Starting phenix.real_space_refine
on Sat Aug 23 09:21:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5o3l_3741/08_2025/5o3l_3741.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5o3l_3741/08_2025/5o3l_3741.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5o3l_3741/08_2025/5o3l_3741.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5o3l_3741/08_2025/5o3l_3741.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5o3l_3741/08_2025/5o3l_3741.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5o3l_3741/08_2025/5o3l_3741.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    3510      2.51       5
     N    1010      2.21       5
     O    1040      1.98       5
     H    5790      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11360
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "B"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "C"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "D"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "E"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "F"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "G"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "H"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "I"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "J"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1136
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Time building chain proxies: 1.97, per 1000 atoms: 0.17
  Number of scatterers: 11360
  At special positions: 0
  Unit cell: (126.88, 104, 56.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O    1040      8.00
     N    1010      7.00
     C    3510      6.00
     H    5790      1.00
    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: 1.08
  Conformation dependent library (CDL) restraints added in 283.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1280

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...

    No hydrogen bonds 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: 0.00

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5780
        1.03 -     1.22: 10
        1.22 -     1.41: 2142
        1.41 -     1.60: 3508
        1.60 -     1.79: 10
  Bond restraints: 11450
  Sorted by residual:
  bond pdb=" CA  HIS G 329 "
       pdb=" CB  HIS G 329 "
    ideal  model  delta    sigma   weight residual
    1.535  1.496  0.040 2.09e-02 2.29e+03 3.57e+00
  bond pdb=" CA  HIS C 329 "
       pdb=" CB  HIS C 329 "
    ideal  model  delta    sigma   weight residual
    1.535  1.496  0.039 2.09e-02 2.29e+03 3.55e+00
  bond pdb=" CA  HIS D 329 "
       pdb=" CB  HIS D 329 "
    ideal  model  delta    sigma   weight residual
    1.535  1.496  0.039 2.09e-02 2.29e+03 3.49e+00
  bond pdb=" CA  HIS H 329 "
       pdb=" CB  HIS H 329 "
    ideal  model  delta    sigma   weight residual
    1.535  1.497  0.039 2.09e-02 2.29e+03 3.44e+00
  bond pdb=" CA  HIS I 329 "
       pdb=" CB  HIS I 329 "
    ideal  model  delta    sigma   weight residual
    1.535  1.497  0.039 2.09e-02 2.29e+03 3.44e+00
  ... (remaining 11445 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 16358
        1.27 -     2.54: 2770
        2.54 -     3.82: 1581
        3.82 -     5.09: 151
        5.09 -     6.36: 40
  Bond angle restraints: 20900
  Sorted by residual:
  angle pdb=" N   GLY I 326 "
        pdb=" CA  GLY I 326 "
        pdb=" C   GLY I 326 "
      ideal   model   delta    sigma   weight residual
     111.21  113.90   -2.69 1.04e+00 9.25e-01 6.67e+00
  angle pdb=" N   GLY D 326 "
        pdb=" CA  GLY D 326 "
        pdb=" C   GLY D 326 "
      ideal   model   delta    sigma   weight residual
     111.21  113.87   -2.66 1.04e+00 9.25e-01 6.54e+00
  angle pdb=" N   GLY G 326 "
        pdb=" CA  GLY G 326 "
        pdb=" C   GLY G 326 "
      ideal   model   delta    sigma   weight residual
     111.21  113.86   -2.65 1.04e+00 9.25e-01 6.49e+00
  angle pdb=" N   GLY J 326 "
        pdb=" CA  GLY J 326 "
        pdb=" C   GLY J 326 "
      ideal   model   delta    sigma   weight residual
     111.21  113.86   -2.65 1.04e+00 9.25e-01 6.47e+00
  angle pdb=" N   GLY A 326 "
        pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     111.21  113.86   -2.65 1.04e+00 9.25e-01 6.47e+00
  ... (remaining 20895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.38: 4790
       15.38 -    30.75: 325
       30.75 -    46.13: 85
       46.13 -    61.50: 65
       61.50 -    76.88: 5
  Dihedral angle restraints: 5270
    sinusoidal: 3000
      harmonic: 2270
  Sorted by residual:
  dihedral pdb=" CA  ILE C 360 "
           pdb=" C   ILE C 360 "
           pdb=" N   THR C 361 "
           pdb=" CA  THR C 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  ILE D 360 "
           pdb=" C   ILE D 360 "
           pdb=" N   THR D 361 "
           pdb=" CA  THR D 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  ILE B 360 "
           pdb=" C   ILE B 360 "
           pdb=" N   THR B 361 "
           pdb=" CA  THR B 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.68   21.32     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 5267 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 371
       0.031 -    0.061: 241
       0.061 -    0.091: 125
       0.091 -    0.122: 108
       0.122 -    0.152: 15
  Chirality restraints: 860
  Sorted by residual:
  chirality pdb=" CB  VAL F 363 "
            pdb=" CA  VAL F 363 "
            pdb=" CG1 VAL F 363 "
            pdb=" CG2 VAL F 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.79e-01
  chirality pdb=" CB  VAL D 363 "
            pdb=" CA  VAL D 363 "
            pdb=" CG1 VAL D 363 "
            pdb=" CG2 VAL D 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.75e-01
  chirality pdb=" CB  VAL B 363 "
            pdb=" CA  VAL B 363 "
            pdb=" CG1 VAL B 363 "
            pdb=" CG2 VAL B 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 857 not shown)

  Planarity restraints: 1650
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 378 "   -0.007 2.00e-02 2.50e+03   1.69e-02 8.58e+00
        pdb=" CG  PHE E 378 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 378 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 378 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 378 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 378 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 378 "    0.006 2.00e-02 2.50e+03
        pdb=" HD1 PHE E 378 "    0.034 2.00e-02 2.50e+03
        pdb=" HD2 PHE E 378 "    0.006 2.00e-02 2.50e+03
        pdb=" HE1 PHE E 378 "   -0.034 2.00e-02 2.50e+03
        pdb=" HE2 PHE E 378 "   -0.006 2.00e-02 2.50e+03
        pdb=" HZ  PHE E 378 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE I 378 "   -0.007 2.00e-02 2.50e+03   1.69e-02 8.56e+00
        pdb=" CG  PHE I 378 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE I 378 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE I 378 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE I 378 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE I 378 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE I 378 "    0.006 2.00e-02 2.50e+03
        pdb=" HD1 PHE I 378 "    0.033 2.00e-02 2.50e+03
        pdb=" HD2 PHE I 378 "    0.006 2.00e-02 2.50e+03
        pdb=" HE1 PHE I 378 "   -0.034 2.00e-02 2.50e+03
        pdb=" HE2 PHE I 378 "   -0.007 2.00e-02 2.50e+03
        pdb=" HZ  PHE I 378 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 378 "   -0.007 2.00e-02 2.50e+03   1.69e-02 8.53e+00
        pdb=" CG  PHE C 378 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 378 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 378 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 378 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 378 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 378 "    0.006 2.00e-02 2.50e+03
        pdb=" HD1 PHE C 378 "    0.034 2.00e-02 2.50e+03
        pdb=" HD2 PHE C 378 "    0.006 2.00e-02 2.50e+03
        pdb=" HE1 PHE C 378 "   -0.034 2.00e-02 2.50e+03
        pdb=" HE2 PHE C 378 "   -0.006 2.00e-02 2.50e+03
        pdb=" HZ  PHE C 378 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1647 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.05: 306
        2.05 -     2.69: 19958
        2.69 -     3.33: 31993
        3.33 -     3.96: 42915
        3.96 -     4.60: 64842
  Nonbonded interactions: 160014
  Sorted by model distance:
  nonbonded pdb=" O   SER D 316 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.419 2.450
  nonbonded pdb=" O   SER H 316 "
            pdb=" HG  SER J 316 "
     model   vdw
     1.419 2.450
  nonbonded pdb=" O   SER B 316 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.419 2.450
  nonbonded pdb=" O   SER F 316 "
            pdb=" HG  SER H 316 "
     model   vdw
     1.420 2.450
  nonbonded pdb=" HG  SER F 320 "
            pdb=" OD1 ASN F 368 "
     model   vdw
     1.420 2.450
  ... (remaining 160009 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'
}

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 individual isotropic
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:             1.300
  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:             0.050
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.030
  Find NCS groups from input model:        0.040
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
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      :  0.012   0.086   5660  Z= 0.511
  Angle     :  1.034   6.304   7580  Z= 0.537
  Chirality :  0.057   0.152    860
  Planarity :  0.010   0.055    960
  Dihedral  :  8.970  44.911   2160
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.39 %
    Favored  : 77.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.67 (0.16), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.08 (0.12), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.003   ARG G 349 
 TYR   0.009   0.003   TYR F 310 
 PHE   0.013   0.005   PHE I 346 
 HIS   0.010   0.004   HIS G 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.01229 ( 5660)
  covalent geometry    : angle       1.03443 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  328 ILE cc_start: 0.7973 (mp) cc_final: 0.7768 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 305
  average time/residue: 0.2532
  time to fit residues: 91.9875
Evaluate side-chains
  217 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
C 359 ASN
C 368 ASN
D 359 ASN
D 368 ASN
E 336 GLN
E 359 ASN
E 368 ASN
F 368 ASN
G 368 ASN
H 368 ASN
H 374 HIS
I 368 ASN
J 368 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.172186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.153109 restraints weight = 27353.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.4612 rms_B_bonded: 3.30
r_work: 0.4651 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4548 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.4548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.5188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5660  Z= 0.167
  Angle     :  0.798   6.956   7580  Z= 0.391
  Chirality :  0.053   0.158    860
  Planarity :  0.007   0.049    960
  Dihedral  :  7.077  19.479    740
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.28 %
    Favored  : 79.72 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.72 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.56 (0.15), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.99 (0.11), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 349 
 TYR   0.015   0.002   TYR C 310 
 PHE   0.011   0.001   PHE F 378 
 HIS   0.005   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 5660)
  covalent geometry    : angle       0.79769 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 243
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 GLU cc_start: 0.8187 (mp0) cc_final: 0.7693 (mp0)
REVERT: B  347 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8341 (mtmm)
REVERT: C  307 GLN cc_start: 0.7886 (tt0) cc_final: 0.6918 (mp10)
REVERT: C  363 VAL cc_start: 0.9288 (t) cc_final: 0.9013 (p)
REVERT: D  363 VAL cc_start: 0.9330 (t) cc_final: 0.9095 (p)
REVERT: D  370 LYS cc_start: 0.8096 (tttm) cc_final: 0.7797 (tttm)
REVERT: D  371 ILE cc_start: 0.8581 (mt) cc_final: 0.8339 (mt)
REVERT: E  336 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7695 (tt0)
REVERT: E  342 GLU cc_start: 0.7525 (mp0) cc_final: 0.7022 (mp0)
REVERT: E  349 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7865 (mtp180)
REVERT: F  363 VAL cc_start: 0.9316 (t) cc_final: 0.9114 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 249
  average time/residue: 0.2230
  time to fit residues: 67.7005
Evaluate side-chains
  234 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 221
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  336 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain I residue  359 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0980
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4818 r_free = 0.4818 target = 0.172142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.152696 restraints weight = 27524.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.4632 rms_B_bonded: 3.40
r_work: 0.4648 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.4542 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.4542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
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      :  0.004   0.065   5660  Z= 0.157
  Angle     :  0.734   5.664   7580  Z= 0.367
  Chirality :  0.051   0.138    860
  Planarity :  0.007   0.049    960
  Dihedral  :  6.631  18.383    740
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.46 %
    Favored  : 82.54 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.72 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.51 (0.15), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.96 (0.11), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I 349 
 TYR   0.010   0.002   TYR A 310 
 PHE   0.005   0.000   PHE H 378 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5660)
  covalent geometry    : angle       0.73358 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 241
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 GLU cc_start: 0.8213 (mp0) cc_final: 0.7713 (mp0)
REVERT: B  347 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8317 (mtmm)
REVERT: C  340 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8520 (tptp)
REVERT: C  363 VAL cc_start: 0.9304 (t) cc_final: 0.9054 (p)
REVERT: D  358 ASP cc_start: 0.8698 (p0) cc_final: 0.8393 (p0)
REVERT: D  363 VAL cc_start: 0.9403 (t) cc_final: 0.9131 (p)
REVERT: E  345 ASP cc_start: 0.7949 (m-30) cc_final: 0.7719 (t0)
REVERT: E  349 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7851 (mtp85)
REVERT: E  358 ASP cc_start: 0.8088 (p0) cc_final: 0.7772 (p0)
REVERT: H  342 GLU cc_start: 0.7949 (mp0) cc_final: 0.7406 (mp0)
REVERT: H  344 LEU cc_start: 0.6514 (mt) cc_final: 0.6309 (mt)
REVERT: I  307 GLN cc_start: 0.7925 (tt0) cc_final: 0.6983 (mp10)
REVERT: I  345 ASP cc_start: 0.7886 (m-30) cc_final: 0.7581 (t0)
REVERT: J  321 LYS cc_start: 0.9051 (tttm) cc_final: 0.8846 (tttm)
  outliers start: 19
  outliers final: 13
  residues processed: 250
  average time/residue: 0.2306
  time to fit residues: 70.4943
Evaluate side-chains
  232 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 218
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain I residue  338 GLU
Chi-restraints excluded: chain I residue  359 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0470
   chunk 47 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.6878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4810 r_free = 0.4810 target = 0.170563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.151214 restraints weight = 27281.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.4574 rms_B_bonded: 3.32
r_work: 0.4599 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.4491 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.4491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.6383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5660  Z= 0.146
  Angle     :  0.693   6.214   7580  Z= 0.343
  Chirality :  0.050   0.138    860
  Planarity :  0.006   0.049    960
  Dihedral  :  6.149  18.224    740
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.90 %
    Favored  : 83.10 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.97 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.39 (0.15), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.87 (0.11), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I 349 
 TYR   0.013   0.002   TYR A 310 
 PHE   0.004   0.001   PHE H 378 
 HIS   0.004   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5660)
  covalent geometry    : angle       0.69346 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 233
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.8628 (mtp180) cc_final: 0.8278 (mtp180)
REVERT: B  311 LYS cc_start: 0.7473 (pptt) cc_final: 0.7100 (pptt)
REVERT: B  347 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8195 (mtmm)
REVERT: B  358 ASP cc_start: 0.8819 (p0) cc_final: 0.8534 (p0)
REVERT: B  372 GLU cc_start: 0.8451 (mp0) cc_final: 0.8222 (mp0)
REVERT: D  358 ASP cc_start: 0.8768 (p0) cc_final: 0.8527 (p0)
REVERT: E  345 ASP cc_start: 0.7966 (m-30) cc_final: 0.7758 (t0)
REVERT: E  358 ASP cc_start: 0.8191 (p0) cc_final: 0.7932 (p0)
REVERT: E  363 VAL cc_start: 0.9298 (t) cc_final: 0.9086 (p)
REVERT: H  342 GLU cc_start: 0.8000 (mp0) cc_final: 0.6860 (mp0)
REVERT: I  307 GLN cc_start: 0.7986 (tt0) cc_final: 0.7014 (mp10)
REVERT: I  340 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7456 (mmmt)
REVERT: I  345 ASP cc_start: 0.8100 (m-30) cc_final: 0.7730 (t0)
REVERT: J  345 ASP cc_start: 0.8331 (m-30) cc_final: 0.7736 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 243
  average time/residue: 0.2295
  time to fit residues: 68.7635
Evaluate side-chains
  230 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 215
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain I residue  359 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0020
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
B 330 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.217453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.164513 restraints weight = 26463.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.4570 rms_B_bonded: 3.51
r_work: 0.4608 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.4495 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.6744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5660  Z= 0.142
  Angle     :  0.679   4.821   7580  Z= 0.333
  Chirality :  0.049   0.147    860
  Planarity :  0.006   0.047    960
  Dihedral  :  5.841  18.054    740
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.92 %
    Favored  : 84.08 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.38 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.22 (0.15), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.74 (0.12), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG I 349 
 TYR   0.011   0.002   TYR E 310 
 PHE   0.003   0.001   PHE I 378 
 HIS   0.006   0.001   HIS J 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5660)
  covalent geometry    : angle       0.67903 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 232
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.6497 (pptt) cc_final: 0.5669 (pttm)
REVERT: A  349 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8302 (mtp180)
REVERT: B  347 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8117 (mtmm)
REVERT: B  358 ASP cc_start: 0.8833 (p0) cc_final: 0.8506 (p0)
REVERT: B  372 GLU cc_start: 0.8469 (mp0) cc_final: 0.8226 (mp0)
REVERT: C  363 VAL cc_start: 0.9266 (t) cc_final: 0.8931 (p)
REVERT: C  370 LYS cc_start: 0.7561 (tttp) cc_final: 0.7332 (tttp)
REVERT: D  358 ASP cc_start: 0.8883 (p0) cc_final: 0.8638 (p0)
REVERT: E  345 ASP cc_start: 0.8224 (m-30) cc_final: 0.7888 (t0)
REVERT: E  363 VAL cc_start: 0.9238 (t) cc_final: 0.8960 (p)
REVERT: G  349 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7635 (mtm-85)
REVERT: G  363 VAL cc_start: 0.9207 (t) cc_final: 0.8974 (p)
REVERT: H  349 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7734 (ttm110)
REVERT: I  307 GLN cc_start: 0.8051 (tt0) cc_final: 0.7089 (mp10)
REVERT: I  340 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7502 (mmmt)
REVERT: I  345 ASP cc_start: 0.8159 (m-30) cc_final: 0.7780 (t0)
REVERT: J  345 ASP cc_start: 0.8272 (m-30) cc_final: 0.7692 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 243
  average time/residue: 0.2221
  time to fit residues: 66.7548
Evaluate side-chains
  238 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 221
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain I residue  359 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
B 368 ASN
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 374 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.212289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.158626 restraints weight = 26614.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.4517 rms_B_bonded: 3.43
r_work: 0.4551 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.4440 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.4440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.7087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5660  Z= 0.191
  Angle     :  0.684   4.783   7580  Z= 0.335
  Chirality :  0.048   0.135    860
  Planarity :  0.006   0.047    960
  Dihedral  :  5.738  18.160    740
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.59 %
    Favored  : 81.41 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 18.59 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.11 (0.16), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.65 (0.12), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I 349 
 TYR   0.015   0.002   TYR A 310 
 PHE   0.005   0.001   PHE I 378 
 HIS   0.005   0.001   HIS H 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 5660)
  covalent geometry    : angle       0.68448 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 246
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.8674 (mtp180) cc_final: 0.8381 (mtp180)
REVERT: B  311 LYS cc_start: 0.7316 (pptt) cc_final: 0.6775 (pptt)
REVERT: B  347 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8049 (mtmm)
REVERT: B  358 ASP cc_start: 0.8823 (p0) cc_final: 0.8461 (p0)
REVERT: B  372 GLU cc_start: 0.8429 (mp0) cc_final: 0.8174 (mp0)
REVERT: C  340 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8698 (tmtt)
REVERT: C  363 VAL cc_start: 0.9279 (t) cc_final: 0.8949 (p)
REVERT: D  358 ASP cc_start: 0.8983 (p0) cc_final: 0.8694 (p0)
REVERT: E  358 ASP cc_start: 0.8672 (p0) cc_final: 0.8408 (p0)
REVERT: E  363 VAL cc_start: 0.9234 (t) cc_final: 0.8992 (p)
REVERT: E  372 GLU cc_start: 0.7666 (mp0) cc_final: 0.7452 (mp0)
REVERT: F  345 ASP cc_start: 0.8285 (m-30) cc_final: 0.7719 (t0)
REVERT: G  342 GLU cc_start: 0.7489 (mp0) cc_final: 0.7043 (mp0)
REVERT: H  349 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7691 (ttm110)
REVERT: I  307 GLN cc_start: 0.8136 (tt0) cc_final: 0.7178 (mp10)
REVERT: I  340 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7515 (mmmt)
REVERT: I  345 ASP cc_start: 0.8385 (m-30) cc_final: 0.8131 (t0)
REVERT: J  345 ASP cc_start: 0.8487 (m-30) cc_final: 0.7985 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 258
  average time/residue: 0.2319
  time to fit residues: 73.5707
Evaluate side-chains
  255 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 237
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  307 GLN
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain F residue  338 GLU
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain J residue  307 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0060
   chunk 30 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
C 368 ASN
E 336 GLN
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 368 ASN
G 368 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.168059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.148851 restraints weight = 26900.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.4568 rms_B_bonded: 3.31
r_work: 0.4586 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4473 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.4473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.7317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5660  Z= 0.129
  Angle     :  0.673   6.836   7580  Z= 0.329
  Chirality :  0.048   0.130    860
  Planarity :  0.006   0.054    960
  Dihedral  :  5.502  17.277    740
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.37 %
    Favored  : 85.63 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 20.62 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.92 (0.17), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.51 (0.13), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG I 349 
 TYR   0.016   0.002   TYR A 310 
 PHE   0.004   0.001   PHE G 378 
 HIS   0.003   0.001   HIS J 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 5660)
  covalent geometry    : angle       0.67285 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 248
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.6150 (pptt) cc_final: 0.5272 (pttm)
REVERT: A  349 ARG cc_start: 0.8689 (mtp180) cc_final: 0.8413 (mtp180)
REVERT: B  353 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8760 (mtpp)
REVERT: B  358 ASP cc_start: 0.8846 (p0) cc_final: 0.8551 (p0)
REVERT: B  372 GLU cc_start: 0.8459 (mp0) cc_final: 0.8241 (mp0)
REVERT: C  340 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8716 (tmtt)
REVERT: C  363 VAL cc_start: 0.9246 (t) cc_final: 0.9042 (p)
REVERT: D  358 ASP cc_start: 0.8979 (p0) cc_final: 0.8673 (p0)
REVERT: E  358 ASP cc_start: 0.8645 (p0) cc_final: 0.8396 (p0)
REVERT: F  345 ASP cc_start: 0.8098 (m-30) cc_final: 0.7727 (t0)
REVERT: H  342 GLU cc_start: 0.7754 (mp0) cc_final: 0.7150 (mp0)
REVERT: H  349 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7733 (ttm110)
REVERT: I  307 GLN cc_start: 0.8142 (tt0) cc_final: 0.7175 (mp10)
REVERT: I  340 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7585 (mmmt)
REVERT: I  345 ASP cc_start: 0.8520 (m-30) cc_final: 0.8206 (t0)
REVERT: J  345 ASP cc_start: 0.8392 (m-30) cc_final: 0.7947 (t0)
REVERT: J  353 LYS cc_start: 0.9273 (mtmt) cc_final: 0.8980 (mtmt)
  outliers start: 20
  outliers final: 15
  residues processed: 259
  average time/residue: 0.2232
  time to fit residues: 70.8261
Evaluate side-chains
  252 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 237
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  307 GLN
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain I residue  358 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
C 368 ASN
E 336 GLN
E 359 ASN
E 368 ASN
G 368 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.167299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.147756 restraints weight = 26675.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.4570 rms_B_bonded: 3.33
r_work: 0.4591 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.4480 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.4480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.7541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5660  Z= 0.150
  Angle     :  0.673   5.659   7580  Z= 0.328
  Chirality :  0.048   0.128    860
  Planarity :  0.006   0.052    960
  Dihedral  :  5.450  17.280    740
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.90 %
    Favored  : 83.10 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.41 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.80 (0.17), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.41 (0.13), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I 349 
 TYR   0.013   0.002   TYR A 310 
 PHE   0.005   0.001   PHE B 346 
 HIS   0.003   0.001   HIS J 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5660)
  covalent geometry    : angle       0.67265 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 245
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.8649 (mtp180) cc_final: 0.8355 (mtp180)
REVERT: B  345 ASP cc_start: 0.8232 (m-30) cc_final: 0.7920 (t0)
REVERT: B  353 LYS cc_start: 0.9124 (mtmt) cc_final: 0.8777 (mtpp)
REVERT: B  358 ASP cc_start: 0.8821 (p0) cc_final: 0.8502 (p0)
REVERT: D  358 ASP cc_start: 0.8949 (p0) cc_final: 0.8615 (p0)
REVERT: E  358 ASP cc_start: 0.8660 (p0) cc_final: 0.8409 (p0)
REVERT: E  370 LYS cc_start: 0.7815 (tttm) cc_final: 0.7342 (ttmt)
REVERT: E  372 GLU cc_start: 0.7689 (mp0) cc_final: 0.7282 (mp0)
REVERT: F  345 ASP cc_start: 0.8213 (m-30) cc_final: 0.7859 (t0)
REVERT: G  349 ARG cc_start: 0.8316 (mtp180) cc_final: 0.7840 (mtm-85)
REVERT: G  372 GLU cc_start: 0.8062 (mp0) cc_final: 0.7619 (mp0)
REVERT: H  349 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7780 (ttm110)
REVERT: H  363 VAL cc_start: 0.9234 (p) cc_final: 0.8978 (p)
REVERT: I  307 GLN cc_start: 0.8160 (tt0) cc_final: 0.7206 (mp10)
REVERT: I  340 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7623 (mmmt)
REVERT: I  345 ASP cc_start: 0.8540 (m-30) cc_final: 0.8289 (t0)
REVERT: J  311 LYS cc_start: 0.5575 (tppt) cc_final: 0.5273 (tppt)
REVERT: J  345 ASP cc_start: 0.8379 (m-30) cc_final: 0.8009 (t0)
REVERT: J  353 LYS cc_start: 0.9312 (mtmt) cc_final: 0.9013 (mtmt)
  outliers start: 23
  outliers final: 21
  residues processed: 255
  average time/residue: 0.2357
  time to fit residues: 74.2156
Evaluate side-chains
  255 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 234
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  307 GLN
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  307 GLN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain I residue  358 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0970
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0770
   chunk 26 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.5736

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

Flipped N/Q/H residues before XYZ refinement:
D 368 ASN
E 336 GLN
F 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.168971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.149955 restraints weight = 26651.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.4586 rms_B_bonded: 3.24
r_work: 0.4605 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.4496 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.4496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.7724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5660  Z= 0.131
  Angle     :  0.681   5.812   7580  Z= 0.331
  Chirality :  0.049   0.243    860
  Planarity :  0.006   0.063    960
  Dihedral  :  5.384  16.937    740
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.21 %
    Favored  : 84.79 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.97 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.70 (0.17), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.33 (0.13), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 349 
 TYR   0.011   0.002   TYR A 310 
 PHE   0.004   0.001   PHE E 346 
 HIS   0.003   0.001   HIS J 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 5660)
  covalent geometry    : angle       0.68135 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 236
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.8661 (mtp180) cc_final: 0.8367 (mtp180)
REVERT: B  345 ASP cc_start: 0.8271 (m-30) cc_final: 0.7897 (t0)
REVERT: B  353 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8772 (mtpp)
REVERT: B  358 ASP cc_start: 0.8830 (p0) cc_final: 0.8522 (p0)
REVERT: D  358 ASP cc_start: 0.9010 (p0) cc_final: 0.8692 (p0)
REVERT: E  370 LYS cc_start: 0.7706 (tttm) cc_final: 0.7262 (ttmt)
REVERT: F  345 ASP cc_start: 0.8201 (m-30) cc_final: 0.7813 (t0)
REVERT: G  349 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7729 (mtm-85)
REVERT: H  349 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7700 (ttm110)
REVERT: I  307 GLN cc_start: 0.8176 (tt0) cc_final: 0.7183 (mp10)
REVERT: I  340 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7588 (mmmt)
REVERT: I  345 ASP cc_start: 0.8553 (m-30) cc_final: 0.8229 (t0)
REVERT: J  311 LYS cc_start: 0.5492 (tppt) cc_final: 0.5254 (tppt)
REVERT: J  345 ASP cc_start: 0.8392 (m-30) cc_final: 0.7965 (t0)
REVERT: J  353 LYS cc_start: 0.9247 (mtmt) cc_final: 0.8922 (mtmt)
  outliers start: 18
  outliers final: 18
  residues processed: 245
  average time/residue: 0.2186
  time to fit residues: 67.1070
Evaluate side-chains
  250 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 232
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  307 GLN
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  307 GLN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain I residue  358 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 60 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
D 368 ASN
E 336 GLN
F 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.167564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.147678 restraints weight = 27093.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.4569 rms_B_bonded: 3.45
r_work: 0.4589 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.4473 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.4473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.7846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5660  Z= 0.149
  Angle     :  0.688   5.823   7580  Z= 0.333
  Chirality :  0.047   0.124    860
  Planarity :  0.006   0.055    960
  Dihedral  :  5.396  18.729    740
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.62 %
    Favored  : 83.38 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.81 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.64 (0.18), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.29 (0.13), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 349 
 TYR   0.010   0.002   TYR A 310 
 PHE   0.004   0.001   PHE H 346 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 5660)
  covalent geometry    : angle       0.68804 ( 7580)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 236
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.8655 (mtp180) cc_final: 0.8349 (mtp180)
REVERT: B  345 ASP cc_start: 0.8287 (m-30) cc_final: 0.7934 (t0)
REVERT: B  353 LYS cc_start: 0.9114 (mtmt) cc_final: 0.8779 (mtpp)
REVERT: B  358 ASP cc_start: 0.8864 (p0) cc_final: 0.8485 (p0)
REVERT: B  372 GLU cc_start: 0.8126 (mp0) cc_final: 0.7898 (mp0)
REVERT: D  358 ASP cc_start: 0.9020 (p0) cc_final: 0.8698 (p0)
REVERT: E  370 LYS cc_start: 0.7788 (tttm) cc_final: 0.7364 (ttmt)
REVERT: E  372 GLU cc_start: 0.7880 (mp0) cc_final: 0.7606 (mp0)
REVERT: F  345 ASP cc_start: 0.8402 (m-30) cc_final: 0.8017 (t0)
REVERT: G  345 ASP cc_start: 0.8505 (m-30) cc_final: 0.7960 (t0)
REVERT: G  349 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7766 (mtm-85)
REVERT: H  349 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7653 (ttm110)
REVERT: I  307 GLN cc_start: 0.8214 (tt0) cc_final: 0.7242 (mp10)
REVERT: I  340 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7634 (mmmt)
REVERT: I  345 ASP cc_start: 0.8580 (m-30) cc_final: 0.8219 (t0)
REVERT: J  311 LYS cc_start: 0.5545 (tppt) cc_final: 0.5312 (tppt)
REVERT: J  345 ASP cc_start: 0.8439 (m-30) cc_final: 0.8078 (t0)
REVERT: J  353 LYS cc_start: 0.9281 (mtmt) cc_final: 0.8973 (mtmt)
REVERT: J  358 ASP cc_start: 0.8231 (p0) cc_final: 0.7112 (t0)
  outliers start: 19
  outliers final: 18
  residues processed: 245
  average time/residue: 0.1984
  time to fit residues: 60.7196
Evaluate side-chains
  253 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 235
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  307 GLN
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  307 GLN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain E residue  307 GLN
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain I residue  358 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0970
   chunk 5 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
C 368 ASN
E 368 ASN
** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.168962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.150045 restraints weight = 26894.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.4592 rms_B_bonded: 3.28
r_work: 0.4611 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.4502 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.4502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.7956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5660  Z= 0.130
  Angle     :  0.668   5.746   7580  Z= 0.323
  Chirality :  0.047   0.125    860
  Planarity :  0.006   0.065    960
  Dihedral  :  5.282  18.782    740
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.93 %
    Favored  : 85.07 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 23.12 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.54 (0.18), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.22 (0.14), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 349 
 TYR   0.011   0.002   TYR F 310 
 PHE   0.004   0.001   PHE G 346 
 HIS   0.004   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 5660)
  covalent geometry    : angle       0.66802 ( 7580)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4004.74 seconds
wall clock time: 69 minutes 2.02 seconds (4142.02 seconds total)