Starting phenix.real_space_refine
on Sat Apr 26 23:04:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qxa_18716/04_2025/8qxa_18716.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qxa_18716/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qxa_18716/04_2025/8qxa_18716.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qxa_18716/04_2025/8qxa_18716.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qxa_18716/04_2025/8qxa_18716.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qxa_18716/04_2025/8qxa_18716.cif"
  }
  resolution = 4.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 2.63, per 1000 atoms: 0.71
  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: 0.83
  Conformation dependent library (CDL) restraints added in 497.7 milliseconds
  

  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: 0.42
  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: 0.75

  Time building geometry restraints manager: 1.00 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: 0.01
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:             0.500
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.060
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.700
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.046   0.009   TRP L 334 
 PHE   0.017   0.003   PHE E 316 

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

*********************** 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  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.7321 (m-80) cc_final: 0.5662 (p90)
REVERT: A  334 TRP cc_start: 0.8104 (p90) cc_final: 0.4302 (m100)
REVERT: B  311 MET cc_start: 0.7816 (ptt) cc_final: 0.7133 (tpt)
REVERT: B  322 MET cc_start: 0.7750 (mtt) cc_final: 0.7470 (mtt)
REVERT: B  334 TRP cc_start: 0.7730 (p90) cc_final: 0.4643 (m100)
REVERT: C  313 PHE cc_start: 0.8056 (m-10) cc_final: 0.7200 (m-80)
REVERT: D  334 TRP cc_start: 0.7983 (p90) cc_final: 0.7649 (p90)
REVERT: E  313 PHE cc_start: 0.8164 (m-10) cc_final: 0.7912 (m-80)
REVERT: G  307 MET cc_start: 0.6436 (ttt) cc_final: 0.6001 (ttt)
REVERT: G  313 PHE cc_start: 0.8053 (m-10) cc_final: 0.7852 (m-80)
REVERT: H  313 PHE cc_start: 0.8675 (m-10) cc_final: 0.8426 (m-10)
REVERT: H  339 MET cc_start: 0.8103 (mtp) cc_final: 0.7756 (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: 0.8224 (m-10)
REVERT: J  339 MET cc_start: 0.8341 (mtp) cc_final: 0.8085 (mtt)
REVERT: L  313 PHE cc_start: 0.8757 (m-10) cc_final: 0.6526 (p90)
REVERT: L  337 MET cc_start: 0.8084 (mtp) cc_final: 0.7336 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1100
  time to fit residues: 33.8236
Evaluate side-chains
  157 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4250 r_free = 0.4250 target = 0.215449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.126530 restraints weight = 5969.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.131571 restraints weight = 3024.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.135114 restraints weight = 1854.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6660
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3744  Z= 0.156
  Angle     :  0.724   5.011   4980  Z= 0.396
  Chirality :  0.039   0.133    480
  Planarity :  0.004   0.043    684
  Dihedral  :  6.611  32.202    528
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.78 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.41 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 334 
 PHE   0.020   0.003   PHE G 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05983 (   45)
  hydrogen bonds       : angle       5.33241 (  135)
  covalent geometry    : bond        0.00347 ( 3744)
  covalent geometry    : angle       0.72381 ( 4980)

*********************** 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
  189 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.7181 (m-80) cc_final: 0.5077 (p90)
REVERT: A  319 ASN cc_start: 0.8244 (m-40) cc_final: 0.7934 (m-40)
REVERT: A  323 MET cc_start: 0.7536 (mtt) cc_final: 0.7130 (mtt)
REVERT: A  343 GLN cc_start: 0.8038 (mt0) cc_final: 0.7774 (tt0)
REVERT: B  311 MET cc_start: 0.7719 (ptp) cc_final: 0.6004 (mmt)
REVERT: B  334 TRP cc_start: 0.8114 (p90) cc_final: 0.3673 (m100)
REVERT: B  340 LEU cc_start: 0.8748 (tt) cc_final: 0.8305 (tt)
REVERT: B  344 GLN cc_start: 0.7655 (mt0) cc_final: 0.6899 (mt0)
REVERT: C  316 PHE cc_start: 0.8282 (m-80) cc_final: 0.7675 (m-80)
REVERT: C  336 MET cc_start: 0.8355 (tmm) cc_final: 0.8151 (tpt)
REVERT: D  311 MET cc_start: 0.8758 (ptm) cc_final: 0.8101 (ptt)
REVERT: D  313 PHE cc_start: 0.8731 (m-10) cc_final: 0.7533 (m-10)
REVERT: D  337 MET cc_start: 0.8885 (mtp) cc_final: 0.7837 (mtp)
REVERT: D  344 GLN cc_start: 0.8125 (mt0) cc_final: 0.7738 (mt0)
REVERT: E  336 MET cc_start: 0.7768 (tmm) cc_final: 0.6827 (tmm)
REVERT: F  307 MET cc_start: 0.8762 (ttt) cc_final: 0.8476 (ttt)
REVERT: F  311 MET cc_start: 0.8132 (ptp) cc_final: 0.7796 (ptm)
REVERT: F  313 PHE cc_start: 0.8504 (m-10) cc_final: 0.8076 (m-80)
REVERT: F  337 MET cc_start: 0.9178 (mtp) cc_final: 0.8829 (mtt)
REVERT: F  344 GLN cc_start: 0.8226 (mt0) cc_final: 0.7372 (mt0)
REVERT: G  317 SER cc_start: 0.8209 (t) cc_final: 0.7646 (m)
REVERT: G  323 MET cc_start: 0.7514 (mtp) cc_final: 0.6854 (mtt)
REVERT: H  334 TRP cc_start: 0.8729 (p90) cc_final: 0.8395 (p90)
REVERT: H  344 GLN cc_start: 0.8343 (mt0) cc_final: 0.7840 (mt0)
REVERT: I  313 PHE cc_start: 0.8270 (m-10) cc_final: 0.7583 (m-80)
REVERT: I  337 MET cc_start: 0.7312 (tpp) cc_final: 0.6751 (tpp)
REVERT: J  311 MET cc_start: 0.7857 (ptp) cc_final: 0.7135 (ptm)
REVERT: J  313 PHE cc_start: 0.8344 (m-10) cc_final: 0.8087 (m-10)
REVERT: J  337 MET cc_start: 0.8610 (mtt) cc_final: 0.8174 (mtp)
REVERT: J  344 GLN cc_start: 0.7968 (mt0) cc_final: 0.7059 (mt0)
REVERT: J  346 GLN cc_start: 0.7829 (mp10) cc_final: 0.7623 (mp10)
REVERT: K  343 GLN cc_start: 0.7773 (mt0) cc_final: 0.7288 (tt0)
REVERT: L  311 MET cc_start: 0.8742 (ptm) cc_final: 0.8478 (ptt)
REVERT: L  344 GLN cc_start: 0.8518 (mt0) cc_final: 0.8235 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1111
  time to fit residues: 26.9486
Evaluate side-chains
  153 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 331 GLN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 345 ASN
** I 331 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.116576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.095493 restraints weight = 5737.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.098888 restraints weight = 3127.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.101476 restraints weight = 2113.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.5473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3744  Z= 0.237
  Angle     :  0.743   6.038   4980  Z= 0.400
  Chirality :  0.038   0.125    480
  Planarity :  0.004   0.037    684
  Dihedral  :  6.857  31.559    528
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 20.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  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 : 0.78 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.39 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.34 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP E 334 
 PHE   0.018   0.003   PHE E 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04964 (   45)
  hydrogen bonds       : angle       6.09405 (  135)
  covalent geometry    : bond        0.00533 ( 3744)
  covalent geometry    : angle       0.74314 ( 4980)

*********************** 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
  159 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8549 (t) cc_final: 0.8000 (m)
REVERT: B  311 MET cc_start: 0.8044 (ptp) cc_final: 0.6650 (mmt)
REVERT: B  344 GLN cc_start: 0.8496 (mt0) cc_final: 0.8247 (mt0)
REVERT: E  317 SER cc_start: 0.8683 (t) cc_final: 0.8370 (m)
REVERT: E  345 ASN cc_start: 0.7510 (m-40) cc_final: 0.7123 (t0)
REVERT: F  307 MET cc_start: 0.9021 (ttt) cc_final: 0.8370 (ttt)
REVERT: F  313 PHE cc_start: 0.9015 (m-10) cc_final: 0.8612 (m-80)
REVERT: F  344 GLN cc_start: 0.8788 (mt0) cc_final: 0.8307 (mt0)
REVERT: G  317 SER cc_start: 0.8653 (t) cc_final: 0.8138 (m)
REVERT: G  323 MET cc_start: 0.7718 (mtp) cc_final: 0.7115 (mtt)
REVERT: H  316 PHE cc_start: 0.8168 (m-80) cc_final: 0.7626 (m-80)
REVERT: H  337 MET cc_start: 0.9097 (mtt) cc_final: 0.8204 (mtt)
REVERT: H  344 GLN cc_start: 0.8796 (mt0) cc_final: 0.8579 (mt0)
REVERT: I  307 MET cc_start: 0.7704 (tpp) cc_final: 0.7053 (tpp)
REVERT: I  336 MET cc_start: 0.8062 (tmm) cc_final: 0.7371 (tmm)
REVERT: J  307 MET cc_start: 0.8774 (ttt) cc_final: 0.8423 (ttt)
REVERT: J  311 MET cc_start: 0.8208 (ptp) cc_final: 0.7803 (ptm)
REVERT: J  313 PHE cc_start: 0.8887 (m-10) cc_final: 0.8143 (m-10)
REVERT: J  331 GLN cc_start: 0.8945 (mt0) cc_final: 0.8682 (mt0)
REVERT: J  337 MET cc_start: 0.8937 (mtt) cc_final: 0.8229 (mtt)
REVERT: J  344 GLN cc_start: 0.8667 (mt0) cc_final: 0.8321 (mt0)
REVERT: L  313 PHE cc_start: 0.8309 (m-10) cc_final: 0.5949 (p90)
REVERT: L  331 GLN cc_start: 0.8645 (mt0) cc_final: 0.8369 (mt0)
REVERT: L  337 MET cc_start: 0.8611 (mtp) cc_final: 0.8250 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1164
  time to fit residues: 23.8933
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  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0010
   chunk 9 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
C 344 GLN
D 319 ASN
D 344 GLN
D 345 ASN
F 345 ASN
G 331 GLN
G 346 GLN
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 345 ASN
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.207277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.119498 restraints weight = 6013.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.123999 restraints weight = 3285.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.127085 restraints weight = 2170.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.5884

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= 0.135
  Angle     :  0.655   5.465   4980  Z= 0.346
  Chirality :  0.037   0.119    480
  Planarity :  0.003   0.026    684
  Dihedral  :  6.339  30.432    528
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  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 : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.32 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP G 334 
 PHE   0.015   0.002   PHE J 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04833 (   45)
  hydrogen bonds       : angle       5.72190 (  135)
  covalent geometry    : bond        0.00311 ( 3744)
  covalent geometry    : angle       0.65527 ( 4980)

*********************** 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
  154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.8334 (t) cc_final: 0.7999 (m)
REVERT: A  319 ASN cc_start: 0.8636 (m-40) cc_final: 0.8371 (m-40)
REVERT: B  311 MET cc_start: 0.7716 (ptp) cc_final: 0.6408 (mmt)
REVERT: B  313 PHE cc_start: 0.8439 (m-80) cc_final: 0.8226 (m-80)
REVERT: B  344 GLN cc_start: 0.8569 (mt0) cc_final: 0.8164 (tt0)
REVERT: C  323 MET cc_start: 0.8034 (mtt) cc_final: 0.7759 (mtt)
REVERT: E  307 MET cc_start: 0.7816 (tpt) cc_final: 0.7509 (tpt)
REVERT: E  317 SER cc_start: 0.8590 (t) cc_final: 0.8334 (m)
REVERT: F  307 MET cc_start: 0.8870 (ttt) cc_final: 0.8345 (ttt)
REVERT: F  339 MET cc_start: 0.8094 (mtp) cc_final: 0.7671 (mtp)
REVERT: F  344 GLN cc_start: 0.8694 (mt0) cc_final: 0.8258 (mt0)
REVERT: G  317 SER cc_start: 0.8711 (t) cc_final: 0.8150 (m)
REVERT: G  323 MET cc_start: 0.7484 (mtp) cc_final: 0.6875 (mtt)
REVERT: H  337 MET cc_start: 0.8480 (mtt) cc_final: 0.7771 (mtt)
REVERT: I  307 MET cc_start: 0.7720 (tpp) cc_final: 0.6710 (tpp)
REVERT: I  317 SER cc_start: 0.8446 (t) cc_final: 0.8186 (m)
REVERT: I  336 MET cc_start: 0.7601 (tmm) cc_final: 0.7107 (tmm)
REVERT: I  337 MET cc_start: 0.7351 (tpp) cc_final: 0.6888 (tpp)
REVERT: J  344 GLN cc_start: 0.8510 (mt0) cc_final: 0.7940 (mt0)
REVERT: K  339 MET cc_start: 0.8275 (mtp) cc_final: 0.7367 (mtp)
REVERT: L  313 PHE cc_start: 0.7916 (m-10) cc_final: 0.5931 (p90)
REVERT: L  344 GLN cc_start: 0.8577 (mt0) cc_final: 0.8341 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1187
  time to fit residues: 23.4275
Evaluate side-chains
  129 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN
C 344 GLN
D 345 ASN
F 345 ASN
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 344 GLN
** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 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 = 0.4167 r_free = 0.4167 target = 0.189929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.111377 restraints weight = 6258.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.115460 restraints weight = 3443.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.118233 restraints weight = 2336.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.6303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3744  Z= 0.245
  Angle     :  0.708   6.497   4980  Z= 0.380
  Chirality :  0.038   0.118    480
  Planarity :  0.003   0.025    684
  Dihedral  :  6.607  29.782    528
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 20.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.40 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.34 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP E 334 
 PHE   0.015   0.002   PHE L 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04872 (   45)
  hydrogen bonds       : angle       5.98974 (  135)
  covalent geometry    : bond        0.00545 ( 3744)
  covalent geometry    : angle       0.70800 ( 4980)

*********************** 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
  145 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.8576 (t) cc_final: 0.8183 (m)
REVERT: B  311 MET cc_start: 0.7787 (ptp) cc_final: 0.6452 (mmt)
REVERT: C  344 GLN cc_start: 0.9041 (mt0) cc_final: 0.7984 (mp10)
REVERT: E  317 SER cc_start: 0.8512 (t) cc_final: 0.8247 (m)
REVERT: F  307 MET cc_start: 0.8933 (ttt) cc_final: 0.8687 (ttt)
REVERT: F  344 GLN cc_start: 0.8710 (mt0) cc_final: 0.8213 (mt0)
REVERT: G  317 SER cc_start: 0.8876 (t) cc_final: 0.8486 (m)
REVERT: G  323 MET cc_start: 0.7514 (mtp) cc_final: 0.6943 (mtt)
REVERT: H  337 MET cc_start: 0.8984 (mtt) cc_final: 0.8429 (mtt)
REVERT: I  307 MET cc_start: 0.7708 (tpp) cc_final: 0.6233 (tpp)
REVERT: I  317 SER cc_start: 0.8428 (t) cc_final: 0.8186 (m)
REVERT: I  336 MET cc_start: 0.7830 (tmm) cc_final: 0.7622 (tmm)
REVERT: J  337 MET cc_start: 0.9083 (mtt) cc_final: 0.8599 (mtt)
REVERT: J  344 GLN cc_start: 0.8568 (mt0) cc_final: 0.8016 (mt0)
REVERT: K  339 MET cc_start: 0.8097 (mtp) cc_final: 0.6972 (mtp)
REVERT: L  344 GLN cc_start: 0.8623 (mt0) cc_final: 0.8285 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1149
  time to fit residues: 21.4462
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  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0370
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
B 344 GLN
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 345 ASN
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 346 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 = 0.4280 r_free = 0.4280 target = 0.207384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.121589 restraints weight = 6052.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.126139 restraints weight = 3210.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.129110 restraints weight = 2102.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.6538

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= 0.117
  Angle     :  0.627   5.858   4980  Z= 0.330
  Chirality :  0.037   0.114    480
  Planarity :  0.002   0.024    684
  Dihedral  :  6.234  30.155    528
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  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 : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.27 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP F 334 
 PHE   0.008   0.002   PHE F 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (   45)
  hydrogen bonds       : angle       5.72143 (  135)
  covalent geometry    : bond        0.00271 ( 3744)
  covalent geometry    : angle       0.62658 ( 4980)

*********************** 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  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.8320 (t) cc_final: 0.7940 (m)
REVERT: A  339 MET cc_start: 0.8054 (mtp) cc_final: 0.7708 (mtm)
REVERT: B  311 MET cc_start: 0.7348 (ptp) cc_final: 0.6280 (mmt)
REVERT: B  327 GLN cc_start: 0.7277 (tt0) cc_final: 0.6810 (mm110)
REVERT: C  344 GLN cc_start: 0.8942 (mt0) cc_final: 0.8260 (mp10)
REVERT: D  313 PHE cc_start: 0.9041 (m-10) cc_final: 0.8802 (m-10)
REVERT: E  307 MET cc_start: 0.7833 (tpt) cc_final: 0.7509 (tpt)
REVERT: E  317 SER cc_start: 0.8379 (t) cc_final: 0.8165 (m)
REVERT: E  336 MET cc_start: 0.7062 (tmm) cc_final: 0.6814 (tmm)
REVERT: F  344 GLN cc_start: 0.8593 (mt0) cc_final: 0.8288 (mt0)
REVERT: G  317 SER cc_start: 0.8790 (t) cc_final: 0.8439 (m)
REVERT: G  323 MET cc_start: 0.7373 (mtp) cc_final: 0.6729 (mtt)
REVERT: I  307 MET cc_start: 0.7763 (tpp) cc_final: 0.6882 (tpp)
REVERT: I  336 MET cc_start: 0.7785 (tmm) cc_final: 0.6977 (tmm)
REVERT: I  337 MET cc_start: 0.7224 (tpp) cc_final: 0.6380 (tpp)
REVERT: J  316 PHE cc_start: 0.8631 (m-10) cc_final: 0.8431 (m-80)
REVERT: J  337 MET cc_start: 0.9018 (mtt) cc_final: 0.8680 (mtt)
REVERT: J  344 GLN cc_start: 0.8519 (mt0) cc_final: 0.8056 (mt0)
REVERT: K  339 MET cc_start: 0.8155 (mtp) cc_final: 0.7599 (mtp)
REVERT: L  313 PHE cc_start: 0.8011 (m-10) cc_final: 0.5651 (p90)
REVERT: L  344 GLN cc_start: 0.8485 (mt0) cc_final: 0.8210 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1076
  time to fit residues: 20.1910
Evaluate side-chains
  119 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.3980
   chunk 16 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN
** L 346 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 = 0.4290 r_free = 0.4290 target = 0.210271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.120276 restraints weight = 5949.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.124632 restraints weight = 3247.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.127669 restraints weight = 2152.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.6730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3744  Z= 0.144
  Angle     :  0.635   5.575   4980  Z= 0.330
  Chirality :  0.036   0.115    480
  Planarity :  0.002   0.022    684
  Dihedral  :  6.128  28.992    528
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.27 (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
 TRP   0.012   0.002   TRP D 334 
 PHE   0.009   0.002   PHE A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04063 (   45)
  hydrogen bonds       : angle       5.57134 (  135)
  covalent geometry    : bond        0.00333 ( 3744)
  covalent geometry    : angle       0.63531 ( 4980)

*********************** 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
  142 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.8447 (t) cc_final: 0.8111 (m)
REVERT: A  339 MET cc_start: 0.7932 (mtp) cc_final: 0.7683 (mtm)
REVERT: B  311 MET cc_start: 0.7714 (ptp) cc_final: 0.6460 (mmt)
REVERT: B  327 GLN cc_start: 0.7284 (tt0) cc_final: 0.6846 (mm110)
REVERT: C  323 MET cc_start: 0.8097 (mtt) cc_final: 0.7852 (mtt)
REVERT: D  307 MET cc_start: 0.9206 (ttm) cc_final: 0.8939 (ttm)
REVERT: D  313 PHE cc_start: 0.9124 (m-10) cc_final: 0.8790 (m-10)
REVERT: D  337 MET cc_start: 0.8361 (mtt) cc_final: 0.8070 (mtt)
REVERT: E  307 MET cc_start: 0.7624 (tpt) cc_final: 0.7135 (tpt)
REVERT: F  344 GLN cc_start: 0.8620 (mt0) cc_final: 0.8336 (mt0)
REVERT: G  317 SER cc_start: 0.8844 (t) cc_final: 0.8509 (m)
REVERT: G  323 MET cc_start: 0.7357 (mtp) cc_final: 0.6738 (mtt)
REVERT: I  307 MET cc_start: 0.7802 (tpp) cc_final: 0.6813 (tpp)
REVERT: I  336 MET cc_start: 0.7630 (tmm) cc_final: 0.7428 (tmm)
REVERT: J  344 GLN cc_start: 0.8571 (mt0) cc_final: 0.7972 (mt0)
REVERT: K  339 MET cc_start: 0.8067 (mtp) cc_final: 0.7564 (mtp)
REVERT: L  313 PHE cc_start: 0.8031 (m-10) cc_final: 0.5737 (p90)
REVERT: L  344 GLN cc_start: 0.8470 (mt0) cc_final: 0.8260 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1108
  time to fit residues: 20.2934
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  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 33 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.209040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.116982 restraints weight = 6054.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.121210 restraints weight = 3312.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.124160 restraints weight = 2213.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.6867

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= 0.191
  Angle     :  0.677   7.937   4980  Z= 0.352
  Chirality :  0.036   0.114    480
  Planarity :  0.003   0.022    684
  Dihedral  :  6.255  28.724    528
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.010   0.002   TRP L 334 
 PHE   0.016   0.002   PHE J 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (   45)
  hydrogen bonds       : angle       5.59072 (  135)
  covalent geometry    : bond        0.00429 ( 3744)
  covalent geometry    : angle       0.67726 ( 4980)

*********************** 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  : 0.537 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8540 (t) cc_final: 0.8197 (m)
REVERT: A  339 MET cc_start: 0.8002 (mtp) cc_final: 0.7698 (mtm)
REVERT: B  311 MET cc_start: 0.7830 (ptp) cc_final: 0.6479 (mmt)
REVERT: D  307 MET cc_start: 0.9199 (ttm) cc_final: 0.8958 (ttm)
REVERT: D  337 MET cc_start: 0.8649 (mtt) cc_final: 0.8310 (mtt)
REVERT: E  333 SER cc_start: 0.8978 (p) cc_final: 0.8772 (p)
REVERT: F  344 GLN cc_start: 0.8575 (mt0) cc_final: 0.8317 (mt0)
REVERT: G  317 SER cc_start: 0.8866 (t) cc_final: 0.8533 (m)
REVERT: G  323 MET cc_start: 0.7292 (mtp) cc_final: 0.6698 (mtt)
REVERT: H  337 MET cc_start: 0.8472 (mtp) cc_final: 0.8133 (mtt)
REVERT: I  337 MET cc_start: 0.6815 (mmt) cc_final: 0.6606 (mmt)
REVERT: J  307 MET cc_start: 0.8622 (ttt) cc_final: 0.8332 (ttt)
REVERT: J  344 GLN cc_start: 0.8514 (mt0) cc_final: 0.8101 (mt0)
REVERT: L  313 PHE cc_start: 0.8189 (m-10) cc_final: 0.5911 (p90)
REVERT: L  337 MET cc_start: 0.8582 (mmm) cc_final: 0.8079 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1186
  time to fit residues: 20.8402
Evaluate side-chains
  118 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 GLN
J 345 ASN
L 344 GLN
** L 346 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 = 0.4238 r_free = 0.4238 target = 0.184049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.116501 restraints weight = 6192.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.120525 restraints weight = 3549.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.123142 restraints weight = 2409.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.7006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3744  Z= 0.233
  Angle     :  0.724   9.993   4980  Z= 0.374
  Chirality :  0.037   0.117    480
  Planarity :  0.003   0.023    684
  Dihedral  :  6.407  28.458    528
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 20.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.35 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 334 
 PHE   0.012   0.002   PHE F 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (   45)
  hydrogen bonds       : angle       5.90520 (  135)
  covalent geometry    : bond        0.00520 ( 3744)
  covalent geometry    : angle       0.72420 ( 4980)

*********************** 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: 0
    poor density    : 133
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8590 (t) cc_final: 0.8212 (m)
REVERT: B  311 MET cc_start: 0.7848 (ptp) cc_final: 0.6572 (mmt)
REVERT: C  323 MET cc_start: 0.8051 (mtt) cc_final: 0.7816 (mtt)
REVERT: C  344 GLN cc_start: 0.8943 (mt0) cc_final: 0.8233 (mp10)
REVERT: D  313 PHE cc_start: 0.9187 (m-10) cc_final: 0.8837 (m-10)
REVERT: D  337 MET cc_start: 0.8733 (mtt) cc_final: 0.8436 (mtt)
REVERT: E  307 MET cc_start: 0.7545 (tpt) cc_final: 0.7339 (tpt)
REVERT: F  344 GLN cc_start: 0.8611 (mt0) cc_final: 0.8365 (mt0)
REVERT: G  317 SER cc_start: 0.8954 (t) cc_final: 0.8641 (m)
REVERT: G  323 MET cc_start: 0.7310 (mtp) cc_final: 0.6702 (mtt)
REVERT: H  346 GLN cc_start: 0.7754 (mp10) cc_final: 0.7436 (mm-40)
REVERT: I  307 MET cc_start: 0.7610 (tpp) cc_final: 0.7020 (tpp)
REVERT: J  344 GLN cc_start: 0.8787 (mt0) cc_final: 0.8510 (mt0)
REVERT: L  313 PHE cc_start: 0.8239 (m-10) cc_final: 0.5904 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1216
  time to fit residues: 20.8073
Evaluate side-chains
  118 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 GLN
J 345 ASN
** 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 = 0.4266 r_free = 0.4266 target = 0.201601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.119161 restraints weight = 5974.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.123578 restraints weight = 3195.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.126544 restraints weight = 2101.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.7166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3744  Z= 0.155
  Angle     :  0.690  11.388   4980  Z= 0.349
  Chirality :  0.037   0.116    480
  Planarity :  0.002   0.022    684
  Dihedral  :  6.224  27.760    528
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.33 (0.20), 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
 TRP   0.008   0.002   TRP D 334 
 PHE   0.012   0.002   PHE J 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (   45)
  hydrogen bonds       : angle       5.61696 (  135)
  covalent geometry    : bond        0.00357 ( 3744)
  covalent geometry    : angle       0.68961 ( 4980)

********************** 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
  134 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8574 (t) cc_final: 0.8234 (m)
REVERT: B  311 MET cc_start: 0.7542 (ptp) cc_final: 0.6487 (mmt)
REVERT: C  323 MET cc_start: 0.7962 (mtt) cc_final: 0.7759 (mtt)
REVERT: C  344 GLN cc_start: 0.8871 (mt0) cc_final: 0.8369 (mp10)
REVERT: D  307 MET cc_start: 0.8848 (ttm) cc_final: 0.8576 (ttm)
REVERT: D  313 PHE cc_start: 0.9185 (m-10) cc_final: 0.8784 (m-10)
REVERT: D  337 MET cc_start: 0.8687 (mtt) cc_final: 0.8337 (mtt)
REVERT: F  337 MET cc_start: 0.8917 (mtt) cc_final: 0.8549 (mtt)
REVERT: F  344 GLN cc_start: 0.8584 (mt0) cc_final: 0.8383 (mt0)
REVERT: G  307 MET cc_start: 0.7649 (tpt) cc_final: 0.7359 (tpt)
REVERT: G  317 SER cc_start: 0.8884 (t) cc_final: 0.8610 (m)
REVERT: G  323 MET cc_start: 0.7274 (mtp) cc_final: 0.6610 (mtt)
REVERT: I  307 MET cc_start: 0.7727 (tpp) cc_final: 0.7025 (tpp)
REVERT: I  337 MET cc_start: 0.7005 (mmt) cc_final: 0.6728 (mmt)
REVERT: J  337 MET cc_start: 0.8489 (mtt) cc_final: 0.8198 (mtt)
REVERT: J  344 GLN cc_start: 0.8642 (mt0) cc_final: 0.8413 (mt0)
REVERT: L  313 PHE cc_start: 0.8064 (m-10) cc_final: 0.6092 (p90)
REVERT: L  337 MET cc_start: 0.8363 (mmm) cc_final: 0.7844 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1129
  time to fit residues: 19.5487
Evaluate side-chains
  117 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0870
   chunk 1 optimal weight:    0.3980
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
F 327 GLN
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.206559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.123842 restraints weight = 5874.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.128522 restraints weight = 3144.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.131675 restraints weight = 2068.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.7339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3744  Z= 0.125
  Angle     :  0.664  10.877   4980  Z= 0.333
  Chirality :  0.037   0.115    480
  Planarity :  0.002   0.022    684
  Dihedral  :  6.142  27.618    528
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.30 (0.21), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 334 
 PHE   0.016   0.002   PHE F 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03697 (   45)
  hydrogen bonds       : angle       5.37126 (  135)
  covalent geometry    : bond        0.00296 ( 3744)
  covalent geometry    : angle       0.66416 ( 4980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1568.42 seconds
wall clock time: 27 minutes 48.79 seconds (1668.79 seconds total)