Starting phenix.real_space_refine
on Wed Sep 17 05:26:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n2e_48836/09_2025/9n2e_48836.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n2e_48836/09_2025/9n2e_48836.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n2e_48836/09_2025/9n2e_48836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n2e_48836/09_2025/9n2e_48836.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n2e_48836/09_2025/9n2e_48836.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n2e_48836/09_2025/9n2e_48836.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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       7      5.16       5
     C    3158      2.51       5
     N     816      2.21       5
     O     947      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4928
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4501
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 561, 4493
          Classifications: {'peptide': 561}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 541}
          Chain breaks: 7
      Conformer: "B"
        Number of residues, atoms: 561, 4493
          Classifications: {'peptide': 561}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 541}
          Chain breaks: 7
          bond proxies already assigned to first conformer: 4587
    Chain: "E"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 427
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 51}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 2.10, per 1000 atoms: 0.43
  Number of scatterers: 4928
  At special positions: 0
  Unit cell: (103.212, 72.468, 108.336, 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       7     16.00
     O     947      8.00
     N     816      7.00
     C    3158      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: 0.36
  Conformation dependent library (CDL) restraints added in 323.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1110

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 4 sheets defined
      16.8% alpha, 38.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 298 through 307
      removed outlier: 3.585A  pdb=" N   LEU A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 324
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 388 through 393
      removed outlier: 3.870A  pdb=" N   GLU A 393 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 418
      removed outlier: 3.739A  pdb=" N   GLY A 418 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 522
      removed outlier: 4.479A  pdb=" N   LYS A 522 " --> pdb=" O   PHE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 641
      removed outlier: 4.068A  pdb=" N   PHE A 640 " --> pdb=" O   PRO A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 655
      removed outlier: 6.661A  pdb=" N   LYS A 652 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   GLU A 653 " --> pdb=" O   ASN A 650 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LYS A 655 " --> pdb=" O   LYS A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 658
      No H-bonds generated for 'chain 'A' and resid 658 through 658'
    Processing helix  chain 'A' and resid 673 through 676
    Processing helix  chain 'A' and resid 702 through 711
    Processing helix  chain 'E' and resid 123 through 129
    Processing helix  chain 'E' and resid 156 through 166
    Processing sheet with id=AA1, first strand: chain 'A' and resid 285 through 292
      removed outlier: 6.532A  pdb=" N   TYR A 285 " --> pdb=" O   ILE A 360 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   PHE A 362 " --> pdb=" O   TYR A 285 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   GLY A 287 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
      removed outlier: 9.017A  pdb=" N   ILE A 364 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
      removed outlier: 9.468A  pdb=" N   ILE A 289 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
      removed outlier: 11.730A  pdb=" N   ILE A 366 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   PHE A 291 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LYS A 354 " --> pdb=" O   ASP A 361 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLU A 363 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   GLU A 352 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ARG A 365 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   ALA A 350 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   THR A 367 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ILE A 348 " --> pdb=" O   THR A 367 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 380
      removed outlier: 5.889A  pdb=" N   VAL A 439 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   LYS A 376 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE A 441 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   THR A 438 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   VAL A 432 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 154 through 155
      removed outlier: 3.581A  pdb=" N   ILE A 896 " --> pdb=" O   TYR A 459 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE A 827 " --> pdb=" O   ILE A 819 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY A 624 " --> pdb=" O   TYR A 726 " (cutoff:3.500A)
      removed outlier: 11.659A  pdb=" N   ARG A 548 " --> pdb=" O   ASN A 540 " (cutoff:3.500A)
      removed outlier: 12.346A  pdb=" N   ASN A 540 " --> pdb=" O   ARG A 548 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLN A 550 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   PHE A 507 " --> pdb=" O   SER A 504 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 761
      removed outlier: 7.177A  pdb=" N   TYR A 760 " --> pdb=" O   ILE A 777 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    220 hydrogen bonds defined for protein.
    608 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: 0.68

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1572
        1.34 -     1.46: 1314
        1.46 -     1.58: 2139
        1.58 -     1.70: 0
        1.70 -     1.82: 14
  Bond restraints: 5039
  Sorted by residual:
  bond pdb=" N   GLY A 731 "
       pdb=" CA  GLY A 731 "
    ideal  model  delta    sigma   weight residual
    1.460  1.448  0.012 1.26e-02 6.30e+03 9.66e-01
  bond pdb=" CA  ASP A 333 "
       pdb=" CB  ASP A 333 "
    ideal  model  delta    sigma   weight residual
    1.535  1.554 -0.019 1.93e-02 2.68e+03 9.53e-01
  bond pdb=" CA  GLY A 731 "
       pdb=" C   GLY A 731 "
    ideal  model  delta    sigma   weight residual
    1.524  1.511  0.012 1.33e-02 5.65e+03 8.49e-01
  bond pdb=" CB  GLU A 740 "
       pdb=" CG  GLU A 740 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 8.36e-01
  bond pdb=" CB  MET A 491 "
       pdb=" CG  MET A 491 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.06e-01
  ... (remaining 5034 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 6679
        2.00 -     4.01: 102
        4.01 -     6.01: 12
        6.01 -     8.02: 4
        8.02 -    10.02: 1
  Bond angle restraints: 6798
  Sorted by residual:
  angle pdb=" N   ILE A 819 "
        pdb=" CA  ILE A 819 "
        pdb=" C   ILE A 819 "
      ideal   model   delta    sigma   weight residual
     112.96  108.99    3.97 1.00e+00 1.00e+00 1.58e+01
  angle pdb=" CB  MET A 491 "
        pdb=" CG  MET A 491 "
        pdb=" SD  MET A 491 "
      ideal   model   delta    sigma   weight residual
     112.70  122.72  -10.02 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" N   VAL A 692 "
        pdb=" CA  VAL A 692 "
        pdb=" C   VAL A 692 "
      ideal   model   delta    sigma   weight residual
     111.88  108.60    3.28 1.06e+00 8.90e-01 9.60e+00
  angle pdb=" N   GLN E 136 "
        pdb=" CA  GLN E 136 "
        pdb=" C   GLN E 136 "
      ideal   model   delta    sigma   weight residual
     110.61  113.80   -3.19 1.25e+00 6.40e-01 6.51e+00
  angle pdb=" CA  MET A 491 "
        pdb=" CB  MET A 491 "
        pdb=" CG  MET A 491 "
      ideal   model   delta    sigma   weight residual
     114.10  118.93   -4.83 2.00e+00 2.50e-01 5.84e+00
  ... (remaining 6793 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 2488
       17.85 -    35.71: 335
       35.71 -    53.56: 89
       53.56 -    71.41: 25
       71.41 -    89.26: 8
  Dihedral angle restraints: 2945
    sinusoidal: 1181
      harmonic: 1764
  Sorted by residual:
  dihedral pdb=" CA  GLN E 136 "
           pdb=" C   GLN E 136 "
           pdb=" N   SER E 137 "
           pdb=" CA  SER E 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.69   17.31     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASP E 134 "
           pdb=" C   ASP E 134 "
           pdb=" N   ARG E 135 "
           pdb=" CA  ARG E 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.70  -17.30     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  THR A 367 "
           pdb=" C   THR A 367 "
           pdb=" N   GLU A 368 "
           pdb=" CA  GLU A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.45  -16.55     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 2942 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 410
       0.032 -    0.064: 196
       0.064 -    0.096: 62
       0.096 -    0.128: 40
       0.128 -    0.160: 3
  Chirality restraints: 711
  Sorted by residual:
  chirality pdb=" CB  ILE A 643 "
            pdb=" CA  ILE A 643 "
            pdb=" CG1 ILE A 643 "
            pdb=" CG2 ILE A 643 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CA  ILE A 377 "
            pdb=" N   ILE A 377 "
            pdb=" C   ILE A 377 "
            pdb=" CB  ILE A 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.41e-01
  chirality pdb=" CA  GLN E 136 "
            pdb=" N   GLN E 136 "
            pdb=" C   GLN E 136 "
            pdb=" CB  GLN E 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.40e-01
  ... (remaining 708 not shown)

  Planarity restraints: 881
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 426 "   -0.030 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO A 427 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 427 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 427 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 299 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.14e+00
        pdb=" CG  ASP A 299 "   -0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 299 "    0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 299 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 516 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO A 517 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 517 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 517 "    0.022 5.00e-02 4.00e+02
  ... (remaining 878 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 2517
        3.00 -     3.47: 4520
        3.47 -     3.95: 7381
        3.95 -     4.42: 8672
        4.42 -     4.90: 14822
  Nonbonded interactions: 37912
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 336 "
            pdb=" ND2 ASN A 336 "
     model   vdw
     2.520 3.120
  nonbonded pdb=" C   THR A 678 "
            pdb=" OG1 THR A 678 "
     model   vdw
     2.520 2.616
  nonbonded pdb=" N   ASP E 134 "
            pdb=" OD1 ASP E 134 "
     model   vdw
     2.529 3.120
  nonbonded pdb=" C   THR A 556 "
            pdb=" OG1 THR A 556 "
     model   vdw
     2.539 2.616
  nonbonded pdb=" N   THR A 556 "
            pdb=" CG2 THR A 556 "
     model   vdw
     2.571 2.832
  ... (remaining 37907 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=0.48 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:             10.830
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     7.580
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
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      :  0.004   0.027   5039  Z= 0.167
  Angle     :  0.650  10.021   6798  Z= 0.361
  Chirality :  0.045   0.160    711
  Planarity :  0.004   0.045    881
  Dihedral  : 18.285  89.263   1835
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 34.03 %
    Favored  : 62.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.34), residues: 596
  helix:  0.47 (0.53), residues: 81
  sheet:  1.12 (0.35), residues: 212
  loop : -1.00 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 135 
 TYR   0.014   0.001   TYR A 373 
 PHE   0.017   0.001   PHE A 552 
 TRP   0.004   0.001   TRP A 890 
 HIS   0.003   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5039)
  covalent geometry    : angle       0.65018 ( 6798)
  hydrogen bonds       : bond        0.11095 (  220)
  hydrogen bonds       : angle       5.57513 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 PHE cc_start: 0.7654 (m-80) cc_final: 0.7393 (m-10)
REVERT: A  512 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8012 (tt)
REVERT: A  532 SER cc_start: 0.8201 (m) cc_final: 0.7812 (t)
REVERT: A  606 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7428 (p)
REVERT: A  721 PHE cc_start: 0.6776 (t80) cc_final: 0.6552 (t80)
REVERT: A  772 ASP cc_start: 0.7507 (p0) cc_final: 0.6942 (t0)
REVERT: A  816 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.6928 (mtm180)
  outliers start: 19
  outliers final: 12
  residues processed: 114
  average time/residue: 0.0870
  time to fit residues: 12.3621
Evaluate side-chains
  112 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  341 ASN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  622 THR
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  816 ARG
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  157 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0970
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 341 ASN
** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 651 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.149555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128110 restraints weight = 10936.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.132852 restraints weight = 4894.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.135843 restraints weight = 2814.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.137743 restraints weight = 1898.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.138581 restraints weight = 1449.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3756 r_free = 0.3756    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3756 r_free = 0.3756    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.0659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5039  Z= 0.211
  Angle     :  0.618   7.776   6798  Z= 0.327
  Chirality :  0.047   0.171    711
  Planarity :  0.004   0.046    881
  Dihedral  :  8.479  59.715    711
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 30.25 %
    Favored  : 63.89 %
  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 aren not related in a simple way.
  whole: -0.13 (0.34), residues: 596
  helix:  0.31 (0.53), residues: 82
  sheet:  1.01 (0.34), residues: 213
  loop : -1.04 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 135 
 TYR   0.016   0.002   TYR A 874 
 PHE   0.025   0.002   PHE A 552 
 TRP   0.004   0.001   TRP A 890 
 HIS   0.005   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 5039)
  covalent geometry    : angle       0.61824 ( 6798)
  hydrogen bonds       : bond        0.03336 (  220)
  hydrogen bonds       : angle       5.19265 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 PHE cc_start: 0.7674 (m-80) cc_final: 0.7369 (m-10)
REVERT: A  512 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7989 (tt)
REVERT: A  532 SER cc_start: 0.8263 (m) cc_final: 0.7862 (t)
REVERT: A  606 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7405 (p)
REVERT: A  788 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8264 (p)
  outliers start: 31
  outliers final: 19
  residues processed: 124
  average time/residue: 0.0761
  time to fit residues: 12.1631
Evaluate side-chains
  122 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  147 ASP
Chi-restraints excluded: chain E residue  149 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0000
   chunk 15 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 37 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0970
   chunk 4 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 502 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.152408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132080 restraints weight = 8823.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136396 restraints weight = 4241.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.139192 restraints weight = 2540.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.141001 restraints weight = 1762.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.142047 restraints weight = 1355.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3806 r_free = 0.3806    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3806 r_free = 0.3806    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.0837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5039  Z= 0.115
  Angle     :  0.571   7.129   6798  Z= 0.297
  Chirality :  0.044   0.146    711
  Planarity :  0.004   0.041    881
  Dihedral  :  7.772  59.443    701
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 31.95 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.34), residues: 596
  helix:  0.50 (0.54), residues: 82
  sheet:  1.19 (0.34), residues: 214
  loop : -0.96 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 395 
 TYR   0.009   0.001   TYR A 828 
 PHE   0.018   0.001   PHE A 552 
 TRP   0.004   0.001   TRP A 518 
 HIS   0.002   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5039)
  covalent geometry    : angle       0.57088 ( 6798)
  hydrogen bonds       : bond        0.02682 (  220)
  hydrogen bonds       : angle       4.92677 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 PHE cc_start: 0.7632 (m-80) cc_final: 0.7304 (m-10)
REVERT: A  512 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7989 (tt)
REVERT: A  532 SER cc_start: 0.8228 (m) cc_final: 0.7845 (t)
REVERT: A  606 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7469 (p)
REVERT: A  853 SER cc_start: 0.7511 (p) cc_final: 0.7121 (p)
  outliers start: 20
  outliers final: 9
  residues processed: 120
  average time/residue: 0.0801
  time to fit residues: 12.1564
Evaluate side-chains
  114 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain E residue  117 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0980
   chunk 2 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0060
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.151058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.127587 restraints weight = 15232.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.133106 restraints weight = 6131.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136612 restraints weight = 3284.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.138856 restraints weight = 2111.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.140280 restraints weight = 1542.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5039  Z= 0.159
  Angle     :  0.583   7.026   6798  Z= 0.305
  Chirality :  0.045   0.129    711
  Planarity :  0.004   0.040    881
  Dihedral  :  7.712  59.722    700
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 32.89 %
    Favored  : 62.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.34), residues: 596
  helix:  0.49 (0.55), residues: 82
  sheet:  1.16 (0.34), residues: 216
  loop : -1.02 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 395 
 TYR   0.012   0.001   TYR A 874 
 PHE   0.020   0.002   PHE A 552 
 TRP   0.003   0.001   TRP A 890 
 HIS   0.004   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 5039)
  covalent geometry    : angle       0.58302 ( 6798)
  hydrogen bonds       : bond        0.02886 (  220)
  hydrogen bonds       : angle       4.96480 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 PHE cc_start: 0.7609 (m-80) cc_final: 0.7230 (m-10)
REVERT: A  430 ARG cc_start: 0.7084 (mmt180) cc_final: 0.6832 (mmm-85)
REVERT: A  512 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7976 (tt)
REVERT: A  532 SER cc_start: 0.8262 (m) cc_final: 0.7806 (p)
REVERT: A  606 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7445 (p)
REVERT: A  788 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8276 (p)
REVERT: A  853 SER cc_start: 0.7513 (p) cc_final: 0.7121 (p)
REVERT: E  134 ASP cc_start: 0.7780 (p0) cc_final: 0.7338 (p0)
  outliers start: 23
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0773
  time to fit residues: 11.9981
Evaluate side-chains
  123 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  157 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0970
   chunk 23 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   chunk 45 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
A 341 ASN
A 502 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.150459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129925 restraints weight = 9313.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.134357 restraints weight = 4435.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.137201 restraints weight = 2622.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.139006 restraints weight = 1811.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.140205 restraints weight = 1390.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3765
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3765 r_free = 0.3765    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3765 r_free = 0.3765    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5039  Z= 0.162
  Angle     :  0.581   6.229   6798  Z= 0.307
  Chirality :  0.045   0.128    711
  Planarity :  0.004   0.047    881
  Dihedral  :  7.789  59.624    700
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 31.95 %
    Favored  : 62.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.34), residues: 596
  helix:  0.47 (0.55), residues: 82
  sheet:  1.14 (0.34), residues: 216
  loop : -1.07 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 852 
 TYR   0.012   0.001   TYR A 874 
 PHE   0.020   0.001   PHE A 552 
 TRP   0.003   0.001   TRP A 890 
 HIS   0.004   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5039)
  covalent geometry    : angle       0.58065 ( 6798)
  hydrogen bonds       : bond        0.02893 (  220)
  hydrogen bonds       : angle       4.94277 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 PHE cc_start: 0.7607 (m-80) cc_final: 0.7220 (m-10)
REVERT: A  512 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7983 (tt)
REVERT: A  532 SER cc_start: 0.8278 (m) cc_final: 0.7872 (p)
REVERT: A  606 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7425 (p)
REVERT: A  788 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8286 (p)
REVERT: A  816 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.6811 (mtm180)
REVERT: A  853 SER cc_start: 0.7502 (p) cc_final: 0.7111 (p)
  outliers start: 30
  outliers final: 19
  residues processed: 127
  average time/residue: 0.0818
  time to fit residues: 13.1869
Evaluate side-chains
  127 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  341 ASN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  816 ARG
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  157 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 0 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.3980
   chunk 57 optimal weight:    0.2980
   chunk 7 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0000
   overall best weight:    0.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 341 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.145571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125490 restraints weight = 9228.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129705 restraints weight = 4450.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132475 restraints weight = 2683.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.134241 restraints weight = 1864.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.135369 restraints weight = 1436.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5039  Z= 0.176
  Angle     :  0.602   6.982   6798  Z= 0.321
  Chirality :  0.046   0.141    711
  Planarity :  0.004   0.046    881
  Dihedral  :  7.767  59.756    700
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 31.76 %
    Favored  : 62.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.34), residues: 596
  helix:  0.41 (0.54), residues: 82
  sheet:  1.15 (0.34), residues: 213
  loop : -1.15 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 852 
 TYR   0.013   0.001   TYR A 874 
 PHE   0.021   0.002   PHE A 552 
 TRP   0.003   0.001   TRP A 890 
 HIS   0.005   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5039)
  covalent geometry    : angle       0.60202 ( 6798)
  hydrogen bonds       : bond        0.02993 (  220)
  hydrogen bonds       : angle       5.02718 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A  430 ARG cc_start: 0.7060 (mmt180) cc_final: 0.6832 (mmm-85)
REVERT: A  512 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7964 (tt)
REVERT: A  532 SER cc_start: 0.8294 (m) cc_final: 0.7887 (p)
REVERT: A  606 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7401 (p)
REVERT: A  788 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8274 (p)
REVERT: A  816 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.6834 (mtm180)
REVERT: E  134 ASP cc_start: 0.7849 (p0) cc_final: 0.7586 (p0)
  outliers start: 29
  outliers final: 21
  residues processed: 124
  average time/residue: 0.0808
  time to fit residues: 12.6189
Evaluate side-chains
  129 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  816 ARG
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  157 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0980
   chunk 49 optimal weight:    0.0040
   chunk 9 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   overall best weight:    0.2592

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

Flipped N/Q/H residues before XYZ refinement:
A 502 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.146594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.126260 restraints weight = 9549.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.130603 restraints weight = 4566.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.133220 restraints weight = 2722.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.135207 restraints weight = 1911.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.136410 restraints weight = 1467.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5039  Z= 0.126
  Angle     :  0.582   8.293   6798  Z= 0.309
  Chirality :  0.044   0.134    711
  Planarity :  0.004   0.045    881
  Dihedral  :  7.528  59.477    700
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 32.33 %
    Favored  : 63.52 %
  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 aren not related in a simple way.
  whole: -0.02 (0.34), residues: 596
  helix:  0.57 (0.55), residues: 82
  sheet:  1.20 (0.34), residues: 214
  loop : -1.13 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 135 
 TYR   0.009   0.001   TYR A 828 
 PHE   0.017   0.001   PHE A 552 
 TRP   0.002   0.000   TRP A 713 
 HIS   0.003   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5039)
  covalent geometry    : angle       0.58191 ( 6798)
  hydrogen bonds       : bond        0.02799 (  220)
  hydrogen bonds       : angle       4.91017 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A  393 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6970 (tm-30)
REVERT: A  512 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7965 (tt)
REVERT: A  532 SER cc_start: 0.8259 (m) cc_final: 0.7847 (p)
REVERT: A  788 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8272 (p)
REVERT: A  816 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6834 (mtm180)
REVERT: A  853 SER cc_start: 0.7541 (p) cc_final: 0.7118 (p)
  outliers start: 22
  outliers final: 18
  residues processed: 123
  average time/residue: 0.0826
  time to fit residues: 12.7754
Evaluate side-chains
  122 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  816 ARG
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  157 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 54 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   chunk 58 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 547 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.144916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.121824 restraints weight = 15892.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.127221 restraints weight = 6416.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.130709 restraints weight = 3465.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.132909 restraints weight = 2235.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134306 restraints weight = 1637.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5039  Z= 0.191
  Angle     :  0.639  10.242   6798  Z= 0.334
  Chirality :  0.046   0.133    711
  Planarity :  0.004   0.047    881
  Dihedral  :  7.542  59.243    699
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 31.76 %
    Favored  : 63.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.34), residues: 596
  helix:  0.29 (0.55), residues: 84
  sheet:  1.14 (0.35), residues: 213
  loop : -1.20 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 852 
 TYR   0.014   0.002   TYR A 874 
 PHE   0.022   0.002   PHE A 552 
 TRP   0.005   0.001   TRP A 890 
 HIS   0.005   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 5039)
  covalent geometry    : angle       0.63883 ( 6798)
  hydrogen bonds       : bond        0.03109 (  220)
  hydrogen bonds       : angle       5.06439 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  393 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6977 (tm-30)
REVERT: A  512 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7965 (tt)
REVERT: A  532 SER cc_start: 0.8290 (m) cc_final: 0.7904 (t)
REVERT: A  788 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8267 (p)
REVERT: A  816 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.6811 (mtm180)
REVERT: E  144 MET cc_start: 0.6394 (mtt) cc_final: 0.6051 (mtt)
  outliers start: 27
  outliers final: 20
  residues processed: 123
  average time/residue: 0.0758
  time to fit residues: 11.9469
Evaluate side-chains
  123 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  816 ARG
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  157 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 13 optimal weight:    0.2980
   chunk 35 optimal weight:    0.0070
   chunk 15 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.2980
   chunk 4 optimal weight:    2.9990
   chunk 56 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.3398

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

Flipped N/Q/H residues before XYZ refinement:
A 502 GLN
A 547 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.146126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.124938 restraints weight = 11282.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.129616 restraints weight = 5091.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.132694 restraints weight = 2940.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.134667 restraints weight = 1973.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.135507 restraints weight = 1486.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3712 r_free = 0.3712    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3712 r_free = 0.3712    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5039  Z= 0.146
  Angle     :  0.612  11.091   6798  Z= 0.320
  Chirality :  0.044   0.131    711
  Planarity :  0.004   0.046    881
  Dihedral  :  7.290  59.449    699
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 32.51 %
    Favored  : 63.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.34), residues: 596
  helix:  0.36 (0.55), residues: 84
  sheet:  1.12 (0.34), residues: 216
  loop : -1.20 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 135 
 TYR   0.010   0.001   TYR A 874 
 PHE   0.019   0.001   PHE A 552 
 TRP   0.002   0.000   TRP A 713 
 HIS   0.003   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5039)
  covalent geometry    : angle       0.61250 ( 6798)
  hydrogen bonds       : bond        0.02824 (  220)
  hydrogen bonds       : angle       4.95976 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  393 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6987 (tm-30)
REVERT: A  512 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7962 (tt)
REVERT: A  532 SER cc_start: 0.8237 (m) cc_final: 0.7853 (t)
REVERT: A  772 ASP cc_start: 0.7481 (p0) cc_final: 0.7010 (t0)
REVERT: A  788 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8259 (p)
REVERT: A  816 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6860 (mtm180)
REVERT: A  853 SER cc_start: 0.7526 (p) cc_final: 0.7126 (p)
REVERT: E  136 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7859 (pp30)
REVERT: E  144 MET cc_start: 0.6447 (mtt) cc_final: 0.6147 (mtt)
  outliers start: 23
  outliers final: 18
  residues processed: 118
  average time/residue: 0.0811
  time to fit residues: 12.1745
Evaluate side-chains
  121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  816 ARG
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  157 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 33 optimal weight:    0.2980
   chunk 17 optimal weight:    0.0770
   chunk 9 optimal weight:    0.0070
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0470
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.2454

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

Flipped N/Q/H residues before XYZ refinement:
A 547 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.147214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.126819 restraints weight = 9613.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.131186 restraints weight = 4574.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.133889 restraints weight = 2726.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.135859 restraints weight = 1901.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136927 restraints weight = 1450.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5039  Z= 0.121
  Angle     :  0.601  11.403   6798  Z= 0.312
  Chirality :  0.044   0.130    711
  Planarity :  0.004   0.046    881
  Dihedral  :  6.996  59.270    698
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 33.08 %
    Favored  : 62.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.34), residues: 596
  helix:  0.49 (0.55), residues: 84
  sheet:  1.16 (0.35), residues: 218
  loop : -1.09 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 135 
 TYR   0.009   0.001   TYR A 828 
 PHE   0.017   0.001   PHE A 552 
 TRP   0.003   0.000   TRP A 890 
 HIS   0.003   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5039)
  covalent geometry    : angle       0.60084 ( 6798)
  hydrogen bonds       : bond        0.02623 (  220)
  hydrogen bonds       : angle       4.81135 (  608)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.5804 (mp10)
REVERT: A  393 GLU cc_start: 0.7310 (tm-30) cc_final: 0.7024 (tm-30)
REVERT: A  504 SER cc_start: 0.8733 (t) cc_final: 0.8328 (m)
REVERT: A  512 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7965 (tt)
REVERT: A  532 SER cc_start: 0.8222 (m) cc_final: 0.7769 (p)
REVERT: A  772 ASP cc_start: 0.7465 (p0) cc_final: 0.7007 (t0)
REVERT: A  788 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8264 (p)
REVERT: A  816 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6860 (mtm180)
REVERT: A  853 SER cc_start: 0.7534 (p) cc_final: 0.7124 (p)
REVERT: E  136 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7886 (pp30)
REVERT: E  144 MET cc_start: 0.6384 (mtt) cc_final: 0.6105 (mtt)
  outliers start: 22
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0811
  time to fit residues: 12.5041
Evaluate side-chains
  122 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  788 THR
Chi-restraints excluded: chain A residue  816 ARG
Chi-restraints excluded: chain A residue  819 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  157 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    0.0000
   chunk 12 optimal weight:    0.2980
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0670
   chunk 37 optimal weight:    0.0170
   chunk 6 optimal weight:    0.0970
   chunk 36 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.0958

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

Flipped N/Q/H residues before XYZ refinement:
A 502 GLN
A 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.154208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.131382 restraints weight = 13884.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136727 restraints weight = 5807.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.140113 restraints weight = 3170.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.142307 restraints weight = 2083.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.143729 restraints weight = 1536.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3817 r_free = 0.3817    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3817 r_free = 0.3817    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5039  Z= 0.094
  Angle     :  0.576  11.032   6798  Z= 0.298
  Chirality :  0.043   0.133    711
  Planarity :  0.004   0.045    881
  Dihedral  :  6.619  59.301    698
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 34.97 %
    Favored  : 62.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.34), residues: 596
  helix:  1.12 (0.57), residues: 79
  sheet:  1.51 (0.35), residues: 210
  loop : -0.97 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 135 
 TYR   0.008   0.001   TYR A 828 
 PHE   0.014   0.001   PHE A 552 
 TRP   0.003   0.001   TRP A 713 
 HIS   0.001   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 5039)
  covalent geometry    : angle       0.57598 ( 6798)
  hydrogen bonds       : bond        0.02337 (  220)
  hydrogen bonds       : angle       4.54262 (  608)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1357.42 seconds
wall clock time: 24 minutes 10.59 seconds (1450.59 seconds total)