Starting phenix.real_space_refine
on Thu Mar  6 02:42:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pdd_13334/03_2025/7pdd_13334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pdd_13334/03_2025/7pdd_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pdd_13334/03_2025/7pdd_13334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pdd_13334/03_2025/7pdd_13334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pdd_13334/03_2025/7pdd_13334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pdd_13334/03_2025/7pdd_13334.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.21, per 1000 atoms: 1.15
  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: 1.28
  Conformation dependent library (CDL) restraints added in 760.5 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: 0.46
  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: 1.30

  Time building geometry restraints manager: 1.55 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:             1.900
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.570
  Find NCS groups from input model:        0.050
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.810
-------------------------------------------------------------------------------
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= 0.254
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.012   0.002   TRP A1031 
 HIS   0.005   0.002   HIS A1170 
 PHE   0.010   0.002   PHE A1224 
 TYR   0.015   0.002   TYR A1241 
 ARG   0.003   0.000   ARG A1165 

*********************** 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  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8592 (m-10) cc_final: 0.8227 (m-80)
REVERT: A  425 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8453 (mtp180)
REVERT: A  429 LEU cc_start: 0.9525 (tp) cc_final: 0.9280 (tt)
REVERT: B   56 TRP cc_start: 0.7689 (t60) cc_final: 0.7441 (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: 0.2876
  time to fit residues: 47.6758
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  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0670
   chunk 32 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.7320

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.096817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.075185 restraints weight = 17467.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.077165 restraints weight = 12186.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.078631 restraints weight = 9410.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4595  Z= 0.200
  Angle     :  0.677   7.255   6189  Z= 0.360
  Chirality :  0.044   0.152    680
  Planarity :  0.004   0.056    803
  Dihedral  :  5.238  24.604    615
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.31), residues: 567
  helix: -0.82 (0.28), residues: 280
  sheet: -2.08 (0.43), residues: 105
  loop : -2.40 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1159 
 HIS   0.004   0.001   HIS B  92 
 PHE   0.013   0.002   PHE A1168 
 TYR   0.019   0.002   TYR A 446 
 ARG   0.005   0.001   ARG B  23 

*********************** 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
  137 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.467 
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: A  423 PHE cc_start: 0.8811 (m-10) cc_final: 0.8396 (m-80)
REVERT: A  425 ARG cc_start: 0.9140 (mtt180) cc_final: 0.8290 (mtp180)
REVERT: A  510 TRP cc_start: 0.7011 (m-90) cc_final: 0.6723 (m-90)
REVERT: A  520 MET cc_start: 0.7356 (ttm) cc_final: 0.7044 (mtp)
REVERT: A  543 TYR cc_start: 0.7550 (m-80) cc_final: 0.6890 (m-80)
REVERT: A 1075 ASN cc_start: 0.7968 (m-40) cc_final: 0.7592 (p0)
REVERT: A 1081 GLU cc_start: 0.7825 (tp30) cc_final: 0.7597 (tp30)
REVERT: A 1084 ARG cc_start: 0.8916 (mtt90) cc_final: 0.8075 (mtt-85)
REVERT: A 1141 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8629 (mm-30)
REVERT: A 1146 MET cc_start: 0.9060 (ppp) cc_final: 0.8809 (ppp)
REVERT: B   56 TRP cc_start: 0.7892 (t60) cc_final: 0.7620 (t-100)
REVERT: B  112 PHE cc_start: 0.7231 (m-80) cc_final: 0.6996 (m-80)
REVERT: B  114 LYS cc_start: 0.8395 (mmtt) cc_final: 0.7995 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2103
  time to fit residues: 35.2799
Evaluate side-chains
  106 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.095954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.076872 restraints weight = 17624.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.078316 restraints weight = 10528.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.079414 restraints weight = 8505.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4595  Z= 0.205
  Angle     :  0.651   8.385   6189  Z= 0.347
  Chirality :  0.043   0.148    680
  Planarity :  0.004   0.055    803
  Dihedral  :  5.106  24.114    615
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.33), residues: 567
  helix: -0.23 (0.29), residues: 281
  sheet: -1.74 (0.45), residues: 105
  loop : -2.23 (0.43), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A1159 
 HIS   0.003   0.001   HIS A 335 
 PHE   0.011   0.001   PHE A1168 
 TYR   0.019   0.002   TYR A 446 
 ARG   0.002   0.000   ARG A 471 

*********************** 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  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  396 LEU cc_start: 0.8644 (tt) cc_final: 0.8248 (tt)
REVERT: A  423 PHE cc_start: 0.8875 (m-10) cc_final: 0.8324 (m-80)
REVERT: A 1075 ASN cc_start: 0.8027 (m-40) cc_final: 0.7660 (p0)
REVERT: A 1084 ARG cc_start: 0.8881 (mtt90) cc_final: 0.8168 (mtt-85)
REVERT: A 1141 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8610 (mm-30)
REVERT: A 1146 MET cc_start: 0.9021 (ppp) cc_final: 0.8753 (ppp)
REVERT: A 1198 MET cc_start: 0.8731 (mtp) cc_final: 0.8251 (tmm)
REVERT: B   16 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8718 (mmtm)
REVERT: B  112 PHE cc_start: 0.7221 (m-80) cc_final: 0.6936 (m-80)
REVERT: B  114 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8040 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1844
  time to fit residues: 28.8206
Evaluate side-chains
  92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0020
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0270
   chunk 5 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.5046

-------------------------------------------------------------------------------
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 = 0.4007 r_free = 0.4007 target = 0.098878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.079535 restraints weight = 17700.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.080688 restraints weight = 10660.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.081020 restraints weight = 8981.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4595  Z= 0.182
  Angle     :  0.649   7.601   6189  Z= 0.345
  Chirality :  0.043   0.149    680
  Planarity :  0.004   0.053    803
  Dihedral  :  4.874  23.427    615
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  5.21 %
    Favored  : 94.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.34), residues: 567
  helix: -0.18 (0.29), residues: 285
  sheet: -1.32 (0.47), residues: 105
  loop : -2.06 (0.45), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP B  56 
 HIS   0.005   0.001   HIS A 530 
 PHE   0.011   0.001   PHE A1168 
 TYR   0.015   0.001   TYR A1083 
 ARG   0.006   0.000   ARG B  23 

*********************** 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
  127 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 PHE cc_start: 0.8746 (m-10) cc_final: 0.8212 (m-80)
REVERT: A 1075 ASN cc_start: 0.8048 (m-40) cc_final: 0.7589 (p0)
REVERT: A 1141 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8393 (mm-30)
REVERT: A 1146 MET cc_start: 0.9021 (ppp) cc_final: 0.8729 (ppp)
REVERT: A 1198 MET cc_start: 0.8580 (mtp) cc_final: 0.8365 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1838
  time to fit residues: 28.6115
Evaluate side-chains
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**
** B 102 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 = 0.4027 r_free = 0.4027 target = 0.100186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.080434 restraints weight = 18022.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.081891 restraints weight = 12433.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.082423 restraints weight = 9197.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4595  Z= 0.196
  Angle     :  0.688   9.240   6189  Z= 0.363
  Chirality :  0.044   0.163    680
  Planarity :  0.004   0.050    803
  Dihedral  :  4.929  23.037    615
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.33), residues: 567
  helix: -0.34 (0.28), residues: 285
  sheet: -0.95 (0.51), residues: 99
  loop : -2.04 (0.44), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP B  56 
 HIS   0.006   0.001   HIS A 530 
 PHE   0.010   0.001   PHE A1168 
 TYR   0.013   0.002   TYR A1083 
 ARG   0.003   0.000   ARG B  89 

*********************** 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
  124 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.508 
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: A  423 PHE cc_start: 0.8603 (m-10) cc_final: 0.8099 (m-80)
REVERT: A  473 ILE cc_start: 0.8833 (tt) cc_final: 0.7762 (tt)
REVERT: A 1141 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8335 (mm-30)
REVERT: A 1146 MET cc_start: 0.8857 (ppp) cc_final: 0.8592 (ppp)
REVERT: B   68 LYS cc_start: 0.8134 (mttt) cc_final: 0.7876 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1848
  time to fit residues: 28.3523
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  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0570
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.7300

-------------------------------------------------------------------------------
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**
A1170 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.099499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.078324 restraints weight = 17895.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.080170 restraints weight = 12922.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.081515 restraints weight = 10113.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4487

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= 0.188
  Angle     :  0.681   9.864   6189  Z= 0.360
  Chirality :  0.044   0.145    680
  Planarity :  0.003   0.047    803
  Dihedral  :  4.858  21.829    615
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.25 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.34), residues: 567
  helix: -0.12 (0.29), residues: 283
  sheet: -0.76 (0.52), residues: 95
  loop : -1.98 (0.43), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B  56 
 HIS   0.004   0.001   HIS A 530 
 PHE   0.011   0.001   PHE A1168 
 TYR   0.012   0.002   TYR A1083 
 ARG   0.004   0.000   ARG A1206 

*********************** 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: 1
    poor density    : 121
  time to evaluate  : 0.524 
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: 0.8520 (m-10) cc_final: 0.8027 (m-80)
REVERT: A  473 ILE cc_start: 0.8275 (tt) cc_final: 0.7405 (tt)
REVERT: A  486 MET cc_start: 0.7576 (mmm) cc_final: 0.7325 (mmm)
REVERT: A 1084 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8011 (mtt-85)
REVERT: A 1141 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8169 (mm-30)
REVERT: B   64 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9117 (pm20)
REVERT: B   68 LYS cc_start: 0.8212 (mttt) cc_final: 0.7731 (mmtt)
REVERT: B  112 PHE cc_start: 0.7318 (m-80) cc_final: 0.7091 (m-80)
REVERT: B  114 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8110 (mmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1833
  time to fit residues: 27.9060
Evaluate side-chains
  93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.0980
   chunk 54 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.098033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.077158 restraints weight = 17340.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.078965 restraints weight = 12532.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.080270 restraints weight = 9823.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4595  Z= 0.233
  Angle     :  0.731  11.550   6189  Z= 0.380
  Chirality :  0.044   0.144    680
  Planarity :  0.004   0.049    803
  Dihedral  :  5.036  21.637    615
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.34), residues: 567
  helix: -0.27 (0.29), residues: 284
  sheet: -0.81 (0.51), residues: 95
  loop : -1.95 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A1159 
 HIS   0.004   0.001   HIS A1170 
 PHE   0.010   0.002   PHE A1168 
 TYR   0.013   0.002   TYR A 446 
 ARG   0.005   0.000   ARG A1206 

*********************** 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
  123 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.473 
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: 0.8583 (m-10) cc_final: 0.8060 (m-80)
REVERT: A  425 ARG cc_start: 0.8850 (ptp-170) cc_final: 0.8577 (ptp-170)
REVERT: A  486 MET cc_start: 0.7791 (mmm) cc_final: 0.7358 (mmm)
REVERT: A 1084 ARG cc_start: 0.8745 (mtt90) cc_final: 0.8192 (mtt-85)
REVERT: A 1141 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8301 (mm-30)
REVERT: B   14 LEU cc_start: 0.7593 (mt) cc_final: 0.7178 (mp)
REVERT: B   56 TRP cc_start: 0.7037 (t-100) cc_final: 0.6809 (t-100)
REVERT: B   68 LYS cc_start: 0.8249 (mttt) cc_final: 0.7868 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1880
  time to fit residues: 28.3595
Evaluate side-chains
  95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 54 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 41 optimal weight:    0.1980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.099525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.078459 restraints weight = 17552.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.080318 restraints weight = 12794.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.081680 restraints weight = 10041.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.4982

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= 0.202
  Angle     :  0.733  10.747   6189  Z= 0.381
  Chirality :  0.045   0.157    680
  Planarity :  0.004   0.048    803
  Dihedral  :  4.900  20.854    615
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.34), residues: 567
  helix: -0.23 (0.29), residues: 285
  sheet: -0.76 (0.50), residues: 95
  loop : -1.78 (0.44), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A1159 
 HIS   0.004   0.001   HIS A 530 
 PHE   0.011   0.001   PHE A1168 
 TYR   0.012   0.001   TYR A 446 
 ARG   0.003   0.000   ARG A1206 

*********************** 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
  123 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.8710 (ttm) cc_final: 0.8326 (ttm)
REVERT: A  423 PHE cc_start: 0.8518 (m-10) cc_final: 0.8013 (m-80)
REVERT: A  425 ARG cc_start: 0.8799 (ptp-170) cc_final: 0.8263 (ptm160)
REVERT: A  486 MET cc_start: 0.7739 (mmm) cc_final: 0.7428 (mmm)
REVERT: A  520 MET cc_start: 0.6229 (ttt) cc_final: 0.5493 (tmm)
REVERT: A  569 TYR cc_start: 0.7795 (m-80) cc_final: 0.7381 (m-80)
REVERT: A 1084 ARG cc_start: 0.8598 (mtt90) cc_final: 0.8161 (mtt-85)
REVERT: A 1134 GLU cc_start: 0.8658 (pp20) cc_final: 0.8010 (pp20)
REVERT: A 1141 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8400 (mm-30)
REVERT: B   20 GLU cc_start: 0.9260 (mp0) cc_final: 0.8981 (pp20)
REVERT: B  114 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8230 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1975
  time to fit residues: 29.8181
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  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0040
   chunk 24 optimal weight:    0.9980
   chunk 43 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.4992

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.100267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.078545 restraints weight = 17004.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.080725 restraints weight = 11623.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.082279 restraints weight = 8768.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.5310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4595  Z= 0.196
  Angle     :  0.727  11.063   6189  Z= 0.378
  Chirality :  0.045   0.179    680
  Planarity :  0.004   0.047    803
  Dihedral  :  4.835  21.944    615
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.34), residues: 567
  helix: -0.21 (0.29), residues: 285
  sheet: -0.61 (0.54), residues: 87
  loop : -1.87 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A1159 
 HIS   0.007   0.001   HIS A 530 
 PHE   0.010   0.001   PHE A1168 
 TYR   0.015   0.001   TYR A 446 
 ARG   0.003   0.000   ARG A1206 

*********************** 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
  121 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.476 
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: 0.8782 (m-10) cc_final: 0.8183 (m-80)
REVERT: A  425 ARG cc_start: 0.8929 (ptp-170) cc_final: 0.8424 (ptm160)
REVERT: A  486 MET cc_start: 0.7985 (mmm) cc_final: 0.7612 (mmm)
REVERT: A  520 MET cc_start: 0.6345 (ttt) cc_final: 0.5498 (tmm)
REVERT: A  569 TYR cc_start: 0.7899 (m-80) cc_final: 0.7546 (m-80)
REVERT: A 1030 ASP cc_start: 0.8190 (t70) cc_final: 0.7758 (t0)
REVERT: A 1134 GLU cc_start: 0.8843 (pp20) cc_final: 0.8343 (pp20)
REVERT: A 1141 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8641 (mm-30)
REVERT: A 1190 ASP cc_start: 0.8636 (p0) cc_final: 0.8226 (p0)
REVERT: A 1198 MET cc_start: 0.8226 (ppp) cc_final: 0.7852 (ppp)
REVERT: B   14 LEU cc_start: 0.7826 (mp) cc_final: 0.7518 (mp)
REVERT: B  114 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8343 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1824
  time to fit residues: 27.3236
Evaluate side-chains
  93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 53 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0770
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0870
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0980
   chunk 29 optimal weight:    0.6980
   chunk 37 optimal weight:    8.9990
   overall best weight:    0.2716

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.100903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.080697 restraints weight = 17197.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.082606 restraints weight = 12388.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.083941 restraints weight = 9623.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4595  Z= 0.192
  Angle     :  0.737  11.366   6189  Z= 0.386
  Chirality :  0.045   0.192    680
  Planarity :  0.003   0.044    803
  Dihedral  :  4.705  21.032    615
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.34), residues: 567
  helix: -0.14 (0.29), residues: 286
  sheet: -0.62 (0.54), residues: 85
  loop : -1.88 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP A1159 
 HIS   0.007   0.001   HIS A 530 
 PHE   0.013   0.001   PHE B 117 
 TYR   0.014   0.001   TYR A 446 
 ARG   0.003   0.000   ARG B  89 

********************** 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
  125 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.522 
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: 0.8483 (m-10) cc_final: 0.7935 (m-80)
REVERT: A  425 ARG cc_start: 0.8769 (ptp-170) cc_final: 0.8231 (ptm160)
REVERT: A  486 MET cc_start: 0.7706 (mmm) cc_final: 0.7455 (mmm)
REVERT: A  520 MET cc_start: 0.5965 (ttt) cc_final: 0.5371 (tmm)
REVERT: A  569 TYR cc_start: 0.7638 (m-80) cc_final: 0.7319 (m-80)
REVERT: A 1030 ASP cc_start: 0.7925 (t70) cc_final: 0.7544 (t0)
REVERT: A 1134 GLU cc_start: 0.8636 (pp20) cc_final: 0.8243 (pp20)
REVERT: A 1146 MET cc_start: 0.8734 (ppp) cc_final: 0.8321 (ppp)
REVERT: A 1190 ASP cc_start: 0.8226 (p0) cc_final: 0.7790 (p0)
REVERT: A 1198 MET cc_start: 0.7996 (ppp) cc_final: 0.7606 (ppp)
REVERT: B   16 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8426 (mmtt)
REVERT: B  114 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8229 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1889
  time to fit residues: 29.1657
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  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 102 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 = 0.3935 r_free = 0.3935 target = 0.095289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.073828 restraints weight = 18136.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.075742 restraints weight = 12590.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.077155 restraints weight = 9656.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.5227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   4595  Z= 0.377
  Angle     :  0.862  11.014   6189  Z= 0.454
  Chirality :  0.048   0.199    680
  Planarity :  0.005   0.052    803
  Dihedral  :  5.487  23.117    615
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 22.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.33), residues: 567
  helix: -0.57 (0.28), residues: 283
  sheet: -0.65 (0.55), residues: 74
  loop : -1.93 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP A1159 
 HIS   0.009   0.002   HIS A 335 
 PHE   0.035   0.003   PHE A1068 
 TYR   0.028   0.003   TYR A1083 
 ARG   0.006   0.001   ARG A1206 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1986.32 seconds
wall clock time: 36 minutes 3.57 seconds (2163.57 seconds total)