Starting phenix.real_space_refine
on Tue Feb 11 07:54:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/1oed_1044/02_2025/1oed_1044.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/1oed_1044/02_2025/1oed_1044.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/1oed_1044/02_2025/1oed_1044.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/1oed_1044/02_2025/1oed_1044.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/1oed_1044/02_2025/1oed_1044.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/1oed_1044/02_2025/1oed_1044.cif"
  }
  resolution = 4.0
  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
-------------------------------------------------------------------------------
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=   1.000
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      37      5.16       5
     C    3331      2.51       5
     N     735      2.21       5
     O     823      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4926
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 978
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 4, 'TRANS': 122}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 995
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 7, 'TRANS': 119}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 982
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 7, 'TRANS': 119}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 978
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 4, 'TRANS': 122}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 993
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Chain breaks: 1
  Time building chain proxies: 3.31, per 1000 atoms: 0.67
  Number of scatterers: 4926
  At special positions: 0
  Unit cell: (96, 88, 67, 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      37     16.00
     O     823      8.00
     N     735      7.00
     C    3331      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: 1.60
  Conformation dependent library (CDL) restraints added in 620.0 milliseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1218

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      92.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 212 through 239
      removed outlier: 3.584A  pdb=" N   VAL A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ASN A 217 " --> pdb=" O   TYR A 213 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
      Proline residue:  A 236  - end of helix
    Processing helix  chain 'A' and resid 242 through 271
      removed outlier: 3.660A  pdb=" N   GLU A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      Proline residue:  A 265  - end of helix
    Processing helix  chain 'A' and resid 275 through 302
      removed outlier: 3.935A  pdb=" N   PHE A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   THR A 281 " --> pdb=" O   TYR A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 437
    Processing helix  chain 'B' and resid 218 through 245
      removed outlier: 3.668A  pdb=" N   VAL B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   TYR B 223 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
      Proline residue:  B 242  - end of helix
    Processing helix  chain 'B' and resid 248 through 277
      removed outlier: 3.500A  pdb=" N   ALA B 255 " --> pdb=" O   LEU B 251 " (cutoff:3.500A)
      Proline residue:  B 271  - end of helix
      removed outlier: 3.781A  pdb=" N   LEU B 275 " --> pdb=" O   PRO B 271 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER B 276 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL B 277 " --> pdb=" O   THR B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 307
      removed outlier: 4.130A  pdb=" N   ILE B 289 " --> pdb=" O   MET B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 462
    Processing helix  chain 'C' and resid 226 through 253
      removed outlier: 4.092A  pdb=" N   ASN C 231 " --> pdb=" O   PHE C 227 " (cutoff:3.500A)
      Proline residue:  C 235  - end of helix
      Proline residue:  C 250  - end of helix
    Processing helix  chain 'C' and resid 256 through 285
      Proline residue:  C 279  - end of helix
    Processing helix  chain 'C' and resid 289 through 316
      removed outlier: 3.916A  pdb=" N   PHE C 294 " --> pdb=" O   LYS C 290 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE C 295 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 484
      Proline residue:  C 463  - end of helix
      Proline residue:  C 481  - end of helix
    Processing helix  chain 'D' and resid 212 through 239
      removed outlier: 3.582A  pdb=" N   VAL D 216 " --> pdb=" O   LEU D 212 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASN D 217 " --> pdb=" O   TYR D 213 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE D 219 " --> pdb=" O   VAL D 215 " (cutoff:3.500A)
      Proline residue:  D 221  - end of helix
      Proline residue:  D 236  - end of helix
    Processing helix  chain 'D' and resid 242 through 271
      removed outlier: 3.660A  pdb=" N   GLU D 262 " --> pdb=" O   LEU D 258 " (cutoff:3.500A)
      Proline residue:  D 265  - end of helix
    Processing helix  chain 'D' and resid 275 through 302
      removed outlier: 3.936A  pdb=" N   PHE D 280 " --> pdb=" O   LYS D 276 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   THR D 281 " --> pdb=" O   TYR D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 437
    Processing helix  chain 'E' and resid 221 through 246
      Proline residue:  E 229  - end of helix
      removed outlier: 3.979A  pdb=" N   SER E 234 " --> pdb=" O   CYS E 230 " (cutoff:3.500A)
      Proline residue:  E 244  - end of helix
    Processing helix  chain 'E' and resid 250 through 280
      Proline residue:  E 274  - end of helix
    Processing helix  chain 'E' and resid 285 through 311
    Processing helix  chain 'E' and resid 445 through 478
      Proline residue:  E 476  - end of helix

    435 hydrogen bonds defined for protein.
    1305 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: 1.31

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 751
        1.31 -     1.43: 1242
        1.43 -     1.56: 2970
        1.56 -     1.69: 6
        1.69 -     1.82: 61
  Bond restraints: 5030
  Sorted by residual:
  bond pdb=" N   PRO B 271 "
       pdb=" CD  PRO B 271 "
    ideal  model  delta    sigma   weight residual
    1.473  1.221  0.252 1.40e-02 5.10e+03 3.23e+02
  bond pdb=" C   ALA A 403 "
       pdb=" O   ALA A 403 "
    ideal  model  delta    sigma   weight residual
    1.231  1.384 -0.153 2.00e-02 2.50e+03 5.87e+01
  bond pdb=" C   ALA D 403 "
       pdb=" O   ALA D 403 "
    ideal  model  delta    sigma   weight residual
    1.231  1.384 -0.153 2.00e-02 2.50e+03 5.86e+01
  bond pdb=" CB  VAL B 445 "
       pdb=" CG1 VAL B 445 "
    ideal  model  delta    sigma   weight residual
    1.521  1.721 -0.200 3.30e-02 9.18e+02 3.69e+01
  bond pdb=" N   PRO B 464 "
       pdb=" CD  PRO B 464 "
    ideal  model  delta    sigma   weight residual
    1.473  1.549 -0.076 1.40e-02 5.10e+03 2.92e+01
  ... (remaining 5025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 5620
        2.74 -     5.47: 1040
        5.47 -     8.21: 136
        8.21 -    10.95: 50
       10.95 -    13.68: 9
  Bond angle restraints: 6855
  Sorted by residual:
  angle pdb=" OE1 GLN E 474 "
        pdb=" CD  GLN E 474 "
        pdb=" NE2 GLN E 474 "
      ideal   model   delta    sigma   weight residual
     122.60  112.76    9.84 1.00e+00 1.00e+00 9.69e+01
  angle pdb=" OE1 GLN A 435 "
        pdb=" CD  GLN A 435 "
        pdb=" NE2 GLN A 435 "
      ideal   model   delta    sigma   weight residual
     122.60  112.77    9.83 1.00e+00 1.00e+00 9.67e+01
  angle pdb=" OE1 GLN E 262 "
        pdb=" CD  GLN E 262 "
        pdb=" NE2 GLN E 262 "
      ideal   model   delta    sigma   weight residual
     122.60  112.81    9.79 1.00e+00 1.00e+00 9.59e+01
  angle pdb=" OE1 GLN E 246 "
        pdb=" CD  GLN E 246 "
        pdb=" NE2 GLN E 246 "
      ideal   model   delta    sigma   weight residual
     122.60  112.84    9.76 1.00e+00 1.00e+00 9.52e+01
  angle pdb=" CA  THR C 462 "
        pdb=" C   THR C 462 "
        pdb=" N   PRO C 463 "
      ideal   model   delta    sigma   weight residual
     120.77  111.31    9.46 9.70e-01 1.06e+00 9.51e+01
  ... (remaining 6850 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 2582
       17.92 -    35.83: 266
       35.83 -    53.75: 111
       53.75 -    71.67: 12
       71.67 -    89.59: 4
  Dihedral angle restraints: 2975
    sinusoidal: 1114
      harmonic: 1861
  Sorted by residual:
  dihedral pdb=" C   PRO E 476 "
           pdb=" N   PRO E 476 "
           pdb=" CA  PRO E 476 "
           pdb=" CB  PRO E 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -109.72  -10.98     0      2.50e+00 1.60e-01 1.93e+01
  dihedral pdb=" C   PRO D 236 "
           pdb=" N   PRO D 236 "
           pdb=" CA  PRO D 236 "
           pdb=" CB  PRO D 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -109.89  -10.81     0      2.50e+00 1.60e-01 1.87e+01
  dihedral pdb=" C   PRO A 236 "
           pdb=" N   PRO A 236 "
           pdb=" CA  PRO A 236 "
           pdb=" CB  PRO A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -109.91  -10.79     0      2.50e+00 1.60e-01 1.86e+01
  ... (remaining 2972 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.276: 898
       0.276 -    0.552: 5
       0.552 -    0.827: 0
       0.827 -    1.103: 0
       1.103 -    1.379: 1
  Chirality restraints: 904
  Sorted by residual:
  chirality pdb=" CB  VAL B 445 "
            pdb=" CA  VAL B 445 "
            pdb=" CG1 VAL B 445 "
            pdb=" CG2 VAL B 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -4.01    1.38 2.00e-01 2.50e+01 4.75e+01
  chirality pdb=" CB  ILE B 446 "
            pdb=" CA  ILE B 446 "
            pdb=" CG1 ILE B 446 "
            pdb=" CG2 ILE B 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.17   -0.52 2.00e-01 2.50e+01 6.82e+00
  chirality pdb=" CA  HIS E 471 "
            pdb=" N   HIS E 471 "
            pdb=" C   HIS E 471 "
            pdb=" CB  HIS E 471 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.48e+00
  ... (remaining 901 not shown)

  Planarity restraints: 798
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO E 476 "   -0.039 2.00e-02 2.50e+03   8.13e-02 6.62e+01
        pdb=" C   PRO E 476 "    0.141 2.00e-02 2.50e+03
        pdb=" O   PRO E 476 "   -0.054 2.00e-02 2.50e+03
        pdb=" N   GLU E 477 "   -0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 275 "    0.026 2.00e-02 2.50e+03   4.99e-02 2.49e+01
        pdb=" C   LEU B 275 "   -0.086 2.00e-02 2.50e+03
        pdb=" O   LEU B 275 "    0.031 2.00e-02 2.50e+03
        pdb=" N   SER B 276 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 445 "    0.019 2.00e-02 2.50e+03   4.20e-02 1.76e+01
        pdb=" C   LYS E 445 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   LYS E 445 "    0.029 2.00e-02 2.50e+03
        pdb=" N   VAL E 446 "    0.024 2.00e-02 2.50e+03
  ... (remaining 795 not shown)

  Histogram of nonbonded interaction distances:
        1.18 -     1.93: 21
        1.93 -     2.67: 595
        2.67 -     3.41: 8998
        3.41 -     4.16: 13035
        4.16 -     4.90: 21585
  Nonbonded interactions: 44234
  Sorted by model distance:
  nonbonded pdb=" O   TYR E 241 "
            pdb=" CG  PRO E 244 "
     model   vdw
     1.183 3.440
  nonbonded pdb=" O   HIS B 460 "
            pdb=" CD  PRO B 464 "
     model   vdw
     1.352 3.440
  nonbonded pdb=" O   TYR E 241 "
            pdb=" CD  PRO E 244 "
     model   vdw
     1.447 3.440
  nonbonded pdb=" O   PHE B 239 "
            pdb=" CD  PRO B 242 "
     model   vdw
     1.624 3.440
  nonbonded pdb=" O   PHE C 459 "
            pdb=" CD  PRO C 463 "
     model   vdw
     1.640 3.440
  ... (remaining 44229 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.050
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.380
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1921
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      :  0.014   0.252   5030  Z= 0.934
  Angle     :  2.288  13.685   6855  Z= 1.670
  Chirality :  0.097   1.379    904
  Planarity :  0.009   0.081    798
  Dihedral  : 17.230  89.585   1757
  Min Nonbonded Distance : 1.183

Molprobity Statistics.
  All-atom Clashscore : 224.94
  Ramachandran Plot:
    Outliers :  2.11 %
    Allowed  :  5.19 %
    Favored  : 92.69 %
  Rotamer:
    Outliers : 19.76 %
    Allowed  : 14.04 %
    Favored  : 66.20 %
  Cbeta Deviations :  0.49 %
  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: -3.67 (0.27), residues: 616
  helix: -2.15 (0.18), residues: 512
  sheet:  None (None), residues: 0
  loop : -2.61 (0.54), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.005   TRP E 453 
 HIS   0.006   0.001   HIS B 460 
 PHE   0.021   0.002   PHE C 247 
 TYR   0.014   0.001   TYR B 220 
 ARG   0.001   0.000   ARG E 310 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 114
    poor density    : 111
  time to evaluate  : 0.633 
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  280 PHE cc_start: 0.4349 (OUTLIER) cc_final: 0.4004 (m-80)
REVERT: A  284 PHE cc_start: 0.2953 (OUTLIER) cc_final: 0.2420 (t80)
REVERT: A  411 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4758 (mm)
REVERT: C  457 SER cc_start: -0.6578 (OUTLIER) cc_final: -0.7210 (m)
REVERT: C  462 THR cc_start: 0.6349 (m) cc_final: 0.5915 (m)
REVERT: C  475 MET cc_start: 0.0883 (OUTLIER) cc_final: -0.0572 (mtt)
REVERT: C  479 ASN cc_start: -0.2803 (OUTLIER) cc_final: -0.3292 (t0)
REVERT: D  243 MET cc_start: 0.3821 (mtt) cc_final: 0.2367 (pmm)
REVERT: D  298 THR cc_start: 0.5185 (OUTLIER) cc_final: 0.4842 (m)
REVERT: D  302 SER cc_start: 0.6645 (OUTLIER) cc_final: 0.5667 (t)
REVERT: E  272 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.4499 (tttt)
REVERT: E  297 ILE cc_start: 0.1827 (OUTLIER) cc_final: 0.1572 (tp)
  outliers start: 114
  outliers final: 46
  residues processed: 198
  average time/residue: 0.1431
  time to fit residues: 36.6915
Evaluate side-chains
  128 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 72
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  280 PHE
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  426 PHE
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ARG
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  437 ARG
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  241 PHE
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain C residue  453 ILE
Chi-restraints excluded: chain C residue  457 SER
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  479 ASN
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  247 ILE
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  289 ILE
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain D residue  302 SER
Chi-restraints excluded: chain D residue  410 LEU
Chi-restraints excluded: chain D residue  422 THR
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  243 LEU
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  269 ILE
Chi-restraints excluded: chain E residue  272 LYS
Chi-restraints excluded: chain E residue  286 TYR
Chi-restraints excluded: chain E residue  297 ILE
Chi-restraints excluded: chain E residue  308 SER
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  453 TRP
Chi-restraints excluded: chain E residue  463 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:   30.0000
   chunk 45 optimal weight:   20.0000
   chunk 25 optimal weight:   50.0000
   chunk 15 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 47 optimal weight:   50.0000
   chunk 18 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 35 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0980
   overall best weight:    7.2190

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

Flipped N/Q/H residues before XYZ refinement:
A 435 GLN
** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 305 ASN
C 479 ASN
D 217 ASN
** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.122109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.105121 restraints weight = 43852.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.105121 restraints weight = 52409.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.105121 restraints weight = 52409.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3375
moved from start:          0.5985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.080   5030  Z= 0.436
  Angle     :  1.144  11.708   6855  Z= 0.582
  Chirality :  0.055   0.316    904
  Planarity :  0.009   0.068    798
  Dihedral  : 13.847  84.525    764
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 39.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers : 10.05 %
    Allowed  : 17.33 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.65 (0.32), residues: 616
  helix: -0.77 (0.21), residues: 567
  sheet:  None (None), residues: 0
  loop : -2.70 (0.83), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.003   TRP E 453 
 HIS   0.007   0.002   HIS D 300 
 PHE   0.036   0.004   PHE B 286 
 TYR   0.033   0.003   TYR C 248 
 ARG   0.004   0.001   ARG D 301 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 73
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 PHE cc_start: 0.7373 (t80) cc_final: 0.7044 (m-10)
REVERT: B  293 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7868 (t80)
REVERT: B  433 MET cc_start: 0.4071 (mpp) cc_final: 0.2080 (mpp)
REVERT: B  440 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6692 (tp)
REVERT: C  257 MET cc_start: -0.3858 (mtt) cc_final: -0.4072 (mtt)
REVERT: C  296 MET cc_start: 0.6323 (mmp) cc_final: 0.5621 (mtp)
REVERT: D  243 MET cc_start: 0.4845 (mtt) cc_final: 0.3731 (pmm)
  outliers start: 58
  outliers final: 21
  residues processed: 115
  average time/residue: 0.1313
  time to fit residues: 20.2752
Evaluate side-chains
  84 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ARG
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain D residue  247 ILE
Chi-restraints excluded: chain D residue  264 ILE
Chi-restraints excluded: chain D residue  281 THR
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain D residue  422 THR
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  286 TYR
Chi-restraints excluded: chain E residue  453 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:   50.0000
   chunk 3 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 51 optimal weight:   30.0000
   chunk 20 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 44 optimal weight:    7.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 ASN
C 305 ASN
C 313 HIS
** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 262 GLN ** 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 = 0.4704 r_free = 0.4704 target = 0.118959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.101478 restraints weight = 44943.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.100907 restraints weight = 53731.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.100543 restraints weight = 61071.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3635
moved from start:          0.8356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   5030  Z= 0.362
  Angle     :  0.987  11.653   6855  Z= 0.487
  Chirality :  0.048   0.278    904
  Planarity :  0.007   0.070    798
  Dihedral  :  9.764  79.081    687
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 27.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 19.24 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.32), residues: 616
  helix: -0.27 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.94 (0.68), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 453 
 HIS   0.009   0.002   HIS B 306 
 PHE   0.023   0.003   PHE D 256 
 TYR   0.009   0.001   TYR A 234 
 ARG   0.004   0.001   ARG B 437 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 71
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 PHE cc_start: 0.7584 (t80) cc_final: 0.7062 (m-10)
REVERT: B  236 ILE cc_start: -0.0358 (OUTLIER) cc_final: -0.0584 (tp)
REVERT: C  296 MET cc_start: 0.6729 (mmp) cc_final: 0.6305 (ptm)
REVERT: C  475 MET cc_start: -0.2564 (ptt) cc_final: -0.3774 (mmt)
REVERT: D  243 MET cc_start: 0.5041 (mtt) cc_final: 0.4286 (pmm)
REVERT: D  435 GLN cc_start: -0.2802 (OUTLIER) cc_final: -0.3123 (mt0)
  outliers start: 31
  outliers final: 15
  residues processed: 96
  average time/residue: 0.1407
  time to fit residues: 18.2028
Evaluate side-chains
  75 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  247 ILE
Chi-restraints excluded: chain D residue  264 ILE
Chi-restraints excluded: chain D residue  422 THR
Chi-restraints excluded: chain D residue  435 GLN
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  286 TYR
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  453 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 45 optimal weight:   40.0000
   chunk 52 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   overall best weight:    5.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 267 GLN
D 300 HIS
E 225 ASN
** E 262 GLN ** 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 = 0.4691 r_free = 0.4691 target = 0.117715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.100598 restraints weight = 45371.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.100573 restraints weight = 55736.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.100541 restraints weight = 56065.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.4383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3694
moved from start:          0.9671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   5030  Z= 0.305
  Angle     :  0.901  11.422   6855  Z= 0.441
  Chirality :  0.046   0.210    904
  Planarity :  0.007   0.068    798
  Dihedral  :  8.365  72.396    674
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 23.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 20.28 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.32), residues: 616
  helix:  0.24 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.34 (0.80), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 453 
 HIS   0.004   0.001   HIS D 299 
 PHE   0.021   0.002   PHE C 314 
 TYR   0.012   0.001   TYR C 248 
 ARG   0.002   0.001   ARG A 301 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 PHE cc_start: 0.7592 (t80) cc_final: 0.7099 (m-10)
REVERT: B  249 MET cc_start: 0.2515 (mmp) cc_final: 0.1700 (pmm)
REVERT: C  296 MET cc_start: 0.6506 (mmp) cc_final: 0.6143 (ptm)
REVERT: C  475 MET cc_start: -0.2450 (ptt) cc_final: -0.3756 (mmt)
REVERT: D  243 MET cc_start: 0.5315 (mtt) cc_final: 0.4516 (pmm)
  outliers start: 28
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1068
  time to fit residues: 14.2263
Evaluate side-chains
  77 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  241 PHE
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  281 THR
Chi-restraints excluded: chain D residue  422 THR
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  268 LEU
Chi-restraints excluded: chain E residue  286 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 48 optimal weight:   20.0000
   chunk 49 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:   20.0000
   chunk 47 optimal weight:   30.0000
   chunk 30 optimal weight:    0.9990
   chunk 46 optimal weight:   30.0000
   chunk 23 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 466 ASN
C 479 ASN
E 225 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.114881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.097924 restraints weight = 44933.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.096939 restraints weight = 56924.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.096827 restraints weight = 63789.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3962
moved from start:          1.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   5030  Z= 0.303
  Angle     :  0.912  13.128   6855  Z= 0.441
  Chirality :  0.046   0.190    904
  Planarity :  0.008   0.068    798
  Dihedral  :  7.111  56.251    668
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 21.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.97 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.33), residues: 616
  helix:  0.70 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.37 (0.79), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.005   TRP E 453 
 HIS   0.005   0.001   HIS B 460 
 PHE   0.021   0.002   PHE D 256 
 TYR   0.015   0.001   TYR B 220 
 ARG   0.005   0.001   ARG D 301 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 PHE cc_start: 0.7700 (t80) cc_final: 0.7116 (m-10)
REVERT: B  249 MET cc_start: 0.3367 (mmp) cc_final: 0.3164 (pmm)
REVERT: B  285 MET cc_start: 0.7056 (tpt) cc_final: 0.6495 (tpt)
REVERT: C  296 MET cc_start: 0.6715 (mmp) cc_final: 0.6347 (ptm)
REVERT: C  475 MET cc_start: -0.2331 (ptt) cc_final: -0.3496 (mmt)
REVERT: D  243 MET cc_start: 0.5026 (mtt) cc_final: 0.4721 (pmm)
REVERT: E  286 TYR cc_start: 0.0989 (OUTLIER) cc_final: 0.0730 (m-10)
  outliers start: 22
  outliers final: 13
  residues processed: 80
  average time/residue: 0.1323
  time to fit residues: 14.5655
Evaluate side-chains
  66 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  241 PHE
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  294 PHE
Chi-restraints excluded: chain C residue  479 ASN
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  268 LEU
Chi-restraints excluded: chain E residue  286 TYR
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 56 optimal weight:   30.0000
   chunk 6 optimal weight:   40.0000
   chunk 51 optimal weight:   20.0000
   chunk 30 optimal weight:   40.0000
   chunk 11 optimal weight:   50.0000
   chunk 50 optimal weight:    8.9990
   chunk 46 optimal weight:   50.0000
   chunk 49 optimal weight:    7.9990
   chunk 34 optimal weight:    8.9990
   chunk 57 optimal weight:   30.0000
   overall best weight:   11.1992

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 477 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.112185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.094492 restraints weight = 44548.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.094335 restraints weight = 55553.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.094080 restraints weight = 68525.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4199
moved from start:          1.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5030  Z= 0.313
  Angle     :  0.928  11.979   6855  Z= 0.454
  Chirality :  0.046   0.187    904
  Planarity :  0.008   0.065    798
  Dihedral  :  6.300  59.827    662
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 23.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 23.05 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.34), residues: 616
  helix:  1.01 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.78 (0.75), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP E 453 
 HIS   0.008   0.002   HIS D 300 
 PHE   0.021   0.003   PHE C 314 
 TYR   0.013   0.002   TYR B 220 
 ARG   0.005   0.001   ARG D 301 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 ASP cc_start: 0.2900 (t70) cc_final: 0.1689 (t70)
REVERT: A  426 PHE cc_start: 0.7631 (t80) cc_final: 0.7011 (m-10)
REVERT: B  249 MET cc_start: 0.3917 (mmt) cc_final: 0.3617 (pmm)
REVERT: B  285 MET cc_start: 0.7180 (tpt) cc_final: 0.6587 (tpt)
REVERT: B  288 MET cc_start: 0.4626 (mmt) cc_final: 0.4410 (mmt)
REVERT: B  289 ILE cc_start: 0.8373 (mm) cc_final: 0.8171 (mm)
REVERT: C  296 MET cc_start: 0.7040 (mmp) cc_final: 0.6621 (ptm)
REVERT: D  243 MET cc_start: 0.5313 (mtt) cc_final: 0.5041 (pmm)
  outliers start: 20
  outliers final: 13
  residues processed: 85
  average time/residue: 0.1304
  time to fit residues: 15.2860
Evaluate side-chains
  77 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  241 PHE
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  294 PHE
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  268 LEU
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:   40.0000
   chunk 35 optimal weight:    9.9990
   chunk 42 optimal weight:   30.0000
   chunk 31 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:   50.0000
   chunk 32 optimal weight:    6.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 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 = 0.4659 r_free = 0.4659 target = 0.112133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.095222 restraints weight = 43427.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.094040 restraints weight = 52914.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.093856 restraints weight = 69375.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.4265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4158
moved from start:          1.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5030  Z= 0.276
  Angle     :  0.923  11.813   6855  Z= 0.438
  Chirality :  0.047   0.450    904
  Planarity :  0.007   0.060    798
  Dihedral  :  5.951  59.530    660
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 22.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.57 %
    Favored  : 73.48 %
  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:  1.36 (0.34), residues: 616
  helix:  1.26 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.76 (0.75), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 453 
 HIS   0.006   0.001   HIS B 306 
 PHE   0.025   0.002   PHE D 256 
 TYR   0.010   0.001   TYR B 220 
 ARG   0.002   0.000   ARG D 301 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A  234 TYR cc_start: 0.8418 (t80) cc_final: 0.8200 (t80)
REVERT: A  426 PHE cc_start: 0.7403 (t80) cc_final: 0.6978 (m-10)
REVERT: B  285 MET cc_start: 0.7007 (tpt) cc_final: 0.6178 (tpp)
REVERT: B  289 ILE cc_start: 0.8348 (mm) cc_final: 0.7646 (mm)
REVERT: C  294 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6319 (m-80)
REVERT: C  296 MET cc_start: 0.6985 (mmp) cc_final: 0.6686 (ptm)
REVERT: D  243 MET cc_start: 0.5322 (mtt) cc_final: 0.5050 (pmm)
REVERT: D  278 MET cc_start: 0.6096 (ppp) cc_final: 0.5338 (ppp)
REVERT: D  282 MET cc_start: -0.0948 (ttt) cc_final: -0.1256 (tpt)
REVERT: E  221 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5538 (m-10)
REVERT: E  272 LYS cc_start: 0.7644 (pttt) cc_final: 0.7137 (pttt)
  outliers start: 17
  outliers final: 11
  residues processed: 82
  average time/residue: 0.1253
  time to fit residues: 14.2863
Evaluate side-chains
  75 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  241 PHE
Chi-restraints excluded: chain C residue  294 PHE
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain D residue  264 ILE
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:   40.0000
   chunk 33 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 5 optimal weight:   30.0000
   chunk 8 optimal weight:   40.0000
   chunk 50 optimal weight:   40.0000
   chunk 10 optimal weight:   40.0000
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 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 = 0.4650 r_free = 0.4650 target = 0.111095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.093435 restraints weight = 43755.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.093113 restraints weight = 47477.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.091986 restraints weight = 65228.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4357
moved from start:          1.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5030  Z= 0.286
  Angle     :  0.955  11.567   6855  Z= 0.451
  Chirality :  0.047   0.379    904
  Planarity :  0.007   0.061    798
  Dihedral  :  6.019  58.520    660
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 22.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 25.30 %
    Favored  : 72.44 %
  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:  1.40 (0.34), residues: 616
  helix:  1.31 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -2.03 (0.78), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 453 
 HIS   0.007   0.001   HIS B 306 
 PHE   0.027   0.002   PHE B 262 
 TYR   0.014   0.002   TYR B 220 
 ARG   0.002   0.000   ARG B 282 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 PHE cc_start: 0.7608 (t80) cc_final: 0.6999 (m-10)
REVERT: C  248 TYR cc_start: 0.2317 (OUTLIER) cc_final: 0.1909 (t80)
REVERT: C  296 MET cc_start: 0.7097 (mmp) cc_final: 0.6816 (ptm)
REVERT: D  278 MET cc_start: 0.6163 (ppp) cc_final: 0.5796 (ppp)
REVERT: D  282 MET cc_start: -0.0752 (ttt) cc_final: -0.1039 (tpt)
REVERT: E  272 LYS cc_start: 0.8118 (pttt) cc_final: 0.7785 (tttt)
  outliers start: 13
  outliers final: 11
  residues processed: 75
  average time/residue: 0.1252
  time to fit residues: 13.2011
Evaluate side-chains
  74 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  241 PHE
Chi-restraints excluded: chain C residue  248 TYR
Chi-restraints excluded: chain C residue  294 PHE
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   chunk 15 optimal weight:    0.1980
   chunk 13 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 50 optimal weight:   30.0000
   chunk 25 optimal weight:    5.9990
   overall best weight:    4.2386

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 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 = 0.4660 r_free = 0.4660 target = 0.111614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.093786 restraints weight = 43565.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.093347 restraints weight = 50803.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.092355 restraints weight = 70620.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4357
moved from start:          1.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5030  Z= 0.272
  Angle     :  0.940  11.437   6855  Z= 0.450
  Chirality :  0.047   0.346    904
  Planarity :  0.007   0.057    798
  Dihedral  :  5.942  56.344    660
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 22.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 25.48 %
    Favored  : 72.44 %
  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:  1.54 (0.34), residues: 616
  helix:  1.42 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.93 (0.75), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 453 
 HIS   0.007   0.001   HIS B 306 
 PHE   0.036   0.002   PHE B 262 
 TYR   0.032   0.002   TYR A 234 
 ARG   0.003   0.000   ARG B 282 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 PHE cc_start: 0.7569 (t80) cc_final: 0.6984 (m-10)
REVERT: B  218 LEU cc_start: 0.8254 (tp) cc_final: 0.8054 (pp)
REVERT: C  248 TYR cc_start: 0.2851 (OUTLIER) cc_final: 0.2373 (t80)
REVERT: C  296 MET cc_start: 0.7130 (mmp) cc_final: 0.6881 (ptm)
REVERT: D  278 MET cc_start: 0.6397 (ppp) cc_final: 0.6071 (ppp)
REVERT: D  282 MET cc_start: -0.0640 (ttt) cc_final: -0.0943 (tpt)
REVERT: E  272 LYS cc_start: 0.8199 (pttt) cc_final: 0.7790 (pttt)
  outliers start: 12
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1255
  time to fit residues: 12.8724
Evaluate side-chains
  71 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain C residue  241 PHE
Chi-restraints excluded: chain C residue  248 TYR
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain D residue  224 LEU
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 6 optimal weight:   30.0000
   chunk 16 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 52 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 460 HIS
** D 300 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 = 0.4651 r_free = 0.4651 target = 0.111356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.092589 restraints weight = 43839.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.091617 restraints weight = 52407.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.091216 restraints weight = 66582.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4602
moved from start:          1.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5030  Z= 0.307
  Angle     :  1.028  14.441   6855  Z= 0.485
  Chirality :  0.050   0.437    904
  Planarity :  0.007   0.060    798
  Dihedral  :  6.375  58.519    660
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 23.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.48 %
    Favored  : 71.92 %
  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 (0.33), residues: 616
  helix:  1.32 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -2.47 (0.71), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP E 453 
 HIS   0.008   0.002   HIS B 306 
 PHE   0.034   0.003   PHE B 262 
 TYR   0.030   0.003   TYR A 234 
 ARG   0.004   0.001   ARG B 282 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 PHE cc_start: 0.7474 (t80) cc_final: 0.6648 (m-10)
REVERT: C  248 TYR cc_start: 0.2798 (OUTLIER) cc_final: 0.2278 (t80)
REVERT: D  278 MET cc_start: 0.6345 (ppp) cc_final: 0.5993 (ppp)
REVERT: D  282 MET cc_start: 0.0028 (ttt) cc_final: -0.0298 (tpt)
  outliers start: 15
  outliers final: 10
  residues processed: 76
  average time/residue: 0.1262
  time to fit residues: 13.6913
Evaluate side-chains
  70 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  241 PHE
Chi-restraints excluded: chain C residue  248 TYR
Chi-restraints excluded: chain C residue  294 PHE
Chi-restraints excluded: chain C residue  466 VAL
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain E residue  221 PHE
Chi-restraints excluded: chain E residue  264 ILE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 36 optimal weight:   30.0000
   chunk 4 optimal weight:   40.0000
   chunk 14 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 18 optimal weight:   20.0000
   chunk 45 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 225 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 = 0.4645 r_free = 0.4645 target = 0.111586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.092624 restraints weight = 42873.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.092440 restraints weight = 50517.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.092440 restraints weight = 56162.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4597
moved from start:          1.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5030  Z= 0.290
  Angle     :  0.998  15.028   6855  Z= 0.475
  Chirality :  0.048   0.398    904
  Planarity :  0.007   0.058    798
  Dihedral  :  5.704  55.991    658
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 22.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 26.86 %
    Favored  : 71.40 %
  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:  1.50 (0.34), residues: 616
  helix:  1.42 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -2.26 (0.78), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 453 
 HIS   0.006   0.001   HIS B 306 
 PHE   0.040   0.002   PHE B 262 
 TYR   0.030   0.002   TYR A 234 
 ARG   0.001   0.000   ARG C 277 

===============================================================================
Job complete
usr+sys time: 1955.32 seconds
wall clock time: 35 minutes 41.11 seconds (2141.11 seconds total)