Starting phenix.real_space_refine
on Tue Mar  3 12:47:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pdd_13334/03_2026/7pdd_13334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pdd_13334/03_2026/7pdd_13334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pdd_13334/03_2026/7pdd_13334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pdd_13334/03_2026/7pdd_13334.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pdd_13334/03_2026/7pdd_13334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pdd_13334/03_2026/7pdd_13334.map"
  }
  resolution = 4.2
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    2847      2.51       5
     N     772      2.21       5
     O     864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4516
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3550
          Classifications: {'peptide': 449}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 9, 'TRANS': 439}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 966
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 3, 'TRANS': 124}
  Time building chain proxies: 1.22, per 1000 atoms: 0.27
  Number of scatterers: 4516
  At special positions: 0
  Unit cell: (94.77, 77.76, 79.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O     864      8.00
     N     772      7.00
     C    2847      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: 0.31
  Conformation dependent library (CDL) restraints added in 345.1 milliseconds
  

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1058

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 4 sheets defined
      50.1% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 321 through 335
    Processing helix  chain 'A' and resid 339 through 348
      removed outlier: 3.552A  pdb=" N   LYS A 348 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 359
      removed outlier: 3.694A  pdb=" N   GLU A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 407
      removed outlier: 3.602A  pdb=" N   MET A 406 " --> pdb=" O   GLY A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 434
    Processing helix  chain 'A' and resid 457 through 481
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 3.779A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 537
    Processing helix  chain 'A' and resid 1021 through 1037
    Processing helix  chain 'A' and resid 1038 through 1047
    Processing helix  chain 'A' and resid 1067 through 1072
      removed outlier: 3.699A  pdb=" N   PHE A1071 " --> pdb=" O   ASN A1067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1097
      removed outlier: 3.912A  pdb=" N   LEU A1097 " --> pdb=" O   PHE A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1157
      removed outlier: 3.878A  pdb=" N   GLN A1137 " --> pdb=" O   GLN A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1189 through 1200
      removed outlier: 4.280A  pdb=" N   ASN A1193 " --> pdb=" O   GLY A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1219
      removed outlier: 3.625A  pdb=" N   LYS A1219 " --> pdb=" O   ARG A1215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 25
    Processing helix  chain 'B' and resid 26 through 36
    Processing helix  chain 'B' and resid 49 through 58
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 82 through 91
    Processing helix  chain 'B' and resid 92 through 102
    Processing helix  chain 'B' and resid 115 through 123
    Processing helix  chain 'B' and resid 125 through 134
    Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439
      removed outlier: 7.373A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER A 394 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 7.373A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER A 394 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   SER A 532 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   THR A 492 " --> pdb=" O   SER A 532 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1109
      removed outlier: 7.182A  pdb=" N   MET A1116 " --> pdb=" O   ILE A1108 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   GLN A1208 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   VAL A1166 " --> pdb=" O   GLN A1208 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR A1241 " --> pdb=" O   VAL A1209 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY A1228 " --> pdb=" O   THR A1240 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    756 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: 0.76

  Time building geometry restraints manager: 0.44 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: 1515
        1.34 -     1.46: 976
        1.46 -     1.58: 2050
        1.58 -     1.70: 0
        1.70 -     1.82: 54
  Bond restraints: 4595
  Sorted by residual:
  bond pdb=" N   ASP A 541 "
       pdb=" CA  ASP A 541 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.69e+00
  bond pdb=" N   GLU A 453 "
       pdb=" CA  GLU A 453 "
    ideal  model  delta    sigma   weight residual
    1.460  1.446  0.014 1.29e-02 6.01e+03 1.11e+00
  bond pdb=" CA  ASN A1035 "
       pdb=" C   ASN A1035 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.011 1.24e-02 6.50e+03 8.21e-01
  bond pdb=" C   GLU A 453 "
       pdb=" O   GLU A 453 "
    ideal  model  delta    sigma   weight residual
    1.248  1.237  0.011 1.26e-02 6.30e+03 7.75e-01
  bond pdb=" CB  PRO A 384 "
       pdb=" CG  PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.492  1.536 -0.044 5.00e-02 4.00e+02 7.66e-01
  ... (remaining 4590 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 5935
        1.58 -     3.15: 212
        3.15 -     4.73: 33
        4.73 -     6.30: 6
        6.30 -     7.88: 3
  Bond angle restraints: 6189
  Sorted by residual:
  angle pdb=" N   TYR A 446 "
        pdb=" CA  TYR A 446 "
        pdb=" C   TYR A 446 "
      ideal   model   delta    sigma   weight residual
     108.79  113.27   -4.48 1.53e+00 4.27e-01 8.58e+00
  angle pdb=" C   TYR A 445 "
        pdb=" N   TYR A 446 "
        pdb=" CA  TYR A 446 "
      ideal   model   delta    sigma   weight residual
     121.62  116.31    5.31 1.83e+00 2.99e-01 8.43e+00
  angle pdb=" C   LYS A 437 "
        pdb=" N   ILE A 438 "
        pdb=" CA  ILE A 438 "
      ideal   model   delta    sigma   weight residual
     121.97  117.45    4.52 1.80e+00 3.09e-01 6.29e+00
  angle pdb=" N   ASN A 409 "
        pdb=" CA  ASN A 409 "
        pdb=" C   ASN A 409 "
      ideal   model   delta    sigma   weight residual
     110.44  113.29   -2.85 1.20e+00 6.94e-01 5.63e+00
  angle pdb=" C   THR A1181 "
        pdb=" N   LYS A1182 "
        pdb=" CA  LYS A1182 "
      ideal   model   delta    sigma   weight residual
     122.39  126.25   -3.86 1.64e+00 3.72e-01 5.54e+00
  ... (remaining 6184 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 2448
       17.24 -    34.48: 248
       34.48 -    51.72: 44
       51.72 -    68.96: 7
       68.96 -    86.20: 5
  Dihedral angle restraints: 2752
    sinusoidal: 1102
      harmonic: 1650
  Sorted by residual:
  dihedral pdb=" CA  THR A1180 "
           pdb=" C   THR A1180 "
           pdb=" N   THR A1181 "
           pdb=" CA  THR A1181 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.99  -23.01     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  TYR A1072 "
           pdb=" C   TYR A1072 "
           pdb=" N   GLU A1073 "
           pdb=" CA  GLU A1073 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.00  -20.00     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  LYS A 321 "
           pdb=" C   LYS A 321 "
           pdb=" N   ASP A 322 "
           pdb=" CA  ASP A 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 2749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 383
       0.029 -    0.059: 186
       0.059 -    0.088: 78
       0.088 -    0.117: 29
       0.117 -    0.146: 4
  Chirality restraints: 680
  Sorted by residual:
  chirality pdb=" CA  ASP A 541 "
            pdb=" N   ASP A 541 "
            pdb=" C   ASP A 541 "
            pdb=" CB  ASP A 541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  ILE A 395 "
            pdb=" N   ILE A 395 "
            pdb=" C   ILE A 395 "
            pdb=" CB  ILE A 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  VAL A 509 "
            pdb=" N   VAL A 509 "
            pdb=" C   VAL A 509 "
            pdb=" CB  VAL A 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 677 not shown)

  Planarity restraints: 803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1037 "    0.032 5.00e-02 4.00e+02   4.77e-02 3.65e+00
        pdb=" N   PRO A1038 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A1038 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1038 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A1072 "    0.007 2.00e-02 2.50e+03   1.36e-02 1.84e+00
        pdb=" C   TYR A1072 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   TYR A1072 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLU A1073 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 453 "    0.020 5.00e-02 4.00e+02   3.04e-02 1.48e+00
        pdb=" N   PRO A 454 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 454 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 454 "    0.017 5.00e-02 4.00e+02
  ... (remaining 800 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 95
        2.65 -     3.22: 4861
        3.22 -     3.78: 7361
        3.78 -     4.34: 9956
        4.34 -     4.90: 15254
  Nonbonded interactions: 37527
  Sorted by model distance:
  nonbonded pdb=" O   SER A 532 "
            pdb=" OG1 THR A 535 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   ALA A 412 "
            pdb=" OG  SER A1052 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" OH  TYR A1226 "
            pdb=" OG1 THR A1229 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   SER A1196 "
            pdb=" OG1 THR A1200 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" NH2 ARG A1206 "
            pdb=" O   PRO A1244 "
     model   vdw
     2.222 3.120
  ... (remaining 37522 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.730
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
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   0.044   4595  Z= 0.199
  Angle     :  0.748   7.879   6189  Z= 0.445
  Chirality :  0.042   0.146    680
  Planarity :  0.004   0.048    803
  Dihedral  : 14.377  86.204   1694
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 20.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.11 (0.29), residues: 567
  helix: -2.34 (0.25), residues: 273
  sheet: -2.54 (0.40), residues: 105
  loop : -3.08 (0.39), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.015   0.002   TYR A1241 
 PHE   0.010   0.002   PHE A1224 
 TRP   0.012   0.002   TRP A1031 
 HIS   0.005   0.002   HIS A1170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 4595)
  covalent geometry    : angle       0.74809 ( 6189)
  hydrogen bonds       : bond        0.14770 (  243)
  hydrogen bonds       : angle       7.01275 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8592 (m-10) cc_final: 0.8223 (m-80)
REVERT: A  425 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8456 (mtp180)
REVERT: A  429 LEU cc_start: 0.9524 (tp) cc_final: 0.9283 (tt)
REVERT: B   56 TRP cc_start: 0.7689 (t60) cc_final: 0.7440 (t-100)
REVERT: B  114 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8269 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0930
  time to fit residues: 15.4491
Evaluate side-chains
  101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1135 HIS
A1154 ASN
A1237 GLN
** B  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.094317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.075110 restraints weight = 18150.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.076177 restraints weight = 10641.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.076422 restraints weight = 8989.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.076734 restraints weight = 8473.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.076927 restraints weight = 8159.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4595  Z= 0.182
  Angle     :  0.703   6.928   6189  Z= 0.377
  Chirality :  0.045   0.150    680
  Planarity :  0.004   0.059    803
  Dihedral  :  5.475  25.258    615
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.31), residues: 567
  helix: -1.09 (0.27), residues: 282
  sheet: -2.12 (0.42), residues: 105
  loop : -2.48 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1084 
 TYR   0.019   0.002   TYR A 446 
 PHE   0.011   0.002   PHE A1168 
 TRP   0.022   0.002   TRP A1159 
 HIS   0.006   0.002   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4595)
  covalent geometry    : angle       0.70290 ( 6189)
  hydrogen bonds       : bond        0.04672 (  243)
  hydrogen bonds       : angle       5.72540 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 PHE cc_start: 0.8382 (m-10) cc_final: 0.8158 (m-10)
REVERT: A  423 PHE cc_start: 0.8927 (m-10) cc_final: 0.8482 (m-80)
REVERT: A  425 ARG cc_start: 0.9163 (mtt180) cc_final: 0.8938 (mtt180)
REVERT: A  543 TYR cc_start: 0.7863 (m-80) cc_final: 0.7041 (m-80)
REVERT: A 1075 ASN cc_start: 0.8140 (m-40) cc_final: 0.7522 (p0)
REVERT: A 1081 GLU cc_start: 0.7970 (tp30) cc_final: 0.7732 (tp30)
REVERT: A 1084 ARG cc_start: 0.8983 (mtt90) cc_final: 0.8203 (mtt-85)
REVERT: A 1141 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8636 (mm-30)
REVERT: A 1146 MET cc_start: 0.9104 (ppp) cc_final: 0.8799 (ppp)
REVERT: A 1238 MET cc_start: 0.9066 (mtp) cc_final: 0.8801 (mtp)
REVERT: B   56 TRP cc_start: 0.7931 (t60) cc_final: 0.7638 (t-100)
REVERT: B   89 ARG cc_start: 0.8215 (ttt180) cc_final: 0.7877 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0817
  time to fit residues: 12.8697
Evaluate side-chains
  101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.095615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.076237 restraints weight = 17895.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.077471 restraints weight = 10622.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.077844 restraints weight = 8844.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.078123 restraints weight = 8386.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.078307 restraints weight = 8156.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4595  Z= 0.138
  Angle     :  0.651   6.841   6189  Z= 0.346
  Chirality :  0.043   0.151    680
  Planarity :  0.004   0.057    803
  Dihedral  :  5.116  24.152    615
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.32), residues: 567
  helix: -0.45 (0.29), residues: 280
  sheet: -1.82 (0.44), residues: 105
  loop : -2.22 (0.43), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1165 
 TYR   0.019   0.002   TYR A 446 
 PHE   0.011   0.002   PHE A1168 
 TRP   0.019   0.002   TRP A1159 
 HIS   0.004   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4595)
  covalent geometry    : angle       0.65099 ( 6189)
  hydrogen bonds       : bond        0.04249 (  243)
  hydrogen bonds       : angle       5.30977 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8840 (m-10) cc_final: 0.8265 (m-80)
REVERT: A  425 ARG cc_start: 0.9163 (mtt180) cc_final: 0.8580 (mtp180)
REVERT: A  465 MET cc_start: 0.8361 (tmm) cc_final: 0.7782 (tmm)
REVERT: A  510 TRP cc_start: 0.6970 (m-90) cc_final: 0.6766 (m-90)
REVERT: A 1075 ASN cc_start: 0.8044 (m-40) cc_final: 0.7688 (p0)
REVERT: A 1084 ARG cc_start: 0.8891 (mtt90) cc_final: 0.8216 (mtt-85)
REVERT: A 1141 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8371 (mm-30)
REVERT: A 1146 MET cc_start: 0.9089 (ppp) cc_final: 0.8798 (ppp)
REVERT: A 1198 MET cc_start: 0.8653 (mtp) cc_final: 0.8180 (tmm)
REVERT: B   16 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8702 (mmtm)
REVERT: B   56 TRP cc_start: 0.7875 (t60) cc_final: 0.7531 (t-100)
REVERT: B  112 PHE cc_start: 0.7327 (m-80) cc_final: 0.7071 (m-80)
REVERT: B  114 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8186 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0838
  time to fit residues: 13.1245
Evaluate side-chains
  98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 21 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0770
   chunk 44 optimal weight:    0.1980
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.2938

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.099091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.077064 restraints weight = 17485.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.079255 restraints weight = 11881.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.080870 restraints weight = 8998.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.082057 restraints weight = 7314.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.082910 restraints weight = 6268.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.3901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   4595  Z= 0.151
  Angle     :  0.684   8.308   6189  Z= 0.359
  Chirality :  0.043   0.156    680
  Planarity :  0.003   0.053    803
  Dihedral  :  4.982  25.334    615
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.79 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.33), residues: 567
  helix: -0.28 (0.28), residues: 284
  sheet: -1.36 (0.46), residues: 105
  loop : -2.05 (0.45), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  23 
 TYR   0.015   0.002   TYR A1083 
 PHE   0.011   0.001   PHE A1168 
 TRP   0.024   0.002   TRP A1159 
 HIS   0.004   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4595)
  covalent geometry    : angle       0.68386 ( 6189)
  hydrogen bonds       : bond        0.04067 (  243)
  hydrogen bonds       : angle       5.34552 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8758 (m-10) cc_final: 0.8289 (m-80)
REVERT: A  483 MET cc_start: 0.5924 (tpt) cc_final: 0.5615 (tpt)
REVERT: A 1075 ASN cc_start: 0.7913 (m-40) cc_final: 0.7648 (p0)
REVERT: A 1084 ARG cc_start: 0.8927 (mtt90) cc_final: 0.8343 (mtt-85)
REVERT: A 1141 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8447 (mm-30)
REVERT: A 1146 MET cc_start: 0.9060 (ppp) cc_final: 0.8751 (ppp)
REVERT: B  112 PHE cc_start: 0.7305 (m-80) cc_final: 0.7062 (m-80)
REVERT: B  114 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8119 (mmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0788
  time to fit residues: 12.5042
Evaluate side-chains
  100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 21 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0270
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
A 389 GLN
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.098705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.078865 restraints weight = 17895.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.080622 restraints weight = 10477.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.080756 restraints weight = 8499.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.081145 restraints weight = 7995.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.081402 restraints weight = 7388.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4595  Z= 0.138
  Angle     :  0.679   6.828   6189  Z= 0.362
  Chirality :  0.044   0.178    680
  Planarity :  0.004   0.051    803
  Dihedral  :  4.961  22.818    615
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.33), residues: 567
  helix: -0.23 (0.29), residues: 285
  sheet: -1.13 (0.49), residues: 99
  loop : -2.10 (0.43), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  89 
 TYR   0.013   0.002   TYR A1083 
 PHE   0.010   0.001   PHE B  57 
 TRP   0.035   0.003   TRP B  56 
 HIS   0.005   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4595)
  covalent geometry    : angle       0.67935 ( 6189)
  hydrogen bonds       : bond        0.04030 (  243)
  hydrogen bonds       : angle       5.19187 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8712 (m-10) cc_final: 0.8149 (m-80)
REVERT: A  483 MET cc_start: 0.5870 (tpt) cc_final: 0.5537 (tpt)
REVERT: A 1084 ARG cc_start: 0.8972 (mtt90) cc_final: 0.8415 (mtt-85)
REVERT: A 1093 PHE cc_start: 0.8901 (m-10) cc_final: 0.8604 (m-80)
REVERT: A 1141 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8556 (mm-30)
REVERT: A 1198 MET cc_start: 0.8312 (ppp) cc_final: 0.7986 (ppp)
REVERT: B  112 PHE cc_start: 0.7393 (m-80) cc_final: 0.7141 (m-80)
REVERT: B  114 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8159 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0743
  time to fit residues: 11.2542
Evaluate side-chains
  99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 25 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 389 GLN
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.099041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.079752 restraints weight = 18091.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.080724 restraints weight = 11207.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.081320 restraints weight = 9789.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.081648 restraints weight = 9004.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.081857 restraints weight = 8148.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.4469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4595  Z= 0.139
  Angle     :  0.675   8.470   6189  Z= 0.355
  Chirality :  0.044   0.145    680
  Planarity :  0.003   0.049    803
  Dihedral  :  4.899  23.217    615
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  3.54 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.33), residues: 567
  helix: -0.14 (0.29), residues: 283
  sheet: -1.04 (0.50), residues: 99
  loop : -2.09 (0.43), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1206 
 TYR   0.013   0.002   TYR A1083 
 PHE   0.009   0.001   PHE A 397 
 TRP   0.036   0.002   TRP B  56 
 HIS   0.005   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4595)
  covalent geometry    : angle       0.67494 ( 6189)
  hydrogen bonds       : bond        0.03932 (  243)
  hydrogen bonds       : angle       5.08269 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8720 (m-10) cc_final: 0.8180 (m-80)
REVERT: A  425 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8507 (mtt180)
REVERT: A  483 MET cc_start: 0.5918 (tpt) cc_final: 0.5568 (tpt)
REVERT: A 1084 ARG cc_start: 0.8936 (mtt90) cc_final: 0.8116 (mtt-85)
REVERT: A 1094 ASP cc_start: 0.7524 (m-30) cc_final: 0.6865 (m-30)
REVERT: A 1141 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8339 (mm-30)
REVERT: A 1198 MET cc_start: 0.8254 (ppp) cc_final: 0.7808 (ppp)
  outliers start: 2
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0693
  time to fit residues: 10.6525
Evaluate side-chains
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0040
   chunk 30 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 40 optimal weight:    0.2980
   chunk 21 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.3190

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

Flipped N/Q/H residues before XYZ refinement:
A 420 ASN
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.100829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.079148 restraints weight = 17993.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.081167 restraints weight = 12719.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.082674 restraints weight = 9858.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.083785 restraints weight = 8113.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.084542 restraints weight = 6998.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.4943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4595  Z= 0.133
  Angle     :  0.680   6.800   6189  Z= 0.359
  Chirality :  0.044   0.156    680
  Planarity :  0.003   0.045    803
  Dihedral  :  4.751  21.761    615
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.33), residues: 567
  helix: -0.16 (0.29), residues: 283
  sheet: -0.98 (0.50), residues: 99
  loop : -1.85 (0.43), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  31 
 TYR   0.012   0.001   TYR A1083 
 PHE   0.009   0.001   PHE A1168 
 TRP   0.028   0.002   TRP B  56 
 HIS   0.003   0.001   HIS A1170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4595)
  covalent geometry    : angle       0.67981 ( 6189)
  hydrogen bonds       : bond        0.04014 (  243)
  hydrogen bonds       : angle       5.14272 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8685 (m-10) cc_final: 0.8150 (m-80)
REVERT: A  425 ARG cc_start: 0.8742 (mtm180) cc_final: 0.8411 (mtt180)
REVERT: A  483 MET cc_start: 0.5779 (tpt) cc_final: 0.5427 (tpt)
REVERT: A  520 MET cc_start: 0.6320 (ttt) cc_final: 0.5527 (tmm)
REVERT: A  569 TYR cc_start: 0.7966 (m-80) cc_final: 0.7615 (m-80)
REVERT: A 1084 ARG cc_start: 0.8889 (mtt90) cc_final: 0.8384 (mtt-85)
REVERT: A 1093 PHE cc_start: 0.8813 (m-10) cc_final: 0.8332 (m-10)
REVERT: A 1094 ASP cc_start: 0.7419 (m-30) cc_final: 0.6862 (m-30)
REVERT: A 1141 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8388 (mm-30)
REVERT: A 1146 MET cc_start: 0.8925 (ppp) cc_final: 0.8333 (ppp)
REVERT: A 1238 MET cc_start: 0.8855 (mtp) cc_final: 0.8645 (mtm)
REVERT: B  112 PHE cc_start: 0.7322 (m-80) cc_final: 0.7110 (m-80)
REVERT: B  114 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8171 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0821
  time to fit residues: 12.5219
Evaluate side-chains
  99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.099263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.078399 restraints weight = 18235.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.079894 restraints weight = 12649.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.081185 restraints weight = 9241.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.081500 restraints weight = 8353.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.081755 restraints weight = 7525.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.4958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4595  Z= 0.159
  Angle     :  0.714   7.398   6189  Z= 0.382
  Chirality :  0.044   0.175    680
  Planarity :  0.004   0.049    803
  Dihedral  :  4.823  20.948    615
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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 are not related in a simple way.
  whole: -1.47 (0.33), residues: 567
  helix: -0.27 (0.29), residues: 283
  sheet: -1.28 (0.49), residues: 97
  loop : -1.68 (0.44), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  31 
 TYR   0.012   0.002   TYR A 446 
 PHE   0.013   0.002   PHE A1068 
 TRP   0.023   0.002   TRP B  56 
 HIS   0.004   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4595)
  covalent geometry    : angle       0.71432 ( 6189)
  hydrogen bonds       : bond        0.04169 (  243)
  hydrogen bonds       : angle       5.19259 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8874 (m-10) cc_final: 0.8280 (m-80)
REVERT: A  425 ARG cc_start: 0.8923 (mtm180) cc_final: 0.8538 (mtt180)
REVERT: A  483 MET cc_start: 0.5835 (tpt) cc_final: 0.5483 (tpt)
REVERT: A  520 MET cc_start: 0.6599 (ttt) cc_final: 0.5592 (tmm)
REVERT: A  569 TYR cc_start: 0.8198 (m-80) cc_final: 0.7749 (m-80)
REVERT: A 1084 ARG cc_start: 0.8958 (mtt90) cc_final: 0.8378 (mtt-85)
REVERT: A 1094 ASP cc_start: 0.7633 (m-30) cc_final: 0.6878 (m-30)
REVERT: A 1141 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8424 (mm-30)
REVERT: A 1238 MET cc_start: 0.8983 (mtp) cc_final: 0.8578 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0794
  time to fit residues: 11.6921
Evaluate side-chains
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    0.2980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 335 HIS
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
** B  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.100996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.078955 restraints weight = 17852.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.081086 restraints weight = 12540.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.082523 restraints weight = 9663.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.083716 restraints weight = 7976.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.084549 restraints weight = 6863.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.5100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4595  Z= 0.142
  Angle     :  0.709   7.576   6189  Z= 0.374
  Chirality :  0.045   0.173    680
  Planarity :  0.004   0.047    803
  Dihedral  :  4.775  21.891    615
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.33), residues: 567
  helix: -0.26 (0.29), residues: 285
  sheet: -1.26 (0.48), residues: 97
  loop : -1.58 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  31 
 TYR   0.022   0.002   TYR A1083 
 PHE   0.019   0.002   PHE A1068 
 TRP   0.023   0.002   TRP B  56 
 HIS   0.004   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4595)
  covalent geometry    : angle       0.70928 ( 6189)
  hydrogen bonds       : bond        0.04060 (  243)
  hydrogen bonds       : angle       5.13877 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8745 (m-10) cc_final: 0.8312 (m-80)
REVERT: A  425 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8207 (mmt180)
REVERT: A  483 MET cc_start: 0.5792 (tpt) cc_final: 0.5466 (tpt)
REVERT: A  520 MET cc_start: 0.6278 (ttt) cc_final: 0.5369 (tmm)
REVERT: A 1084 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8371 (mtt-85)
REVERT: A 1094 ASP cc_start: 0.7455 (m-30) cc_final: 0.6737 (m-30)
REVERT: A 1141 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8363 (mm-30)
REVERT: A 1238 MET cc_start: 0.8851 (mtp) cc_final: 0.8640 (mtm)
REVERT: B  114 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8271 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0728
  time to fit residues: 10.7140
Evaluate side-chains
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 41 optimal weight:    0.3980
   chunk 35 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
** B  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.099556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.077167 restraints weight = 17835.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.079314 restraints weight = 12463.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.080853 restraints weight = 9532.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.081983 restraints weight = 7823.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.082762 restraints weight = 6737.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4595  Z= 0.154
  Angle     :  0.723   8.258   6189  Z= 0.383
  Chirality :  0.045   0.175    680
  Planarity :  0.004   0.048    803
  Dihedral  :  4.830  21.714    615
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.33), residues: 567
  helix: -0.26 (0.29), residues: 285
  sheet: -1.30 (0.50), residues: 93
  loop : -1.65 (0.43), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  31 
 TYR   0.021   0.002   TYR A1083 
 PHE   0.017   0.002   PHE A1068 
 TRP   0.017   0.002   TRP B  56 
 HIS   0.007   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4595)
  covalent geometry    : angle       0.72332 ( 6189)
  hydrogen bonds       : bond        0.04131 (  243)
  hydrogen bonds       : angle       5.28346 (  756)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 MET cc_start: 0.8367 (ppp) cc_final: 0.7935 (ppp)
REVERT: A  423 PHE cc_start: 0.8907 (m-10) cc_final: 0.8416 (m-80)
REVERT: A  425 ARG cc_start: 0.8894 (mtm180) cc_final: 0.8232 (mmt180)
REVERT: A  483 MET cc_start: 0.5790 (tpt) cc_final: 0.5437 (tpt)
REVERT: A  520 MET cc_start: 0.6450 (ttt) cc_final: 0.5551 (tmm)
REVERT: A 1030 ASP cc_start: 0.8094 (t70) cc_final: 0.7694 (t0)
REVERT: A 1094 ASP cc_start: 0.7539 (m-30) cc_final: 0.6781 (m-30)
REVERT: A 1141 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8356 (mm-30)
REVERT: A 1190 ASP cc_start: 0.8715 (p0) cc_final: 0.8285 (p0)
REVERT: A 1238 MET cc_start: 0.8904 (mtp) cc_final: 0.8642 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0743
  time to fit residues: 10.8637
Evaluate side-chains
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 11 optimal weight:    0.1980
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 31 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 49 optimal weight:    0.4980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
** B  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.101346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.079168 restraints weight = 17606.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.081279 restraints weight = 12281.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.082893 restraints weight = 9477.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.084079 restraints weight = 7714.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.084928 restraints weight = 6601.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.5466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4595  Z= 0.139
  Angle     :  0.714   8.612   6189  Z= 0.376
  Chirality :  0.045   0.171    680
  Planarity :  0.004   0.044    803
  Dihedral  :  4.724  21.186    615
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.33), residues: 567
  helix: -0.22 (0.29), residues: 286
  sheet: -1.30 (0.50), residues: 93
  loop : -1.54 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  31 
 TYR   0.017   0.001   TYR A1083 
 PHE   0.014   0.001   PHE B 117 
 TRP   0.021   0.002   TRP B  56 
 HIS   0.007   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4595)
  covalent geometry    : angle       0.71437 ( 6189)
  hydrogen bonds       : bond        0.04023 (  243)
  hydrogen bonds       : angle       5.20365 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1010.03 seconds
wall clock time: 18 minutes 3.32 seconds (1083.32 seconds total)