Starting phenix.real_space_refine
on Fri Aug 22 14:00:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qxa_18716/08_2025/8qxa_18716.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qxa_18716/08_2025/8qxa_18716.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qxa_18716/08_2025/8qxa_18716.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qxa_18716/08_2025/8qxa_18716.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qxa_18716/08_2025/8qxa_18716.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qxa_18716/08_2025/8qxa_18716.map"
  }
  resolution = 4.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      84      5.16       5
     C    2232      2.51       5
     N     660      2.21       5
     O     720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3696
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "B"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "C"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "D"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "E"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "F"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "G"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "H"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "I"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "J"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "K"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "L"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
  Time building chain proxies: 0.79, per 1000 atoms: 0.21
  Number of scatterers: 3696
  At special positions: 0
  Unit cell: (107.12, 71.76, 48.88, 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      84     16.00
     O     720      8.00
     N     660      7.00
     C    2232      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.19
  Conformation dependent library (CDL) restraints added in 122.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  888

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318
      removed outlier: 6.301A  pdb=" N   SER A 317 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   SER C 317 " --> pdb=" O   ILE E 318 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   SER E 317 " --> pdb=" O   ILE G 318 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   SER G 317 " --> pdb=" O   ILE I 318 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   SER I 317 " --> pdb=" O   ILE K 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 323 through 324
      removed outlier: 7.079A  pdb=" N   MET A 323 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   MET C 323 " --> pdb=" O   ALA E 324 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   MET E 323 " --> pdb=" O   ALA G 324 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   MET G 323 " --> pdb=" O   ALA I 324 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   MET I 323 " --> pdb=" O   ALA K 324 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 331
    Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340
    Processing sheet with id=AA5, first strand: chain 'B' and resid 326 through 332
      removed outlier: 6.812A  pdb=" N   GLN D 327 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   GLN F 327 " --> pdb=" O   ALA D 326 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   GLN H 327 " --> pdb=" O   ALA F 326 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   GLN J 327 " --> pdb=" O   ALA H 326 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   GLN L 327 " --> pdb=" O   ALA J 326 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 338

    45 hydrogen bonds defined for protein.
    135 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.33

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 881
        1.33 -     1.46: 745
        1.46 -     1.58: 1950
        1.58 -     1.71: 0
        1.71 -     1.84: 168
  Bond restraints: 3744
  Sorted by residual:
  bond pdb=" N   GLY I 308 "
       pdb=" CA  GLY I 308 "
    ideal  model  delta    sigma   weight residual
    1.444  1.476 -0.032 9.60e-03 1.09e+04 1.11e+01
  bond pdb=" N   GLY K 308 "
       pdb=" CA  GLY K 308 "
    ideal  model  delta    sigma   weight residual
    1.444  1.476 -0.031 9.60e-03 1.09e+04 1.07e+01
  bond pdb=" N   GLY G 308 "
       pdb=" CA  GLY G 308 "
    ideal  model  delta    sigma   weight residual
    1.444  1.476 -0.031 9.60e-03 1.09e+04 1.05e+01
  bond pdb=" N   GLY A 308 "
       pdb=" CA  GLY A 308 "
    ideal  model  delta    sigma   weight residual
    1.444  1.475 -0.031 9.60e-03 1.09e+04 1.04e+01
  bond pdb=" N   GLY E 308 "
       pdb=" CA  GLY E 308 "
    ideal  model  delta    sigma   weight residual
    1.444  1.475 -0.031 9.60e-03 1.09e+04 1.02e+01
  ... (remaining 3739 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 3660
        2.41 -     4.83: 1144
        4.83 -     7.24: 146
        7.24 -     9.65: 24
        9.65 -    12.06: 6
  Bond angle restraints: 4980
  Sorted by residual:
  angle pdb=" N   GLN K 327 "
        pdb=" CA  GLN K 327 "
        pdb=" C   GLN K 327 "
      ideal   model   delta    sigma   weight residual
     112.23  100.17   12.06 1.26e+00 6.30e-01 9.17e+01
  angle pdb=" N   GLN I 327 "
        pdb=" CA  GLN I 327 "
        pdb=" C   GLN I 327 "
      ideal   model   delta    sigma   weight residual
     112.23  100.18   12.05 1.26e+00 6.30e-01 9.15e+01
  angle pdb=" N   GLN A 327 "
        pdb=" CA  GLN A 327 "
        pdb=" C   GLN A 327 "
      ideal   model   delta    sigma   weight residual
     112.23  100.18   12.05 1.26e+00 6.30e-01 9.15e+01
  angle pdb=" N   GLN G 327 "
        pdb=" CA  GLN G 327 "
        pdb=" C   GLN G 327 "
      ideal   model   delta    sigma   weight residual
     112.23  100.19   12.04 1.26e+00 6.30e-01 9.13e+01
  angle pdb=" N   GLN C 327 "
        pdb=" CA  GLN C 327 "
        pdb=" C   GLN C 327 "
      ideal   model   delta    sigma   weight residual
     112.23  100.20   12.03 1.26e+00 6.30e-01 9.12e+01
  ... (remaining 4975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.02 -    17.06: 1896
       17.06 -    34.10: 216
       34.10 -    51.14: 42
       51.14 -    68.18: 12
       68.18 -    85.22: 30
  Dihedral angle restraints: 2196
    sinusoidal: 780
      harmonic: 1416
  Sorted by residual:
  dihedral pdb=" N   MET L 307 "
           pdb=" CA  MET L 307 "
           pdb=" CB  MET L 307 "
           pdb=" CG  MET L 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.07   51.07     3      1.50e+01 4.44e-03 8.97e+00
  dihedral pdb=" N   MET D 307 "
           pdb=" CA  MET D 307 "
           pdb=" CB  MET D 307 "
           pdb=" CG  MET D 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.06   51.06     3      1.50e+01 4.44e-03 8.97e+00
  dihedral pdb=" N   MET H 307 "
           pdb=" CA  MET H 307 "
           pdb=" CB  MET H 307 "
           pdb=" CG  MET H 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.05   51.05     3      1.50e+01 4.44e-03 8.97e+00
  ... (remaining 2193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 150
       0.049 -    0.097: 127
       0.097 -    0.144: 125
       0.144 -    0.192: 54
       0.192 -    0.240: 24
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  TRP B 334 "
            pdb=" N   TRP B 334 "
            pdb=" C   TRP B 334 "
            pdb=" CB  TRP B 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  TRP J 334 "
            pdb=" N   TRP J 334 "
            pdb=" C   TRP J 334 "
            pdb=" CB  TRP J 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  TRP H 334 "
            pdb=" N   TRP H 334 "
            pdb=" C   TRP H 334 "
            pdb=" CB  TRP H 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 477 not shown)

  Planarity restraints: 684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA J 326 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.74e+00
        pdb=" C   ALA J 326 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ALA J 326 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLN J 327 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F 326 "    0.015 2.00e-02 2.50e+03   2.95e-02 8.70e+00
        pdb=" C   ALA F 326 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ALA F 326 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLN F 327 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 326 "    0.014 2.00e-02 2.50e+03   2.95e-02 8.69e+00
        pdb=" C   ALA D 326 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ALA D 326 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLN D 327 "    0.018 2.00e-02 2.50e+03
  ... (remaining 681 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 1399
        2.92 -     3.41: 3236
        3.41 -     3.91: 6325
        3.91 -     4.40: 6764
        4.40 -     4.90: 13333
  Nonbonded interactions: 31057
  Sorted by model distance:
  nonbonded pdb=" N   ALA I 325 "
            pdb=" O   ALA I 325 "
     model   vdw
     2.420 2.496
  nonbonded pdb=" N   ALA A 325 "
            pdb=" O   ALA A 325 "
     model   vdw
     2.421 2.496
  nonbonded pdb=" N   ALA C 325 "
            pdb=" O   ALA C 325 "
     model   vdw
     2.421 2.496
  nonbonded pdb=" N   ALA K 325 "
            pdb=" O   ALA K 325 "
     model   vdw
     2.421 2.496
  nonbonded pdb=" N   ALA G 325 "
            pdb=" O   ALA G 325 "
     model   vdw
     2.421 2.496
  ... (remaining 31052 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.010
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.044   3744  Z= 1.012
  Angle     :  2.245  12.063   4980  Z= 1.658
  Chirality :  0.104   0.240    480
  Planarity :  0.009   0.030    684
  Dihedral  : 18.942  85.216   1308
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 27.59 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.36 (0.17), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.003   PHE E 316 
 TRP   0.046   0.009   TRP L 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.01374 ( 3744)
  covalent geometry    : angle       2.24470 ( 4980)
  hydrogen bonds       : bond        0.28191 (   45)
  hydrogen bonds       : angle       9.27540 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.7321 (m-80) cc_final: 0.5670 (p90)
REVERT: A  334 TRP cc_start: 0.8104 (p90) cc_final: 0.4301 (m100)
REVERT: B  311 MET cc_start: 0.7816 (ptt) cc_final: 0.7129 (tpt)
REVERT: B  322 MET cc_start: 0.7750 (mtt) cc_final: 0.7481 (mtt)
REVERT: B  334 TRP cc_start: 0.7730 (p90) cc_final: 0.4653 (m100)
REVERT: C  313 PHE cc_start: 0.8056 (m-10) cc_final: 0.7197 (m-80)
REVERT: D  334 TRP cc_start: 0.7983 (p90) cc_final: 0.7643 (p90)
REVERT: E  313 PHE cc_start: 0.8164 (m-10) cc_final: 0.7914 (m-80)
REVERT: G  307 MET cc_start: 0.6436 (ttt) cc_final: 0.5999 (ttt)
REVERT: G  313 PHE cc_start: 0.8053 (m-10) cc_final: 0.7853 (m-80)
REVERT: H  313 PHE cc_start: 0.8675 (m-10) cc_final: 0.8422 (m-10)
REVERT: H  339 MET cc_start: 0.8103 (mtp) cc_final: 0.7754 (mtp)
REVERT: I  334 TRP cc_start: 0.7956 (p90) cc_final: 0.7736 (p90)
REVERT: J  313 PHE cc_start: 0.8531 (m-10) cc_final: 0.8231 (m-10)
REVERT: J  339 MET cc_start: 0.8341 (mtp) cc_final: 0.8087 (mtt)
REVERT: L  313 PHE cc_start: 0.8757 (m-10) cc_final: 0.6530 (p90)
REVERT: L  337 MET cc_start: 0.8084 (mtp) cc_final: 0.7341 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.0393
  time to fit residues: 12.5700
Evaluate side-chains
  158 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
C 346 GLN
D 319 ASN
D 345 ASN
E 346 GLN
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 319 ASN
H 345 ASN
** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 319 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.210139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.122564 restraints weight = 6064.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.127494 restraints weight = 3161.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.130811 restraints weight = 1961.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.133116 restraints weight = 1391.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.134681 restraints weight = 1064.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3744  Z= 0.188
  Angle     :  0.755   5.716   4980  Z= 0.410
  Chirality :  0.038   0.132    480
  Planarity :  0.005   0.044    684
  Dihedral  :  6.710  31.611    528
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.58 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.43 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.025   0.003   PHE G 316 
 TRP   0.013   0.002   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 3744)
  covalent geometry    : angle       0.75523 ( 4980)
  hydrogen bonds       : bond        0.05947 (   45)
  hydrogen bonds       : angle       5.52980 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.7621 (m-80) cc_final: 0.5287 (p90)
REVERT: A  323 MET cc_start: 0.7771 (mtt) cc_final: 0.7488 (mtt)
REVERT: A  343 GLN cc_start: 0.8292 (mt0) cc_final: 0.7919 (tt0)
REVERT: B  311 MET cc_start: 0.8113 (ptp) cc_final: 0.6353 (mmt)
REVERT: B  334 TRP cc_start: 0.8219 (p90) cc_final: 0.3908 (m100)
REVERT: B  340 LEU cc_start: 0.8930 (tt) cc_final: 0.8565 (tt)
REVERT: B  344 GLN cc_start: 0.8256 (mt0) cc_final: 0.7992 (mt0)
REVERT: C  316 PHE cc_start: 0.8346 (m-80) cc_final: 0.8013 (m-80)
REVERT: D  337 MET cc_start: 0.9149 (mtp) cc_final: 0.8089 (mtp)
REVERT: E  316 PHE cc_start: 0.8485 (m-80) cc_final: 0.8220 (m-80)
REVERT: F  307 MET cc_start: 0.8861 (ttt) cc_final: 0.8592 (ttt)
REVERT: F  337 MET cc_start: 0.9136 (mtp) cc_final: 0.8890 (mtt)
REVERT: F  344 GLN cc_start: 0.8673 (mt0) cc_final: 0.8043 (mt0)
REVERT: G  313 PHE cc_start: 0.8623 (m-10) cc_final: 0.8190 (m-10)
REVERT: G  317 SER cc_start: 0.8653 (t) cc_final: 0.7990 (m)
REVERT: G  323 MET cc_start: 0.7711 (mtp) cc_final: 0.7084 (mtt)
REVERT: H  337 MET cc_start: 0.8594 (mtp) cc_final: 0.8240 (mtt)
REVERT: H  344 GLN cc_start: 0.8884 (mt0) cc_final: 0.8328 (mt0)
REVERT: I  313 PHE cc_start: 0.8568 (m-10) cc_final: 0.7557 (m-80)
REVERT: I  317 SER cc_start: 0.8474 (t) cc_final: 0.7998 (m)
REVERT: I  336 MET cc_start: 0.7550 (tmm) cc_final: 0.6726 (tmm)
REVERT: I  337 MET cc_start: 0.7316 (tpp) cc_final: 0.6668 (tpp)
REVERT: J  311 MET cc_start: 0.7896 (ptp) cc_final: 0.7558 (ptm)
REVERT: J  313 PHE cc_start: 0.8696 (m-10) cc_final: 0.8432 (m-10)
REVERT: J  337 MET cc_start: 0.8724 (mtt) cc_final: 0.8202 (mtp)
REVERT: J  344 GLN cc_start: 0.8356 (mt0) cc_final: 0.7909 (mt0)
REVERT: K  323 MET cc_start: 0.7685 (mtt) cc_final: 0.7471 (mtt)
REVERT: K  343 GLN cc_start: 0.8251 (mt0) cc_final: 0.7761 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0369
  time to fit residues: 9.0653
Evaluate side-chains
  148 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 37 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0270
   chunk 29 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7842

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN
B 345 ASN
C 344 GLN
D 331 GLN
D 344 GLN
G 346 GLN
H 345 ASN
J 345 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.220183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.124986 restraints weight = 5880.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.129985 restraints weight = 3052.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.133333 restraints weight = 1913.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.135614 restraints weight = 1362.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.137069 restraints weight = 1057.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6748
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3744  Z= 0.125
  Angle     :  0.662   6.770   4980  Z= 0.352
  Chirality :  0.037   0.125    480
  Planarity :  0.003   0.029    684
  Dihedral  :  6.316  31.517    528
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.31 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.003   PHE E 313 
 TRP   0.015   0.002   TRP H 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3744)
  covalent geometry    : angle       0.66230 ( 4980)
  hydrogen bonds       : bond        0.04975 (   45)
  hydrogen bonds       : angle       5.54198 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.7320 (m-80) cc_final: 0.4699 (p90)
REVERT: A  319 ASN cc_start: 0.8274 (m-40) cc_final: 0.7990 (m-40)
REVERT: A  323 MET cc_start: 0.7871 (mtt) cc_final: 0.7350 (mtt)
REVERT: B  311 MET cc_start: 0.7768 (ptp) cc_final: 0.6000 (mmt)
REVERT: B  313 PHE cc_start: 0.8429 (m-10) cc_final: 0.7954 (m-80)
REVERT: B  322 MET cc_start: 0.7992 (mtt) cc_final: 0.7783 (mtt)
REVERT: B  344 GLN cc_start: 0.8324 (mt0) cc_final: 0.7806 (tt0)
REVERT: C  316 PHE cc_start: 0.8087 (m-80) cc_final: 0.7741 (m-80)
REVERT: C  323 MET cc_start: 0.8135 (mtt) cc_final: 0.7844 (mtt)
REVERT: C  337 MET cc_start: 0.6626 (ptt) cc_final: 0.6309 (ptt)
REVERT: D  307 MET cc_start: 0.8941 (ttm) cc_final: 0.8647 (ttm)
REVERT: D  313 PHE cc_start: 0.8294 (m-10) cc_final: 0.6981 (m-80)
REVERT: E  317 SER cc_start: 0.8436 (t) cc_final: 0.8124 (m)
REVERT: F  337 MET cc_start: 0.9171 (mtp) cc_final: 0.8743 (mtt)
REVERT: F  339 MET cc_start: 0.8036 (mtm) cc_final: 0.7588 (mtm)
REVERT: F  344 GLN cc_start: 0.8365 (mt0) cc_final: 0.7861 (mt0)
REVERT: G  317 SER cc_start: 0.8448 (t) cc_final: 0.7878 (m)
REVERT: G  323 MET cc_start: 0.7365 (mtp) cc_final: 0.6665 (mtt)
REVERT: H  316 PHE cc_start: 0.7629 (m-80) cc_final: 0.6826 (m-80)
REVERT: H  339 MET cc_start: 0.8206 (mtp) cc_final: 0.7887 (mtp)
REVERT: H  344 GLN cc_start: 0.8229 (mt0) cc_final: 0.7994 (mt0)
REVERT: I  307 MET cc_start: 0.7807 (tpp) cc_final: 0.6862 (tpp)
REVERT: I  317 SER cc_start: 0.8278 (t) cc_final: 0.7998 (m)
REVERT: I  336 MET cc_start: 0.8005 (tmm) cc_final: 0.6881 (tmm)
REVERT: I  337 MET cc_start: 0.7328 (tpp) cc_final: 0.6216 (tpp)
REVERT: J  307 MET cc_start: 0.8654 (ttt) cc_final: 0.8422 (ttt)
REVERT: J  311 MET cc_start: 0.7911 (ptp) cc_final: 0.7258 (ptm)
REVERT: J  313 PHE cc_start: 0.8330 (m-10) cc_final: 0.7702 (m-10)
REVERT: J  322 MET cc_start: 0.8621 (mtt) cc_final: 0.8390 (mtt)
REVERT: J  337 MET cc_start: 0.8760 (mtt) cc_final: 0.8337 (mtp)
REVERT: J  344 GLN cc_start: 0.8162 (mt0) cc_final: 0.7778 (mt0)
REVERT: K  322 MET cc_start: 0.6364 (mtp) cc_final: 0.6068 (mtp)
REVERT: L  311 MET cc_start: 0.8675 (ptt) cc_final: 0.8381 (ptp)
REVERT: L  313 PHE cc_start: 0.8276 (m-10) cc_final: 0.5893 (p90)
REVERT: L  337 MET cc_start: 0.8467 (mtp) cc_final: 0.8147 (mtt)
REVERT: L  345 ASN cc_start: 0.8228 (m-40) cc_final: 0.7844 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0401
  time to fit residues: 9.0189
Evaluate side-chains
  137 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    8.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
C 331 GLN
D 319 ASN
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 345 ASN
H 345 ASN
J 345 ASN
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.115420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.093883 restraints weight = 5680.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.097163 restraints weight = 3182.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.099366 restraints weight = 2175.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.100995 restraints weight = 1685.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.102074 restraints weight = 1395.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.5831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3744  Z= 0.282
  Angle     :  0.757   8.735   4980  Z= 0.405
  Chirality :  0.038   0.124    480
  Planarity :  0.004   0.028    684
  Dihedral  :  6.691  30.974    528
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 20.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.86 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.58 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.35 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.020   0.003   PHE A 313 
 TRP   0.013   0.003   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00626 ( 3744)
  covalent geometry    : angle       0.75713 ( 4980)
  hydrogen bonds       : bond        0.04915 (   45)
  hydrogen bonds       : angle       6.12291 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.8637 (t) cc_final: 0.8210 (m)
REVERT: B  311 MET cc_start: 0.8053 (ptp) cc_final: 0.6411 (mmt)
REVERT: B  313 PHE cc_start: 0.8659 (m-10) cc_final: 0.8199 (m-10)
REVERT: D  313 PHE cc_start: 0.8778 (m-10) cc_final: 0.8052 (m-80)
REVERT: E  317 SER cc_start: 0.8710 (t) cc_final: 0.8385 (m)
REVERT: F  307 MET cc_start: 0.8655 (ttm) cc_final: 0.8280 (ttp)
REVERT: F  344 GLN cc_start: 0.8848 (mt0) cc_final: 0.8484 (mt0)
REVERT: G  317 SER cc_start: 0.8815 (t) cc_final: 0.8311 (m)
REVERT: G  323 MET cc_start: 0.7713 (mtp) cc_final: 0.7119 (mtt)
REVERT: H  337 MET cc_start: 0.8628 (mtt) cc_final: 0.8179 (mtt)
REVERT: I  307 MET cc_start: 0.7763 (tpp) cc_final: 0.6910 (tpp)
REVERT: I  336 MET cc_start: 0.7732 (tmm) cc_final: 0.7431 (tmm)
REVERT: I  337 MET cc_start: 0.7699 (tpp) cc_final: 0.7075 (tpp)
REVERT: J  331 GLN cc_start: 0.8954 (mt0) cc_final: 0.8729 (mt0)
REVERT: J  344 GLN cc_start: 0.8605 (mt0) cc_final: 0.8329 (mt0)
REVERT: K  317 SER cc_start: 0.8525 (t) cc_final: 0.8279 (m)
REVERT: L  344 GLN cc_start: 0.8467 (mt0) cc_final: 0.8210 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0373
  time to fit residues: 7.5323
Evaluate side-chains
  125 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0030
   overall best weight:    0.9594

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

Flipped N/Q/H residues before XYZ refinement:
B 344 GLN
C 344 GLN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 331 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.211783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.119246 restraints weight = 6006.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.123841 restraints weight = 3207.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.126959 restraints weight = 2106.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.129058 restraints weight = 1562.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.129913 restraints weight = 1257.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.6218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3744  Z= 0.136
  Angle     :  0.641   7.015   4980  Z= 0.337
  Chirality :  0.036   0.122    480
  Planarity :  0.003   0.025    684
  Dihedral  :  6.313  29.898    528
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.29 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.002   PHE J 313 
 TRP   0.010   0.002   TRP H 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3744)
  covalent geometry    : angle       0.64062 ( 4980)
  hydrogen bonds       : bond        0.04426 (   45)
  hydrogen bonds       : angle       5.86332 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8312 (t) cc_final: 0.7991 (m)
REVERT: A  339 MET cc_start: 0.7902 (mtp) cc_final: 0.7631 (mtm)
REVERT: B  311 MET cc_start: 0.7682 (ptp) cc_final: 0.6168 (mmt)
REVERT: D  311 MET cc_start: 0.7972 (ptt) cc_final: 0.7738 (ptt)
REVERT: D  313 PHE cc_start: 0.8966 (m-10) cc_final: 0.8664 (m-10)
REVERT: E  317 SER cc_start: 0.8707 (t) cc_final: 0.8433 (m)
REVERT: F  337 MET cc_start: 0.8865 (mtt) cc_final: 0.8510 (mtt)
REVERT: F  344 GLN cc_start: 0.8659 (mt0) cc_final: 0.8429 (mt0)
REVERT: G  317 SER cc_start: 0.8754 (t) cc_final: 0.8308 (m)
REVERT: G  323 MET cc_start: 0.7500 (mtp) cc_final: 0.6838 (mtt)
REVERT: I  307 MET cc_start: 0.7722 (tpp) cc_final: 0.6774 (tpp)
REVERT: I  336 MET cc_start: 0.7661 (tmm) cc_final: 0.7387 (tmm)
REVERT: I  337 MET cc_start: 0.7637 (tpp) cc_final: 0.5893 (tpp)
REVERT: K  317 SER cc_start: 0.8489 (t) cc_final: 0.8214 (m)
REVERT: L  313 PHE cc_start: 0.8256 (m-10) cc_final: 0.5955 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0372
  time to fit residues: 7.4097
Evaluate side-chains
  124 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 2 optimal weight:    0.2980
   chunk 27 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
E 331 GLN
G 331 GLN
** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN
** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.210600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.125094 restraints weight = 5917.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.129793 restraints weight = 3200.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.132959 restraints weight = 2109.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.134929 restraints weight = 1573.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.136453 restraints weight = 1284.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.6706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3744  Z= 0.121
  Angle     :  0.628   5.964   4980  Z= 0.333
  Chirality :  0.036   0.117    480
  Planarity :  0.003   0.024    684
  Dihedral  :  6.214  29.456    528
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.18 (0.21), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.013   0.002   PHE L 316 
 TRP   0.011   0.002   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3744)
  covalent geometry    : angle       0.62796 ( 4980)
  hydrogen bonds       : bond        0.04175 (   45)
  hydrogen bonds       : angle       5.55098 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8253 (t) cc_final: 0.7909 (m)
REVERT: A  339 MET cc_start: 0.7940 (mtp) cc_final: 0.7540 (mtm)
REVERT: B  311 MET cc_start: 0.7519 (ptp) cc_final: 0.5877 (mmt)
REVERT: B  313 PHE cc_start: 0.8384 (m-10) cc_final: 0.8114 (m-80)
REVERT: D  311 MET cc_start: 0.7798 (ptt) cc_final: 0.7376 (ptt)
REVERT: E  317 SER cc_start: 0.8580 (t) cc_final: 0.8283 (m)
REVERT: F  307 MET cc_start: 0.8751 (ttm) cc_final: 0.8505 (ttp)
REVERT: F  337 MET cc_start: 0.8807 (mtt) cc_final: 0.8512 (mtt)
REVERT: F  344 GLN cc_start: 0.8532 (mt0) cc_final: 0.8124 (mt0)
REVERT: G  317 SER cc_start: 0.8615 (t) cc_final: 0.8167 (m)
REVERT: G  323 MET cc_start: 0.7306 (mtp) cc_final: 0.6636 (mtt)
REVERT: H  331 GLN cc_start: 0.8771 (mt0) cc_final: 0.8326 (pt0)
REVERT: H  337 MET cc_start: 0.8529 (mtt) cc_final: 0.7462 (mtt)
REVERT: I  307 MET cc_start: 0.7887 (tpp) cc_final: 0.6863 (tpp)
REVERT: I  313 PHE cc_start: 0.8387 (m-10) cc_final: 0.8105 (m-80)
REVERT: I  336 MET cc_start: 0.8056 (tmm) cc_final: 0.7678 (tmm)
REVERT: I  337 MET cc_start: 0.7400 (tpp) cc_final: 0.6388 (tpp)
REVERT: J  311 MET cc_start: 0.8392 (ptm) cc_final: 0.8070 (ptm)
REVERT: J  337 MET cc_start: 0.8642 (mtt) cc_final: 0.8324 (mtt)
REVERT: K  307 MET cc_start: 0.7291 (tpp) cc_final: 0.6995 (tpp)
REVERT: L  313 PHE cc_start: 0.8131 (m-10) cc_final: 0.5891 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0389
  time to fit residues: 7.5220
Evaluate side-chains
  122 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN
** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.113473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.091910 restraints weight = 6090.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.094846 restraints weight = 3414.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.096923 restraints weight = 2358.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.098013 restraints weight = 1839.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.099055 restraints weight = 1588.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.6772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.043   3744  Z= 0.391
  Angle     :  0.843   6.971   4980  Z= 0.453
  Chirality :  0.040   0.146    480
  Planarity :  0.004   0.024    684
  Dihedral  :  6.838  29.966    528
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 23.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.28 (0.21), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.003   PHE K 313 
 TRP   0.012   0.003   TRP H 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00849 ( 3744)
  covalent geometry    : angle       0.84285 ( 4980)
  hydrogen bonds       : bond        0.04814 (   45)
  hydrogen bonds       : angle       6.40869 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8579 (t) cc_final: 0.8199 (m)
REVERT: B  311 MET cc_start: 0.7700 (ptp) cc_final: 0.6074 (tpt)
REVERT: D  307 MET cc_start: 0.8399 (ttt) cc_final: 0.7988 (ttt)
REVERT: D  337 MET cc_start: 0.8730 (mtt) cc_final: 0.8352 (mtt)
REVERT: E  317 SER cc_start: 0.8777 (t) cc_final: 0.8518 (m)
REVERT: E  322 MET cc_start: 0.7998 (mtp) cc_final: 0.7796 (mtp)
REVERT: F  331 GLN cc_start: 0.8962 (mt0) cc_final: 0.8746 (mt0)
REVERT: G  317 SER cc_start: 0.8932 (t) cc_final: 0.8533 (m)
REVERT: G  323 MET cc_start: 0.7556 (mtp) cc_final: 0.6964 (mtt)
REVERT: H  337 MET cc_start: 0.8730 (mtt) cc_final: 0.8197 (mtt)
REVERT: I  307 MET cc_start: 0.7792 (tpp) cc_final: 0.7033 (tpp)
REVERT: I  336 MET cc_start: 0.7807 (tmm) cc_final: 0.7571 (tmm)
REVERT: I  337 MET cc_start: 0.7673 (tpp) cc_final: 0.7166 (tpp)
REVERT: L  337 MET cc_start: 0.8459 (mmm) cc_final: 0.8062 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0427
  time to fit residues: 7.7299
Evaluate side-chains
  125 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C 331 GLN
F 327 GLN
** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN
** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.209690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.123028 restraints weight = 5903.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.127395 restraints weight = 3204.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.130437 restraints weight = 2135.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.132298 restraints weight = 1598.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.133711 restraints weight = 1316.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.7028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3744  Z= 0.132
  Angle     :  0.652   6.509   4980  Z= 0.339
  Chirality :  0.037   0.114    480
  Planarity :  0.003   0.022    684
  Dihedral  :  6.220  29.078    528
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.27 (0.21), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.002   PHE F 316 
 TRP   0.010   0.002   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3744)
  covalent geometry    : angle       0.65164 ( 4980)
  hydrogen bonds       : bond        0.04146 (   45)
  hydrogen bonds       : angle       5.80125 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.8447 (t) cc_final: 0.8163 (m)
REVERT: B  311 MET cc_start: 0.7438 (ptp) cc_final: 0.5945 (tpt)
REVERT: D  313 PHE cc_start: 0.9109 (m-10) cc_final: 0.8533 (m-10)
REVERT: D  337 MET cc_start: 0.8331 (mtt) cc_final: 0.8034 (mmm)
REVERT: E  317 SER cc_start: 0.8784 (t) cc_final: 0.8470 (m)
REVERT: E  333 SER cc_start: 0.9142 (p) cc_final: 0.8931 (p)
REVERT: F  307 MET cc_start: 0.8528 (ttm) cc_final: 0.8289 (ttp)
REVERT: F  313 PHE cc_start: 0.9306 (m-10) cc_final: 0.8582 (m-80)
REVERT: G  317 SER cc_start: 0.8849 (t) cc_final: 0.8472 (m)
REVERT: G  323 MET cc_start: 0.7315 (mtp) cc_final: 0.6823 (mtt)
REVERT: H  307 MET cc_start: 0.8173 (ttt) cc_final: 0.7568 (ttt)
REVERT: H  336 MET cc_start: 0.8132 (tpt) cc_final: 0.7789 (tpt)
REVERT: H  337 MET cc_start: 0.8815 (mtt) cc_final: 0.8119 (mtt)
REVERT: I  307 MET cc_start: 0.7843 (tpp) cc_final: 0.6892 (tpp)
REVERT: I  337 MET cc_start: 0.7564 (tpp) cc_final: 0.6861 (tpp)
REVERT: J  311 MET cc_start: 0.8216 (ptm) cc_final: 0.8000 (ptm)
REVERT: J  337 MET cc_start: 0.8476 (mtt) cc_final: 0.8107 (mtt)
REVERT: L  313 PHE cc_start: 0.8255 (m-10) cc_final: 0.6073 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0383
  time to fit residues: 6.8898
Evaluate side-chains
  120 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 35 optimal weight:    0.3980
   chunk 29 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0040
   chunk 30 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
B 327 GLN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 345 ASN
** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.212008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.125799 restraints weight = 5831.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.130263 restraints weight = 3154.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.133082 restraints weight = 2080.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.134644 restraints weight = 1579.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.136423 restraints weight = 1332.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.7134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3744  Z= 0.117
  Angle     :  0.656   7.669   4980  Z= 0.335
  Chirality :  0.036   0.113    480
  Planarity :  0.002   0.024    684
  Dihedral  :  5.996  28.482    528
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.29 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.26 (0.21), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE D 316 
 TRP   0.008   0.001   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3744)
  covalent geometry    : angle       0.65641 ( 4980)
  hydrogen bonds       : bond        0.03776 (   45)
  hydrogen bonds       : angle       5.57032 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8314 (t) cc_final: 0.8018 (m)
REVERT: B  311 MET cc_start: 0.7536 (ptp) cc_final: 0.6002 (mmt)
REVERT: D  337 MET cc_start: 0.8183 (mtt) cc_final: 0.7740 (mmm)
REVERT: E  317 SER cc_start: 0.8691 (t) cc_final: 0.8447 (m)
REVERT: E  337 MET cc_start: 0.7725 (ptt) cc_final: 0.7395 (ptt)
REVERT: F  337 MET cc_start: 0.8918 (mtt) cc_final: 0.8219 (mtt)
REVERT: G  317 SER cc_start: 0.8741 (t) cc_final: 0.8346 (m)
REVERT: G  323 MET cc_start: 0.7176 (mtp) cc_final: 0.6537 (mtt)
REVERT: H  307 MET cc_start: 0.8549 (ttt) cc_final: 0.7817 (ttt)
REVERT: H  336 MET cc_start: 0.8765 (tpt) cc_final: 0.8496 (tpt)
REVERT: H  337 MET cc_start: 0.8916 (mtt) cc_final: 0.7683 (mtt)
REVERT: I  307 MET cc_start: 0.7989 (tpp) cc_final: 0.7043 (tpp)
REVERT: I  336 MET cc_start: 0.7848 (tmm) cc_final: 0.6897 (tmm)
REVERT: I  337 MET cc_start: 0.7299 (tpp) cc_final: 0.6156 (tpp)
REVERT: L  313 PHE cc_start: 0.8216 (m-10) cc_final: 0.5747 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0446
  time to fit residues: 7.8968
Evaluate side-chains
  116 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0670
   overall best weight:    1.3320

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

Flipped N/Q/H residues before XYZ refinement:
C 331 GLN
C 344 GLN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 344 GLN
H 345 ASN
** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.211708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.122444 restraints weight = 5974.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.126914 restraints weight = 3236.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.129905 restraints weight = 2134.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.132083 restraints weight = 1606.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.133360 restraints weight = 1291.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.7243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3744  Z= 0.166
  Angle     :  0.702   9.051   4980  Z= 0.353
  Chirality :  0.036   0.118    480
  Planarity :  0.003   0.027    684
  Dihedral  :  6.185  28.508    528
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.33 (0.21), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.014   0.002   PHE J 316 
 TRP   0.007   0.002   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3744)
  covalent geometry    : angle       0.70172 ( 4980)
  hydrogen bonds       : bond        0.03839 (   45)
  hydrogen bonds       : angle       5.68019 (  135)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.8376 (t) cc_final: 0.8020 (m)
REVERT: B  311 MET cc_start: 0.7705 (ptp) cc_final: 0.5990 (mmt)
REVERT: C  344 GLN cc_start: 0.9031 (mt0) cc_final: 0.7863 (mp10)
REVERT: D  313 PHE cc_start: 0.8777 (m-10) cc_final: 0.8530 (m-10)
REVERT: E  317 SER cc_start: 0.8703 (t) cc_final: 0.8439 (m)
REVERT: F  307 MET cc_start: 0.8587 (ttm) cc_final: 0.8382 (ttp)
REVERT: F  337 MET cc_start: 0.9119 (mtt) cc_final: 0.8549 (mtt)
REVERT: G  317 SER cc_start: 0.8779 (t) cc_final: 0.8354 (m)
REVERT: G  323 MET cc_start: 0.7087 (mtp) cc_final: 0.6478 (mtt)
REVERT: H  337 MET cc_start: 0.8707 (mtt) cc_final: 0.7746 (mtt)
REVERT: H  345 ASN cc_start: 0.8567 (m-40) cc_final: 0.8302 (m-40)
REVERT: I  307 MET cc_start: 0.7993 (tpp) cc_final: 0.6941 (tpp)
REVERT: I  336 MET cc_start: 0.7874 (tmm) cc_final: 0.6990 (tmm)
REVERT: I  337 MET cc_start: 0.7360 (tpp) cc_final: 0.6267 (tpp)
REVERT: I  344 GLN cc_start: 0.8570 (mt0) cc_final: 0.8317 (mt0)
REVERT: K  339 MET cc_start: 0.7663 (mtp) cc_final: 0.6749 (mtp)
REVERT: L  313 PHE cc_start: 0.8077 (m-10) cc_final: 0.5820 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0441
  time to fit residues: 7.6379
Evaluate side-chains
  122 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.208991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.124100 restraints weight = 5889.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.128591 restraints weight = 3217.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.131413 restraints weight = 2130.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.133591 restraints weight = 1623.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.134829 restraints weight = 1313.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.7353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3744  Z= 0.147
  Angle     :  0.678   8.499   4980  Z= 0.342
  Chirality :  0.036   0.118    480
  Planarity :  0.003   0.029    684
  Dihedral  :  6.160  28.908    528
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.36 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE J 316 
 TRP   0.008   0.002   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3744)
  covalent geometry    : angle       0.67799 ( 4980)
  hydrogen bonds       : bond        0.03661 (   45)
  hydrogen bonds       : angle       5.67750 (  135)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 726.32 seconds
wall clock time: 13 minutes 10.33 seconds (790.33 seconds total)