Starting phenix.real_space_refine
on Tue Mar  3 16:33:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6l47_0831/03_2026/6l47_0831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l47_0831/03_2026/6l47_0831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l47_0831/03_2026/6l47_0831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l47_0831/03_2026/6l47_0831.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6l47_0831/03_2026/6l47_0831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l47_0831/03_2026/6l47_0831.map"
  }
  resolution = 3.5
  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=   0.015 sd=   0.713
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      38      5.16       5
     C    4796      2.51       5
     N    1066      2.21       5
     O    1100      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 7000
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 416, 3444
          Classifications: {'peptide': 416}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 19, 'TRANS': 396}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 67
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 59
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 1, 'E5L': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.25, per 1000 atoms: 0.32
  Number of scatterers: 7000
  At special positions: 0
  Unit cell: (141.075, 86.735, 76.285, 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      38     16.00
     O    1100      8.00
     N    1066      7.00
     C    4796      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 365 " - pdb=" SG  CYS A 516 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 528 " - pdb=" SG  CYS A 548 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 516 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 528 " - pdb=" SG  CYS B 548 " distance=2.03

  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: 0.56
  Conformation dependent library (CDL) restraints added in 191.5 milliseconds
  

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1604

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      76.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 135 through 165
    Processing helix  chain 'A' and resid 172 through 178
    Processing helix  chain 'A' and resid 180 through 213
      Proline residue:  A 199  - end of helix
      removed outlier: 4.092A  pdb=" N   SER A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 247
      removed outlier: 3.870A  pdb=" N   GLY A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
      removed outlier: 3.637A  pdb=" N   VAL A 243 " --> pdb=" O   PRO A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 285
      removed outlier: 3.676A  pdb=" N   PHE A 254 " --> pdb=" O   PRO A 250 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      Proline residue:  A 276  - end of helix
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 3.573A  pdb=" N   TYR A 297 " --> pdb=" O   THR A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 346
      removed outlier: 3.658A  pdb=" N   PHE A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 369
    Processing helix  chain 'A' and resid 369 through 395
    Processing helix  chain 'A' and resid 412 through 419
    Processing helix  chain 'A' and resid 421 through 439
    Processing helix  chain 'A' and resid 446 through 467
      removed outlier: 4.618A  pdb=" N   LEU A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   VAL A 452 " --> pdb=" O   ALA A 448 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   CYS A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 487
    Processing helix  chain 'A' and resid 498 through 528
      removed outlier: 3.642A  pdb=" N   CYS A 528 " --> pdb=" O   ALA A 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 133
    Processing helix  chain 'B' and resid 135 through 165
    Processing helix  chain 'B' and resid 172 through 178
    Processing helix  chain 'B' and resid 180 through 213
      Proline residue:  B 199  - end of helix
      removed outlier: 4.092A  pdb=" N   SER B 213 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 247
      removed outlier: 3.870A  pdb=" N   GLY B 238 " --> pdb=" O   VAL B 234 " (cutoff:3.500A)
      Proline residue:  B 239  - end of helix
      removed outlier: 3.636A  pdb=" N   VAL B 243 " --> pdb=" O   PRO B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 285
      removed outlier: 3.675A  pdb=" N   PHE B 254 " --> pdb=" O   PRO B 250 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE B 255 " --> pdb=" O   ALA B 251 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE B 256 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
      Proline residue:  B 276  - end of helix
    Processing helix  chain 'B' and resid 293 through 301
      removed outlier: 3.573A  pdb=" N   TYR B 297 " --> pdb=" O   THR B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 346
      removed outlier: 3.658A  pdb=" N   PHE B 335 " --> pdb=" O   PHE B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 369
    Processing helix  chain 'B' and resid 369 through 395
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 421 through 439
    Processing helix  chain 'B' and resid 446 through 467
      removed outlier: 4.618A  pdb=" N   LEU B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   VAL B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   CYS B 467 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 487
    Processing helix  chain 'B' and resid 498 through 528
      removed outlier: 3.642A  pdb=" N   CYS B 528 " --> pdb=" O   ALA B 524 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1428 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1940
        1.34 -     1.46: 2208
        1.46 -     1.58: 3064
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 7272
  Sorted by residual:
  bond pdb=" C   E5L A1001 "
       pdb=" C2  E5L A1001 "
    ideal  model  delta    sigma   weight residual
    1.394  1.482 -0.088 2.00e-02 2.50e+03 1.94e+01
  bond pdb=" C   E5L B1001 "
       pdb=" C2  E5L B1001 "
    ideal  model  delta    sigma   weight residual
    1.394  1.482 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" C   E5L B1001 "
       pdb=" C1  E5L B1001 "
    ideal  model  delta    sigma   weight residual
    1.399  1.485 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C   E5L A1001 "
       pdb=" C1  E5L A1001 "
    ideal  model  delta    sigma   weight residual
    1.399  1.485 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" N   E5L A1001 "
       pdb=" C   E5L A1001 "
    ideal  model  delta    sigma   weight residual
    1.407  1.353  0.054 2.00e-02 2.50e+03 7.34e+00
  ... (remaining 7267 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 9603
        1.80 -     3.59: 249
        3.59 -     5.39: 66
        5.39 -     7.18: 14
        7.18 -     8.98: 2
  Bond angle restraints: 9934
  Sorted by residual:
  angle pdb=" C   HIS A 386 "
        pdb=" N   CYS A 387 "
        pdb=" CA  CYS A 387 "
      ideal   model   delta    sigma   weight residual
     120.68  115.11    5.57 1.70e+00 3.46e-01 1.07e+01
  angle pdb=" C   HIS B 386 "
        pdb=" N   CYS B 387 "
        pdb=" CA  CYS B 387 "
      ideal   model   delta    sigma   weight residual
     120.68  115.11    5.57 1.70e+00 3.46e-01 1.07e+01
  angle pdb=" C17 CLR B1002 "
        pdb=" C20 CLR B1002 "
        pdb=" C21 CLR B1002 "
      ideal   model   delta    sigma   weight residual
     113.17  104.19    8.98 3.00e+00 1.11e-01 8.96e+00
  angle pdb=" C17 CLR A1002 "
        pdb=" C20 CLR A1002 "
        pdb=" C21 CLR A1002 "
      ideal   model   delta    sigma   weight residual
     113.17  104.22    8.95 3.00e+00 1.11e-01 8.91e+00
  angle pdb=" N   VAL A 198 "
        pdb=" CA  VAL A 198 "
        pdb=" C   VAL A 198 "
      ideal   model   delta    sigma   weight residual
     108.88  114.15   -5.27 2.16e+00 2.14e-01 5.95e+00
  ... (remaining 9929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.43: 3675
       14.43 -    28.86: 365
       28.86 -    43.29: 102
       43.29 -    57.72: 20
       57.72 -    72.15: 4
  Dihedral angle restraints: 4166
    sinusoidal: 1680
      harmonic: 2486
  Sorted by residual:
  dihedral pdb=" CA  ARG A 309 "
           pdb=" C   ARG A 309 "
           pdb=" N   ASP A 310 "
           pdb=" CA  ASP A 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.38  -21.62     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  ARG B 309 "
           pdb=" C   ARG B 309 "
           pdb=" N   ASP B 310 "
           pdb=" CA  ASP B 310 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.40  -21.60     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  LYS A 212 "
           pdb=" C   LYS A 212 "
           pdb=" N   SER A 213 "
           pdb=" CA  SER A 213 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.15  -20.85     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 4163 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 890
       0.057 -    0.115: 164
       0.115 -    0.172: 12
       0.172 -    0.230: 2
       0.230 -    0.287: 2
  Chirality restraints: 1070
  Sorted by residual:
  chirality pdb=" C17 CLR A1002 "
            pdb=" C13 CLR A1002 "
            pdb=" C16 CLR A1002 "
            pdb=" C20 CLR A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" C17 CLR B1002 "
            pdb=" C13 CLR B1002 "
            pdb=" C16 CLR B1002 "
            pdb=" C20 CLR B1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C20 CLR A1002 "
            pdb=" C17 CLR A1002 "
            pdb=" C21 CLR A1002 "
            pdb=" C22 CLR A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.81   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1067 not shown)

  Planarity restraints: 1180
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   E5L A1001 "    0.201 2.00e-02 2.50e+03   1.26e-01 2.00e+02
        pdb=" C   E5L A1001 "   -0.158 2.00e-02 2.50e+03
        pdb=" C3  E5L A1001 "    0.045 2.00e-02 2.50e+03
        pdb=" C4  E5L A1001 "   -0.110 2.00e-02 2.50e+03
        pdb=" O3  E5L A1001 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   E5L B1001 "   -0.201 2.00e-02 2.50e+03   1.26e-01 2.00e+02
        pdb=" C   E5L B1001 "    0.157 2.00e-02 2.50e+03
        pdb=" C3  E5L B1001 "   -0.046 2.00e-02 2.50e+03
        pdb=" C4  E5L B1001 "    0.110 2.00e-02 2.50e+03
        pdb=" O3  E5L B1001 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 385 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.67e+00
        pdb=" C   LEU B 385 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LEU B 385 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   HIS B 386 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1177 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1864
        2.79 -     3.32: 6882
        3.32 -     3.85: 11886
        3.85 -     4.37: 12772
        4.37 -     4.90: 21603
  Nonbonded interactions: 55007
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 284 "
            pdb=" OG  SER B 286 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OE1 GLU A 284 "
            pdb=" OG  SER A 286 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   THR B 419 "
            pdb=" OG1 THR B 419 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   THR A 419 "
            pdb=" OG1 THR A 419 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OH  TYR B 299 "
            pdb=" O   LEU B 396 "
     model   vdw
     2.370 3.040
  ... (remaining 55002 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:             0.700
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.910
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088   7276  Z= 0.212
  Angle     :  0.763   8.981   9942  Z= 0.388
  Chirality :  0.045   0.287   1070
  Planarity :  0.008   0.126   1180
  Dihedral  : 12.692  72.148   2550
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.73 %
    Favored  : 89.27 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 10.58 %
    Favored  : 86.07 %
  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: -3.09 (0.26), residues: 820
  helix: -1.17 (0.19), residues: 586
  sheet:  None (None), residues: 0
  loop : -4.15 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 418 
 TYR   0.016   0.002   TYR A 308 
 PHE   0.020   0.002   PHE B 230 
 TRP   0.011   0.001   TRP B 407 
 HIS   0.004   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 7272)
  covalent geometry    : angle       0.76081 ( 9934)
  SS BOND              : bond        0.02212 (    4)
  SS BOND              : angle       1.97082 (    8)
  hydrogen bonds       : bond        0.12137 (  476)
  hydrogen bonds       : angle       7.08949 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 235
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7802 (ptpp)
REVERT: A  273 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: A  339 TYR cc_start: 0.8713 (m-80) cc_final: 0.8279 (m-80)
REVERT: A  342 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7278 (tm-30)
REVERT: A  371 LEU cc_start: 0.8659 (tm) cc_final: 0.7920 (mm)
REVERT: A  422 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8447 (p)
REVERT: A  426 ASP cc_start: 0.8348 (m-30) cc_final: 0.8025 (m-30)
REVERT: B  223 HIS cc_start: 0.8844 (m90) cc_final: 0.8627 (m170)
REVERT: B  273 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8215 (tm-30)
REVERT: B  339 TYR cc_start: 0.8716 (m-80) cc_final: 0.8278 (m-80)
REVERT: B  342 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7268 (tm-30)
REVERT: B  371 LEU cc_start: 0.8656 (tm) cc_final: 0.7906 (mm)
REVERT: B  422 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8440 (p)
REVERT: B  426 ASP cc_start: 0.8360 (m-30) cc_final: 0.8051 (m-30)
  outliers start: 24
  outliers final: 10
  residues processed: 251
  average time/residue: 0.0850
  time to fit residues: 28.1045
Evaluate side-chains
  177 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  548 CYS
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  548 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 460 HIS
B 460 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.123504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.102917 restraints weight = 16503.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.106321 restraints weight = 8157.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.108531 restraints weight = 5178.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.109836 restraints weight = 3837.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.111402 restraints weight = 3175.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7276  Z= 0.155
  Angle     :  0.711   8.300   9942  Z= 0.365
  Chirality :  0.042   0.163   1070
  Planarity :  0.006   0.052   1180
  Dihedral  :  7.546  47.605   1110
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.37 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 16.02 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.29), residues: 820
  helix: -0.05 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.75 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 272 
 TYR   0.033   0.002   TYR A 308 
 PHE   0.028   0.002   PHE B 270 
 TRP   0.014   0.001   TRP A 438 
 HIS   0.003   0.001   HIS B 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7272)
  covalent geometry    : angle       0.71018 ( 9934)
  SS BOND              : bond        0.00211 (    4)
  SS BOND              : angle       1.05131 (    8)
  hydrogen bonds       : bond        0.04263 (  476)
  hydrogen bonds       : angle       5.77806 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 170
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ILE cc_start: 0.8770 (pt) cc_final: 0.8438 (mt)
REVERT: A  180 LYS cc_start: 0.8046 (mttt) cc_final: 0.7627 (mtmm)
REVERT: A  201 PHE cc_start: 0.8685 (t80) cc_final: 0.8469 (t80)
REVERT: A  259 GLU cc_start: 0.8589 (tp30) cc_final: 0.8298 (tp30)
REVERT: A  260 GLN cc_start: 0.9248 (pt0) cc_final: 0.8690 (tt0)
REVERT: A  327 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8371 (m-80)
REVERT: A  342 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: A  396 LEU cc_start: 0.9531 (tp) cc_final: 0.9326 (tp)
REVERT: A  418 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7651 (ttp-110)
REVERT: A  453 PHE cc_start: 0.8320 (m-10) cc_final: 0.7930 (m-80)
REVERT: A  471 PHE cc_start: 0.7031 (p90) cc_final: 0.6318 (m-80)
REVERT: A  475 LEU cc_start: 0.8445 (tt) cc_final: 0.8217 (tt)
REVERT: B  180 LYS cc_start: 0.8041 (mttt) cc_final: 0.7626 (mtmm)
REVERT: B  201 PHE cc_start: 0.8719 (t80) cc_final: 0.8461 (t80)
REVERT: B  259 GLU cc_start: 0.8641 (tp30) cc_final: 0.8371 (tp30)
REVERT: B  327 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8366 (m-80)
REVERT: B  342 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7557 (tm-30)
REVERT: B  387 CYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8430 (p)
REVERT: B  418 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7665 (ttp-110)
REVERT: B  422 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8341 (p)
REVERT: B  426 ASP cc_start: 0.8477 (m-30) cc_final: 0.8158 (m-30)
REVERT: B  453 PHE cc_start: 0.8289 (m-10) cc_final: 0.7943 (m-80)
REVERT: B  471 PHE cc_start: 0.7036 (p90) cc_final: 0.6340 (m-80)
REVERT: B  475 LEU cc_start: 0.8412 (tt) cc_final: 0.8180 (tt)
  outliers start: 45
  outliers final: 29
  residues processed: 194
  average time/residue: 0.0692
  time to fit residues: 18.6038
Evaluate side-chains
  183 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain A residue  548 CYS
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  131 GLU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  405 LYS
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  548 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0020
   chunk 54 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.8790

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.125718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.106884 restraints weight = 15837.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.109977 restraints weight = 7660.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.112384 restraints weight = 4847.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.113945 restraints weight = 3483.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.115032 restraints weight = 2763.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7276  Z= 0.134
  Angle     :  0.652   7.302   9942  Z= 0.332
  Chirality :  0.041   0.159   1070
  Planarity :  0.006   0.048   1180
  Dihedral  :  6.818  54.902   1107
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 19.64 %
    Favored  : 75.35 %
  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: -0.91 (0.30), residues: 820
  helix:  0.37 (0.21), residues: 618
  sheet:  None (None), residues: 0
  loop : -3.65 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 262 
 TYR   0.028   0.002   TYR A 308 
 PHE   0.034   0.002   PHE B 270 
 TRP   0.015   0.001   TRP A 438 
 HIS   0.003   0.001   HIS B 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7272)
  covalent geometry    : angle       0.65178 ( 9934)
  SS BOND              : bond        0.00261 (    4)
  SS BOND              : angle       0.86625 (    8)
  hydrogen bonds       : bond        0.03917 (  476)
  hydrogen bonds       : angle       5.61639 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 181
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8771 (tt)
REVERT: A  146 ILE cc_start: 0.8509 (pt) cc_final: 0.8285 (mt)
REVERT: A  201 PHE cc_start: 0.8650 (t80) cc_final: 0.8416 (t80)
REVERT: A  327 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8252 (m-80)
REVERT: A  342 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7593 (tm-30)
REVERT: A  426 ASP cc_start: 0.8316 (m-30) cc_final: 0.8016 (m-30)
REVERT: A  462 TYR cc_start: 0.9067 (t80) cc_final: 0.8776 (t80)
REVERT: A  471 PHE cc_start: 0.7001 (p90) cc_final: 0.6679 (m-80)
REVERT: A  472 TYR cc_start: 0.8329 (t80) cc_final: 0.7731 (t80)
REVERT: B  132 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8767 (tt)
REVERT: B  180 LYS cc_start: 0.8018 (mttt) cc_final: 0.7630 (mtmm)
REVERT: B  200 TYR cc_start: 0.9040 (t80) cc_final: 0.8792 (t80)
REVERT: B  327 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8331 (m-80)
REVERT: B  342 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: B  422 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8447 (p)
REVERT: B  426 ASP cc_start: 0.8409 (m-30) cc_final: 0.8072 (m-30)
REVERT: B  462 TYR cc_start: 0.9037 (t80) cc_final: 0.8822 (t80)
REVERT: B  471 PHE cc_start: 0.7064 (p90) cc_final: 0.6425 (m-80)
REVERT: B  472 TYR cc_start: 0.8369 (t80) cc_final: 0.7773 (t80)
  outliers start: 36
  outliers final: 22
  residues processed: 201
  average time/residue: 0.0662
  time to fit residues: 18.8904
Evaluate side-chains
  174 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  514 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 78 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.108055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.088571 restraints weight = 16479.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.091834 restraints weight = 7758.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.094125 restraints weight = 4795.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.095702 restraints weight = 3447.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.096722 restraints weight = 2736.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7276  Z= 0.223
  Angle     :  0.723  10.114   9942  Z= 0.370
  Chirality :  0.044   0.182   1070
  Planarity :  0.006   0.054   1180
  Dihedral  :  6.584  46.603   1105
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.10 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  7.80 %
    Allowed  : 20.33 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.71 (0.30), residues: 820
  helix:  0.61 (0.20), residues: 616
  sheet:  None (None), residues: 0
  loop : -3.87 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 272 
 TYR   0.020   0.002   TYR B 336 
 PHE   0.029   0.002   PHE A 227 
 TRP   0.013   0.001   TRP A 438 
 HIS   0.009   0.002   HIS B 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 7272)
  covalent geometry    : angle       0.72320 ( 9934)
  SS BOND              : bond        0.00360 (    4)
  SS BOND              : angle       1.00268 (    8)
  hydrogen bonds       : bond        0.04081 (  476)
  hydrogen bonds       : angle       5.66257 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 146
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8521 (tt)
REVERT: A  180 LYS cc_start: 0.8022 (mttt) cc_final: 0.7708 (mtmm)
REVERT: A  201 PHE cc_start: 0.8777 (t80) cc_final: 0.8534 (t80)
REVERT: A  265 MET cc_start: 0.8330 (ttm) cc_final: 0.7962 (ttm)
REVERT: A  327 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8329 (m-80)
REVERT: A  342 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7642 (tm-30)
REVERT: A  402 MET cc_start: 0.8678 (ppp) cc_final: 0.7665 (ppp)
REVERT: A  418 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7695 (ttp-110)
REVERT: A  462 TYR cc_start: 0.9044 (t80) cc_final: 0.8749 (t80)
REVERT: B  132 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8511 (tt)
REVERT: B  160 ASP cc_start: 0.8651 (t0) cc_final: 0.8397 (t0)
REVERT: B  180 LYS cc_start: 0.8029 (mttt) cc_final: 0.7721 (mtmm)
REVERT: B  265 MET cc_start: 0.8363 (ttm) cc_final: 0.7994 (ttm)
REVERT: B  273 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: B  279 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9399 (tt)
REVERT: B  327 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8279 (m-80)
REVERT: B  342 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7643 (tm-30)
REVERT: B  462 TYR cc_start: 0.9034 (t80) cc_final: 0.8757 (t80)
  outliers start: 56
  outliers final: 36
  residues processed: 182
  average time/residue: 0.0635
  time to fit residues: 16.4789
Evaluate side-chains
  177 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  260 GLN
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 PHE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain B residue  514 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 73 optimal weight:    0.0170
   chunk 74 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.6024

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

Flipped N/Q/H residues before XYZ refinement:
A 415 ASN
B 415 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.120402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.102417 restraints weight = 15983.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.105698 restraints weight = 7290.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.108067 restraints weight = 4365.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.109503 restraints weight = 3019.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.110555 restraints weight = 2342.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7276  Z= 0.146
  Angle     :  0.663   8.208   9942  Z= 0.335
  Chirality :  0.042   0.187   1070
  Planarity :  0.006   0.069   1180
  Dihedral  :  6.276  48.444   1104
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 23.40 %
    Favored  : 71.31 %
  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: -0.49 (0.30), residues: 820
  helix:  0.79 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -3.83 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 272 
 TYR   0.039   0.002   TYR A 308 
 PHE   0.031   0.002   PHE B 270 
 TRP   0.014   0.001   TRP B 438 
 HIS   0.007   0.001   HIS B 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7272)
  covalent geometry    : angle       0.66257 ( 9934)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       0.91417 (    8)
  hydrogen bonds       : bond        0.03951 (  476)
  hydrogen bonds       : angle       5.57631 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8534 (tt)
REVERT: A  180 LYS cc_start: 0.8080 (mttt) cc_final: 0.7787 (mtmm)
REVERT: A  253 ARG cc_start: 0.8695 (mtt90) cc_final: 0.8477 (mmt90)
REVERT: A  259 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8222 (mp0)
REVERT: A  265 MET cc_start: 0.8339 (ttm) cc_final: 0.7871 (ttm)
REVERT: A  327 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8240 (m-80)
REVERT: A  342 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7566 (tm-30)
REVERT: A  402 MET cc_start: 0.8638 (ppp) cc_final: 0.7959 (ppp)
REVERT: A  426 ASP cc_start: 0.8286 (m-30) cc_final: 0.8056 (m-30)
REVERT: A  462 TYR cc_start: 0.9017 (t80) cc_final: 0.8780 (t80)
REVERT: A  471 PHE cc_start: 0.7199 (p90) cc_final: 0.6716 (m-80)
REVERT: B  132 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8517 (tt)
REVERT: B  180 LYS cc_start: 0.8055 (mttt) cc_final: 0.7756 (mtmm)
REVERT: B  253 ARG cc_start: 0.8675 (mtt90) cc_final: 0.8171 (mtt-85)
REVERT: B  259 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8223 (mp0)
REVERT: B  265 MET cc_start: 0.8374 (ttm) cc_final: 0.7921 (ttm)
REVERT: B  273 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: B  279 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9388 (tt)
REVERT: B  327 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8171 (m-80)
REVERT: B  342 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7569 (tm-30)
REVERT: B  471 PHE cc_start: 0.7189 (p90) cc_final: 0.6739 (m-80)
  outliers start: 38
  outliers final: 28
  residues processed: 178
  average time/residue: 0.0687
  time to fit residues: 17.0853
Evaluate side-chains
  177 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 142
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  260 GLN
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 PHE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  260 GLN
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain B residue  514 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 73 optimal weight:    0.0020
   chunk 81 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 = 0.3878 r_free = 0.3878 target = 0.125302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.107336 restraints weight = 15788.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.110768 restraints weight = 7194.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.113056 restraints weight = 4279.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.114683 restraints weight = 2993.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.115790 restraints weight = 2292.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7276  Z= 0.127
  Angle     :  0.652   9.726   9942  Z= 0.324
  Chirality :  0.041   0.159   1070
  Planarity :  0.005   0.054   1180
  Dihedral  :  6.015  50.589   1104
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 24.93 %
    Favored  : 70.89 %
  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: -0.17 (0.31), residues: 820
  helix:  0.99 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -3.65 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 262 
 TYR   0.026   0.002   TYR A 308 
 PHE   0.032   0.001   PHE B 270 
 TRP   0.014   0.001   TRP B 438 
 HIS   0.006   0.001   HIS B 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7272)
  covalent geometry    : angle       0.65175 ( 9934)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       0.77848 (    8)
  hydrogen bonds       : bond        0.03766 (  476)
  hydrogen bonds       : angle       5.40660 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8621 (tt)
REVERT: A  180 LYS cc_start: 0.8058 (mttt) cc_final: 0.7746 (mtmm)
REVERT: A  259 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8142 (mp0)
REVERT: A  265 MET cc_start: 0.8295 (ttm) cc_final: 0.7828 (ttm)
REVERT: A  283 LYS cc_start: 0.9361 (tmmt) cc_final: 0.8786 (mttt)
REVERT: A  308 TYR cc_start: 0.8062 (t80) cc_final: 0.7834 (t80)
REVERT: A  327 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8195 (m-80)
REVERT: A  335 PHE cc_start: 0.8445 (m-80) cc_final: 0.7877 (m-80)
REVERT: A  342 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: A  395 MET cc_start: 0.8102 (ttt) cc_final: 0.7890 (tmm)
REVERT: A  402 MET cc_start: 0.8414 (ppp) cc_final: 0.7784 (ppp)
REVERT: A  471 PHE cc_start: 0.7196 (p90) cc_final: 0.6765 (m-80)
REVERT: A  472 TYR cc_start: 0.7816 (t80) cc_final: 0.7381 (t80)
REVERT: B  132 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8541 (tt)
REVERT: B  180 LYS cc_start: 0.8047 (mttt) cc_final: 0.7736 (mtmm)
REVERT: B  259 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8108 (mp0)
REVERT: B  265 MET cc_start: 0.8333 (ttm) cc_final: 0.7874 (ttm)
REVERT: B  273 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: B  279 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9378 (tt)
REVERT: B  327 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8146 (m-80)
REVERT: B  342 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7560 (tm-30)
REVERT: B  395 MET cc_start: 0.8216 (ttt) cc_final: 0.7939 (tmm)
REVERT: B  471 PHE cc_start: 0.7162 (p90) cc_final: 0.6844 (m-80)
REVERT: B  472 TYR cc_start: 0.7861 (t80) cc_final: 0.7426 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 183
  average time/residue: 0.0747
  time to fit residues: 18.7643
Evaluate side-chains
  174 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 PHE
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0050
   chunk 53 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.3398

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.120587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.102539 restraints weight = 15726.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.105806 restraints weight = 7386.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.108141 restraints weight = 4508.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.109573 restraints weight = 3185.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.110562 restraints weight = 2512.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.4296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7276  Z= 0.139
  Angle     :  0.668  11.785   9942  Z= 0.332
  Chirality :  0.043   0.206   1070
  Planarity :  0.005   0.046   1180
  Dihedral  :  5.771  49.132   1102
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 24.51 %
    Favored  : 71.03 %
  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: -0.20 (0.31), residues: 820
  helix:  0.94 (0.21), residues: 618
  sheet:  None (None), residues: 0
  loop : -3.61 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 272 
 TYR   0.026   0.002   TYR A 308 
 PHE   0.029   0.001   PHE B 270 
 TRP   0.013   0.001   TRP B 438 
 HIS   0.009   0.002   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7272)
  covalent geometry    : angle       0.66794 ( 9934)
  SS BOND              : bond        0.00255 (    4)
  SS BOND              : angle       0.84972 (    8)
  hydrogen bonds       : bond        0.03733 (  476)
  hydrogen bonds       : angle       5.44639 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8585 (tt)
REVERT: A  180 LYS cc_start: 0.8097 (mttt) cc_final: 0.7821 (mtmm)
REVERT: A  259 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8211 (mp0)
REVERT: A  265 MET cc_start: 0.8316 (ttm) cc_final: 0.7866 (ttm)
REVERT: A  327 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8219 (m-80)
REVERT: A  335 PHE cc_start: 0.8415 (m-80) cc_final: 0.7844 (m-80)
REVERT: A  342 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7511 (tm-30)
REVERT: A  395 MET cc_start: 0.8200 (ttt) cc_final: 0.7952 (tmm)
REVERT: A  402 MET cc_start: 0.8470 (ppp) cc_final: 0.7922 (ppp)
REVERT: A  471 PHE cc_start: 0.7182 (p90) cc_final: 0.6781 (m-80)
REVERT: A  472 TYR cc_start: 0.7779 (t80) cc_final: 0.7380 (t80)
REVERT: B  132 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8561 (tt)
REVERT: B  265 MET cc_start: 0.8403 (ttm) cc_final: 0.7986 (ttm)
REVERT: B  273 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8040 (tm-30)
REVERT: B  279 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9390 (tt)
REVERT: B  327 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8162 (m-80)
REVERT: B  342 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: B  395 MET cc_start: 0.8249 (ttt) cc_final: 0.7965 (tmm)
REVERT: B  471 PHE cc_start: 0.7261 (p90) cc_final: 0.6829 (m-80)
REVERT: B  472 TYR cc_start: 0.7795 (t80) cc_final: 0.7336 (t80)
  outliers start: 32
  outliers final: 21
  residues processed: 175
  average time/residue: 0.0776
  time to fit residues: 18.6677
Evaluate side-chains
  169 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 PHE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  369 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 35 optimal weight:    0.4980
   chunk 81 optimal weight:    0.0170
   chunk 44 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0980
   overall best weight:    0.5220

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

Flipped N/Q/H residues before XYZ refinement:
A 526 GLN
B 526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.123098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.105226 restraints weight = 15617.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.108661 restraints weight = 7265.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.110908 restraints weight = 4369.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.112552 restraints weight = 3085.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.113512 restraints weight = 2372.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.4589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7276  Z= 0.131
  Angle     :  0.675  12.843   9942  Z= 0.334
  Chirality :  0.043   0.212   1070
  Planarity :  0.005   0.042   1180
  Dihedral  :  5.728  50.260   1102
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.49 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.14 (0.31), residues: 820
  helix:  1.03 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.63 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 139 
 TYR   0.026   0.001   TYR B 322 
 PHE   0.030   0.001   PHE A 270 
 TRP   0.018   0.001   TRP A 438 
 HIS   0.010   0.002   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7272)
  covalent geometry    : angle       0.67451 ( 9934)
  SS BOND              : bond        0.00215 (    4)
  SS BOND              : angle       0.84221 (    8)
  hydrogen bonds       : bond        0.03734 (  476)
  hydrogen bonds       : angle       5.39948 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8436 (tt)
REVERT: A  138 ILE cc_start: 0.7833 (mm) cc_final: 0.7543 (mm)
REVERT: A  180 LYS cc_start: 0.8097 (mttt) cc_final: 0.7819 (mtmm)
REVERT: A  253 ARG cc_start: 0.8340 (mmt90) cc_final: 0.8121 (mtt-85)
REVERT: A  259 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8195 (mp0)
REVERT: A  265 MET cc_start: 0.8336 (ttm) cc_final: 0.7899 (ttm)
REVERT: A  327 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8114 (m-80)
REVERT: A  335 PHE cc_start: 0.8411 (m-80) cc_final: 0.7851 (m-80)
REVERT: A  342 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7628 (tm-30)
REVERT: A  395 MET cc_start: 0.8161 (ttt) cc_final: 0.7928 (tmm)
REVERT: A  402 MET cc_start: 0.8437 (ppp) cc_final: 0.7910 (ppp)
REVERT: A  471 PHE cc_start: 0.7231 (p90) cc_final: 0.6910 (m-80)
REVERT: A  472 TYR cc_start: 0.7717 (t80) cc_final: 0.7420 (t80)
REVERT: A  484 MET cc_start: 0.6898 (ttt) cc_final: 0.6652 (ttm)
REVERT: B  132 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8489 (tt)
REVERT: B  180 LYS cc_start: 0.8077 (mttt) cc_final: 0.7797 (mtmm)
REVERT: B  265 MET cc_start: 0.8371 (ttm) cc_final: 0.7950 (ttm)
REVERT: B  273 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8104 (tm-30)
REVERT: B  279 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9391 (tt)
REVERT: B  327 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8039 (m-80)
REVERT: B  342 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: B  395 MET cc_start: 0.8255 (ttt) cc_final: 0.7993 (tmm)
REVERT: B  425 HIS cc_start: 0.7623 (t70) cc_final: 0.7375 (t-90)
REVERT: B  471 PHE cc_start: 0.7289 (p90) cc_final: 0.6899 (m-80)
REVERT: B  472 TYR cc_start: 0.7705 (t80) cc_final: 0.7413 (t80)
  outliers start: 34
  outliers final: 24
  residues processed: 181
  average time/residue: 0.0648
  time to fit residues: 16.5736
Evaluate side-chains
  183 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 PHE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  526 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0030
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.6990

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.123204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.105398 restraints weight = 15522.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.108752 restraints weight = 7202.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.111135 restraints weight = 4364.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.112595 restraints weight = 3055.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.113744 restraints weight = 2386.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7276  Z= 0.137
  Angle     :  0.689  14.163   9942  Z= 0.341
  Chirality :  0.043   0.232   1070
  Planarity :  0.005   0.041   1180
  Dihedral  :  5.463  39.963   1100
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 27.02 %
    Favored  : 68.66 %
  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: -0.16 (0.31), residues: 820
  helix:  1.02 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.62 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 139 
 TYR   0.027   0.001   TYR B 322 
 PHE   0.033   0.001   PHE A 270 
 TRP   0.013   0.001   TRP B 438 
 HIS   0.012   0.002   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7272)
  covalent geometry    : angle       0.68886 ( 9934)
  SS BOND              : bond        0.00180 (    4)
  SS BOND              : angle       0.72868 (    8)
  hydrogen bonds       : bond        0.03798 (  476)
  hydrogen bonds       : angle       5.37468 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8496 (tt)
REVERT: A  138 ILE cc_start: 0.7791 (mm) cc_final: 0.7492 (mm)
REVERT: A  180 LYS cc_start: 0.8156 (mttt) cc_final: 0.7866 (mtmm)
REVERT: A  259 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8134 (mp0)
REVERT: A  265 MET cc_start: 0.8322 (ttm) cc_final: 0.7898 (ttm)
REVERT: A  327 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8151 (m-80)
REVERT: A  335 PHE cc_start: 0.8406 (m-80) cc_final: 0.7871 (m-80)
REVERT: A  342 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7583 (tm-30)
REVERT: A  395 MET cc_start: 0.8152 (ttt) cc_final: 0.7919 (tmm)
REVERT: A  402 MET cc_start: 0.8437 (ppp) cc_final: 0.7957 (ppp)
REVERT: A  471 PHE cc_start: 0.7190 (p90) cc_final: 0.6932 (m-80)
REVERT: A  472 TYR cc_start: 0.7671 (t80) cc_final: 0.7428 (t80)
REVERT: A  484 MET cc_start: 0.6843 (ttt) cc_final: 0.6586 (ttm)
REVERT: B  132 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8602 (tt)
REVERT: B  180 LYS cc_start: 0.8129 (mttt) cc_final: 0.7846 (mtmm)
REVERT: B  265 MET cc_start: 0.8362 (ttm) cc_final: 0.7928 (ttm)
REVERT: B  273 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: B  279 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9339 (tt)
REVERT: B  327 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8079 (m-80)
REVERT: B  342 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: B  395 MET cc_start: 0.8246 (ttt) cc_final: 0.7979 (tmm)
REVERT: B  402 MET cc_start: 0.8239 (ppp) cc_final: 0.7567 (ppp)
REVERT: B  422 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8569 (p)
REVERT: B  425 HIS cc_start: 0.7651 (t70) cc_final: 0.7426 (t-90)
REVERT: B  471 PHE cc_start: 0.7210 (p90) cc_final: 0.6915 (m-80)
REVERT: B  472 TYR cc_start: 0.7658 (t80) cc_final: 0.7384 (t80)
REVERT: B  484 MET cc_start: 0.6898 (ttt) cc_final: 0.6632 (ttm)
  outliers start: 31
  outliers final: 22
  residues processed: 176
  average time/residue: 0.0682
  time to fit residues: 16.7524
Evaluate side-chains
  176 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 PHE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 4 optimal weight:    0.3980
   chunk 41 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 526 GLN
B 526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.124628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.106668 restraints weight = 15483.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.110177 restraints weight = 7219.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.112525 restraints weight = 4349.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.114031 restraints weight = 3048.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.115183 restraints weight = 2378.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.4918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7276  Z= 0.134
  Angle     :  0.700  14.546   9942  Z= 0.341
  Chirality :  0.043   0.238   1070
  Planarity :  0.005   0.044   1180
  Dihedral  :  5.392  38.979   1100
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 27.72 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.31), residues: 820
  helix:  1.04 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.61 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 253 
 TYR   0.025   0.001   TYR B 322 
 PHE   0.032   0.001   PHE A 270 
 TRP   0.014   0.001   TRP B 438 
 HIS   0.012   0.002   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7272)
  covalent geometry    : angle       0.69995 ( 9934)
  SS BOND              : bond        0.00168 (    4)
  SS BOND              : angle       0.70729 (    8)
  hydrogen bonds       : bond        0.03692 (  476)
  hydrogen bonds       : angle       5.32144 ( 1428)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8415 (tt)
REVERT: A  138 ILE cc_start: 0.7621 (mm) cc_final: 0.7322 (mm)
REVERT: A  180 LYS cc_start: 0.8157 (mttt) cc_final: 0.7875 (mtmm)
REVERT: A  265 MET cc_start: 0.8302 (ttm) cc_final: 0.7841 (ttm)
REVERT: A  327 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.8072 (m-80)
REVERT: A  335 PHE cc_start: 0.8363 (m-80) cc_final: 0.7804 (m-80)
REVERT: A  342 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: A  395 MET cc_start: 0.8235 (ttt) cc_final: 0.7921 (tmm)
REVERT: A  402 MET cc_start: 0.8454 (ppp) cc_final: 0.8005 (ppp)
REVERT: A  471 PHE cc_start: 0.7244 (p90) cc_final: 0.6922 (m-80)
REVERT: A  484 MET cc_start: 0.6886 (ttt) cc_final: 0.6627 (ttm)
REVERT: B  132 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8512 (tt)
REVERT: B  180 LYS cc_start: 0.8143 (mttt) cc_final: 0.7875 (mtmm)
REVERT: B  260 GLN cc_start: 0.9440 (pt0) cc_final: 0.8908 (tt0)
REVERT: B  265 MET cc_start: 0.8408 (ttm) cc_final: 0.7984 (ttm)
REVERT: B  273 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: B  279 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9367 (tt)
REVERT: B  327 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7980 (m-80)
REVERT: B  342 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: B  395 MET cc_start: 0.8295 (ttt) cc_final: 0.7968 (tmm)
REVERT: B  402 MET cc_start: 0.8220 (ppp) cc_final: 0.7591 (ppp)
REVERT: B  425 HIS cc_start: 0.7367 (t70) cc_final: 0.7122 (t-90)
REVERT: B  471 PHE cc_start: 0.7239 (p90) cc_final: 0.6918 (m-80)
REVERT: B  472 TYR cc_start: 0.7466 (t80) cc_final: 0.7220 (t80)
REVERT: B  484 MET cc_start: 0.6957 (ttt) cc_final: 0.6664 (ttm)
  outliers start: 28
  outliers final: 20
  residues processed: 171
  average time/residue: 0.0719
  time to fit residues: 17.2387
Evaluate side-chains
  173 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 PHE
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  526 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 57 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 526 GLN
B 390 ASN
B 526 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.124785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.107004 restraints weight = 15583.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.110505 restraints weight = 7206.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.112899 restraints weight = 4324.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.114458 restraints weight = 3021.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.115536 restraints weight = 2331.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.4930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.149   7276  Z= 0.266
  Angle     :  1.393  59.198   9942  Z= 0.786
  Chirality :  0.055   0.645   1070
  Planarity :  0.005   0.041   1180
  Dihedral  :  5.201  36.207   1096
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 28.69 %
    Favored  : 67.83 %
  Cbeta Deviations :  0.25 %
  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: -0.16 (0.31), residues: 820
  helix:  1.02 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.61 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 253 
 TYR   0.045   0.002   TYR A 308 
 PHE   0.029   0.001   PHE A 270 
 TRP   0.012   0.001   TRP B 438 
 HIS   0.010   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 ( 7272)
  covalent geometry    : angle       1.39342 ( 9934)
  SS BOND              : bond        0.00160 (    4)
  SS BOND              : angle       0.72087 (    8)
  hydrogen bonds       : bond        0.03745 (  476)
  hydrogen bonds       : angle       5.31911 ( 1428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1140.67 seconds
wall clock time: 20 minutes 22.31 seconds (1222.31 seconds total)