Starting phenix.real_space_refine
on Tue Mar  3 13:50:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wwb_32865/03_2026/7wwb_32865.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wwb_32865/03_2026/7wwb_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_32865/03_2026/7wwb_32865.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wwb_32865/03_2026/7wwb_32865.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wwb_32865/03_2026/7wwb_32865.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wwb_32865/03_2026/7wwb_32865.cif"
  }
  resolution = 3.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.018 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.49, per 1000 atoms: 0.27
  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: 0.49
  Conformation dependent library (CDL) restraints added in 234.0 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: 0.11
  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: 0.62

  Time building geometry restraints manager: 0.64 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: 0.01
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:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.450
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.450
-------------------------------------------------------------------------------
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= 0.476
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  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
 ARG   0.001   0.000   ARG B 311 
 TYR   0.001   0.000   TYR B 415 
 PHE   0.001   0.000   PHE B 348 
 TRP   0.001   0.000   TRP B 386 
 HIS   0.001   0.000   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00825 ( 5564)
  covalent geometry    : angle       0.96944 ( 7568)
  hydrogen bonds       : bond        0.21072 (  428)
  hydrogen bonds       : angle       6.93898 ( 1260)

*********************** 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  : 0.207 
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: 0.7160 (ptt-90)
REVERT: A  326 LYS cc_start: 0.8897 (mttt) cc_final: 0.8602 (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: 0.6193 (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: 0.6957 (mmt180)
REVERT: B  463 ILE cc_start: 0.8796 (mt) cc_final: 0.8573 (mm)
REVERT: B  508 SER cc_start: 0.8865 (m) cc_final: 0.8507 (t)
REVERT: B  516 LYS cc_start: 0.6949 (mttt) cc_final: 0.6378 (mptt)
REVERT: B  534 THR cc_start: 0.8810 (m) cc_final: 0.8595 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.0744
  time to fit residues: 27.3892
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  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0670
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   overall best weight:    0.6718

-------------------------------------------------------------------------------
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 = 0.3896 r_free = 0.3896 target = 0.157930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.122139 restraints weight = 9226.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.125580 restraints weight = 5769.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.127963 restraints weight = 4369.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.129303 restraints weight = 3682.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.130470 restraints weight = 3327.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5564  Z= 0.150
  Angle     :  0.668   7.600   7568  Z= 0.336
  Chirality :  0.037   0.179    930
  Planarity :  0.004   0.028    860
  Dihedral  :  4.691  32.950    836
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 15.27 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.34), residues: 642
  helix:  2.68 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -2.45 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 614 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.019   0.001   PHE B  44 
 TRP   0.009   0.001   TRP B 487 
 HIS   0.003   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5564)
  covalent geometry    : angle       0.66796 ( 7568)
  hydrogen bonds       : bond        0.05367 (  428)
  hydrogen bonds       : angle       4.17807 ( 1260)

*********************** 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
  219 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 184
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 MET cc_start: 0.8011 (mmp) cc_final: 0.7675 (mmp)
REVERT: A  342 PHE cc_start: 0.7850 (t80) cc_final: 0.7432 (m-10)
REVERT: A  397 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7682 (mp0)
REVERT: A  433 ASN cc_start: 0.7513 (p0) cc_final: 0.7141 (m-40)
REVERT: A  516 LYS cc_start: 0.6418 (mttt) cc_final: 0.6186 (mmtp)
REVERT: A  528 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7221 (mpt180)
REVERT: A  538 PHE cc_start: 0.8608 (t80) cc_final: 0.7689 (t80)
REVERT: A  542 LEU cc_start: 0.8695 (mp) cc_final: 0.8471 (mp)
REVERT: A  578 PHE cc_start: 0.8162 (t80) cc_final: 0.7754 (t80)
REVERT: A  581 LEU cc_start: 0.8985 (mt) cc_final: 0.8740 (tt)
REVERT: B   21 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6957 (pp)
REVERT: B  340 TRP cc_start: 0.6788 (m-10) cc_final: 0.6568 (m-10)
REVERT: B  516 LYS cc_start: 0.7050 (mttt) cc_final: 0.6234 (mmtt)
  outliers start: 35
  outliers final: 19
  residues processed: 212
  average time/residue: 0.0633
  time to fit residues: 17.6563
Evaluate side-chains
  180 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
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  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  588 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  459 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 13 optimal weight:    0.6980
   chunk 61 optimal weight:    8.9990
   chunk 63 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.159079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.123098 restraints weight = 9090.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.126608 restraints weight = 5717.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.128953 restraints weight = 4367.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.130388 restraints weight = 3724.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.131086 restraints weight = 3377.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.5866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5564  Z= 0.157
  Angle     :  0.657   7.104   7568  Z= 0.332
  Chirality :  0.039   0.172    930
  Planarity :  0.004   0.036    860
  Dihedral  :  4.830  37.844    836
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 17.11 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.10 (0.34), residues: 642
  helix:  2.84 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.84 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 457 
 TYR   0.028   0.002   TYR A 438 
 PHE   0.021   0.001   PHE B  48 
 TRP   0.016   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 439 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5564)
  covalent geometry    : angle       0.65724 ( 7568)
  hydrogen bonds       : bond        0.05223 (  428)
  hydrogen bonds       : angle       4.03024 ( 1260)

*********************** 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
  209 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 174
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  307 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7585 (tpt)
REVERT: A  342 PHE cc_start: 0.7761 (t80) cc_final: 0.7439 (m-10)
REVERT: A  397 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7636 (mp0)
REVERT: A  466 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8699 (tm-30)
REVERT: A  501 TYR cc_start: 0.9258 (m-10) cc_final: 0.8980 (m-10)
REVERT: A  528 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7253 (mpt180)
REVERT: A  538 PHE cc_start: 0.8701 (t80) cc_final: 0.7857 (t80)
REVERT: A  581 LEU cc_start: 0.9027 (mt) cc_final: 0.8660 (tt)
REVERT: B  244 LEU cc_start: 0.9060 (tt) cc_final: 0.8814 (mm)
REVERT: B  438 TYR cc_start: 0.8102 (m-80) cc_final: 0.7734 (m-80)
REVERT: B  454 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8161 (ttmm)
REVERT: B  506 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8856 (mm)
REVERT: B  516 LYS cc_start: 0.7371 (mttt) cc_final: 0.6827 (mmtt)
REVERT: B  592 MET cc_start: 0.8228 (ttm) cc_final: 0.8020 (ttm)
  outliers start: 35
  outliers final: 24
  residues processed: 200
  average time/residue: 0.0638
  time to fit residues: 16.8275
Evaluate side-chains
  169 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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  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  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  488 CYS
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  556 ILE
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   33 LEU
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  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 1 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.148721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.114191 restraints weight = 9242.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.117214 restraints weight = 5884.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.119231 restraints weight = 4508.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.120428 restraints weight = 3834.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.120717 restraints weight = 3493.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.6670

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= 0.182
  Angle     :  0.690   7.602   7568  Z= 0.351
  Chirality :  0.040   0.187    930
  Planarity :  0.004   0.037    860
  Dihedral  :  5.198  31.510    836
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  7.21 %
    Allowed  : 19.80 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.85 (0.34), residues: 642
  helix:  2.68 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.97 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 614 
 TYR   0.031   0.002   TYR A 438 
 PHE   0.022   0.002   PHE B 343 
 TRP   0.013   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 439 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 5564)
  covalent geometry    : angle       0.68999 ( 7568)
  hydrogen bonds       : bond        0.05345 (  428)
  hydrogen bonds       : angle       4.10502 ( 1260)

*********************** 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
  194 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 151
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7621 (OUTLIER) cc_final: 0.7113 (m-10)
REVERT: A  307 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7620 (tpt)
REVERT: A  342 PHE cc_start: 0.7838 (t80) cc_final: 0.7416 (m-10)
REVERT: A  384 MET cc_start: 0.5415 (mpp) cc_final: 0.5125 (mpp)
REVERT: A  393 ILE cc_start: 0.8482 (mm) cc_final: 0.8056 (mt)
REVERT: A  397 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7623 (mp0)
REVERT: A  445 LYS cc_start: 0.8305 (tptm) cc_final: 0.7808 (tptm)
REVERT: A  449 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8808 (mp)
REVERT: A  538 PHE cc_start: 0.8674 (t80) cc_final: 0.8270 (t80)
REVERT: A  581 LEU cc_start: 0.9015 (mt) cc_final: 0.8629 (tt)
REVERT: B   42 MET cc_start: 0.8732 (tpt) cc_final: 0.8237 (tpp)
REVERT: B  242 TRP cc_start: 0.7722 (OUTLIER) cc_final: 0.6872 (t60)
REVERT: B  397 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8470 (mm-30)
REVERT: B  454 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8124 (ttpt)
REVERT: B  516 LYS cc_start: 0.7298 (mttt) cc_final: 0.6761 (mmtt)
  outliers start: 43
  outliers final: 30
  residues processed: 181
  average time/residue: 0.0584
  time to fit residues: 14.3760
Evaluate side-chains
  176 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
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  240 LEU
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  486 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  509 THR
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  577 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  577 LEU
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 13 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.151499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.119121 restraints weight = 9309.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121260 restraints weight = 6429.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.122289 restraints weight = 4655.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.123507 restraints weight = 4096.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.123640 restraints weight = 3721.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.7070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5564  Z= 0.138
  Angle     :  0.642   8.362   7568  Z= 0.325
  Chirality :  0.038   0.169    930
  Planarity :  0.004   0.027    860
  Dihedral  :  4.899  29.625    836
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 21.48 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.91 (0.34), residues: 642
  helix:  2.72 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.96 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 614 
 TYR   0.019   0.002   TYR A 438 
 PHE   0.021   0.001   PHE B 343 
 TRP   0.009   0.001   TRP A 386 
 HIS   0.002   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5564)
  covalent geometry    : angle       0.64164 ( 7568)
  hydrogen bonds       : bond        0.04534 (  428)
  hydrogen bonds       : angle       3.92907 ( 1260)

*********************** 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
  193 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 152
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7638 (OUTLIER) cc_final: 0.7135 (m-10)
REVERT: A  307 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7647 (tpt)
REVERT: A  342 PHE cc_start: 0.7755 (t80) cc_final: 0.7399 (m-10)
REVERT: A  343 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7867 (t80)
REVERT: A  384 MET cc_start: 0.5697 (mpp) cc_final: 0.5477 (mpp)
REVERT: A  393 ILE cc_start: 0.8351 (mm) cc_final: 0.7939 (mt)
REVERT: A  397 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7399 (mp0)
REVERT: A  445 LYS cc_start: 0.8235 (tptm) cc_final: 0.7820 (tptm)
REVERT: A  449 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8788 (mp)
REVERT: A  458 MET cc_start: 0.7759 (tpt) cc_final: 0.7341 (tpt)
REVERT: A  538 PHE cc_start: 0.8641 (t80) cc_final: 0.8412 (t80)
REVERT: A  581 LEU cc_start: 0.9026 (mt) cc_final: 0.8646 (tt)
REVERT: A  599 LEU cc_start: 0.8893 (tp) cc_final: 0.8344 (tt)
REVERT: B   42 MET cc_start: 0.8673 (tpt) cc_final: 0.8243 (tpp)
REVERT: B  242 TRP cc_start: 0.7632 (OUTLIER) cc_final: 0.6922 (t60)
REVERT: B  354 MET cc_start: 0.7229 (ttp) cc_final: 0.6807 (tmm)
REVERT: B  397 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8451 (mm-30)
REVERT: B  419 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7093 (p0)
REVERT: B  438 TYR cc_start: 0.7924 (m-80) cc_final: 0.7697 (m-10)
REVERT: B  454 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8236 (ttmt)
REVERT: B  516 LYS cc_start: 0.7408 (mttt) cc_final: 0.6916 (mmtt)
  outliers start: 41
  outliers final: 28
  residues processed: 177
  average time/residue: 0.0522
  time to fit residues: 12.8290
Evaluate side-chains
  176 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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  343 PHE
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  488 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 A residue  573 ILE
Chi-restraints excluded: chain A residue  588 SER
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  459 ILE
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
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 44 optimal weight:    0.0370
   chunk 34 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.1462

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.150755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.117562 restraints weight = 9466.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.119355 restraints weight = 6855.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121308 restraints weight = 4989.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.121183 restraints weight = 4298.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121305 restraints weight = 4086.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.7319

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= 0.148
  Angle     :  0.651   7.606   7568  Z= 0.330
  Chirality :  0.038   0.201    930
  Planarity :  0.004   0.027    860
  Dihedral  :  5.066  30.236    836
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 21.81 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.93 (0.34), residues: 642
  helix:  2.72 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.87 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 614 
 TYR   0.018   0.002   TYR B 351 
 PHE   0.023   0.001   PHE B 342 
 TRP   0.014   0.001   TRP B 386 
 HIS   0.002   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5564)
  covalent geometry    : angle       0.65068 ( 7568)
  hydrogen bonds       : bond        0.04677 (  428)
  hydrogen bonds       : angle       3.96004 ( 1260)

*********************** 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
  191 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7679 (OUTLIER) cc_final: 0.7153 (m-10)
REVERT: A  307 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7660 (tpt)
REVERT: A  342 PHE cc_start: 0.7794 (t80) cc_final: 0.7363 (m-10)
REVERT: A  343 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7877 (t80)
REVERT: A  393 ILE cc_start: 0.8480 (mm) cc_final: 0.8031 (mt)
REVERT: A  397 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7351 (mp0)
REVERT: A  445 LYS cc_start: 0.8211 (tptm) cc_final: 0.7850 (tptm)
REVERT: A  449 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8773 (mp)
REVERT: A  458 MET cc_start: 0.7868 (tpt) cc_final: 0.7454 (tpt)
REVERT: A  581 LEU cc_start: 0.9022 (mt) cc_final: 0.8649 (tt)
REVERT: A  599 LEU cc_start: 0.8896 (tp) cc_final: 0.8400 (tt)
REVERT: B  242 TRP cc_start: 0.7443 (OUTLIER) cc_final: 0.6755 (t60)
REVERT: B  354 MET cc_start: 0.7425 (ttp) cc_final: 0.6951 (tmm)
REVERT: B  397 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8583 (mm-30)
REVERT: B  438 TYR cc_start: 0.8071 (m-80) cc_final: 0.7742 (m-10)
REVERT: B  454 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8339 (ttmt)
REVERT: B  516 LYS cc_start: 0.7406 (mttt) cc_final: 0.6913 (mmtt)
REVERT: B  545 VAL cc_start: 0.8800 (t) cc_final: 0.8585 (p)
REVERT: B  549 CYS cc_start: 0.8751 (m) cc_final: 0.8492 (m)
  outliers start: 44
  outliers final: 32
  residues processed: 175
  average time/residue: 0.0548
  time to fit residues: 13.2993
Evaluate side-chains
  178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   22 GLU
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  335 VAL
Chi-restraints excluded: chain A residue  343 PHE
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  450 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  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  588 SER
Chi-restraints excluded: chain A residue  594 VAL
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  459 ILE
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.155578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.121794 restraints weight = 9311.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.124395 restraints weight = 6634.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.125581 restraints weight = 4670.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.126138 restraints weight = 4274.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.126440 restraints weight = 4023.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.7554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5564  Z= 0.144
  Angle     :  0.664   9.915   7568  Z= 0.329
  Chirality :  0.038   0.170    930
  Planarity :  0.004   0.026    860
  Dihedral  :  4.990  29.888    836
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  7.21 %
    Allowed  : 23.32 %
    Favored  : 69.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.97 (0.34), residues: 642
  helix:  2.75 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.88 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 418 
 TYR   0.017   0.002   TYR B 351 
 PHE   0.025   0.002   PHE A 538 
 TRP   0.015   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5564)
  covalent geometry    : angle       0.66401 ( 7568)
  hydrogen bonds       : bond        0.04514 (  428)
  hydrogen bonds       : angle       3.92082 ( 1260)

*********************** 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
  191 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 148
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 TRP cc_start: 0.7743 (OUTLIER) cc_final: 0.7168 (m-10)
REVERT: A  307 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7681 (tpt)
REVERT: A  342 PHE cc_start: 0.7788 (t80) cc_final: 0.7364 (m-10)
REVERT: A  393 ILE cc_start: 0.8489 (mm) cc_final: 0.8046 (mt)
REVERT: A  397 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7343 (mp0)
REVERT: A  445 LYS cc_start: 0.8228 (tptm) cc_final: 0.7960 (tptm)
REVERT: A  449 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8860 (mp)
REVERT: A  458 MET cc_start: 0.7845 (tpt) cc_final: 0.7457 (tpt)
REVERT: A  581 LEU cc_start: 0.9017 (mt) cc_final: 0.8641 (tt)
REVERT: A  599 LEU cc_start: 0.8897 (tp) cc_final: 0.8383 (tt)
REVERT: B  242 TRP cc_start: 0.7520 (OUTLIER) cc_final: 0.6939 (t60)
REVERT: B  354 MET cc_start: 0.7281 (ttp) cc_final: 0.6847 (tmm)
REVERT: B  397 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8527 (mm-30)
REVERT: B  438 TYR cc_start: 0.8124 (m-80) cc_final: 0.7751 (m-10)
REVERT: B  454 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8326 (ttmt)
REVERT: B  516 LYS cc_start: 0.7384 (mttt) cc_final: 0.6954 (mmtt)
REVERT: B  545 VAL cc_start: 0.8817 (t) cc_final: 0.8548 (p)
REVERT: B  549 CYS cc_start: 0.8889 (m) cc_final: 0.8584 (m)
  outliers start: 43
  outliers final: 32
  residues processed: 178
  average time/residue: 0.0539
  time to fit residues: 13.3756
Evaluate side-chains
  178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
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  450 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  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  545 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   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  353 ILE
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.151903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.119455 restraints weight = 9537.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121434 restraints weight = 6693.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122602 restraints weight = 4902.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.123663 restraints weight = 4258.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123847 restraints weight = 3953.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.7751

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= 0.133
  Angle     :  0.640   8.724   7568  Z= 0.320
  Chirality :  0.038   0.180    930
  Planarity :  0.003   0.025    860
  Dihedral  :  4.873  29.373    836
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 24.50 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.34), residues: 642
  helix:  2.78 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.84 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 418 
 TYR   0.018   0.002   TYR B 351 
 PHE   0.026   0.001   PHE B 342 
 TRP   0.010   0.001   TRP A 385 
 HIS   0.002   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5564)
  covalent geometry    : angle       0.63953 ( 7568)
  hydrogen bonds       : bond        0.04307 (  428)
  hydrogen bonds       : angle       3.89032 ( 1260)

*********************** 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
  189 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 151
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.7254 (m-10)
REVERT: A  307 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7683 (tpt)
REVERT: A  342 PHE cc_start: 0.7819 (t80) cc_final: 0.7276 (m-10)
REVERT: A  393 ILE cc_start: 0.8429 (mm) cc_final: 0.7964 (mt)
REVERT: A  397 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7391 (mp0)
REVERT: A  445 LYS cc_start: 0.8197 (tptm) cc_final: 0.7944 (tptm)
REVERT: A  449 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8849 (mp)
REVERT: A  458 MET cc_start: 0.7850 (tpt) cc_final: 0.7452 (tpt)
REVERT: A  581 LEU cc_start: 0.8965 (mt) cc_final: 0.8593 (tt)
REVERT: A  599 LEU cc_start: 0.8827 (tp) cc_final: 0.8301 (tt)
REVERT: B  397 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8553 (mm-30)
REVERT: B  438 TYR cc_start: 0.8045 (m-80) cc_final: 0.7666 (m-10)
REVERT: B  454 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8285 (ttmt)
REVERT: B  516 LYS cc_start: 0.7296 (mttt) cc_final: 0.6865 (mmtt)
REVERT: B  545 VAL cc_start: 0.8901 (t) cc_final: 0.8589 (p)
REVERT: B  549 CYS cc_start: 0.8831 (m) cc_final: 0.8497 (m)
  outliers start: 38
  outliers final: 32
  residues processed: 179
  average time/residue: 0.0535
  time to fit residues: 13.4371
Evaluate side-chains
  179 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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  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  450 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  488 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  545 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  594 VAL
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  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 38 optimal weight:    0.2980
   chunk 44 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.157868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.123310 restraints weight = 9288.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.126525 restraints weight = 5849.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.128847 restraints weight = 4468.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.130103 restraints weight = 3779.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.131175 restraints weight = 3424.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.7946

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= 0.126
  Angle     :  0.651  11.077   7568  Z= 0.321
  Chirality :  0.038   0.195    930
  Planarity :  0.003   0.026    860
  Dihedral  :  4.654  30.468    836
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 26.34 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.03 (0.34), residues: 642
  helix:  2.96 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.19 (0.53), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 418 
 TYR   0.019   0.002   TYR B 351 
 PHE   0.027   0.001   PHE B 343 
 TRP   0.009   0.001   TRP A 385 
 HIS   0.002   0.000   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5564)
  covalent geometry    : angle       0.65143 ( 7568)
  hydrogen bonds       : bond        0.04017 (  428)
  hydrogen bonds       : angle       3.82458 ( 1260)

*********************** 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
  183 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.7215 (m-10)
REVERT: A  307 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7693 (tpt)
REVERT: A  393 ILE cc_start: 0.8344 (mm) cc_final: 0.7917 (mt)
REVERT: A  397 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7345 (mp0)
REVERT: A  445 LYS cc_start: 0.8211 (tptm) cc_final: 0.7985 (tptm)
REVERT: A  458 MET cc_start: 0.7846 (tpt) cc_final: 0.7555 (tpt)
REVERT: A  538 PHE cc_start: 0.8650 (t80) cc_final: 0.8176 (t80)
REVERT: A  581 LEU cc_start: 0.8953 (mt) cc_final: 0.8574 (tt)
REVERT: A  599 LEU cc_start: 0.8693 (tp) cc_final: 0.8119 (tt)
REVERT: B  354 MET cc_start: 0.7303 (ttp) cc_final: 0.6879 (tmm)
REVERT: B  438 TYR cc_start: 0.7894 (m-80) cc_final: 0.7524 (m-10)
REVERT: B  454 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8207 (ttmt)
REVERT: B  462 TYR cc_start: 0.8587 (t80) cc_final: 0.8081 (t80)
REVERT: B  516 LYS cc_start: 0.7538 (mttt) cc_final: 0.7072 (mmtt)
REVERT: B  545 VAL cc_start: 0.8863 (t) cc_final: 0.8555 (p)
REVERT: B  549 CYS cc_start: 0.8802 (m) cc_final: 0.8489 (m)
  outliers start: 34
  outliers final: 24
  residues processed: 172
  average time/residue: 0.0523
  time to fit residues: 12.6029
Evaluate side-chains
  169 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
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  397 GLU
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  455 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  529 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
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  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.157233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.122670 restraints weight = 9310.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.125978 restraints weight = 5902.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.128180 restraints weight = 4494.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.129619 restraints weight = 3808.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.130314 restraints weight = 3433.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.8033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5564  Z= 0.133
  Angle     :  0.670  10.525   7568  Z= 0.331
  Chirality :  0.039   0.241    930
  Planarity :  0.004   0.025    860
  Dihedral  :  4.712  31.176    836
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 27.68 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.07 (0.34), residues: 642
  helix:  3.00 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.22 (0.52), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 418 
 TYR   0.020   0.001   TYR B 351 
 PHE   0.029   0.002   PHE B 342 
 TRP   0.021   0.001   TRP A 352 
 HIS   0.002   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5564)
  covalent geometry    : angle       0.66984 ( 7568)
  hydrogen bonds       : bond        0.04172 (  428)
  hydrogen bonds       : angle       3.87365 ( 1260)

********************** 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
  171 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.7187 (m-10)
REVERT: A  307 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7718 (tpt)
REVERT: A  393 ILE cc_start: 0.8444 (mm) cc_final: 0.8013 (mt)
REVERT: A  397 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7393 (mp0)
REVERT: A  458 MET cc_start: 0.7905 (tpt) cc_final: 0.7613 (tpt)
REVERT: A  501 TYR cc_start: 0.9069 (m-10) cc_final: 0.8855 (m-10)
REVERT: A  516 LYS cc_start: 0.6100 (mmtp) cc_final: 0.5639 (mmtt)
REVERT: A  538 PHE cc_start: 0.8622 (t80) cc_final: 0.8032 (t80)
REVERT: A  581 LEU cc_start: 0.8882 (mt) cc_final: 0.8549 (tt)
REVERT: A  599 LEU cc_start: 0.8787 (tp) cc_final: 0.8257 (tt)
REVERT: B  354 MET cc_start: 0.7355 (ttp) cc_final: 0.6849 (tmm)
REVERT: B  397 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8586 (mm-30)
REVERT: B  438 TYR cc_start: 0.7908 (m-80) cc_final: 0.7599 (m-10)
REVERT: B  454 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8163 (ttmt)
REVERT: B  462 TYR cc_start: 0.8573 (t80) cc_final: 0.8084 (t80)
REVERT: B  516 LYS cc_start: 0.7348 (mttt) cc_final: 0.6917 (mmtt)
REVERT: B  545 VAL cc_start: 0.8819 (t) cc_final: 0.8526 (p)
REVERT: B  549 CYS cc_start: 0.8811 (m) cc_final: 0.8468 (m)
  outliers start: 26
  outliers final: 23
  residues processed: 164
  average time/residue: 0.0516
  time to fit residues: 11.9120
Evaluate side-chains
  168 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
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  397 GLU
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
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  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 533 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.156262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122083 restraints weight = 9227.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.125359 restraints weight = 5828.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127548 restraints weight = 4425.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.128934 restraints weight = 3743.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.129519 restraints weight = 3390.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.8063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   5564  Z= 0.137
  Angle     :  0.663   9.648   7568  Z= 0.331
  Chirality :  0.039   0.250    930
  Planarity :  0.004   0.025    860
  Dihedral  :  4.711  31.168    836
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 27.35 %
    Favored  : 67.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.11 (0.34), residues: 642
  helix:  2.99 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.04 (0.56), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 418 
 TYR   0.020   0.001   TYR B 351 
 PHE   0.028   0.001   PHE A 538 
 TRP   0.017   0.001   TRP A 352 
 HIS   0.002   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5564)
  covalent geometry    : angle       0.66258 ( 7568)
  hydrogen bonds       : bond        0.04293 (  428)
  hydrogen bonds       : angle       3.89654 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 945.33 seconds
wall clock time: 16 minutes 59.99 seconds (1019.99 seconds total)