Starting phenix.real_space_refine
on Fri Jul 25 05:03:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6l47_0831/07_2025/6l47_0831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l47_0831/07_2025/6l47_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6l47_0831/07_2025/6l47_0831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l47_0831/07_2025/6l47_0831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l47_0831/07_2025/6l47_0831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l47_0831/07_2025/6l47_0831.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.015 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 2, 'ARG:plan': 5, '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: 6.00, per 1000 atoms: 0.86
  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: 1.77
  Conformation dependent library (CDL) restraints added in 849.0 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: 0.54
  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: 1.48

  Time building geometry restraints manager: 2.04 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: 0.04
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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.940
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.830
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (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
 TRP   0.011   0.001   TRP B 407 
 HIS   0.004   0.001   HIS A 425 
 PHE   0.020   0.002   PHE B 230 
 TYR   0.016   0.002   TYR A 308 
 ARG   0.003   0.000   ARG B 418 

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

*********************** 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  : 0.778 
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: 0.8712 (m-80) cc_final: 0.8279 (m-80)
REVERT: A  342 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7277 (tm-30)
REVERT: A  371 LEU cc_start: 0.8659 (tm) cc_final: 0.7921 (mm)
REVERT: A  422 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8447 (p)
REVERT: A  426 ASP cc_start: 0.8349 (m-30) cc_final: 0.8024 (m-30)
REVERT: B  223 HIS cc_start: 0.8844 (m90) cc_final: 0.8626 (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: 0.7267 (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: 0.8359 (m-30) cc_final: 0.8051 (m-30)
  outliers start: 24
  outliers final: 10
  residues processed: 251
  average time/residue: 0.2125
  time to fit residues: 69.4678
Evaluate side-chains
  178 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 166
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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 69 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0670
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.6126

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.119897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.099759 restraints weight = 16374.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.103003 restraints weight = 8184.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.105086 restraints weight = 5249.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7276  Z= 0.161
  Angle     :  0.713   8.361   9942  Z= 0.367
  Chirality :  0.042   0.164   1070
  Planarity :  0.006   0.053   1180
  Dihedral  :  7.563  47.916   1110
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 16.16 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.29), residues: 820
  helix: -0.02 (0.20), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.73 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 438 
 HIS   0.003   0.001   HIS B 425 
 PHE   0.028   0.002   PHE B 270 
 TYR   0.034   0.002   TYR A 308 
 ARG   0.008   0.001   ARG B 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04277 (  476)
  hydrogen bonds       : angle       5.78794 ( 1428)
  SS BOND              : bond        0.00277 (    4)
  SS BOND              : angle       1.06347 (    8)
  covalent geometry    : bond        0.00356 ( 7272)
  covalent geometry    : angle       0.71241 ( 9934)

*********************** 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
  211 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 166
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 LYS cc_start: 0.8017 (mttt) cc_final: 0.7589 (mtmm)
REVERT: A  201 PHE cc_start: 0.8714 (t80) cc_final: 0.8498 (t80)
REVERT: A  259 GLU cc_start: 0.8620 (tp30) cc_final: 0.8320 (tp30)
REVERT: A  260 GLN cc_start: 0.9256 (pt0) cc_final: 0.8695 (tt0)
REVERT: A  327 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8363 (m-80)
REVERT: A  342 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: A  396 LEU cc_start: 0.9561 (tp) cc_final: 0.9336 (tp)
REVERT: A  418 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7622 (ttp-110)
REVERT: A  453 PHE cc_start: 0.8373 (m-10) cc_final: 0.7991 (m-80)
REVERT: A  471 PHE cc_start: 0.7184 (p90) cc_final: 0.6344 (m-80)
REVERT: A  475 LEU cc_start: 0.8355 (tt) cc_final: 0.8134 (tt)
REVERT: A  503 MET cc_start: 0.8967 (ttp) cc_final: 0.8749 (ttp)
REVERT: B  180 LYS cc_start: 0.8015 (mttt) cc_final: 0.7591 (mtmm)
REVERT: B  201 PHE cc_start: 0.8749 (t80) cc_final: 0.8493 (t80)
REVERT: B  259 GLU cc_start: 0.8660 (tp30) cc_final: 0.8388 (tp30)
REVERT: B  327 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8292 (m-80)
REVERT: B  342 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: B  387 CYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8436 (p)
REVERT: B  396 LEU cc_start: 0.9556 (tp) cc_final: 0.9343 (tp)
REVERT: B  422 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8368 (p)
REVERT: B  426 ASP cc_start: 0.8498 (m-30) cc_final: 0.8180 (m-30)
REVERT: B  453 PHE cc_start: 0.8363 (m-10) cc_final: 0.8013 (m-80)
REVERT: B  471 PHE cc_start: 0.7178 (p90) cc_final: 0.6367 (m-80)
REVERT: B  503 MET cc_start: 0.8974 (ttp) cc_final: 0.8754 (ttp)
  outliers start: 45
  outliers final: 30
  residues processed: 191
  average time/residue: 0.1711
  time to fit residues: 44.2805
Evaluate side-chains
  184 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 150
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  131 GLU
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  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  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 62 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 59 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0030
   overall best weight:    0.7998

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.126074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.107242 restraints weight = 16116.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.110439 restraints weight = 7670.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.112751 restraints weight = 4781.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2968

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= 0.132
  Angle     :  0.646   7.307   9942  Z= 0.329
  Chirality :  0.040   0.155   1070
  Planarity :  0.005   0.045   1180
  Dihedral  :  6.800  55.096   1107
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 19.22 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.30), residues: 820
  helix:  0.37 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -3.47 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 438 
 HIS   0.003   0.001   HIS B 223 
 PHE   0.035   0.002   PHE B 270 
 TYR   0.025   0.002   TYR A 308 
 ARG   0.005   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  476)
  hydrogen bonds       : angle       5.60608 ( 1428)
  SS BOND              : bond        0.00244 (    4)
  SS BOND              : angle       0.83197 (    8)
  covalent geometry    : bond        0.00281 ( 7272)
  covalent geometry    : angle       0.64542 ( 9934)

*********************** 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
  224 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 182
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 PHE cc_start: 0.8697 (t80) cc_final: 0.8459 (t80)
REVERT: A  327 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8192 (m-80)
REVERT: A  342 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: A  426 ASP cc_start: 0.8341 (m-30) cc_final: 0.8024 (m-30)
REVERT: A  462 TYR cc_start: 0.9052 (t80) cc_final: 0.8762 (t80)
REVERT: A  472 TYR cc_start: 0.8373 (t80) cc_final: 0.7774 (t80)
REVERT: B  200 TYR cc_start: 0.9066 (t80) cc_final: 0.8844 (t80)
REVERT: B  306 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8847 (tp)
REVERT: B  327 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8237 (m-80)
REVERT: B  342 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7595 (tm-30)
REVERT: B  422 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8431 (p)
REVERT: B  426 ASP cc_start: 0.8453 (m-30) cc_final: 0.8112 (m-30)
REVERT: B  462 TYR cc_start: 0.9052 (t80) cc_final: 0.8820 (t80)
REVERT: B  471 PHE cc_start: 0.7262 (p90) cc_final: 0.6399 (m-80)
REVERT: B  472 TYR cc_start: 0.8411 (t80) cc_final: 0.7780 (t80)
  outliers start: 42
  outliers final: 23
  residues processed: 202
  average time/residue: 0.1554
  time to fit residues: 43.4911
Evaluate side-chains
  173 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
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  467 CYS
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
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  306 LEU
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  369 SER
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  467 CYS
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 63 optimal weight:    8.9990
   chunk 60 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
B 205 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.119974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.102015 restraints weight = 15995.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.105341 restraints weight = 7316.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.107641 restraints weight = 4391.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7276  Z= 0.155
  Angle     :  0.681   9.819   9942  Z= 0.342
  Chirality :  0.042   0.172   1070
  Planarity :  0.006   0.055   1180
  Dihedral  :  6.330  47.716   1105
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.24 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 20.61 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.30), residues: 820
  helix:  0.63 (0.20), residues: 614
  sheet:  None (None), residues: 0
  loop : -3.87 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 438 
 HIS   0.008   0.001   HIS B 425 
 PHE   0.029   0.001   PHE B 270 
 TYR   0.028   0.002   TYR B 308 
 ARG   0.004   0.001   ARG B 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  476)
  hydrogen bonds       : angle       5.56962 ( 1428)
  SS BOND              : bond        0.00387 (    4)
  SS BOND              : angle       0.82769 (    8)
  covalent geometry    : bond        0.00342 ( 7272)
  covalent geometry    : angle       0.68119 ( 9934)

*********************** 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
  196 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 151
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 LYS cc_start: 0.8011 (mttt) cc_final: 0.7658 (mtmm)
REVERT: A  201 PHE cc_start: 0.8772 (t80) cc_final: 0.8517 (t80)
REVERT: A  265 MET cc_start: 0.8252 (ttm) cc_final: 0.7813 (ttm)
REVERT: A  306 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8869 (tp)
REVERT: A  327 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8157 (m-80)
REVERT: A  342 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: A  402 MET cc_start: 0.8502 (ppp) cc_final: 0.7617 (ppp)
REVERT: A  418 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7713 (ttp-110)
REVERT: A  426 ASP cc_start: 0.8459 (m-30) cc_final: 0.8194 (m-30)
REVERT: A  462 TYR cc_start: 0.9017 (t80) cc_final: 0.8772 (t80)
REVERT: A  471 PHE cc_start: 0.7532 (p90) cc_final: 0.6812 (m-80)
REVERT: B  180 LYS cc_start: 0.7995 (mttt) cc_final: 0.7642 (mtmm)
REVERT: B  265 MET cc_start: 0.8284 (ttm) cc_final: 0.7940 (ttm)
REVERT: B  273 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7668 (tm-30)
REVERT: B  327 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8153 (m-80)
REVERT: B  342 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: B  422 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8451 (p)
REVERT: B  426 ASP cc_start: 0.8530 (m-30) cc_final: 0.8233 (m-30)
REVERT: B  462 TYR cc_start: 0.8997 (t80) cc_final: 0.8771 (t80)
REVERT: B  471 PHE cc_start: 0.7549 (p90) cc_final: 0.6802 (m-80)
  outliers start: 45
  outliers final: 27
  residues processed: 179
  average time/residue: 0.1645
  time to fit residues: 40.1704
Evaluate side-chains
  171 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  146 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  230 PHE
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  306 LEU
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  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  146 ILE
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  230 PHE
Chi-restraints excluded: chain B residue  255 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  422 VAL
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 80 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.121431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.103571 restraints weight = 15773.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.106832 restraints weight = 7217.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.109218 restraints weight = 4343.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7276  Z= 0.147
  Angle     :  0.672   8.796   9942  Z= 0.337
  Chirality :  0.043   0.184   1070
  Planarity :  0.005   0.041   1180
  Dihedral  :  6.241  48.430   1105
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.63 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 21.59 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.30), residues: 820
  helix:  0.76 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -3.77 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 438 
 HIS   0.007   0.001   HIS B 425 
 PHE   0.029   0.001   PHE B 270 
 TYR   0.017   0.002   TYR B 322 
 ARG   0.006   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03836 (  476)
  hydrogen bonds       : angle       5.58722 ( 1428)
  SS BOND              : bond        0.00262 (    4)
  SS BOND              : angle       0.85798 (    8)
  covalent geometry    : bond        0.00327 ( 7272)
  covalent geometry    : angle       0.67169 ( 9934)

*********************** 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
  187 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 LYS cc_start: 0.8053 (mttt) cc_final: 0.7654 (mtmm)
REVERT: A  265 MET cc_start: 0.8251 (ttm) cc_final: 0.7759 (ttm)
REVERT: A  327 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8173 (m-80)
REVERT: A  342 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7600 (tm-30)
REVERT: A  402 MET cc_start: 0.8607 (ppp) cc_final: 0.7630 (ppp)
REVERT: A  418 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7481 (mtm-85)
REVERT: A  422 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8280 (p)
REVERT: A  426 ASP cc_start: 0.8386 (m-30) cc_final: 0.8048 (m-30)
REVERT: A  471 PHE cc_start: 0.7398 (p90) cc_final: 0.6757 (m-80)
REVERT: B  180 LYS cc_start: 0.8055 (mttt) cc_final: 0.7623 (mtmm)
REVERT: B  259 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8278 (mp0)
REVERT: B  265 MET cc_start: 0.8308 (ttm) cc_final: 0.7841 (ttm)
REVERT: B  273 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: B  327 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8153 (m-80)
REVERT: B  342 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: B  422 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8511 (p)
REVERT: B  426 ASP cc_start: 0.8466 (m-30) cc_final: 0.8182 (m-30)
REVERT: B  471 PHE cc_start: 0.7402 (p90) cc_final: 0.6712 (m-80)
  outliers start: 38
  outliers final: 27
  residues processed: 176
  average time/residue: 0.1711
  time to fit residues: 41.2567
Evaluate side-chains
  172 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
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  230 PHE
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  260 GLN
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  422 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
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  255 ILE
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  260 GLN
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  422 VAL
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 33 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 76 optimal weight:    0.4980
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.8988

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.117082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.098395 restraints weight = 15855.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.101684 restraints weight = 7459.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.103956 restraints weight = 4600.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3950

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= 0.156
  Angle     :  0.679   9.575   9942  Z= 0.340
  Chirality :  0.043   0.199   1070
  Planarity :  0.005   0.040   1180
  Dihedral  :  6.252  48.179   1105
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.37 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 22.28 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.30), residues: 820
  helix:  0.82 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -3.79 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 438 
 HIS   0.008   0.001   HIS B 223 
 PHE   0.030   0.001   PHE B 270 
 TYR   0.020   0.002   TYR B 322 
 ARG   0.004   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  476)
  hydrogen bonds       : angle       5.57189 ( 1428)
  SS BOND              : bond        0.00281 (    4)
  SS BOND              : angle       0.90369 (    8)
  covalent geometry    : bond        0.00349 ( 7272)
  covalent geometry    : angle       0.67911 ( 9934)

*********************** 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
  187 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 146
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 LYS cc_start: 0.8096 (mttt) cc_final: 0.7708 (mtmm)
REVERT: A  253 ARG cc_start: 0.8730 (mtt90) cc_final: 0.8509 (mmt90)
REVERT: A  259 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8181 (mp0)
REVERT: A  265 MET cc_start: 0.8343 (ttm) cc_final: 0.7811 (ttm)
REVERT: A  306 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8955 (tp)
REVERT: A  327 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8320 (m-80)
REVERT: A  342 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7545 (tm-30)
REVERT: A  395 MET cc_start: 0.8225 (ttt) cc_final: 0.7973 (tmm)
REVERT: A  402 MET cc_start: 0.8660 (ppp) cc_final: 0.7728 (ppp)
REVERT: A  418 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7583 (mtm-85)
REVERT: A  422 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8350 (p)
REVERT: A  426 ASP cc_start: 0.8297 (m-30) cc_final: 0.7954 (m-30)
REVERT: A  471 PHE cc_start: 0.7382 (p90) cc_final: 0.6759 (m-80)
REVERT: A  472 TYR cc_start: 0.8036 (t80) cc_final: 0.7736 (t80)
REVERT: B  180 LYS cc_start: 0.8067 (mttt) cc_final: 0.7688 (mtmm)
REVERT: B  253 ARG cc_start: 0.8703 (mtt90) cc_final: 0.8495 (mmt90)
REVERT: B  259 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8194 (mp0)
REVERT: B  265 MET cc_start: 0.8365 (ttm) cc_final: 0.7940 (ttm)
REVERT: B  273 GLU cc_start: 0.8624 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: B  327 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8288 (m-80)
REVERT: B  342 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7622 (tm-30)
REVERT: B  395 MET cc_start: 0.8263 (ttt) cc_final: 0.7984 (tmm)
REVERT: B  402 MET cc_start: 0.8441 (ppp) cc_final: 0.7688 (ppp)
REVERT: B  422 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8622 (p)
REVERT: B  426 ASP cc_start: 0.8354 (m-30) cc_final: 0.8105 (m-30)
REVERT: B  471 PHE cc_start: 0.7338 (p90) cc_final: 0.6745 (m-80)
REVERT: B  472 TYR cc_start: 0.8046 (t80) cc_final: 0.7717 (t80)
  outliers start: 41
  outliers final: 32
  residues processed: 171
  average time/residue: 0.1806
  time to fit residues: 41.4756
Evaluate side-chains
  177 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 138
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  174 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  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
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  422 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  174 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  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  422 VAL
Chi-restraints excluded: chain B residue  514 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
A 415 ASN
B 415 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.118863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.100675 restraints weight = 15908.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.104033 restraints weight = 7284.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.106058 restraints weight = 4366.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7276  Z= 0.167
  Angle     :  0.689  10.978   9942  Z= 0.344
  Chirality :  0.045   0.248   1070
  Planarity :  0.005   0.039   1180
  Dihedral  :  6.322  47.417   1105
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 22.70 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.30), residues: 820
  helix:  0.86 (0.21), residues: 618
  sheet:  None (None), residues: 0
  loop : -3.81 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 438 
 HIS   0.008   0.002   HIS B 223 
 PHE   0.031   0.001   PHE B 270 
 TYR   0.022   0.002   TYR A 308 
 ARG   0.004   0.000   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03912 (  476)
  hydrogen bonds       : angle       5.58828 ( 1428)
  SS BOND              : bond        0.00290 (    4)
  SS BOND              : angle       0.93065 (    8)
  covalent geometry    : bond        0.00377 ( 7272)
  covalent geometry    : angle       0.68852 ( 9934)

*********************** 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
  198 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 152
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 LYS cc_start: 0.8090 (mttt) cc_final: 0.7731 (mtmm)
REVERT: A  253 ARG cc_start: 0.8744 (mtt90) cc_final: 0.8167 (mtt-85)
REVERT: A  259 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8115 (mp0)
REVERT: A  265 MET cc_start: 0.8357 (ttm) cc_final: 0.7842 (ttm)
REVERT: A  306 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8899 (tp)
REVERT: A  327 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8365 (m-80)
REVERT: A  342 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7623 (tm-30)
REVERT: A  395 MET cc_start: 0.8222 (ttt) cc_final: 0.7978 (tmm)
REVERT: A  402 MET cc_start: 0.8738 (ppp) cc_final: 0.8048 (ppp)
REVERT: A  422 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8285 (p)
REVERT: A  426 ASP cc_start: 0.8317 (m-30) cc_final: 0.7959 (m-30)
REVERT: A  471 PHE cc_start: 0.7377 (p90) cc_final: 0.6687 (m-80)
REVERT: A  472 TYR cc_start: 0.8016 (t80) cc_final: 0.7607 (t80)
REVERT: B  180 LYS cc_start: 0.8064 (mttt) cc_final: 0.7677 (mtmm)
REVERT: B  253 ARG cc_start: 0.8730 (mtt90) cc_final: 0.8496 (mmt90)
REVERT: B  259 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8255 (mp0)
REVERT: B  265 MET cc_start: 0.8375 (ttm) cc_final: 0.7980 (ttm)
REVERT: B  273 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: B  327 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8329 (m-80)
REVERT: B  342 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7594 (tm-30)
REVERT: B  395 MET cc_start: 0.8247 (ttt) cc_final: 0.7989 (tmm)
REVERT: B  402 MET cc_start: 0.8504 (ppp) cc_final: 0.7784 (ppp)
REVERT: B  422 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8545 (p)
REVERT: B  426 ASP cc_start: 0.8371 (m-30) cc_final: 0.8089 (m-30)
REVERT: B  471 PHE cc_start: 0.7301 (p90) cc_final: 0.6686 (m-80)
REVERT: B  472 TYR cc_start: 0.7939 (t80) cc_final: 0.7508 (t80)
  outliers start: 46
  outliers final: 34
  residues processed: 180
  average time/residue: 0.1891
  time to fit residues: 45.6519
Evaluate side-chains
  185 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  174 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  306 LEU
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  422 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  174 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  301 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  422 VAL
Chi-restraints excluded: chain B residue  514 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0020
   chunk 40 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.5792

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.120156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.102025 restraints weight = 15557.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.105375 restraints weight = 7186.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.107640 restraints weight = 4350.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.4393

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= 0.137
  Angle     :  0.698  12.800   9942  Z= 0.339
  Chirality :  0.043   0.227   1070
  Planarity :  0.005   0.041   1180
  Dihedral  :  6.368  49.678   1105
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 24.93 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.31), residues: 820
  helix:  0.95 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -3.69 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 438 
 HIS   0.010   0.001   HIS A 223 
 PHE   0.029   0.001   PHE B 270 
 TYR   0.032   0.002   TYR A 336 
 ARG   0.008   0.000   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  476)
  hydrogen bonds       : angle       5.54629 ( 1428)
  SS BOND              : bond        0.00183 (    4)
  SS BOND              : angle       0.75474 (    8)
  covalent geometry    : bond        0.00299 ( 7272)
  covalent geometry    : angle       0.69790 ( 9934)

*********************** 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
  198 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8137 (mp0)
REVERT: A  265 MET cc_start: 0.8257 (ttm) cc_final: 0.7688 (ttm)
REVERT: A  306 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8808 (tp)
REVERT: A  327 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8293 (m-80)
REVERT: A  342 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: A  395 MET cc_start: 0.8188 (ttt) cc_final: 0.7967 (tmm)
REVERT: A  402 MET cc_start: 0.8649 (ppp) cc_final: 0.7934 (ppp)
REVERT: A  422 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8103 (p)
REVERT: A  426 ASP cc_start: 0.8286 (m-30) cc_final: 0.7978 (m-30)
REVERT: A  471 PHE cc_start: 0.7448 (p90) cc_final: 0.6913 (m-80)
REVERT: A  472 TYR cc_start: 0.7775 (t80) cc_final: 0.7347 (t80)
REVERT: B  259 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8283 (mp0)
REVERT: B  265 MET cc_start: 0.8339 (ttm) cc_final: 0.7933 (ttm)
REVERT: B  273 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: B  327 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8213 (m-80)
REVERT: B  342 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7579 (tm-30)
REVERT: B  390 ASN cc_start: 0.8166 (m-40) cc_final: 0.7858 (m-40)
REVERT: B  395 MET cc_start: 0.8231 (ttt) cc_final: 0.7956 (tmm)
REVERT: B  402 MET cc_start: 0.8363 (ppp) cc_final: 0.7685 (ppp)
REVERT: B  422 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8457 (p)
REVERT: B  426 ASP cc_start: 0.8323 (m-30) cc_final: 0.8008 (m-30)
REVERT: B  471 PHE cc_start: 0.7410 (p90) cc_final: 0.6839 (m-80)
REVERT: B  472 TYR cc_start: 0.7860 (t80) cc_final: 0.7484 (t80)
REVERT: B  484 MET cc_start: 0.6820 (ttt) cc_final: 0.6576 (ttm)
  outliers start: 36
  outliers final: 29
  residues processed: 180
  average time/residue: 0.1970
  time to fit residues: 47.3150
Evaluate side-chains
  185 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 149
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  174 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  259 GLU
Chi-restraints excluded: chain A residue  260 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
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  422 VAL
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  174 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  259 GLU
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  369 SER
Chi-restraints excluded: chain B residue  422 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 61 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 6 optimal weight:    0.2980
   chunk 12 optimal weight:    8.9990
   chunk 47 optimal weight:    0.2980
   chunk 42 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.121608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.103969 restraints weight = 15836.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.107139 restraints weight = 7439.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.109377 restraints weight = 4545.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7276  Z= 0.137
  Angle     :  0.709  14.128   9942  Z= 0.343
  Chirality :  0.043   0.219   1070
  Planarity :  0.005   0.041   1180
  Dihedral  :  6.333  49.867   1105
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 25.21 %
    Favored  : 69.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.31), residues: 820
  helix:  0.95 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -3.61 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 438 
 HIS   0.012   0.002   HIS B 223 
 PHE   0.031   0.001   PHE B 270 
 TYR   0.034   0.002   TYR A 336 
 ARG   0.009   0.000   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03822 (  476)
  hydrogen bonds       : angle       5.51918 ( 1428)
  SS BOND              : bond        0.00180 (    4)
  SS BOND              : angle       0.71480 (    8)
  covalent geometry    : bond        0.00301 ( 7272)
  covalent geometry    : angle       0.70852 ( 9934)

*********************** 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
  191 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 152
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 LYS cc_start: 0.8128 (mttt) cc_final: 0.7781 (mtmm)
REVERT: A  259 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8104 (mp0)
REVERT: A  265 MET cc_start: 0.8322 (ttm) cc_final: 0.7777 (ttm)
REVERT: A  306 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8893 (tp)
REVERT: A  327 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8325 (m-80)
REVERT: A  342 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: A  395 MET cc_start: 0.8181 (ttt) cc_final: 0.7953 (tmm)
REVERT: A  402 MET cc_start: 0.8630 (ppp) cc_final: 0.7966 (ppp)
REVERT: A  422 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8168 (p)
REVERT: A  426 ASP cc_start: 0.8059 (m-30) cc_final: 0.7797 (m-30)
REVERT: A  471 PHE cc_start: 0.7286 (p90) cc_final: 0.6856 (m-80)
REVERT: A  472 TYR cc_start: 0.7778 (t80) cc_final: 0.7558 (t80)
REVERT: B  180 LYS cc_start: 0.8128 (mttt) cc_final: 0.7760 (mtmm)
REVERT: B  259 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8196 (mp0)
REVERT: B  265 MET cc_start: 0.8414 (ttm) cc_final: 0.7980 (ttm)
REVERT: B  273 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: B  327 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8282 (m-80)
REVERT: B  342 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: B  390 ASN cc_start: 0.8201 (m-40) cc_final: 0.7933 (m-40)
REVERT: B  395 MET cc_start: 0.8205 (ttt) cc_final: 0.7949 (tmm)
REVERT: B  402 MET cc_start: 0.8363 (ppp) cc_final: 0.7724 (ppp)
REVERT: B  422 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8433 (p)
REVERT: B  426 ASP cc_start: 0.8194 (m-30) cc_final: 0.7922 (m-30)
REVERT: B  471 PHE cc_start: 0.7261 (p90) cc_final: 0.6870 (m-80)
REVERT: B  472 TYR cc_start: 0.7802 (t80) cc_final: 0.7372 (t80)
REVERT: B  484 MET cc_start: 0.6873 (ttt) cc_final: 0.6646 (ttm)
  outliers start: 39
  outliers final: 29
  residues processed: 172
  average time/residue: 0.1807
  time to fit residues: 42.3144
Evaluate side-chains
  181 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 145
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
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  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  260 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
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  422 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  174 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  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  369 SER
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  514 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 79 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3859 r_free = 0.3859 target = 0.123661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.105577 restraints weight = 16032.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.108948 restraints weight = 7526.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.111099 restraints weight = 4560.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.4761

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= 0.139
  Angle     :  0.722  14.911   9942  Z= 0.347
  Chirality :  0.044   0.219   1070
  Planarity :  0.005   0.041   1180
  Dihedral  :  6.340  50.615   1105
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 25.49 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.31), residues: 820
  helix:  0.93 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.64 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 438 
 HIS   0.013   0.002   HIS B 223 
 PHE   0.030   0.001   PHE B 270 
 TYR   0.034   0.002   TYR A 336 
 ARG   0.008   0.001   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03903 (  476)
  hydrogen bonds       : angle       5.48743 ( 1428)
  SS BOND              : bond        0.00230 (    4)
  SS BOND              : angle       0.82409 (    8)
  covalent geometry    : bond        0.00305 ( 7272)
  covalent geometry    : angle       0.72152 ( 9934)

********************** 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
  182 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 LYS cc_start: 0.8163 (mttt) cc_final: 0.7836 (mtmm)
REVERT: A  259 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8162 (mp0)
REVERT: A  265 MET cc_start: 0.8351 (ttm) cc_final: 0.7828 (ttm)
REVERT: A  306 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8862 (tp)
REVERT: A  327 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8315 (m-80)
REVERT: A  342 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7610 (tm-30)
REVERT: A  365 CYS cc_start: 0.7612 (t) cc_final: 0.7277 (t)
REVERT: A  395 MET cc_start: 0.8191 (ttt) cc_final: 0.7953 (tmm)
REVERT: A  402 MET cc_start: 0.8651 (ppp) cc_final: 0.8020 (ppp)
REVERT: A  422 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8150 (p)
REVERT: A  426 ASP cc_start: 0.8093 (m-30) cc_final: 0.7814 (m-30)
REVERT: A  471 PHE cc_start: 0.7364 (p90) cc_final: 0.6892 (m-80)
REVERT: A  472 TYR cc_start: 0.7793 (t80) cc_final: 0.7391 (t80)
REVERT: A  484 MET cc_start: 0.6766 (ttt) cc_final: 0.6546 (ttm)
REVERT: B  180 LYS cc_start: 0.8169 (mttt) cc_final: 0.7831 (mtmm)
REVERT: B  259 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8277 (mp0)
REVERT: B  265 MET cc_start: 0.8428 (ttm) cc_final: 0.8006 (ttm)
REVERT: B  273 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: B  327 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8225 (m-80)
REVERT: B  342 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7753 (tm-30)
REVERT: B  390 ASN cc_start: 0.8228 (m-40) cc_final: 0.7858 (m-40)
REVERT: B  395 MET cc_start: 0.8240 (ttt) cc_final: 0.7959 (tmm)
REVERT: B  402 MET cc_start: 0.8401 (ppp) cc_final: 0.7777 (ppp)
REVERT: B  422 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8416 (p)
REVERT: B  426 ASP cc_start: 0.8153 (m-30) cc_final: 0.7931 (m-30)
REVERT: B  471 PHE cc_start: 0.7388 (p90) cc_final: 0.6888 (m-80)
REVERT: B  472 TYR cc_start: 0.7589 (t80) cc_final: 0.7274 (t80)
REVERT: B  484 MET cc_start: 0.6877 (ttt) cc_final: 0.6537 (ttm)
  outliers start: 36
  outliers final: 26
  residues processed: 165
  average time/residue: 0.1829
  time to fit residues: 40.8814
Evaluate side-chains
  177 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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  174 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  260 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 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  422 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  174 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  255 ILE
Chi-restraints excluded: chain B residue  259 GLU
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  526 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
A 526 GLN
B 526 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.121233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.102909 restraints weight = 15634.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.106178 restraints weight = 7421.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.108460 restraints weight = 4573.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.4800

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= 0.141
  Angle     :  0.718  15.129   9942  Z= 0.345
  Chirality :  0.043   0.216   1070
  Planarity :  0.005   0.040   1180
  Dihedral  :  5.801  45.459   1099
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.91 %
    Favored  : 69.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.31), residues: 820
  helix:  0.97 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.64 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 438 
 HIS   0.013   0.002   HIS B 223 
 PHE   0.032   0.001   PHE B 270 
 TYR   0.030   0.001   TYR B 322 
 ARG   0.009   0.001   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  476)
  hydrogen bonds       : angle       5.43193 ( 1428)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       0.80403 (    8)
  covalent geometry    : bond        0.00314 ( 7272)
  covalent geometry    : angle       0.71830 ( 9934)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2329.16 seconds
wall clock time: 41 minutes 8.43 seconds (2468.43 seconds total)