid 5 through 7'
    Processing helix  chain 'A' and resid 21 through 33
      removed outlier: 3.531A  pdb=" N   LEU A  25 " --> pdb=" O   GLY A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 58
    Processing helix  chain 'A' and resid 87 through 98
      removed outlier: 3.626A  pdb=" N   THR A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 126
    Processing helix  chain 'A' and resid 142 through 154
    Processing helix  chain 'A' and resid 167 through 171
      removed outlier: 3.627A  pdb=" N   GLY A 170 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 200
      No H-bonds generated for 'chain 'A' and resid 198 through 200'
    Processing helix  chain 'A' and resid 201 through 220
    Processing helix  chain 'A' and resid 235 through 248
      removed outlier: 4.231A  pdb=" N   GLU A 240 " --> pdb=" O   ASP A 236 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 275
    Processing helix  chain 'A' and resid 411 through 426
    Processing helix  chain 'A' and resid 446 through 459
    Processing helix  chain 'A' and resid 555 through 557
      No H-bonds generated for 'chain 'A' and resid 555 through 557'
    Processing helix  chain 'A' and resid 558 through 571
    Processing helix  chain 'A' and resid 598 through 617
      removed outlier: 3.534A  pdb=" N   PHE A 602 " --> pdb=" O   ASN A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 646
    Processing helix  chain 'A' and resid 670 through 672
      No H-bonds generated for 'chain 'A' and resid 670 through 672'
    Processing helix  chain 'A' and resid 674 through 684
      removed outlier: 3.512A  pdb=" N   ALA A 678 " --> pdb=" O   SER A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 716
      removed outlier: 3.553A  pdb=" N   GLN A 704 " --> pdb=" O   PRO A 700 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70
      removed outlier: 6.834A  pdb=" N   LYS A  10 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ILE A  79 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE A  12 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ALA A 101 " --> pdb=" O   ILE A 130 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   LEU A 132 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   ASN A 134 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   LEU A 105 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   VAL A 159 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 9.626A  pdb=" N   CYS A 256 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 164
    Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 343
      removed outlier: 6.964A  pdb=" N   SER A 302 " --> pdb=" O   MET A 323 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328
      removed outlier: 3.510A  pdb=" N   LEU A 361 " --> pdb=" O   VAL A 327 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350
      removed outlier: 4.477A  pdb=" N   ILE A 347 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434
      removed outlier: 3.585A  pdb=" N   GLN A 439 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   THR A 440 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   TYR A 400 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 580
    Processing sheet with id=AA8, first strand: chain 'A' and resid 482 through 488
      removed outlier: 3.539A  pdb=" N   ALA A 482 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   GLU A 500 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   GLY A 590 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   HIS A 502 " --> pdb=" O   TYR A 588 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   LYS A 542 " --> pdb=" O   VAL A 583 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   VAL A 585 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   VAL A 587 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 654
      removed outlier: 6.706A  pdb=" N   VAL A 664 " --> pdb=" O   MET A 652 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   MET A 654 " --> pdb=" O   LYS A 662 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS A 662 " --> pdb=" O   MET A 654 " (cutoff:3.500A)

    225 hydrogen bonds defined for protein.
    645 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1743
        1.33 -     1.45: 846
        1.45 -     1.57: 3124
        1.57 -     1.69: 5
        1.69 -     1.81: 61
  Bond restraints: 5779
  Sorted by residual:
  bond pdb=" N   GLU A 476 "
       pdb=" CA  GLU A 476 "
    ideal  model  delta    sigma   weight residual
    1.452  1.488 -0.035 1.25e-02 6.40e+03 7.96e+00
  bond pdb=" N   GLU A 697 "
       pdb=" CA  GLU A 697 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.32e-02 5.74e+03 6.38e+00
  bond pdb=" N   TYR A 474 "
       pdb=" CA  TYR A 474 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.030 1.22e-02 6.72e+03 6.21e+00
  bond pdb=" N   LYS A  22 "
       pdb=" CA  LYS A  22 "
    ideal  model  delta    sigma   weight residual
    1.460  1.490 -0.030 1.22e-02 6.72e+03 6.10e+00
  bond pdb=" N   SER A 695 "
       pdb=" CA  SER A 695 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.029 1.21e-02 6.83e+03 5.63e+00
  ... (remaining 5774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 7554
        1.63 -     3.26: 201
        3.26 -     4.89: 30
        4.89 -     6.52: 5
        6.52 -     8.15: 5
  Bond angle restraints: 7795
  Sorted by residual:
  angle pdb=" N   GLU A 425 "
        pdb=" CA  GLU A 425 "
        pdb=" C   GLU A 425 "
      ideal   model   delta    sigma   weight residual
     111.28  107.47    3.81 1.09e+00 8.42e-01 1.22e+01
  angle pdb=" CA  GLU A 697 "
        pdb=" C   GLU A 697 "
        pdb=" O   GLU A 697 "
      ideal   model   delta    sigma   weight residual
     121.36  118.00    3.36 1.06e+00 8.90e-01 1.00e+01
  angle pdb=" N   GLU A 424 "
        pdb=" CA  GLU A 424 "
        pdb=" C   GLU A 424 "
      ideal   model   delta    sigma   weight residual
     111.71  108.17    3.54 1.15e+00 7.56e-01 9.47e+00
  angle pdb=" CA  GLU A 476 "
        pdb=" C   GLU A 476 "
        pdb=" O   GLU A 476 "
      ideal   model   delta    sigma   weight residual
     121.82  118.12    3.70 1.21e+00 6.83e-01 9.36e+00
  angle pdb=" CA  TYR A 696 "
        pdb=" C   TYR A 696 "
        pdb=" O   TYR A 696 "
      ideal   model   delta    sigma   weight residual
     121.55  118.32    3.23 1.06e+00 8.90e-01 9.28e+00
  ... (remaining 7790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.34: 3265
       22.34 -    44.68: 233
       44.68 -    67.02: 10
       67.02 -    89.36: 3
       89.36 -   111.70: 4
  Dihedral angle restraints: 3515
    sinusoidal: 1461
      harmonic: 2054
  Sorted by residual:
  dihedral pdb=" C8  GTP A 802 "
           pdb=" C1' GTP A 802 "
           pdb=" N9  GTP A 802 "
           pdb=" O4' GTP A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   -7.11  111.70     1      2.00e+01 2.50e-03 3.29e+01
  dihedral pdb=" C5' GTP A 802 "
           pdb=" O5' GTP A 802 "
           pdb=" PA  GTP A 802 "
           pdb=" O3A GTP A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  178.40 -109.13     1      2.00e+01 2.50e-03 3.19e+01
  dihedral pdb=" CA  MET A 224 "
           pdb=" C   MET A 224 "
           pdb=" N   GLU A 225 "
           pdb=" CA  GLU A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.71  -20.29     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 3512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 573
       0.037 -    0.073: 172
       0.073 -    0.110: 76
       0.110 -    0.146: 22
       0.146 -    0.183: 3
  Chirality restraints: 846
  Sorted by residual:
  chirality pdb=" CB  ILE A 535 "
            pdb=" CA  ILE A 535 "
            pdb=" CG1 ILE A 535 "
            pdb=" CG2 ILE A 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.37e-01
  chirality pdb=" CA  GLU A 424 "
            pdb=" N   GLU A 424 "
            pdb=" C   GLU A 424 "
            pdb=" CB  GLU A 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" CA  ARG A 423 "
            pdb=" N   ARG A 423 "
            pdb=" C   ARG A 423 "
            pdb=" CB  ARG A 423 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.15 2.00e-01 2.50e+01 5.98e-01
  ... (remaining 843 not shown)

  Planarity restraints: 1012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 632 "   -0.028 5.00e-02 4.00e+02   4.21e-02 2.83e+00
        pdb=" N   PRO A 633 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 633 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 633 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 276 "    0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO A 277 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  21 "   -0.005 2.00e-02 2.50e+03   1.05e-02 1.10e+00
        pdb=" C   GLY A  21 "    0.018 2.00e-02 2.50e+03
        pdb=" O   GLY A  21 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   LYS A  22 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1009 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 65
        2.56 -     3.15: 4775
        3.15 -     3.73: 9308
        3.73 -     4.32: 11920
        4.32 -     4.90: 19654
  Nonbonded interactions: 45722
  Sorted by model distance:
  nonbonded pdb="MG    MG A 801 "
            pdb=" O3A GTP A 802 "
     model   vdw
     1.977 2.170
  nonbonded pdb="MG    MG A 801 "
            pdb=" O3G GTP A 802 "
     model   vdw
     2.168 2.170
  nonbonded pdb=" N   THR A  23 "
            pdb="MG    MG A 801 "
     model   vdw
     2.183 2.250
  nonbonded pdb=" OH  TYR A 400 "
            pdb=" NH2 ARG A 402 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NZ  LYS A 291 "
            pdb=" OH  TYR A 388 "
     model   vdw
     2.267 3.120
  ... (remaining 45717 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=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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.370
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5779  Z= 0.172
  Angle     :  0.636   8.154   7795  Z= 0.347
  Chirality :  0.046   0.183    846
  Planarity :  0.004   0.042   1012
  Dihedral  : 14.277 111.705   2203
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.33), residues: 716
  helix:  1.11 (0.39), residues: 202
  sheet: -0.03 (0.41), residues: 195
  loop : -0.97 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 343 
 TYR   0.008   0.001   TYR A 696 
 PHE   0.011   0.001   PHE A 610 
 TRP   0.006   0.001   TRP A 455 
 HIS   0.009   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 5779)
  covalent geometry    : angle       0.63593 ( 7795)
  hydrogen bonds       : bond        0.19381 (  225)
  hydrogen bonds       : angle       8.31932 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.8795 (ptm) cc_final: 0.8594 (ttt)
REVERT: A  251 MET cc_start: 0.8929 (tmm) cc_final: 0.8647 (tmm)
REVERT: A  263 MET cc_start: 0.8783 (mmp) cc_final: 0.8097 (mmp)
REVERT: A  323 MET cc_start: 0.8461 (mmp) cc_final: 0.8205 (mmm)
REVERT: A  563 MET cc_start: 0.9575 (mmp) cc_final: 0.9122 (mmm)
REVERT: A  650 MET cc_start: 0.9167 (mpp) cc_final: 0.8874 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0577
  time to fit residues: 3.8428
Evaluate side-chains
  36 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:   30.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    3.1562

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 443 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.040755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.032543 restraints weight = 47519.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.033691 restraints weight = 28132.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.034511 restraints weight = 19232.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.035071 restraints weight = 14489.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.035517 restraints weight = 11712.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5779  Z= 0.132
  Angle     :  0.608  10.112   7795  Z= 0.303
  Chirality :  0.044   0.151    846
  Planarity :  0.004   0.041   1012
  Dihedral  :  7.638 112.980    787
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.99 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.33), residues: 716
  helix:  1.25 (0.37), residues: 207
  sheet: -0.16 (0.39), residues: 206
  loop : -0.95 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 402 
 TYR   0.013   0.001   TYR A 121 
 PHE   0.011   0.001   PHE A 255 
 TRP   0.009   0.001   TRP A 429 
 HIS   0.008   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5779)
  covalent geometry    : angle       0.60776 ( 7795)
  hydrogen bonds       : bond        0.04066 (  225)
  hydrogen bonds       : angle       5.88354 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  206 MET cc_start: 0.9250 (mmp) cc_final: 0.8994 (mmt)
REVERT: A  251 MET cc_start: 0.8837 (tmm) cc_final: 0.8602 (tmm)
REVERT: A  263 MET cc_start: 0.8621 (mmp) cc_final: 0.7948 (mmp)
REVERT: A  303 LEU cc_start: 0.9331 (mt) cc_final: 0.9059 (mt)
REVERT: A  323 MET cc_start: 0.8450 (mmp) cc_final: 0.8169 (mmm)
REVERT: A  389 LYS cc_start: 0.8657 (pttm) cc_final: 0.8074 (tppt)
REVERT: A  422 MET cc_start: 0.9355 (mmm) cc_final: 0.9064 (mmm)
REVERT: A  563 MET cc_start: 0.9406 (mmp) cc_final: 0.9092 (mmm)
REVERT: A  650 MET cc_start: 0.9120 (mpp) cc_final: 0.8702 (mpp)
  outliers start: 3
  outliers final: 1
  residues processed: 44
  average time/residue: 0.0611
  time to fit residues: 3.9305
Evaluate side-chains
  38 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 44 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   chunk 28 optimal weight:    0.6980
   chunk 23 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 59 optimal weight:   20.0000
   overall best weight:    5.7388

-------------------------------------------------------------------------------
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 = 0.3060 r_free = 0.3060 target = 0.039241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.031095 restraints weight = 48205.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.032169 restraints weight = 28883.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.032925 restraints weight = 20029.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.033512 restraints weight = 15309.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.033892 restraints weight = 12404.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5779  Z= 0.183
  Angle     :  0.603   8.950   7795  Z= 0.303
  Chirality :  0.044   0.141    846
  Planarity :  0.004   0.034   1012
  Dihedral  :  7.684 111.450    787
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 10.93 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.32), residues: 716
  helix:  1.32 (0.37), residues: 207
  sheet:  0.02 (0.39), residues: 201
  loop : -0.97 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 402 
 TYR   0.014   0.001   TYR A 121 
 PHE   0.012   0.001   PHE A 255 
 TRP   0.012   0.001   TRP A 429 
 HIS   0.006   0.002   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 5779)
  covalent geometry    : angle       0.60303 ( 7795)
  hydrogen bonds       : bond        0.03772 (  225)
  hydrogen bonds       : angle       5.50676 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 MET cc_start: 0.9295 (mmp) cc_final: 0.9026 (mmt)
REVERT: A  251 MET cc_start: 0.8831 (tmm) cc_final: 0.8607 (tmm)
REVERT: A  263 MET cc_start: 0.8731 (mmp) cc_final: 0.7978 (mmp)
REVERT: A  394 LYS cc_start: 0.9332 (tppt) cc_final: 0.9097 (tptp)
REVERT: A  422 MET cc_start: 0.9476 (mmm) cc_final: 0.9141 (mmm)
REVERT: A  424 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9037 (mm-30)
REVERT: A  563 MET cc_start: 0.9352 (mmp) cc_final: 0.9127 (mmm)
REVERT: A  567 MET cc_start: 0.9350 (mpp) cc_final: 0.9124 (mpp)
REVERT: A  650 MET cc_start: 0.9149 (mpp) cc_final: 0.8495 (mpp)
REVERT: A  691 MET cc_start: 0.8668 (ttm) cc_final: 0.8295 (ttt)
  outliers start: 8
  outliers final: 4
  residues processed: 46
  average time/residue: 0.0674
  time to fit residues: 4.4106
Evaluate side-chains
  41 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 31 optimal weight:    0.0670
   chunk 41 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0770
   chunk 11 optimal weight:    9.9990
   chunk 13 optimal weight:   20.0000
   chunk 63 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 10 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    2.6280

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 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 = 0.3085 r_free = 0.3085 target = 0.039825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.031666 restraints weight = 47977.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.032724 restraints weight = 28301.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.033545 restraints weight = 19681.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.034117 restraints weight = 14808.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.034549 restraints weight = 11957.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5779  Z= 0.112
  Angle     :  0.561   8.967   7795  Z= 0.276
  Chirality :  0.044   0.175    846
  Planarity :  0.003   0.033   1012
  Dihedral  :  7.245 105.736    787
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.70 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.33), residues: 716
  helix:  1.63 (0.37), residues: 207
  sheet:  0.07 (0.42), residues: 185
  loop : -0.95 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 239 
 TYR   0.009   0.001   TYR A 626 
 PHE   0.015   0.001   PHE A 255 
 TRP   0.006   0.001   TRP A 429 
 HIS   0.006   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 5779)
  covalent geometry    : angle       0.56118 ( 7795)
  hydrogen bonds       : bond        0.03172 (  225)
  hydrogen bonds       : angle       4.99350 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 MET cc_start: 0.9175 (mmp) cc_final: 0.8898 (mmt)
REVERT: A  251 MET cc_start: 0.8783 (tmm) cc_final: 0.8557 (tmm)
REVERT: A  263 MET cc_start: 0.8515 (mmp) cc_final: 0.7818 (mmp)
REVERT: A  303 LEU cc_start: 0.9336 (mt) cc_final: 0.9095 (mt)
REVERT: A  422 MET cc_start: 0.9424 (mmm) cc_final: 0.9145 (mmm)
REVERT: A  424 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8906 (mm-30)
REVERT: A  563 MET cc_start: 0.9313 (mmp) cc_final: 0.9048 (mmm)
REVERT: A  567 MET cc_start: 0.9287 (mpp) cc_final: 0.9057 (mpp)
REVERT: A  691 MET cc_start: 0.8666 (ttm) cc_final: 0.8408 (ttt)
  outliers start: 4
  outliers final: 4
  residues processed: 43
  average time/residue: 0.0670
  time to fit residues: 4.2390
Evaluate side-chains
  41 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 33 optimal weight:   20.0000
   chunk 17 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 715 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.039080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.030911 restraints weight = 48760.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.031996 restraints weight = 29145.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.032753 restraints weight = 20155.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.033305 restraints weight = 15355.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.033764 restraints weight = 12517.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5779  Z= 0.166
  Angle     :  0.583   8.046   7795  Z= 0.291
  Chirality :  0.043   0.178    846
  Planarity :  0.004   0.032   1012
  Dihedral  :  7.408 107.161    787
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.19 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.32), residues: 716
  helix:  1.62 (0.37), residues: 207
  sheet:  0.14 (0.42), residues: 184
  loop : -1.04 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.012   0.001   TYR A 121 
 PHE   0.012   0.001   PHE A 255 
 TRP   0.013   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5779)
  covalent geometry    : angle       0.58262 ( 7795)
  hydrogen bonds       : bond        0.03310 (  225)
  hydrogen bonds       : angle       4.95214 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 MET cc_start: 0.9145 (mmp) cc_final: 0.8936 (mmp)
REVERT: A  251 MET cc_start: 0.8803 (tmm) cc_final: 0.8569 (tmm)
REVERT: A  323 MET cc_start: 0.8749 (mmm) cc_final: 0.8397 (mmm)
REVERT: A  422 MET cc_start: 0.9561 (mmm) cc_final: 0.9283 (mmm)
REVERT: A  424 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8919 (mm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 40
  average time/residue: 0.0502
  time to fit residues: 3.0305
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  447 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 60 optimal weight:    9.9990
   chunk 47 optimal weight:    7.9990
   chunk 43 optimal weight:    7.9990
   chunk 31 optimal weight:    0.2980
   chunk 10 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   overall best weight:    4.6586

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.039232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.031027 restraints weight = 48480.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.032103 restraints weight = 29224.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.032889 restraints weight = 20251.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.033414 restraints weight = 15412.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.033872 restraints weight = 12643.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5779  Z= 0.150
  Angle     :  0.582   8.101   7795  Z= 0.286
  Chirality :  0.043   0.189    846
  Planarity :  0.003   0.033   1012
  Dihedral  :  7.320 106.530    787
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.50 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.33), residues: 716
  helix:  1.69 (0.37), residues: 207
  sheet:  0.23 (0.43), residues: 185
  loop : -1.14 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.011   0.001   TYR A 121 
 PHE   0.010   0.001   PHE A 255 
 TRP   0.010   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5779)
  covalent geometry    : angle       0.58175 ( 7795)
  hydrogen bonds       : bond        0.03170 (  225)
  hydrogen bonds       : angle       4.84596 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 MET cc_start: 0.8817 (tpp) cc_final: 0.8580 (tpp)
REVERT: A  206 MET cc_start: 0.9038 (mmp) cc_final: 0.8807 (mmt)
REVERT: A  208 MET cc_start: 0.8976 (ttm) cc_final: 0.8730 (ttt)
REVERT: A  251 MET cc_start: 0.8819 (tmm) cc_final: 0.8596 (tmm)
REVERT: A  303 LEU cc_start: 0.9361 (mt) cc_final: 0.9089 (mt)
REVERT: A  323 MET cc_start: 0.8724 (mmm) cc_final: 0.8294 (mmm)
REVERT: A  422 MET cc_start: 0.9549 (mmm) cc_final: 0.9256 (mmm)
REVERT: A  424 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8908 (mm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 43
  average time/residue: 0.0522
  time to fit residues: 3.2914
Evaluate side-chains
  41 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:   20.0000
   chunk 3 optimal weight:    8.9990
   chunk 15 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.3049 r_free = 0.3049 target = 0.038916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.030708 restraints weight = 49587.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.031761 restraints weight = 29809.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.032511 restraints weight = 20759.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.033087 restraints weight = 15793.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.033526 restraints weight = 12889.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5779  Z= 0.196
  Angle     :  0.622   8.082   7795  Z= 0.310
  Chirality :  0.044   0.176    846
  Planarity :  0.004   0.033   1012
  Dihedral  :  7.515 107.982    787
  Min Nonbonded Distance : 1.822

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.64 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.32), residues: 716
  helix:  1.50 (0.37), residues: 207
  sheet:  0.16 (0.43), residues: 183
  loop : -1.14 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 239 
 TYR   0.013   0.001   TYR A 626 
 PHE   0.012   0.001   PHE A 525 
 TRP   0.014   0.002   TRP A 429 
 HIS   0.004   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 5779)
  covalent geometry    : angle       0.62158 ( 7795)
  hydrogen bonds       : bond        0.03439 (  225)
  hydrogen bonds       : angle       5.02002 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9395 (mm)
REVERT: A  208 MET cc_start: 0.8965 (ttm) cc_final: 0.8740 (ttt)
REVERT: A  251 MET cc_start: 0.8842 (tmm) cc_final: 0.8593 (tmm)
REVERT: A  323 MET cc_start: 0.8709 (mmm) cc_final: 0.8303 (mmm)
REVERT: A  422 MET cc_start: 0.9579 (mmm) cc_final: 0.9297 (mmm)
REVERT: A  424 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8934 (mm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0533
  time to fit residues: 3.4202
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   95 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 51 optimal weight:   30.0000
   chunk 37 optimal weight:    0.5980
   chunk 40 optimal weight:    9.9990
   chunk 27 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0060
   chunk 43 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:   30.0000
   overall best weight:    2.6400

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 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 = 0.3087 r_free = 0.3087 target = 0.039804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.031455 restraints weight = 47076.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.032557 restraints weight = 28352.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.033347 restraints weight = 19755.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.033862 restraints weight = 15086.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.034336 restraints weight = 12409.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5779  Z= 0.113
  Angle     :  0.616   9.343   7795  Z= 0.294
  Chirality :  0.044   0.180    846
  Planarity :  0.003   0.033   1012
  Dihedral  :  7.137 104.466    787
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 18.11 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.33), residues: 716
  helix:  1.60 (0.38), residues: 208
  sheet:  0.12 (0.45), residues: 168
  loop : -1.12 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.009   0.001   TYR A 626 
 PHE   0.008   0.001   PHE A 255 
 TRP   0.005   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 5779)
  covalent geometry    : angle       0.61609 ( 7795)
  hydrogen bonds       : bond        0.03090 (  225)
  hydrogen bonds       : angle       4.75417 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 MET cc_start: 0.9158 (mmm) cc_final: 0.8944 (mmt)
REVERT: A  251 MET cc_start: 0.8776 (tmm) cc_final: 0.8530 (tmm)
REVERT: A  303 LEU cc_start: 0.9352 (mt) cc_final: 0.9063 (mt)
REVERT: A  323 MET cc_start: 0.8704 (mmm) cc_final: 0.8256 (mmm)
REVERT: A  422 MET cc_start: 0.9487 (mmm) cc_final: 0.9169 (mmm)
REVERT: A  424 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8914 (mm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 45
  average time/residue: 0.0725
  time to fit residues: 4.5932
Evaluate side-chains
  42 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 63 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3065 r_free = 0.3065 target = 0.039191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.031160 restraints weight = 48413.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.032219 restraints weight = 29169.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.032991 restraints weight = 20226.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.033425 restraints weight = 15286.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.033924 restraints weight = 12718.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5779  Z= 0.183
  Angle     :  0.658  10.218   7795  Z= 0.322
  Chirality :  0.044   0.178    846
  Planarity :  0.004   0.032   1012
  Dihedral  :  7.401 106.869    787
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 18.92 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.32), residues: 716
  helix:  1.51 (0.37), residues: 207
  sheet:  0.07 (0.42), residues: 182
  loop : -1.06 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 239 
 TYR   0.012   0.001   TYR A 626 
 PHE   0.012   0.001   PHE A 525 
 TRP   0.014   0.002   TRP A 429 
 HIS   0.004   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 5779)
  covalent geometry    : angle       0.65809 ( 7795)
  hydrogen bonds       : bond        0.03343 (  225)
  hydrogen bonds       : angle       4.87747 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.8932 (ttm) cc_final: 0.8692 (ttt)
REVERT: A  251 MET cc_start: 0.8832 (tmm) cc_final: 0.8584 (tmm)
REVERT: A  303 LEU cc_start: 0.9368 (mt) cc_final: 0.9078 (mt)
REVERT: A  323 MET cc_start: 0.8746 (mmm) cc_final: 0.8431 (mmm)
REVERT: A  422 MET cc_start: 0.9573 (mmm) cc_final: 0.9280 (mmm)
REVERT: A  424 GLU cc_start: 0.9394 (mm-30) cc_final: 0.8932 (mm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 40
  average time/residue: 0.0587
  time to fit residues: 3.5966
Evaluate side-chains
  39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 54 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 62 optimal weight:    0.6980
   chunk 65 optimal weight:   30.0000
   chunk 7 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 30 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    6.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 488 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.038884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.030938 restraints weight = 49036.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.031974 restraints weight = 29553.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.032742 restraints weight = 20571.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.033320 restraints weight = 15608.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.033728 restraints weight = 12582.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5779  Z= 0.201
  Angle     :  0.699  12.298   7795  Z= 0.340
  Chirality :  0.045   0.171    846
  Planarity :  0.004   0.032   1012
  Dihedral  :  7.533 107.856    787
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 19.25 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.32), residues: 716
  helix:  1.23 (0.37), residues: 207
  sheet: -0.14 (0.41), residues: 189
  loop : -1.12 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.016   0.001   TYR A 626 
 PHE   0.013   0.001   PHE A 525 
 TRP   0.015   0.002   TRP A 429 
 HIS   0.004   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 5779)
  covalent geometry    : angle       0.69903 ( 7795)
  hydrogen bonds       : bond        0.03557 (  225)
  hydrogen bonds       : angle       5.05043 (  645)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.9008 (mpp) cc_final: 0.8757 (mpp)
REVERT: A   95 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9397 (mm)
REVERT: A  208 MET cc_start: 0.8939 (ttm) cc_final: 0.8695 (ttt)
REVERT: A  251 MET cc_start: 0.8806 (tmm) cc_final: 0.8589 (tmm)
REVERT: A  269 MET cc_start: 0.9583 (mmt) cc_final: 0.9383 (mmp)
REVERT: A  323 MET cc_start: 0.8720 (mmm) cc_final: 0.8417 (mmm)
REVERT: A  422 MET cc_start: 0.9558 (mmm) cc_final: 0.9264 (mmm)
REVERT: A  424 GLU cc_start: 0.9392 (mm-30) cc_final: 0.8924 (mm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 40
  average time/residue: 0.0535
  time to fit residues: 3.2463
Evaluate side-chains
  39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   95 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 24 optimal weight:   30.0000
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 34 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 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 = 0.3069 r_free = 0.3069 target = 0.039243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.031256 restraints weight = 48238.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.032316 restraints weight = 28869.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.033072 restraints weight = 20133.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.033695 restraints weight = 15348.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.034125 restraints weight = 12299.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5779  Z= 0.150
  Angle     :  0.674  11.137   7795  Z= 0.324
  Chirality :  0.044   0.176    846
  Planarity :  0.003   0.032   1012
  Dihedral  :  7.323 105.678    787
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 19.41 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.32), residues: 716
  helix:  1.35 (0.38), residues: 207
  sheet: -0.12 (0.42), residues: 182
  loop : -1.06 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 239 
 TYR   0.015   0.001   TYR A 626 
 PHE   0.009   0.001   PHE A 525 
 TRP   0.009   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5779)
  covalent geometry    : angle       0.67423 ( 7795)
  hydrogen bonds       : bond        0.03290 (  225)
  hydrogen bonds       : angle       4.91251 (  645)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 839.56 seconds
wall clock time: 15 minutes 15.59 seconds (915.59 seconds total)