Starting phenix.real_space_refine
on Mon Jan 13 19:22:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qxa_18716/01_2025/8qxa_18716.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qxa_18716/01_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_18716/01_2025/8qxa_18716.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qxa_18716/01_2025/8qxa_18716.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qxa_18716/01_2025/8qxa_18716.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qxa_18716/01_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-5571/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: 2.52, per 1000 atoms: 0.68
  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: 0.81
  Conformation dependent library (CDL) restraints added in 460.2 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: 0.43
  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: 0.78

  Time building geometry restraints manager: 0.91 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:             0.520
  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:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.770
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.450
-------------------------------------------------------------------------------
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= 0.923
  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 

*********************** 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  : 0.392 
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: 0.1072
  time to fit residues: 33.1444
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  : 0.398 
-------------------------------------------------------------------------------
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 = 0.215450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.126516 restraints weight = 5969.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.131606 restraints weight = 3026.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.135139 restraints weight = 1851.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
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= 0.238
  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 

*********************** 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  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.7187 (m-80) cc_final: 0.5080 (p90)
REVERT: A  319 ASN cc_start: 0.8245 (m-40) cc_final: 0.7936 (m-40)
REVERT: A  323 MET cc_start: 0.7538 (mtt) cc_final: 0.7132 (mtt)
REVERT: A  343 GLN cc_start: 0.8036 (mt0) cc_final: 0.7773 (tt0)
REVERT: B  311 MET cc_start: 0.7725 (ptp) cc_final: 0.6010 (mmt)
REVERT: B  334 TRP cc_start: 0.8115 (p90) cc_final: 0.3674 (m100)
REVERT: B  340 LEU cc_start: 0.8746 (tt) cc_final: 0.8303 (tt)
REVERT: B  344 GLN cc_start: 0.7647 (mt0) cc_final: 0.6890 (mt0)
REVERT: C  316 PHE cc_start: 0.8282 (m-80) cc_final: 0.7678 (m-80)
REVERT: C  336 MET cc_start: 0.8353 (tmm) cc_final: 0.8151 (tpt)
REVERT: D  311 MET cc_start: 0.8753 (ptm) cc_final: 0.8104 (ptt)
REVERT: D  313 PHE cc_start: 0.8738 (m-10) cc_final: 0.7541 (m-10)
REVERT: D  337 MET cc_start: 0.8884 (mtp) cc_final: 0.7838 (mtp)
REVERT: D  344 GLN cc_start: 0.8119 (mt0) cc_final: 0.7731 (mt0)
REVERT: E  336 MET cc_start: 0.7764 (tmm) cc_final: 0.6827 (tmm)
REVERT: F  307 MET cc_start: 0.8762 (ttt) cc_final: 0.8473 (ttt)
REVERT: F  311 MET cc_start: 0.8134 (ptp) cc_final: 0.7799 (ptm)
REVERT: F  313 PHE cc_start: 0.8510 (m-10) cc_final: 0.8083 (m-80)
REVERT: F  337 MET cc_start: 0.9179 (mtp) cc_final: 0.8829 (mtt)
REVERT: F  344 GLN cc_start: 0.8214 (mt0) cc_final: 0.7362 (mt0)
REVERT: G  317 SER cc_start: 0.8210 (t) cc_final: 0.7647 (m)
REVERT: G  323 MET cc_start: 0.7516 (mtp) cc_final: 0.6855 (mtt)
REVERT: H  334 TRP cc_start: 0.8726 (p90) cc_final: 0.8393 (p90)
REVERT: H  344 GLN cc_start: 0.8335 (mt0) cc_final: 0.7830 (mt0)
REVERT: I  313 PHE cc_start: 0.8274 (m-10) cc_final: 0.7587 (m-80)
REVERT: I  337 MET cc_start: 0.7312 (tpp) cc_final: 0.6751 (tpp)
REVERT: J  311 MET cc_start: 0.7858 (ptp) cc_final: 0.7138 (ptm)
REVERT: J  313 PHE cc_start: 0.8347 (m-10) cc_final: 0.8087 (m-10)
REVERT: J  337 MET cc_start: 0.8611 (mtt) cc_final: 0.8175 (mtp)
REVERT: J  344 GLN cc_start: 0.7960 (mt0) cc_final: 0.7050 (mt0)
REVERT: J  346 GLN cc_start: 0.7828 (mp10) cc_final: 0.7624 (mp10)
REVERT: K  343 GLN cc_start: 0.7771 (mt0) cc_final: 0.7286 (tt0)
REVERT: L  311 MET cc_start: 0.8742 (ptm) cc_final: 0.8480 (ptt)
REVERT: L  344 GLN cc_start: 0.8519 (mt0) cc_final: 0.8235 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1204
  time to fit residues: 29.3553
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:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.115195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.094404 restraints weight = 5738.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.097844 restraints weight = 3166.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.100170 restraints weight = 2128.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.5450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3744  Z= 0.386
  Angle     :  0.757   6.250   4980  Z= 0.406
  Chirality :  0.038   0.124    480
  Planarity :  0.004   0.037    684
  Dihedral  :  6.877  31.628    528
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 21.53
  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: -4.41 (0.19), 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   0.014   0.003   TRP E 334 
 PHE   0.018   0.003   PHE E 313 

*********************** 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  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.8570 (t) cc_final: 0.8017 (m)
REVERT: B  311 MET cc_start: 0.8067 (ptp) cc_final: 0.6628 (mmt)
REVERT: D  337 MET cc_start: 0.9017 (mtp) cc_final: 0.8802 (mtt)
REVERT: E  317 SER cc_start: 0.8744 (t) cc_final: 0.8291 (m)
REVERT: E  345 ASN cc_start: 0.7510 (m-40) cc_final: 0.7129 (t0)
REVERT: F  307 MET cc_start: 0.9005 (ttt) cc_final: 0.8302 (ttt)
REVERT: F  313 PHE cc_start: 0.9014 (m-10) cc_final: 0.8683 (m-80)
REVERT: F  344 GLN cc_start: 0.8784 (mt0) cc_final: 0.8289 (mt0)
REVERT: G  323 MET cc_start: 0.7732 (mtp) cc_final: 0.7130 (mtt)
REVERT: H  316 PHE cc_start: 0.8230 (m-80) cc_final: 0.7825 (m-80)
REVERT: H  337 MET cc_start: 0.9091 (mtt) cc_final: 0.8151 (mtt)
REVERT: H  344 GLN cc_start: 0.8810 (mt0) cc_final: 0.8578 (mt0)
REVERT: I  307 MET cc_start: 0.7734 (tpp) cc_final: 0.7025 (tpp)
REVERT: I  336 MET cc_start: 0.8062 (tmm) cc_final: 0.7372 (tmm)
REVERT: J  307 MET cc_start: 0.8772 (ttt) cc_final: 0.8352 (ttt)
REVERT: J  311 MET cc_start: 0.8224 (ptp) cc_final: 0.7798 (ptm)
REVERT: J  313 PHE cc_start: 0.8917 (m-10) cc_final: 0.8454 (m-10)
REVERT: J  331 GLN cc_start: 0.8976 (mt0) cc_final: 0.8685 (mt0)
REVERT: J  344 GLN cc_start: 0.8664 (mt0) cc_final: 0.8323 (mt0)
REVERT: L  331 GLN cc_start: 0.8667 (mt0) cc_final: 0.8368 (mt0)
REVERT: L  337 MET cc_start: 0.8638 (mtp) cc_final: 0.8386 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1152
  time to fit residues: 23.7076
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  : 0.399 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0010
   chunk 9 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
B 344 GLN
D 319 ASN
D 344 GLN
D 345 ASN
F 345 ASN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.212237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.118785 restraints weight = 6064.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.123378 restraints weight = 3281.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.126210 restraints weight = 2164.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.5878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3744  Z= 0.199
  Angle     :  0.648   6.101   4980  Z= 0.342
  Chirality :  0.037   0.120    480
  Planarity :  0.003   0.027    684
  Dihedral  :  6.286  30.325    528
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 17.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  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: -4.31 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E 334 
 PHE   0.011   0.002   PHE F 313 

*********************** 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
  150 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8412 (t) cc_final: 0.8051 (m)
REVERT: A  323 MET cc_start: 0.7311 (mtt) cc_final: 0.6783 (mtt)
REVERT: B  311 MET cc_start: 0.7830 (ptp) cc_final: 0.6496 (mmt)
REVERT: C  323 MET cc_start: 0.8049 (mtt) cc_final: 0.7816 (mtt)
REVERT: E  307 MET cc_start: 0.7799 (tpt) cc_final: 0.7504 (tpt)
REVERT: E  317 SER cc_start: 0.8562 (t) cc_final: 0.8292 (m)
REVERT: F  307 MET cc_start: 0.8839 (ttt) cc_final: 0.8216 (ttt)
REVERT: F  313 PHE cc_start: 0.9169 (m-10) cc_final: 0.8761 (m-80)
REVERT: F  344 GLN cc_start: 0.8669 (mt0) cc_final: 0.8297 (mt0)
REVERT: G  317 SER cc_start: 0.8722 (t) cc_final: 0.8201 (m)
REVERT: G  323 MET cc_start: 0.7521 (mtp) cc_final: 0.6912 (mtt)
REVERT: H  316 PHE cc_start: 0.8144 (m-80) cc_final: 0.7729 (m-80)
REVERT: H  337 MET cc_start: 0.8549 (mtt) cc_final: 0.7876 (mtt)
REVERT: I  307 MET cc_start: 0.7690 (tpp) cc_final: 0.6604 (tpp)
REVERT: I  317 SER cc_start: 0.8467 (t) cc_final: 0.8222 (m)
REVERT: I  336 MET cc_start: 0.7675 (tmm) cc_final: 0.7154 (tmm)
REVERT: I  337 MET cc_start: 0.7296 (tpp) cc_final: 0.6808 (tpp)
REVERT: J  307 MET cc_start: 0.8721 (ttt) cc_final: 0.8471 (ttt)
REVERT: J  313 PHE cc_start: 0.8845 (m-10) cc_final: 0.8608 (m-10)
REVERT: J  337 MET cc_start: 0.9047 (mtt) cc_final: 0.8260 (mtt)
REVERT: J  344 GLN cc_start: 0.8498 (mt0) cc_final: 0.7935 (mt0)
REVERT: K  307 MET cc_start: 0.7060 (tpp) cc_final: 0.6683 (tpp)
REVERT: K  322 MET cc_start: 0.6587 (mtp) cc_final: 0.6358 (mtp)
REVERT: K  339 MET cc_start: 0.8321 (mtp) cc_final: 0.7418 (mtp)
REVERT: L  313 PHE cc_start: 0.8091 (m-10) cc_final: 0.5980 (p90)
REVERT: L  344 GLN cc_start: 0.8552 (mt0) cc_final: 0.8350 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1187
  time to fit residues: 22.8660
Evaluate side-chains
  128 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 345 ASN
** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4228 r_free = 0.4228 target = 0.201689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.117726 restraints weight = 6133.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.122165 restraints weight = 3300.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.125315 restraints weight = 2188.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.6246

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= 0.235
  Angle     :  0.628   4.616   4980  Z= 0.337
  Chirality :  0.037   0.115    480
  Planarity :  0.003   0.025    684
  Dihedral  :  6.269  29.407    528
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  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 (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 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E 334 
 PHE   0.010   0.002   PHE H 316 

*********************** 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
  146 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8343 (t) cc_final: 0.7954 (m)
REVERT: A  323 MET cc_start: 0.7308 (mtt) cc_final: 0.7041 (mtp)
REVERT: B  311 MET cc_start: 0.7577 (ptp) cc_final: 0.6298 (mmt)
REVERT: D  313 PHE cc_start: 0.9126 (m-10) cc_final: 0.8880 (m-10)
REVERT: E  307 MET cc_start: 0.7849 (tpt) cc_final: 0.7525 (tpt)
REVERT: E  317 SER cc_start: 0.8490 (t) cc_final: 0.8255 (m)
REVERT: F  344 GLN cc_start: 0.8693 (mt0) cc_final: 0.8191 (mt0)
REVERT: G  317 SER cc_start: 0.8813 (t) cc_final: 0.8363 (m)
REVERT: G  323 MET cc_start: 0.7445 (mtp) cc_final: 0.6804 (mtt)
REVERT: H  316 PHE cc_start: 0.8177 (m-80) cc_final: 0.7905 (m-80)
REVERT: H  337 MET cc_start: 0.8874 (mtt) cc_final: 0.8573 (mtp)
REVERT: I  307 MET cc_start: 0.7712 (tpp) cc_final: 0.6898 (tpp)
REVERT: I  317 SER cc_start: 0.8382 (t) cc_final: 0.8134 (m)
REVERT: I  337 MET cc_start: 0.7277 (tpp) cc_final: 0.6896 (tpp)
REVERT: J  307 MET cc_start: 0.8877 (ttt) cc_final: 0.8618 (ttt)
REVERT: J  311 MET cc_start: 0.8222 (ptp) cc_final: 0.7973 (ptm)
REVERT: J  344 GLN cc_start: 0.8464 (mt0) cc_final: 0.7969 (mt0)
REVERT: L  313 PHE cc_start: 0.8147 (m-10) cc_final: 0.5918 (p90)
REVERT: L  337 MET cc_start: 0.8633 (mtt) cc_final: 0.7999 (mtt)
REVERT: L  344 GLN cc_start: 0.8492 (mt0) cc_final: 0.8248 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1147
  time to fit residues: 21.6255
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  : 0.372 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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**
E 331 GLN
** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 345 ASN
J 345 ASN
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 331 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 = 0.4230 r_free = 0.4230 target = 0.202068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.113168 restraints weight = 6094.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.117409 restraints weight = 3350.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.120112 restraints weight = 2239.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.6517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3744  Z= 0.352
  Angle     :  0.693   4.939   4980  Z= 0.371
  Chirality :  0.037   0.116    480
  Planarity :  0.003   0.025    684
  Dihedral  :  6.570  29.597    528
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.16 %
    Favored  : 96.55 %
  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 : -3.25 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP D 334 
 PHE   0.018   0.002   PHE J 316 

*********************** 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
  142 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8456 (t) cc_final: 0.8038 (m)
REVERT: B  311 MET cc_start: 0.8073 (ptp) cc_final: 0.6339 (mmt)
REVERT: B  313 PHE cc_start: 0.8520 (m-80) cc_final: 0.8311 (m-80)
REVERT: D  313 PHE cc_start: 0.9121 (m-10) cc_final: 0.8727 (m-10)
REVERT: E  317 SER cc_start: 0.8544 (t) cc_final: 0.8331 (m)
REVERT: F  344 GLN cc_start: 0.8648 (mt0) cc_final: 0.8292 (mt0)
REVERT: G  317 SER cc_start: 0.8856 (t) cc_final: 0.8486 (m)
REVERT: G  323 MET cc_start: 0.7493 (mtp) cc_final: 0.6902 (mtt)
REVERT: H  337 MET cc_start: 0.9074 (mtt) cc_final: 0.8760 (mtt)
REVERT: H  346 GLN cc_start: 0.7811 (mp10) cc_final: 0.7281 (mp10)
REVERT: I  307 MET cc_start: 0.7632 (tpp) cc_final: 0.7185 (tpp)
REVERT: I  317 SER cc_start: 0.8436 (t) cc_final: 0.8192 (m)
REVERT: I  322 MET cc_start: 0.7425 (mtp) cc_final: 0.7214 (mtp)
REVERT: I  337 MET cc_start: 0.7358 (tpp) cc_final: 0.6937 (tpp)
REVERT: J  331 GLN cc_start: 0.8654 (mt0) cc_final: 0.8389 (mt0)
REVERT: J  337 MET cc_start: 0.8997 (mtt) cc_final: 0.8578 (mtt)
REVERT: J  344 GLN cc_start: 0.8598 (mt0) cc_final: 0.8259 (mt0)
REVERT: K  307 MET cc_start: 0.7403 (tpp) cc_final: 0.7118 (ttt)
REVERT: L  313 PHE cc_start: 0.8363 (m-10) cc_final: 0.6091 (p90)
REVERT: L  337 MET cc_start: 0.8400 (mtt) cc_final: 0.7748 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 142
  average time/residue: 0.1153
  time to fit residues: 21.0812
Evaluate side-chains
  122 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 45 optimal weight:    0.4980
   chunk 34 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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**
G 331 GLN
G 344 GLN
L 344 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.200939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.119183 restraints weight = 5953.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.123559 restraints weight = 3190.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.126486 restraints weight = 2106.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.6836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3744  Z= 0.231
  Angle     :  0.676   7.683   4980  Z= 0.347
  Chirality :  0.037   0.115    480
  Planarity :  0.003   0.023    684
  Dihedral  :  6.396  29.253    528
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  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: -4.26 (0.20), 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   0.010   0.002   TRP D 334 
 PHE   0.017   0.002   PHE L 316 

*********************** 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
  139 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8423 (t) cc_final: 0.7993 (m)
REVERT: A  323 MET cc_start: 0.7030 (mtt) cc_final: 0.6686 (mtp)
REVERT: B  311 MET cc_start: 0.7880 (ptp) cc_final: 0.6380 (mmt)
REVERT: E  317 SER cc_start: 0.8415 (t) cc_final: 0.8178 (m)
REVERT: F  344 GLN cc_start: 0.8678 (mt0) cc_final: 0.8319 (mt0)
REVERT: G  317 SER cc_start: 0.8797 (t) cc_final: 0.8445 (m)
REVERT: G  323 MET cc_start: 0.7363 (mtp) cc_final: 0.6747 (mtt)
REVERT: H  337 MET cc_start: 0.8759 (mtt) cc_final: 0.8090 (mtt)
REVERT: H  346 GLN cc_start: 0.7598 (mp10) cc_final: 0.7254 (mp10)
REVERT: I  307 MET cc_start: 0.7786 (tpp) cc_final: 0.6872 (tpp)
REVERT: I  337 MET cc_start: 0.7361 (tpp) cc_final: 0.7015 (tpp)
REVERT: J  331 GLN cc_start: 0.8728 (mt0) cc_final: 0.8451 (mt0)
REVERT: J  337 MET cc_start: 0.8576 (mtt) cc_final: 0.8282 (mtt)
REVERT: J  344 GLN cc_start: 0.8650 (mt0) cc_final: 0.8380 (mt0)
REVERT: K  307 MET cc_start: 0.7554 (tpp) cc_final: 0.7339 (ttt)
REVERT: K  339 MET cc_start: 0.8176 (mtp) cc_final: 0.7685 (mtp)
REVERT: L  313 PHE cc_start: 0.8230 (m-10) cc_final: 0.6032 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1150
  time to fit residues: 20.6826
Evaluate side-chains
  123 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 33 optimal weight:    0.1980
   chunk 15 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    0.3980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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**
** E 331 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 = 0.4317 r_free = 0.4317 target = 0.210801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.120713 restraints weight = 5939.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.125161 restraints weight = 3200.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.128154 restraints weight = 2124.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.7012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3744  Z= 0.225
  Angle     :  0.652   7.340   4980  Z= 0.337
  Chirality :  0.037   0.114    480
  Planarity :  0.002   0.023    684
  Dihedral  :  6.212  28.475    528
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  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: -4.26 (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
 TRP   0.010   0.002   TRP D 334 
 PHE   0.014   0.002   PHE J 316 

*********************** 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
  137 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8496 (t) cc_final: 0.8215 (m)
REVERT: A  339 MET cc_start: 0.8055 (mtp) cc_final: 0.7682 (mtm)
REVERT: B  311 MET cc_start: 0.7569 (ptp) cc_final: 0.6421 (mmt)
REVERT: E  333 SER cc_start: 0.8935 (p) cc_final: 0.8721 (p)
REVERT: F  344 GLN cc_start: 0.8672 (mt0) cc_final: 0.8401 (mt0)
REVERT: G  307 MET cc_start: 0.7795 (tpp) cc_final: 0.7545 (tpp)
REVERT: G  317 SER cc_start: 0.8846 (t) cc_final: 0.8568 (m)
REVERT: G  323 MET cc_start: 0.7413 (mtp) cc_final: 0.6903 (mtt)
REVERT: H  331 GLN cc_start: 0.8848 (mt0) cc_final: 0.8628 (pt0)
REVERT: H  337 MET cc_start: 0.8659 (mtt) cc_final: 0.8449 (mtt)
REVERT: I  307 MET cc_start: 0.7576 (tpp) cc_final: 0.6488 (tpp)
REVERT: I  337 MET cc_start: 0.7312 (tpp) cc_final: 0.7010 (tpp)
REVERT: J  307 MET cc_start: 0.8588 (ttt) cc_final: 0.8051 (ttt)
REVERT: J  331 GLN cc_start: 0.8657 (mt0) cc_final: 0.8354 (mt0)
REVERT: J  344 GLN cc_start: 0.8541 (mt0) cc_final: 0.8265 (mt0)
REVERT: K  339 MET cc_start: 0.8254 (mtp) cc_final: 0.7669 (mtp)
REVERT: L  313 PHE cc_start: 0.8094 (m-10) cc_final: 0.5955 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1213
  time to fit residues: 21.4777
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  : 0.387 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0040
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.6796

-------------------------------------------------------------------------------
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**
G 344 GLN
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN
** J 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 = 0.4305 r_free = 0.4305 target = 0.208991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.118151 restraints weight = 5987.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.122495 restraints weight = 3346.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.125461 restraints weight = 2264.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.7124

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= 0.296
  Angle     :  0.696   7.050   4980  Z= 0.360
  Chirality :  0.036   0.119    480
  Planarity :  0.003   0.023    684
  Dihedral  :  6.391  28.649    528
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  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: -4.30 (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   0.010   0.002   TRP D 334 
 PHE   0.014   0.002   PHE J 316 

*********************** 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
  130 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8578 (t) cc_final: 0.8245 (m)
REVERT: A  339 MET cc_start: 0.8013 (mtp) cc_final: 0.7689 (mtm)
REVERT: B  311 MET cc_start: 0.7780 (ptp) cc_final: 0.6335 (mmm)
REVERT: C  344 GLN cc_start: 0.8903 (mt0) cc_final: 0.8255 (mp10)
REVERT: D  337 MET cc_start: 0.8632 (mtt) cc_final: 0.8286 (mtt)
REVERT: E  333 SER cc_start: 0.8965 (p) cc_final: 0.8743 (p)
REVERT: F  336 MET cc_start: 0.8134 (tpt) cc_final: 0.7843 (tpt)
REVERT: G  317 SER cc_start: 0.8906 (t) cc_final: 0.8614 (m)
REVERT: G  323 MET cc_start: 0.7343 (mtp) cc_final: 0.6719 (mtt)
REVERT: H  307 MET cc_start: 0.8225 (ttt) cc_final: 0.7343 (ttt)
REVERT: H  337 MET cc_start: 0.8305 (mtt) cc_final: 0.8089 (mtt)
REVERT: I  307 MET cc_start: 0.7542 (tpp) cc_final: 0.6730 (tpp)
REVERT: I  337 MET cc_start: 0.7339 (tpp) cc_final: 0.7066 (tpp)
REVERT: J  331 GLN cc_start: 0.8762 (mt0) cc_final: 0.8464 (mt0)
REVERT: J  337 MET cc_start: 0.8842 (mtt) cc_final: 0.8112 (mmt)
REVERT: J  344 GLN cc_start: 0.8580 (mt0) cc_final: 0.8277 (mt0)
REVERT: L  313 PHE cc_start: 0.8061 (m-10) cc_final: 0.6116 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1234
  time to fit residues: 20.4752
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  : 0.381 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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**
** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 344 GLN
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 345 ASN
** J 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 = 0.4351 r_free = 0.4351 target = 0.218090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.124447 restraints weight = 5716.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.128927 restraints weight = 3187.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.131934 restraints weight = 2128.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.7232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3744  Z= 0.207
  Angle     :  0.666   6.982   4980  Z= 0.340
  Chirality :  0.036   0.114    480
  Planarity :  0.002   0.022    684
  Dihedral  :  6.137  27.959    528
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 : -3.26 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP J 334 
 PHE   0.014   0.002   PHE F 313 

********************** 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
  128 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  317 SER cc_start: 0.8517 (t) cc_final: 0.8193 (m)
REVERT: A  339 MET cc_start: 0.8001 (mtp) cc_final: 0.7652 (mtm)
REVERT: B  311 MET cc_start: 0.7311 (ptp) cc_final: 0.5966 (tpt)
REVERT: C  344 GLN cc_start: 0.8842 (mt0) cc_final: 0.8184 (mp10)
REVERT: D  337 MET cc_start: 0.8566 (mtt) cc_final: 0.7885 (mtt)
REVERT: E  337 MET cc_start: 0.7545 (ptt) cc_final: 0.7221 (ptt)
REVERT: G  317 SER cc_start: 0.8858 (t) cc_final: 0.8570 (m)
REVERT: G  323 MET cc_start: 0.7476 (mtp) cc_final: 0.6869 (mtt)
REVERT: H  337 MET cc_start: 0.8321 (mtt) cc_final: 0.7840 (mtt)
REVERT: I  337 MET cc_start: 0.7260 (tpp) cc_final: 0.6957 (tpp)
REVERT: J  331 GLN cc_start: 0.8702 (mt0) cc_final: 0.8431 (mt0)
REVERT: J  344 GLN cc_start: 0.8506 (mt0) cc_final: 0.8276 (mt0)
REVERT: L  313 PHE cc_start: 0.7432 (m-10) cc_final: 0.5853 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1171
  time to fit residues: 19.1736
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  : 0.355 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 35 optimal weight:    0.4980
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0870
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.9164

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.205268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.117154 restraints weight = 5925.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.121476 restraints weight = 3327.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.124353 restraints weight = 2250.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.7268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3744  Z= 0.322
  Angle     :  0.728   8.271   4980  Z= 0.371
  Chirality :  0.037   0.116    480
  Planarity :  0.003   0.025    684
  Dihedral  :  6.415  27.708    528
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  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: -4.38 (0.21), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.16), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP L 334 
 PHE   0.012   0.002   PHE F 313 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1484.78 seconds
wall clock time: 27 minutes 16.98 seconds (1636.98 seconds total)