Starting phenix.real_space_refine
on Tue Feb 11 12:05:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wwb_32865/02_2025/7wwb_32865.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wwb_32865/02_2025/7wwb_32865.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wwb_32865/02_2025/7wwb_32865.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wwb_32865/02_2025/7wwb_32865.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wwb_32865/02_2025/7wwb_32865.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wwb_32865/02_2025/7wwb_32865.cif"
  }
  resolution = 3.86
  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=   0.018 sd=   0.094
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      60      5.16       5
     C    3682      2.51       5
     N     834      2.21       5
     O     852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 5428
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2679
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 8, 'TRANS': 324}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2679
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 8, 'TRANS': 324}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 35
          Unusual residues: {'CHT': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 35
          Unusual residues: {'CHT': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.77, per 1000 atoms: 0.69
  Number of scatterers: 5428
  At special positions: 0
  Unit cell: (107.613, 120.657, 82.612, 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      60     16.00
     O     852      8.00
     N     834      7.00
     C    3682      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: 1.48
  Conformation dependent library (CDL) restraints added in 675.1 milliseconds
  

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1276

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      83.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 51
    Processing helix  chain 'A' and resid 228 through 245
      removed outlier: 5.997A  pdb=" N   ARG A 234 " --> pdb=" O   MET A 230 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   TYR A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ARG A 238 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 309
    Processing helix  chain 'A' and resid 310 through 331
    Processing helix  chain 'A' and resid 333 through 336
    Processing helix  chain 'A' and resid 337 through 356
      removed outlier: 3.515A  pdb=" N   THR A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 416
      removed outlier: 3.614A  pdb=" N   ILE A 393 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 430
    Processing helix  chain 'A' and resid 431 through 438
    Processing helix  chain 'A' and resid 439 through 466
      removed outlier: 3.545A  pdb=" N   VAL A 443 " --> pdb=" O   HIS A 439 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A 453 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      Proline residue:  A 456  - end of helix
    Processing helix  chain 'A' and resid 479 through 508
    Processing helix  chain 'A' and resid 510 through 525
    Processing helix  chain 'A' and resid 525 through 554
    Processing helix  chain 'A' and resid 573 through 607
    Processing helix  chain 'B' and resid 29 through 51
    Processing helix  chain 'B' and resid 228 through 245
      removed outlier: 5.997A  pdb=" N   ARG B 234 " --> pdb=" O   MET B 230 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR B 235 " --> pdb=" O   VAL B 231 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ARG B 238 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 309
    Processing helix  chain 'B' and resid 310 through 331
    Processing helix  chain 'B' and resid 333 through 336
    Processing helix  chain 'B' and resid 337 through 356
      removed outlier: 3.516A  pdb=" N   THR B 341 " --> pdb=" O   GLN B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 416
      removed outlier: 3.615A  pdb=" N   ILE B 393 " --> pdb=" O   VAL B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 430
    Processing helix  chain 'B' and resid 431 through 438
    Processing helix  chain 'B' and resid 439 through 466
      removed outlier: 3.544A  pdb=" N   VAL B 443 " --> pdb=" O   HIS B 439 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL B 453 " --> pdb=" O   ILE B 449 " (cutoff:3.500A)
      Proline residue:  B 456  - end of helix
    Processing helix  chain 'B' and resid 479 through 508
    Processing helix  chain 'B' and resid 510 through 525
    Processing helix  chain 'B' and resid 525 through 554
    Processing helix  chain 'B' and resid 573 through 607

    428 hydrogen bonds defined for protein.
    1260 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: 1.61

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 756
        1.30 -     1.43: 1504
        1.43 -     1.56: 3180
        1.56 -     1.68: 34
        1.68 -     1.81: 90
  Bond restraints: 5564
  Sorted by residual:
  bond pdb=" C   GLN B 337 "
       pdb=" O   GLN B 337 "
    ideal  model  delta    sigma   weight residual
    1.243  1.177  0.066 9.90e-03 1.02e+04 4.38e+01
  bond pdb=" C   GLN A 337 "
       pdb=" O   GLN A 337 "
    ideal  model  delta    sigma   weight residual
    1.243  1.178  0.065 9.90e-03 1.02e+04 4.35e+01
  bond pdb=" C   PHE B 339 "
       pdb=" O   PHE B 339 "
    ideal  model  delta    sigma   weight residual
    1.236  1.190  0.046 1.29e-02 6.01e+03 1.26e+01
  bond pdb=" C   PHE A 339 "
       pdb=" O   PHE A 339 "
    ideal  model  delta    sigma   weight residual
    1.236  1.190  0.046 1.29e-02 6.01e+03 1.25e+01
  bond pdb=" C17 CLR A 702 "
       pdb=" C20 CLR A 702 "
    ideal  model  delta    sigma   weight residual
    1.535  1.596 -0.061 2.00e-02 2.50e+03 9.18e+00
  ... (remaining 5559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 7256
        2.16 -     4.32: 268
        4.32 -     6.48: 32
        6.48 -     8.64: 8
        8.64 -    10.80: 4
  Bond angle restraints: 7568
  Sorted by residual:
  angle pdb=" C   PHE B 339 "
        pdb=" N   TRP B 340 "
        pdb=" CA  TRP B 340 "
      ideal   model   delta    sigma   weight residual
     120.31  109.51   10.80 1.52e+00 4.33e-01 5.05e+01
  angle pdb=" C   PHE A 339 "
        pdb=" N   TRP A 340 "
        pdb=" CA  TRP A 340 "
      ideal   model   delta    sigma   weight residual
     120.31  109.53   10.78 1.52e+00 4.33e-01 5.03e+01
  angle pdb=" N   ILE A 428 "
        pdb=" CA  ILE A 428 "
        pdb=" C   ILE A 428 "
      ideal   model   delta    sigma   weight residual
     113.53  107.83    5.70 9.80e-01 1.04e+00 3.38e+01
  angle pdb=" N   ILE B 428 "
        pdb=" CA  ILE B 428 "
        pdb=" C   ILE B 428 "
      ideal   model   delta    sigma   weight residual
     113.53  107.85    5.68 9.80e-01 1.04e+00 3.36e+01
  angle pdb=" C   PHE B 336 "
        pdb=" N   GLN B 337 "
        pdb=" CA  GLN B 337 "
      ideal   model   delta    sigma   weight residual
     120.58  128.05   -7.47 1.32e+00 5.74e-01 3.20e+01
  ... (remaining 7563 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 3222
       17.14 -    34.28: 68
       34.28 -    51.42: 6
       51.42 -    68.56: 4
       68.56 -    85.70: 4
  Dihedral angle restraints: 3304
    sinusoidal: 1350
      harmonic: 1954
  Sorted by residual:
  dihedral pdb=" CA  TYR B 438 "
           pdb=" C   TYR B 438 "
           pdb=" N   HIS B 439 "
           pdb=" CA  HIS B 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.84  -20.16     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  TYR A 438 "
           pdb=" C   TYR A 438 "
           pdb=" N   HIS A 439 "
           pdb=" CA  HIS A 439 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.85  -20.15     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CB  GLU B 591 "
           pdb=" CG  GLU B 591 "
           pdb=" CD  GLU B 591 "
           pdb=" OE1 GLU B 591 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.70   85.70     1      3.00e+01 1.11e-03 9.87e+00
  ... (remaining 3301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 642
       0.063 -    0.125: 240
       0.125 -    0.188: 32
       0.188 -    0.251: 8
       0.251 -    0.313: 8
  Chirality restraints: 930
  Sorted by residual:
  chirality pdb=" C13 CLR A 702 "
            pdb=" C12 CLR A 702 "
            pdb=" C14 CLR A 702 "
            pdb=" C17 CLR A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -3.25    0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C13 CLR B 702 "
            pdb=" C12 CLR B 702 "
            pdb=" C14 CLR B 702 "
            pdb=" C17 CLR B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -3.25    0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C14 CLR B 702 "
            pdb=" C13 CLR B 702 "
            pdb=" C15 CLR B 702 "
            pdb=" C8  CLR B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.63    0.31 2.00e-01 2.50e+01 2.38e+00
  ... (remaining 927 not shown)

  Planarity restraints: 860
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 343 "   -0.012 2.00e-02 2.50e+03   2.39e-02 5.71e+00
        pdb=" C   PHE A 343 "    0.041 2.00e-02 2.50e+03
        pdb=" O   PHE A 343 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A 344 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 343 "    0.012 2.00e-02 2.50e+03   2.39e-02 5.70e+00
        pdb=" C   PHE B 343 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   PHE B 343 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ALA B 344 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 493 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.17e+00
        pdb=" C   LEU B 493 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   LEU B 493 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN B 494 "    0.013 2.00e-02 2.50e+03
  ... (remaining 857 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 2767
        2.99 -     3.47: 5843
        3.47 -     3.94: 8642
        3.94 -     4.42: 9683
        4.42 -     4.90: 15145
  Nonbonded interactions: 42080
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 326 "
            pdb=" OD2 ASP B 619 "
     model   vdw
     2.511 3.120
  nonbonded pdb=" NZ  LYS A 326 "
            pdb=" OD2 ASP A 619 "
     model   vdw
     2.512 3.120
  nonbonded pdb=" O   CYS B  26 "
            pdb=" OG1 THR B  27 "
     model   vdw
     2.531 3.040
  nonbonded pdb=" O   CYS A  26 "
            pdb=" OG1 THR A  27 "
     model   vdw
     2.531 3.040
  nonbonded pdb=" N   PHE B 336 "
            pdb=" N   GLN B 337 "
     model   vdw
     2.561 2.560
  ... (remaining 42075 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.800
  Find NCS groups from input model:        0.090
  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:   20.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
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      :  0.008   0.066   5564  Z= 0.529
  Angle     :  0.969  10.801   7568  Z= 0.650
  Chirality :  0.066   0.313    930
  Planarity :  0.006   0.026    860
  Dihedral  :  9.324  85.703   2028
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 0.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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:  0.18 (0.31), residues: 642
  helix:  0.69 (0.21), residues: 518
  sheet:  None (None), residues: 0
  loop : -2.08 (0.51), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 386 
 HIS   0.001   0.000   HIS B 464 
 PHE   0.001   0.000   PHE B 348 
 TYR   0.001   0.000   TYR B 415 
 ARG   0.001   0.000   ARG B 311 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8669 (mt) cc_final: 0.8421 (mt)
REVERT: A  234 ARG cc_start: 0.7483 (ptt180) cc_final: 0.7161 (ptt-90)
REVERT: A  326 LYS cc_start: 0.8897 (mttt) cc_final: 0.8603 (ttmm)
REVERT: A  342 PHE cc_start: 0.7578 (t80) cc_final: 0.7357 (m-10)
REVERT: A  352 TRP cc_start: 0.8852 (t60) cc_final: 0.8616 (t60)
REVERT: A  354 MET cc_start: 0.8206 (mmm) cc_final: 0.7948 (tpp)
REVERT: A  438 TYR cc_start: 0.7244 (m-80) cc_final: 0.7021 (m-10)
REVERT: A  516 LYS cc_start: 0.6466 (mttt) cc_final: 0.6192 (mmtp)
REVERT: A  528 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7031 (mpt180)
REVERT: A  581 LEU cc_start: 0.8942 (mt) cc_final: 0.8654 (tt)
REVERT: B  340 TRP cc_start: 0.6592 (m-10) cc_final: 0.5815 (m100)
REVERT: B  437 ARG cc_start: 0.7457 (tpt90) cc_final: 0.6958 (mmt180)
REVERT: B  463 ILE cc_start: 0.8796 (mt) cc_final: 0.8568 (mm)
REVERT: B  508 SER cc_start: 0.8865 (m) cc_final: 0.8506 (t)
REVERT: B  516 LYS cc_start: 0.6949 (mttt) cc_final: 0.6379 (mptt)
REVERT: B  534 THR cc_start: 0.8810 (m) cc_final: 0.8596 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1804
  time to fit residues: 65.5952
Evaluate side-chains
  178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
A 466 GLN
B 439 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.154974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120157 restraints weight = 9006.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.123309 restraints weight = 5591.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.125582 restraints weight = 4277.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5564  Z= 0.217
  Angle     :  0.680   7.472   7568  Z= 0.344
  Chirality :  0.039   0.184    930
  Planarity :  0.004   0.028    860
  Dihedral  :  4.735  31.905    836
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 14.93 %
    Favored  : 78.69 %
  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:  2.68 (0.34), residues: 642
  helix:  2.65 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -2.41 (0.50), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 340 
 HIS   0.002   0.001   HIS B 330 
 PHE   0.020   0.001   PHE B  44 
 TYR   0.012   0.001   TYR B 415 
 ARG   0.006   0.001   ARG B 614 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 185
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 TYR cc_start: 0.7197 (m-80) cc_final: 0.6985 (m-80)
REVERT: A  342 PHE cc_start: 0.7882 (t80) cc_final: 0.7449 (m-10)
REVERT: A  397 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7717 (mp0)
REVERT: A  433 ASN cc_start: 0.7516 (p0) cc_final: 0.7146 (m-40)
REVERT: A  445 LYS cc_start: 0.8205 (tptm) cc_final: 0.7909 (tptm)
REVERT: A  528 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7081 (mpt180)
REVERT: A  538 PHE cc_start: 0.8630 (t80) cc_final: 0.7730 (t80)
REVERT: A  542 LEU cc_start: 0.8734 (mp) cc_final: 0.8503 (mp)
REVERT: A  578 PHE cc_start: 0.8198 (t80) cc_final: 0.7778 (t80)
REVERT: A  581 LEU cc_start: 0.9005 (mt) cc_final: 0.8775 (tt)
REVERT: B   21 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7086 (pp)
REVERT: B   22 GLU cc_start: 0.7806 (mp0) cc_final: 0.7587 (mp0)
REVERT: B  234 ARG cc_start: 0.8777 (ptp90) cc_final: 0.8493 (ptp90)
REVERT: B  340 TRP cc_start: 0.6943 (m-10) cc_final: 0.6651 (m-10)
REVERT: B  508 SER cc_start: 0.8822 (m) cc_final: 0.8609 (t)
REVERT: B  516 LYS cc_start: 0.7093 (mttt) cc_final: 0.6316 (mmtt)
  outliers start: 38
  outliers final: 26
  residues processed: 216
  average time/residue: 0.1749
  time to fit residues: 48.6439
Evaluate side-chains
  181 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  396 SER
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  603 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 439 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.160310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124384 restraints weight = 9064.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.127992 restraints weight = 5658.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.130402 restraints weight = 4305.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.5818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5564  Z= 0.204
  Angle     :  0.635   7.115   7568  Z= 0.319
  Chirality :  0.037   0.175    930
  Planarity :  0.004   0.030    860
  Dihedral  :  4.711  34.675    836
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 16.95 %
    Favored  : 76.34 %
  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:  2.90 (0.34), residues: 642
  helix:  2.66 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.20 (0.59), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 439 
 PHE   0.023   0.001   PHE B  48 
 TYR   0.028   0.002   TYR A 438 
 ARG   0.005   0.001   ARG B 614 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 175
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A  230 MET cc_start: 0.7959 (mmp) cc_final: 0.7707 (mmp)
REVERT: A  307 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7647 (tpt)
REVERT: A  342 PHE cc_start: 0.7819 (t80) cc_final: 0.7159 (m-10)
REVERT: A  349 TRP cc_start: 0.9055 (m-10) cc_final: 0.8680 (m-10)
REVERT: A  397 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7622 (mp0)
REVERT: A  466 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8691 (tm-30)
REVERT: A  501 TYR cc_start: 0.9243 (m-10) cc_final: 0.8976 (m-10)
REVERT: A  528 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7207 (mpt180)
REVERT: A  538 PHE cc_start: 0.8654 (t80) cc_final: 0.7808 (t80)
REVERT: A  581 LEU cc_start: 0.9020 (mt) cc_final: 0.8663 (tt)
REVERT: A  599 LEU cc_start: 0.8830 (tp) cc_final: 0.8543 (tp)
REVERT: B  244 LEU cc_start: 0.9070 (tt) cc_final: 0.8781 (mm)
REVERT: B  340 TRP cc_start: 0.7070 (m-10) cc_final: 0.6738 (m-10)
REVERT: B  454 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8314 (ttmm)
REVERT: B  516 LYS cc_start: 0.7244 (mttt) cc_final: 0.6714 (mmtt)
  outliers start: 40
  outliers final: 22
  residues processed: 203
  average time/residue: 0.1537
  time to fit residues: 41.0176
Evaluate side-chains
  168 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 33 optimal weight:    8.9990
   chunk 37 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.159129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.125292 restraints weight = 9332.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.128110 restraints weight = 6428.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.129908 restraints weight = 4412.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.6473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5564  Z= 0.194
  Angle     :  0.637   8.716   7568  Z= 0.321
  Chirality :  0.038   0.201    930
  Planarity :  0.004   0.028    860
  Dihedral  :  4.776  30.197    836
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 21.48 %
    Favored  : 72.48 %
  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:  2.97 (0.34), residues: 642
  helix:  2.76 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.91 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  31 
 HIS   0.002   0.001   HIS B 330 
 PHE   0.025   0.001   PHE B 343 
 TYR   0.024   0.001   TYR A 438 
 ARG   0.004   0.001   ARG B 614 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 0.581 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7588 (OUTLIER) cc_final: 0.7203 (m-10)
REVERT: A  307 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7659 (tpt)
REVERT: A  342 PHE cc_start: 0.7816 (t80) cc_final: 0.7160 (m-10)
REVERT: A  347 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8956 (tt)
REVERT: A  349 TRP cc_start: 0.9058 (m-10) cc_final: 0.8695 (m-10)
REVERT: A  384 MET cc_start: 0.5018 (mpp) cc_final: 0.4569 (mpp)
REVERT: A  393 ILE cc_start: 0.8200 (mm) cc_final: 0.7883 (mt)
REVERT: A  397 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7495 (mp0)
REVERT: A  445 LYS cc_start: 0.8371 (tptm) cc_final: 0.7873 (tptm)
REVERT: A  449 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8916 (mp)
REVERT: A  501 TYR cc_start: 0.9226 (m-10) cc_final: 0.8981 (m-10)
REVERT: A  528 ARG cc_start: 0.7680 (mtt90) cc_final: 0.7346 (mpt180)
REVERT: A  538 PHE cc_start: 0.8601 (t80) cc_final: 0.8171 (t80)
REVERT: A  581 LEU cc_start: 0.8998 (mt) cc_final: 0.8604 (tt)
REVERT: B   42 MET cc_start: 0.8599 (tpt) cc_final: 0.8129 (tpp)
REVERT: B  242 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.6953 (t60)
REVERT: B  244 LEU cc_start: 0.8889 (tt) cc_final: 0.8642 (mm)
REVERT: B  397 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8496 (mm-30)
REVERT: B  438 TYR cc_start: 0.7861 (m-80) cc_final: 0.7471 (m-10)
REVERT: B  454 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8222 (ttmt)
REVERT: B  516 LYS cc_start: 0.7310 (mttt) cc_final: 0.6819 (mmtt)
  outliers start: 36
  outliers final: 22
  residues processed: 193
  average time/residue: 0.1467
  time to fit residues: 37.9333
Evaluate side-chains
  178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  455 ILE
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 466 GLN
B 608 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.145457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111641 restraints weight = 9368.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.113459 restraints weight = 6977.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.114600 restraints weight = 5425.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.6968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   5564  Z= 0.386
  Angle     :  0.761   7.988   7568  Z= 0.394
  Chirality :  0.044   0.245    930
  Planarity :  0.004   0.035    860
  Dihedral  :  6.008  48.547    836
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 22.32 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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:  2.42 (0.33), residues: 642
  helix:  2.36 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.12 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 340 
 HIS   0.004   0.001   HIS B 330 
 PHE   0.024   0.002   PHE B 343 
 TYR   0.025   0.002   TYR A 438 
 ARG   0.003   0.001   ARG A 457 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 152
  time to evaluate  : 0.576 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7671 (OUTLIER) cc_final: 0.7042 (m-10)
REVERT: A  307 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7756 (ppp)
REVERT: A  342 PHE cc_start: 0.7913 (t80) cc_final: 0.7361 (m-10)
REVERT: A  347 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8957 (tt)
REVERT: A  392 LEU cc_start: 0.7930 (tp) cc_final: 0.7704 (tp)
REVERT: A  397 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7423 (mp0)
REVERT: A  445 LYS cc_start: 0.8423 (tptm) cc_final: 0.7933 (tptm)
REVERT: A  449 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8848 (mp)
REVERT: A  516 LYS cc_start: 0.6431 (mttt) cc_final: 0.6171 (mmtp)
REVERT: A  538 PHE cc_start: 0.8745 (t80) cc_final: 0.8454 (t80)
REVERT: A  581 LEU cc_start: 0.9143 (mt) cc_final: 0.8775 (tt)
REVERT: B   42 MET cc_start: 0.8748 (tpt) cc_final: 0.8369 (tpp)
REVERT: B  242 TRP cc_start: 0.7690 (OUTLIER) cc_final: 0.6851 (t60)
REVERT: B  516 LYS cc_start: 0.7419 (mttt) cc_final: 0.6798 (mmtt)
  outliers start: 47
  outliers final: 30
  residues processed: 184
  average time/residue: 0.1469
  time to fit residues: 36.0619
Evaluate side-chains
  182 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  387 TYR
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  455 ILE
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 61 optimal weight:    0.0970
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
B 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.151451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.118690 restraints weight = 9264.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.120718 restraints weight = 6552.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.122010 restraints weight = 4735.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.7287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5564  Z= 0.188
  Angle     :  0.644   8.071   7568  Z= 0.325
  Chirality :  0.039   0.235    930
  Planarity :  0.003   0.027    860
  Dihedral  :  5.021  35.940    836
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 26.17 %
    Favored  : 68.46 %
  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:  2.83 (0.34), residues: 642
  helix:  2.69 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -2.11 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 386 
 HIS   0.002   0.001   HIS B 330 
 PHE   0.024   0.001   PHE B 343 
 TYR   0.019   0.002   TYR A 438 
 ARG   0.004   0.001   ARG B 614 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 0.595 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7761 (OUTLIER) cc_final: 0.7227 (m-10)
REVERT: A  307 MET cc_start: 0.7975 (tpp) cc_final: 0.7612 (tpt)
REVERT: A  342 PHE cc_start: 0.7860 (t80) cc_final: 0.7329 (m-10)
REVERT: A  393 ILE cc_start: 0.8394 (mm) cc_final: 0.7944 (mt)
REVERT: A  397 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7390 (mp0)
REVERT: A  445 LYS cc_start: 0.8189 (tptm) cc_final: 0.7732 (tptm)
REVERT: A  449 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8754 (mp)
REVERT: A  458 MET cc_start: 0.7780 (tpt) cc_final: 0.7349 (tpt)
REVERT: A  460 LEU cc_start: 0.8628 (mp) cc_final: 0.8367 (tt)
REVERT: A  508 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8698 (t)
REVERT: A  581 LEU cc_start: 0.9034 (mt) cc_final: 0.8665 (tt)
REVERT: A  599 LEU cc_start: 0.8869 (tp) cc_final: 0.8594 (tp)
REVERT: B  242 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.6946 (t60)
REVERT: B  397 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8576 (mm-30)
REVERT: B  438 TYR cc_start: 0.7915 (m-80) cc_final: 0.7558 (m-10)
REVERT: B  454 LYS cc_start: 0.9042 (tppp) cc_final: 0.8376 (ttmt)
REVERT: B  516 LYS cc_start: 0.7368 (mttt) cc_final: 0.6878 (mmtt)
  outliers start: 32
  outliers final: 22
  residues processed: 176
  average time/residue: 0.1450
  time to fit residues: 34.0373
Evaluate side-chains
  172 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  387 TYR
Chi-restraints excluded: chain B residue  419 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.155903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.123349 restraints weight = 9158.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.125472 restraints weight = 6406.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.126809 restraints weight = 4636.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.7577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5564  Z= 0.193
  Angle     :  0.649   9.723   7568  Z= 0.327
  Chirality :  0.039   0.235    930
  Planarity :  0.004   0.027    860
  Dihedral  :  4.940  38.206    836
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 25.84 %
    Favored  : 68.29 %
  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:  2.95 (0.34), residues: 642
  helix:  2.77 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -2.03 (0.55), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 386 
 HIS   0.002   0.001   HIS B 322 
 PHE   0.019   0.001   PHE A 578 
 TYR   0.026   0.002   TYR A 438 
 ARG   0.003   0.000   ARG B 418 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 152
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 TRP cc_start: 0.7782 (OUTLIER) cc_final: 0.7199 (m-10)
REVERT: A  307 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7640 (tpt)
REVERT: A  343 PHE cc_start: 0.8083 (t80) cc_final: 0.7854 (t80)
REVERT: A  393 ILE cc_start: 0.8439 (mm) cc_final: 0.8034 (mt)
REVERT: A  397 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7388 (mp0)
REVERT: A  458 MET cc_start: 0.7817 (tpt) cc_final: 0.7405 (tpt)
REVERT: A  460 LEU cc_start: 0.8627 (mp) cc_final: 0.8327 (tt)
REVERT: A  581 LEU cc_start: 0.8974 (mt) cc_final: 0.8618 (tt)
REVERT: A  599 LEU cc_start: 0.8916 (tp) cc_final: 0.8397 (tt)
REVERT: B  242 TRP cc_start: 0.7539 (OUTLIER) cc_final: 0.6891 (t60)
REVERT: B  438 TYR cc_start: 0.7936 (m-80) cc_final: 0.7719 (m-10)
REVERT: B  462 TYR cc_start: 0.8553 (t80) cc_final: 0.8081 (t80)
REVERT: B  516 LYS cc_start: 0.7423 (mttt) cc_final: 0.6934 (mmtt)
REVERT: B  545 VAL cc_start: 0.8803 (t) cc_final: 0.8567 (p)
REVERT: B  549 CYS cc_start: 0.8852 (m) cc_final: 0.8602 (m)
  outliers start: 35
  outliers final: 23
  residues processed: 179
  average time/residue: 0.1279
  time to fit residues: 31.7562
Evaluate side-chains
  173 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  419 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.149274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.116338 restraints weight = 9425.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.118204 restraints weight = 6753.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120028 restraints weight = 4903.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.7677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5564  Z= 0.231
  Angle     :  0.689   9.007   7568  Z= 0.347
  Chirality :  0.040   0.240    930
  Planarity :  0.004   0.029    860
  Dihedral  :  5.135  41.967    836
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 26.34 %
    Favored  : 67.28 %
  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:  2.96 (0.34), residues: 642
  helix:  2.73 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.80 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 330 
 PHE   0.026   0.002   PHE B 343 
 TYR   0.028   0.002   TYR A 438 
 ARG   0.004   0.000   ARG B 418 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7716 (OUTLIER) cc_final: 0.7088 (m-10)
REVERT: A  307 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7624 (tpt)
REVERT: A  343 PHE cc_start: 0.8114 (t80) cc_final: 0.7876 (t80)
REVERT: A  393 ILE cc_start: 0.8641 (mm) cc_final: 0.8192 (mt)
REVERT: A  397 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7401 (mp0)
REVERT: A  458 MET cc_start: 0.7779 (tpt) cc_final: 0.7478 (tpt)
REVERT: A  459 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8985 (tp)
REVERT: A  508 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8647 (t)
REVERT: A  538 PHE cc_start: 0.8703 (t80) cc_final: 0.8218 (t80)
REVERT: A  542 LEU cc_start: 0.8394 (mp) cc_final: 0.8143 (tt)
REVERT: A  581 LEU cc_start: 0.8999 (mt) cc_final: 0.8656 (tt)
REVERT: A  599 LEU cc_start: 0.8971 (tp) cc_final: 0.8444 (tt)
REVERT: B   42 MET cc_start: 0.8944 (tpp) cc_final: 0.8679 (tpp)
REVERT: B  242 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.6571 (t60)
REVERT: B  354 MET cc_start: 0.7291 (ttp) cc_final: 0.6805 (tmm)
REVERT: B  462 TYR cc_start: 0.8603 (t80) cc_final: 0.8101 (t80)
REVERT: B  516 LYS cc_start: 0.7418 (mttt) cc_final: 0.6919 (mmtt)
REVERT: B  545 VAL cc_start: 0.8820 (t) cc_final: 0.8566 (p)
REVERT: B  549 CYS cc_start: 0.8886 (m) cc_final: 0.8614 (m)
  outliers start: 38
  outliers final: 28
  residues processed: 175
  average time/residue: 0.1353
  time to fit residues: 32.8496
Evaluate side-chains
  174 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 140
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  419 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.150692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.119311 restraints weight = 9383.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.121668 restraints weight = 6368.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.122831 restraints weight = 4518.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.7854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5564  Z= 0.193
  Angle     :  0.657   7.923   7568  Z= 0.334
  Chirality :  0.039   0.246    930
  Planarity :  0.004   0.028    860
  Dihedral  :  4.951  39.764    836
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 27.18 %
    Favored  : 66.78 %
  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:  2.98 (0.34), residues: 642
  helix:  2.77 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.91 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.021   0.001   PHE A 538 
 TYR   0.026   0.002   TYR A 438 
 ARG   0.004   0.000   ARG B 418 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 0.593 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7707 (OUTLIER) cc_final: 0.7089 (m-10)
REVERT: A  307 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7671 (tpt)
REVERT: A  343 PHE cc_start: 0.8062 (t80) cc_final: 0.7817 (t80)
REVERT: A  393 ILE cc_start: 0.8457 (mm) cc_final: 0.8005 (mt)
REVERT: A  397 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7368 (mp0)
REVERT: A  438 TYR cc_start: 0.7937 (m-80) cc_final: 0.7731 (m-10)
REVERT: A  458 MET cc_start: 0.7766 (tpt) cc_final: 0.7490 (tpt)
REVERT: A  459 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8955 (tp)
REVERT: A  460 LEU cc_start: 0.8660 (mp) cc_final: 0.8349 (tt)
REVERT: A  508 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8609 (t)
REVERT: A  516 LYS cc_start: 0.5975 (mmtp) cc_final: 0.5546 (mmtt)
REVERT: A  538 PHE cc_start: 0.8702 (t80) cc_final: 0.8225 (t80)
REVERT: A  581 LEU cc_start: 0.8935 (mt) cc_final: 0.8577 (tt)
REVERT: A  599 LEU cc_start: 0.8880 (tp) cc_final: 0.8319 (tt)
REVERT: B  438 TYR cc_start: 0.7776 (m-80) cc_final: 0.7555 (m-10)
REVERT: B  462 TYR cc_start: 0.8563 (t80) cc_final: 0.8095 (t80)
REVERT: B  516 LYS cc_start: 0.7380 (mttt) cc_final: 0.6918 (mmtt)
REVERT: B  545 VAL cc_start: 0.8815 (t) cc_final: 0.8612 (p)
REVERT: B  549 CYS cc_start: 0.8840 (m) cc_final: 0.8592 (m)
  outliers start: 36
  outliers final: 25
  residues processed: 173
  average time/residue: 0.1338
  time to fit residues: 31.8211
Evaluate side-chains
  169 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  419 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.8384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.155570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.123480 restraints weight = 9194.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.126173 restraints weight = 6266.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127537 restraints weight = 4435.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.7969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   5564  Z= 0.200
  Angle     :  0.691   8.440   7568  Z= 0.343
  Chirality :  0.040   0.247    930
  Planarity :  0.004   0.028    860
  Dihedral  :  4.945  39.398    836
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 28.86 %
    Favored  : 66.61 %
  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:  3.01 (0.34), residues: 642
  helix:  2.77 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.83 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.030   0.002   PHE B 342 
 TYR   0.025   0.002   TYR B 235 
 ARG   0.003   0.000   ARG B 418 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 0.658 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.7137 (m-10)
REVERT: A  307 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7716 (tpt)
REVERT: A  343 PHE cc_start: 0.8043 (t80) cc_final: 0.7785 (t80)
REVERT: A  393 ILE cc_start: 0.8472 (mm) cc_final: 0.8047 (mt)
REVERT: A  397 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7400 (mp0)
REVERT: A  458 MET cc_start: 0.7790 (tpt) cc_final: 0.7520 (tpt)
REVERT: A  459 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8960 (tp)
REVERT: A  460 LEU cc_start: 0.8669 (mp) cc_final: 0.8358 (tt)
REVERT: A  538 PHE cc_start: 0.8680 (t80) cc_final: 0.8320 (t80)
REVERT: A  581 LEU cc_start: 0.8910 (mt) cc_final: 0.8566 (tt)
REVERT: A  599 LEU cc_start: 0.8881 (tp) cc_final: 0.8330 (tt)
REVERT: B  438 TYR cc_start: 0.7805 (m-80) cc_final: 0.7550 (m-10)
REVERT: B  462 TYR cc_start: 0.8593 (t80) cc_final: 0.8095 (t80)
REVERT: B  516 LYS cc_start: 0.7381 (mttt) cc_final: 0.6938 (mmtt)
REVERT: B  545 VAL cc_start: 0.8871 (t) cc_final: 0.8627 (p)
REVERT: B  549 CYS cc_start: 0.8800 (m) cc_final: 0.8520 (m)
  outliers start: 27
  outliers final: 21
  residues processed: 166
  average time/residue: 0.1354
  time to fit residues: 31.1252
Evaluate side-chains
  166 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  419 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.155682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.123899 restraints weight = 9334.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126308 restraints weight = 6279.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.127846 restraints weight = 4509.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.8061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   5564  Z= 0.195
  Angle     :  0.681   7.566   7568  Z= 0.340
  Chirality :  0.040   0.238    930
  Planarity :  0.004   0.029    860
  Dihedral  :  4.911  37.780    836
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 28.52 %
    Favored  : 66.78 %
  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:  3.01 (0.34), residues: 642
  helix:  2.78 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.84 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.026   0.001   PHE B 343 
 TYR   0.019   0.002   TYR B 351 
 ARG   0.003   0.000   ARG B 418 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1772.35 seconds
wall clock time: 32 minutes 35.46 seconds (1955.46 seconds total)