Starting phenix.real_space_refine
on Tue Feb  3 18:53:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w1o_65552/02_2026/9w1o_65552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w1o_65552/02_2026/9w1o_65552.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w1o_65552/02_2026/9w1o_65552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w1o_65552/02_2026/9w1o_65552.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w1o_65552/02_2026/9w1o_65552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w1o_65552/02_2026/9w1o_65552.map"
  }
  resolution = 3.2
  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=   0.028
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
     P       2      5.49       5
     S      38      5.16       5
     C    4094      2.51       5
     N     992      2.21       5
     O    1098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6224
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3107
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 15, 'TRANS': 391}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'PO4': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.69, per 1000 atoms: 0.27
  Number of scatterers: 6224
  At special positions: 0
  Unit cell: (108.73, 112.05, 62.25, 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      38     16.00
     P       2     15.00
     O    1098      8.00
     N     992      7.00
     C    4094      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: 0.39
  Conformation dependent library (CDL) restraints added in 318.4 milliseconds
  

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      87.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 27
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 34 through 42
    Processing helix  chain 'A' and resid 45 through 72
      removed outlier: 4.028A  pdb=" N   ASP A  72 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 96
    Processing helix  chain 'A' and resid 99 through 116
    Processing helix  chain 'A' and resid 117 through 129
      removed outlier: 3.753A  pdb=" N   CYS A 121 " --> pdb=" O   GLY A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 133
    Processing helix  chain 'A' and resid 134 through 163
      removed outlier: 3.979A  pdb=" N   MET A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 164 through 186
      removed outlier: 3.554A  pdb=" N   PHE A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 222
    Processing helix  chain 'A' and resid 223 through 253
      removed outlier: 4.179A  pdb=" N   TRP A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   GLN A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   PHE A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 291
    Processing helix  chain 'A' and resid 300 through 321
      removed outlier: 5.247A  pdb=" N   PHE A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 356
      Proline residue:  A 345  - end of helix
    Processing helix  chain 'A' and resid 361 through 391
      removed outlier: 3.723A  pdb=" N   VAL A 369 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   MET A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      Proline residue:  A 383  - end of helix
    Processing helix  chain 'A' and resid 392 through 414
    Processing helix  chain 'A' and resid 415 through 417
      No H-bonds generated for 'chain 'A' and resid 415 through 417'
    Processing helix  chain 'B' and resid 6 through 27
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 34 through 42
    Processing helix  chain 'B' and resid 45 through 72
      removed outlier: 4.028A  pdb=" N   ASP B  72 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 96
    Processing helix  chain 'B' and resid 99 through 116
    Processing helix  chain 'B' and resid 117 through 129
      removed outlier: 3.753A  pdb=" N   CYS B 121 " --> pdb=" O   GLY B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 133
    Processing helix  chain 'B' and resid 134 through 163
      removed outlier: 3.979A  pdb=" N   MET B 145 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      Proline residue:  B 153  - end of helix
    Processing helix  chain 'B' and resid 164 through 186
      removed outlier: 3.554A  pdb=" N   PHE B 181 " --> pdb=" O   VAL B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 222
    Processing helix  chain 'B' and resid 223 through 253
      removed outlier: 4.178A  pdb=" N   TRP B 227 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   GLN B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   PHE B 249 " --> pdb=" O   ASP B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 291
    Processing helix  chain 'B' and resid 300 through 321
      removed outlier: 5.247A  pdb=" N   PHE B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 356
      Proline residue:  B 345  - end of helix
    Processing helix  chain 'B' and resid 361 through 391
      removed outlier: 3.723A  pdb=" N   VAL B 369 " --> pdb=" O   SER B 365 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   MET B 372 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      Proline residue:  B 383  - end of helix
    Processing helix  chain 'B' and resid 392 through 414
    Processing helix  chain 'B' and resid 415 through 417
      No H-bonds generated for 'chain 'B' and resid 415 through 417'

    534 hydrogen bonds defined for protein.
    1596 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: 0.94

  Time building geometry restraints manager: 0.49 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: 1141
        1.33 -     1.45: 1754
        1.45 -     1.57: 3439
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6396
  Sorted by residual:
  bond pdb=" O3  PO4 A 501 "
       pdb=" P   PO4 A 501 "
    ideal  model  delta    sigma   weight residual
    1.569  1.510  0.059 2.00e-02 2.50e+03 8.82e+00
  bond pdb=" O4  PO4 B 501 "
       pdb=" P   PO4 B 501 "
    ideal  model  delta    sigma   weight residual
    1.568  1.509  0.059 2.00e-02 2.50e+03 8.80e+00
  bond pdb=" O4  PO4 A 501 "
       pdb=" P   PO4 A 501 "
    ideal  model  delta    sigma   weight residual
    1.568  1.509  0.059 2.00e-02 2.50e+03 8.76e+00
  bond pdb=" O3  PO4 B 501 "
       pdb=" P   PO4 B 501 "
    ideal  model  delta    sigma   weight residual
    1.569  1.510  0.059 2.00e-02 2.50e+03 8.68e+00
  bond pdb=" O2  PO4 B 501 "
       pdb=" P   PO4 B 501 "
    ideal  model  delta    sigma   weight residual
    1.567  1.509  0.058 2.00e-02 2.50e+03 8.38e+00
  ... (remaining 6391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 8360
        2.17 -     4.34: 274
        4.34 -     6.52: 52
        6.52 -     8.69: 14
        8.69 -    10.86: 6
  Bond angle restraints: 8706
  Sorted by residual:
  angle pdb=" N   TRP B 118 "
        pdb=" CA  TRP B 118 "
        pdb=" C   TRP B 118 "
      ideal   model   delta    sigma   weight residual
     109.81  117.13   -7.32 2.21e+00 2.05e-01 1.10e+01
  angle pdb=" N   TRP A 118 "
        pdb=" CA  TRP A 118 "
        pdb=" C   TRP A 118 "
      ideal   model   delta    sigma   weight residual
     109.81  117.11   -7.30 2.21e+00 2.05e-01 1.09e+01
  angle pdb=" N   GLY A 117 "
        pdb=" CA  GLY A 117 "
        pdb=" C   GLY A 117 "
      ideal   model   delta    sigma   weight residual
     113.18  120.95   -7.77 2.37e+00 1.78e-01 1.08e+01
  angle pdb=" N   GLY B 117 "
        pdb=" CA  GLY B 117 "
        pdb=" C   GLY B 117 "
      ideal   model   delta    sigma   weight residual
     113.18  120.95   -7.77 2.37e+00 1.78e-01 1.07e+01
  angle pdb=" N   PRO B 119 "
        pdb=" CA  PRO B 119 "
        pdb=" C   PRO B 119 "
      ideal   model   delta    sigma   weight residual
     110.70  114.63   -3.93 1.22e+00 6.72e-01 1.04e+01
  ... (remaining 8701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.27: 3418
       15.27 -    30.53: 162
       30.53 -    45.80: 32
       45.80 -    61.06: 4
       61.06 -    76.33: 2
  Dihedral angle restraints: 3618
    sinusoidal: 1312
      harmonic: 2306
  Sorted by residual:
  dihedral pdb=" CA  TRP A 137 "
           pdb=" C   TRP A 137 "
           pdb=" N   TRP A 138 "
           pdb=" CA  TRP A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  TRP B 137 "
           pdb=" C   TRP B 137 "
           pdb=" N   TRP B 138 "
           pdb=" CA  TRP B 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  PRO A 119 "
           pdb=" C   PRO A 119 "
           pdb=" N   PRO A 120 "
           pdb=" CA  PRO A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.19   17.81     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 3615 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 774
       0.063 -    0.126: 187
       0.126 -    0.189: 19
       0.189 -    0.252: 2
       0.252 -    0.315: 2
  Chirality restraints: 984
  Sorted by residual:
  chirality pdb=" CB  VAL B  34 "
            pdb=" CA  VAL B  34 "
            pdb=" CG1 VAL B  34 "
            pdb=" CG2 VAL B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CB  VAL A  34 "
            pdb=" CA  VAL A  34 "
            pdb=" CG1 VAL A  34 "
            pdb=" CG2 VAL A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" CA  LEU B 382 "
            pdb=" N   LEU B 382 "
            pdb=" C   LEU B 382 "
            pdb=" CB  LEU B 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.73e-01
  ... (remaining 981 not shown)

  Planarity restraints: 1064
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 119 "   -0.045 5.00e-02 4.00e+02   6.78e-02 7.36e+00
        pdb=" N   PRO A 120 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 120 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 120 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 119 "    0.045 5.00e-02 4.00e+02   6.78e-02 7.35e+00
        pdb=" N   PRO B 120 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 120 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 120 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 344 "    0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO B 345 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 345 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 345 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1061 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1496
        2.78 -     3.31: 5934
        3.31 -     3.84: 11187
        3.84 -     4.37: 12495
        4.37 -     4.90: 22391
  Nonbonded interactions: 53503
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 317 "
            pdb=" OG1 THR B 321 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   LEU A 317 "
            pdb=" OG1 THR A 321 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   PHE B  26 "
            pdb=" OG1 THR B  30 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   PHE A  26 "
            pdb=" OG1 THR A  30 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   LEU B 141 "
            pdb=" OG  SER B 144 "
     model   vdw
     2.259 3.040
  ... (remaining 53498 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'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             3.100
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.620
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
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      :  0.008   0.070   6396  Z= 0.351
  Angle     :  0.989  10.862   8706  Z= 0.509
  Chirality :  0.054   0.315    984
  Planarity :  0.009   0.068   1064
  Dihedral  :  9.764  76.330   2154
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  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 are not related in a simple way.
  whole: -2.88 (0.24), residues: 806
  helix: -1.82 (0.15), residues: 676
  sheet:  None (None), residues: 0
  loop : -0.96 (0.52), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 319 
 TYR   0.030   0.003   TYR A 343 
 PHE   0.038   0.004   PHE A 103 
 TRP   0.039   0.004   TRP A 138 
 HIS   0.007   0.002   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00825 ( 6396)
  covalent geometry    : angle       0.98921 ( 8706)
  hydrogen bonds       : bond        0.10295 (  534)
  hydrogen bonds       : angle       6.47074 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   93 PHE cc_start: 0.7538 (m-10) cc_final: 0.7221 (m-10)
REVERT: A  263 SER cc_start: 0.8291 (t) cc_final: 0.7876 (m)
REVERT: A  307 MET cc_start: 0.8523 (mtt) cc_final: 0.7920 (mtp)
REVERT: A  312 THR cc_start: 0.8586 (m) cc_final: 0.8318 (m)
REVERT: A  389 LYS cc_start: 0.8259 (tttt) cc_final: 0.7937 (ttmt)
REVERT: B  127 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8313 (mmtp)
REVERT: B  263 SER cc_start: 0.8267 (t) cc_final: 0.7834 (m)
REVERT: B  307 MET cc_start: 0.8495 (mtt) cc_final: 0.7984 (mtp)
REVERT: B  312 THR cc_start: 0.8651 (m) cc_final: 0.8410 (m)
REVERT: B  389 LYS cc_start: 0.8263 (tttt) cc_final: 0.8015 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0880
  time to fit residues: 16.1541
Evaluate side-chains
  99 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   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  91 ASN
A 114 GLN
A 146 ASN
B 114 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.134140 restraints weight = 7762.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.88
r_work: 0.3408 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6396  Z= 0.173
  Angle     :  0.617   6.271   8706  Z= 0.319
  Chirality :  0.040   0.155    984
  Planarity :  0.006   0.057   1064
  Dihedral  :  4.699  15.603    866
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  7.32 %
    Favored  : 91.62 %
  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 are not related in a simple way.
  whole:  0.29 (0.29), residues: 806
  helix:  0.38 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -0.10 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 423 
 TYR   0.014   0.001   TYR B  25 
 PHE   0.017   0.002   PHE B 103 
 TRP   0.017   0.002   TRP B 227 
 HIS   0.001   0.000   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6396)
  covalent geometry    : angle       0.61707 ( 8706)
  hydrogen bonds       : bond        0.04950 (  534)
  hydrogen bonds       : angle       4.70678 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A   93 PHE cc_start: 0.7570 (m-10) cc_final: 0.7292 (m-80)
REVERT: A  133 GLN cc_start: 0.8121 (mt0) cc_final: 0.7921 (pt0)
REVERT: A  166 ARG cc_start: 0.7547 (mtt-85) cc_final: 0.7285 (mtt-85)
REVERT: A  181 PHE cc_start: 0.8415 (m-80) cc_final: 0.8132 (m-80)
REVERT: A  263 SER cc_start: 0.8008 (t) cc_final: 0.7566 (m)
REVERT: A  312 THR cc_start: 0.8571 (m) cc_final: 0.8353 (m)
REVERT: A  351 VAL cc_start: 0.8966 (t) cc_final: 0.8699 (m)
REVERT: A  389 LYS cc_start: 0.8378 (tttt) cc_final: 0.8158 (tttm)
REVERT: B  127 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8203 (mmtp)
REVERT: B  133 GLN cc_start: 0.8386 (mt0) cc_final: 0.7388 (mm-40)
REVERT: B  181 PHE cc_start: 0.8321 (m-80) cc_final: 0.8077 (m-80)
REVERT: B  263 SER cc_start: 0.8012 (t) cc_final: 0.7547 (m)
REVERT: B  351 VAL cc_start: 0.8955 (t) cc_final: 0.8607 (m)
REVERT: B  389 LYS cc_start: 0.8433 (tttt) cc_final: 0.8211 (tttm)
  outliers start: 7
  outliers final: 5
  residues processed: 114
  average time/residue: 0.0811
  time to fit residues: 11.9852
Evaluate side-chains
  106 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  365 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0970
   chunk 61 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 114 GLN
B 146 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.155860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.133228 restraints weight = 7622.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.87
r_work: 0.3390 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6396  Z= 0.166
  Angle     :  0.565   6.467   8706  Z= 0.292
  Chirality :  0.040   0.162    984
  Planarity :  0.005   0.054   1064
  Dihedral  :  4.386  16.083    866
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  8.54 %
    Favored  : 89.33 %
  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 are not related in a simple way.
  whole:  1.57 (0.30), residues: 806
  helix:  1.29 (0.20), residues: 674
  sheet:  None (None), residues: 0
  loop :  0.07 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 166 
 TYR   0.009   0.001   TYR A  25 
 PHE   0.017   0.002   PHE A 103 
 TRP   0.015   0.002   TRP B 227 
 HIS   0.002   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6396)
  covalent geometry    : angle       0.56455 ( 8706)
  hydrogen bonds       : bond        0.04778 (  534)
  hydrogen bonds       : angle       4.36665 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   93 PHE cc_start: 0.7666 (m-10) cc_final: 0.7370 (m-80)
REVERT: A  116 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7539 (tt)
REVERT: A  133 GLN cc_start: 0.8076 (mt0) cc_final: 0.7174 (mm-40)
REVERT: A  166 ARG cc_start: 0.7428 (mtt-85) cc_final: 0.7155 (mtt-85)
REVERT: A  263 SER cc_start: 0.8025 (t) cc_final: 0.7565 (m)
REVERT: A  264 SER cc_start: 0.8434 (m) cc_final: 0.8059 (p)
REVERT: A  328 LYS cc_start: 0.8176 (tttt) cc_final: 0.7860 (tttm)
REVERT: A  351 VAL cc_start: 0.9015 (t) cc_final: 0.8719 (m)
REVERT: A  389 LYS cc_start: 0.8424 (tttt) cc_final: 0.8174 (tttm)
REVERT: B  116 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7455 (tt)
REVERT: B  127 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8195 (mmtp)
REVERT: B  133 GLN cc_start: 0.8357 (mt0) cc_final: 0.7403 (mm-40)
REVERT: B  166 ARG cc_start: 0.7399 (mtt-85) cc_final: 0.7085 (mmt90)
REVERT: B  263 SER cc_start: 0.8000 (t) cc_final: 0.7539 (m)
REVERT: B  264 SER cc_start: 0.8463 (m) cc_final: 0.8083 (p)
REVERT: B  328 LYS cc_start: 0.8197 (tttt) cc_final: 0.7965 (tttm)
REVERT: B  389 LYS cc_start: 0.8550 (tttt) cc_final: 0.8317 (tttm)
  outliers start: 14
  outliers final: 5
  residues processed: 114
  average time/residue: 0.0710
  time to fit residues: 10.6731
Evaluate side-chains
  99 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  365 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
B 114 GLN
B 146 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.155007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.131636 restraints weight = 7716.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 1.90
r_work: 0.3383 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6396  Z= 0.174
  Angle     :  0.561   5.392   8706  Z= 0.289
  Chirality :  0.040   0.179    984
  Planarity :  0.005   0.053   1064
  Dihedral  :  4.231  16.341    866
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  :  8.84 %
    Favored  : 87.80 %
  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 are not related in a simple way.
  whole:  2.15 (0.30), residues: 806
  helix:  1.68 (0.20), residues: 674
  sheet:  None (None), residues: 0
  loop :  0.37 (0.61), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 423 
 TYR   0.013   0.001   TYR A  24 
 PHE   0.015   0.002   PHE A 340 
 TRP   0.014   0.002   TRP B 227 
 HIS   0.002   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6396)
  covalent geometry    : angle       0.56111 ( 8706)
  hydrogen bonds       : bond        0.04749 (  534)
  hydrogen bonds       : angle       4.27911 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   93 PHE cc_start: 0.7822 (m-10) cc_final: 0.7530 (m-80)
REVERT: A  116 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7631 (tt)
REVERT: A  133 GLN cc_start: 0.8108 (mt0) cc_final: 0.7239 (mm-40)
REVERT: A  166 ARG cc_start: 0.7462 (mtt-85) cc_final: 0.7208 (mtt-85)
REVERT: A  219 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7655 (mt-10)
REVERT: A  263 SER cc_start: 0.8114 (t) cc_final: 0.7637 (m)
REVERT: A  264 SER cc_start: 0.8496 (m) cc_final: 0.8065 (p)
REVERT: A  328 LYS cc_start: 0.8278 (tttt) cc_final: 0.8072 (tttm)
REVERT: A  351 VAL cc_start: 0.9077 (t) cc_final: 0.8773 (m)
REVERT: A  389 LYS cc_start: 0.8518 (tttt) cc_final: 0.8273 (tttm)
REVERT: B  116 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7550 (tt)
REVERT: B  127 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8295 (mmtp)
REVERT: B  133 GLN cc_start: 0.8376 (mt0) cc_final: 0.7458 (mm-40)
REVERT: B  166 ARG cc_start: 0.7413 (mtt-85) cc_final: 0.6814 (mmt180)
REVERT: B  263 SER cc_start: 0.8102 (t) cc_final: 0.7634 (m)
REVERT: B  264 SER cc_start: 0.8540 (m) cc_final: 0.8115 (p)
REVERT: B  328 LYS cc_start: 0.8243 (tttt) cc_final: 0.8008 (tttm)
REVERT: B  389 LYS cc_start: 0.8554 (tttt) cc_final: 0.8321 (tttm)
  outliers start: 22
  outliers final: 11
  residues processed: 112
  average time/residue: 0.0778
  time to fit residues: 11.3788
Evaluate side-chains
  103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  365 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 58 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.155834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.132093 restraints weight = 7788.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.95
r_work: 0.3385 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6396  Z= 0.155
  Angle     :  0.543   5.319   8706  Z= 0.280
  Chirality :  0.039   0.152    984
  Planarity :  0.005   0.054   1064
  Dihedral  :  4.120  16.472    866
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 10.52 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.30), residues: 806
  helix:  1.93 (0.20), residues: 674
  sheet:  None (None), residues: 0
  loop :  0.52 (0.61), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 423 
 TYR   0.010   0.001   TYR A  24 
 PHE   0.014   0.002   PHE A 338 
 TRP   0.013   0.001   TRP B 227 
 HIS   0.001   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6396)
  covalent geometry    : angle       0.54330 ( 8706)
  hydrogen bonds       : bond        0.04601 (  534)
  hydrogen bonds       : angle       4.19386 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   93 PHE cc_start: 0.7920 (m-10) cc_final: 0.7603 (m-80)
REVERT: A  116 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7624 (tt)
REVERT: A  133 GLN cc_start: 0.8100 (mt0) cc_final: 0.7267 (mm-40)
REVERT: A  166 ARG cc_start: 0.7478 (mtt-85) cc_final: 0.6809 (mmt180)
REVERT: A  219 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7680 (mt-10)
REVERT: A  263 SER cc_start: 0.8120 (t) cc_final: 0.7645 (m)
REVERT: A  264 SER cc_start: 0.8534 (m) cc_final: 0.8132 (p)
REVERT: A  328 LYS cc_start: 0.8306 (tttt) cc_final: 0.8083 (tttm)
REVERT: A  351 VAL cc_start: 0.9086 (t) cc_final: 0.8800 (m)
REVERT: A  389 LYS cc_start: 0.8505 (tttt) cc_final: 0.8274 (tttm)
REVERT: B  116 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7574 (tt)
REVERT: B  127 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8298 (mmtp)
REVERT: B  133 GLN cc_start: 0.8329 (mt0) cc_final: 0.7509 (mm-40)
REVERT: B  166 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6778 (mmt180)
REVERT: B  263 SER cc_start: 0.8118 (t) cc_final: 0.7654 (m)
REVERT: B  264 SER cc_start: 0.8556 (m) cc_final: 0.8163 (p)
REVERT: B  328 LYS cc_start: 0.8332 (tttt) cc_final: 0.8108 (tttm)
REVERT: B  389 LYS cc_start: 0.8585 (tttt) cc_final: 0.8366 (tttm)
  outliers start: 21
  outliers final: 11
  residues processed: 112
  average time/residue: 0.0871
  time to fit residues: 12.8093
Evaluate side-chains
  103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  365 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 79 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 52 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 114 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 = 0.3773 r_free = 0.3773 target = 0.153840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.129896 restraints weight = 7680.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.94
r_work: 0.3408 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6396  Z= 0.151
  Angle     :  0.548   5.458   8706  Z= 0.280
  Chirality :  0.039   0.152    984
  Planarity :  0.005   0.054   1064
  Dihedral  :  4.043  16.510    866
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 10.98 %
    Favored  : 85.67 %
  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 are not related in a simple way.
  whole:  2.74 (0.30), residues: 806
  helix:  2.09 (0.20), residues: 670
  sheet:  None (None), residues: 0
  loop :  0.56 (0.59), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 423 
 TYR   0.011   0.001   TYR B  24 
 PHE   0.014   0.002   PHE B 103 
 TRP   0.013   0.002   TRP B 227 
 HIS   0.001   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6396)
  covalent geometry    : angle       0.54829 ( 8706)
  hydrogen bonds       : bond        0.04534 (  534)
  hydrogen bonds       : angle       4.13272 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  116 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7585 (tt)
REVERT: A  133 GLN cc_start: 0.8126 (mt0) cc_final: 0.7258 (mm-40)
REVERT: A  166 ARG cc_start: 0.7442 (mtt-85) cc_final: 0.6775 (mmt180)
REVERT: A  181 PHE cc_start: 0.8546 (m-80) cc_final: 0.8166 (m-80)
REVERT: A  263 SER cc_start: 0.8075 (t) cc_final: 0.7601 (m)
REVERT: A  264 SER cc_start: 0.8502 (m) cc_final: 0.8107 (p)
REVERT: A  328 LYS cc_start: 0.8276 (tttt) cc_final: 0.8070 (tttm)
REVERT: A  351 VAL cc_start: 0.9044 (t) cc_final: 0.8757 (m)
REVERT: A  389 LYS cc_start: 0.8452 (tttt) cc_final: 0.8228 (tttm)
REVERT: A  391 TYR cc_start: 0.8074 (m-80) cc_final: 0.7322 (m-80)
REVERT: B  116 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7554 (tt)
REVERT: B  127 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8263 (mmtp)
REVERT: B  133 GLN cc_start: 0.8293 (mt0) cc_final: 0.7420 (mm-40)
REVERT: B  166 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.6740 (mmt180)
REVERT: B  263 SER cc_start: 0.8094 (t) cc_final: 0.7625 (m)
REVERT: B  264 SER cc_start: 0.8514 (m) cc_final: 0.8121 (p)
REVERT: B  328 LYS cc_start: 0.8266 (tttt) cc_final: 0.8043 (tttm)
REVERT: B  389 LYS cc_start: 0.8565 (tttt) cc_final: 0.8345 (tttm)
  outliers start: 22
  outliers final: 16
  residues processed: 111
  average time/residue: 0.0672
  time to fit residues: 9.8492
Evaluate side-chains
  105 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain B residue   11 THR
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  311 MET
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  394 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 114 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 = 0.3761 r_free = 0.3761 target = 0.152680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128629 restraints weight = 7615.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.91
r_work: 0.3369 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6396  Z= 0.162
  Angle     :  0.553   5.844   8706  Z= 0.282
  Chirality :  0.039   0.152    984
  Planarity :  0.005   0.054   1064
  Dihedral  :  4.017  16.529    866
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 11.74 %
    Favored  : 84.91 %
  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 are not related in a simple way.
  whole:  2.82 (0.30), residues: 806
  helix:  2.12 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.76 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 423 
 TYR   0.012   0.001   TYR A  24 
 PHE   0.015   0.002   PHE B 103 
 TRP   0.013   0.001   TRP B 227 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6396)
  covalent geometry    : angle       0.55345 ( 8706)
  hydrogen bonds       : bond        0.04568 (  534)
  hydrogen bonds       : angle       4.16011 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   93 PHE cc_start: 0.7950 (m-10) cc_final: 0.7590 (m-80)
REVERT: A  116 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7642 (tt)
REVERT: A  133 GLN cc_start: 0.8106 (mt0) cc_final: 0.7272 (mm-40)
REVERT: A  166 ARG cc_start: 0.7432 (mtt-85) cc_final: 0.6750 (mmt180)
REVERT: A  181 PHE cc_start: 0.8557 (m-80) cc_final: 0.8283 (m-80)
REVERT: A  263 SER cc_start: 0.8142 (t) cc_final: 0.7661 (m)
REVERT: A  264 SER cc_start: 0.8524 (m) cc_final: 0.8155 (p)
REVERT: A  328 LYS cc_start: 0.8302 (tttt) cc_final: 0.8083 (tttm)
REVERT: A  351 VAL cc_start: 0.9074 (t) cc_final: 0.8776 (m)
REVERT: A  389 LYS cc_start: 0.8499 (tttt) cc_final: 0.8251 (tttm)
REVERT: A  391 TYR cc_start: 0.8201 (m-80) cc_final: 0.7636 (m-80)
REVERT: B  116 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7593 (tt)
REVERT: B  127 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8314 (mmtp)
REVERT: B  133 GLN cc_start: 0.8287 (mt0) cc_final: 0.7500 (mm-40)
REVERT: B  166 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.6701 (mmt180)
REVERT: B  263 SER cc_start: 0.8157 (t) cc_final: 0.7678 (m)
REVERT: B  264 SER cc_start: 0.8542 (m) cc_final: 0.8195 (p)
REVERT: B  328 LYS cc_start: 0.8302 (tttt) cc_final: 0.8072 (tttm)
REVERT: B  389 LYS cc_start: 0.8576 (tttt) cc_final: 0.8334 (tttm)
  outliers start: 22
  outliers final: 16
  residues processed: 108
  average time/residue: 0.0721
  time to fit residues: 10.3881
Evaluate side-chains
  105 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain B residue   74 MET
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  311 MET
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  394 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0970
   chunk 38 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 ASN
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.155145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.131353 restraints weight = 7615.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.90
r_work: 0.3375 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6396  Z= 0.153
  Angle     :  0.548   5.948   8706  Z= 0.279
  Chirality :  0.039   0.147    984
  Planarity :  0.005   0.054   1064
  Dihedral  :  3.993  16.859    866
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 12.04 %
    Favored  : 84.15 %
  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 are not related in a simple way.
  whole:  2.89 (0.30), residues: 806
  helix:  2.15 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.87 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 423 
 TYR   0.012   0.001   TYR B  24 
 PHE   0.015   0.002   PHE B 103 
 TRP   0.012   0.001   TRP B 227 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6396)
  covalent geometry    : angle       0.54835 ( 8706)
  hydrogen bonds       : bond        0.04503 (  534)
  hydrogen bonds       : angle       4.13334 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A   93 PHE cc_start: 0.7959 (m-10) cc_final: 0.7610 (m-80)
REVERT: A  116 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7617 (tt)
REVERT: A  133 GLN cc_start: 0.8097 (mt0) cc_final: 0.7261 (mm-40)
REVERT: A  166 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.6740 (mmt180)
REVERT: A  181 PHE cc_start: 0.8546 (m-80) cc_final: 0.8151 (m-80)
REVERT: A  263 SER cc_start: 0.8137 (t) cc_final: 0.7653 (m)
REVERT: A  264 SER cc_start: 0.8521 (m) cc_final: 0.8198 (p)
REVERT: A  328 LYS cc_start: 0.8285 (tttt) cc_final: 0.8063 (tttm)
REVERT: A  351 VAL cc_start: 0.9062 (t) cc_final: 0.8767 (m)
REVERT: A  389 LYS cc_start: 0.8504 (tttt) cc_final: 0.8266 (tttm)
REVERT: A  391 TYR cc_start: 0.8179 (m-80) cc_final: 0.7527 (m-80)
REVERT: B  116 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7641 (tt)
REVERT: B  127 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8310 (mmtp)
REVERT: B  133 GLN cc_start: 0.8288 (mt0) cc_final: 0.7454 (mm-40)
REVERT: B  166 ARG cc_start: 0.7344 (mtt-85) cc_final: 0.6676 (mmt180)
REVERT: B  263 SER cc_start: 0.8143 (t) cc_final: 0.7658 (m)
REVERT: B  264 SER cc_start: 0.8522 (m) cc_final: 0.8185 (p)
REVERT: B  328 LYS cc_start: 0.8289 (tttt) cc_final: 0.8067 (tttm)
REVERT: B  389 LYS cc_start: 0.8570 (tttt) cc_final: 0.8333 (tttm)
REVERT: B  391 TYR cc_start: 0.8119 (m-80) cc_final: 0.7651 (m-80)
  outliers start: 25
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0792
  time to fit residues: 11.5617
Evaluate side-chains
  111 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain B residue   11 THR
Chi-restraints excluded: chain B residue   74 MET
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  311 MET
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  394 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0470
   chunk 33 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 ASN
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.153854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.129963 restraints weight = 7584.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.91
r_work: 0.3376 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6396  Z= 0.140
  Angle     :  0.538   5.792   8706  Z= 0.274
  Chirality :  0.039   0.144    984
  Planarity :  0.005   0.053   1064
  Dihedral  :  3.954  16.975    866
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.11 %
    Favored  : 83.84 %
  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 are not related in a simple way.
  whole:  2.97 (0.30), residues: 806
  helix:  2.20 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.91 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  28 
 TYR   0.011   0.001   TYR B  24 
 PHE   0.015   0.002   PHE B 103 
 TRP   0.012   0.001   TRP B 227 
 HIS   0.002   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6396)
  covalent geometry    : angle       0.53783 ( 8706)
  hydrogen bonds       : bond        0.04421 (  534)
  hydrogen bonds       : angle       4.09890 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  116 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7534 (tt)
REVERT: A  133 GLN cc_start: 0.8097 (mt0) cc_final: 0.7218 (mm-40)
REVERT: A  166 ARG cc_start: 0.7336 (mtt-85) cc_final: 0.6662 (mmt180)
REVERT: A  263 SER cc_start: 0.8026 (t) cc_final: 0.7545 (m)
REVERT: A  264 SER cc_start: 0.8459 (m) cc_final: 0.8163 (p)
REVERT: A  328 LYS cc_start: 0.8208 (tttt) cc_final: 0.7985 (tttm)
REVERT: A  351 VAL cc_start: 0.9004 (t) cc_final: 0.8705 (m)
REVERT: A  389 LYS cc_start: 0.8445 (tttt) cc_final: 0.8203 (tttm)
REVERT: A  391 TYR cc_start: 0.8186 (m-80) cc_final: 0.7635 (m-80)
REVERT: B  116 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7484 (tt)
REVERT: B  127 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8181 (mmtp)
REVERT: B  133 GLN cc_start: 0.8246 (mt0) cc_final: 0.7389 (mm-40)
REVERT: B  263 SER cc_start: 0.8032 (t) cc_final: 0.7555 (m)
REVERT: B  264 SER cc_start: 0.8440 (m) cc_final: 0.8154 (p)
REVERT: B  328 LYS cc_start: 0.8191 (tttt) cc_final: 0.7956 (tttm)
REVERT: B  389 LYS cc_start: 0.8500 (tttt) cc_final: 0.8260 (tttm)
REVERT: B  391 TYR cc_start: 0.8189 (m-80) cc_final: 0.7386 (m-80)
  outliers start: 20
  outliers final: 14
  residues processed: 107
  average time/residue: 0.0714
  time to fit residues: 10.0415
Evaluate side-chains
  106 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain B residue   11 THR
Chi-restraints excluded: chain B residue   74 MET
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  311 MET
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  365 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
A 354 ASN
** B  91 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.152682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.128532 restraints weight = 7592.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.90
r_work: 0.3352 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6396  Z= 0.186
  Angle     :  0.579   5.504   8706  Z= 0.293
  Chirality :  0.041   0.148    984
  Planarity :  0.005   0.054   1064
  Dihedral  :  3.992  16.840    866
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.26 %
    Favored  : 83.54 %
  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 are not related in a simple way.
  whole:  2.92 (0.30), residues: 806
  helix:  2.17 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.88 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  28 
 TYR   0.013   0.001   TYR B  24 
 PHE   0.017   0.002   PHE B 103 
 TRP   0.014   0.002   TRP B 227 
 HIS   0.002   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 6396)
  covalent geometry    : angle       0.57923 ( 8706)
  hydrogen bonds       : bond        0.04658 (  534)
  hydrogen bonds       : angle       4.20723 ( 1596)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   93 PHE cc_start: 0.7936 (m-10) cc_final: 0.7604 (m-80)
REVERT: A  116 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7586 (tt)
REVERT: A  133 GLN cc_start: 0.8135 (mt0) cc_final: 0.7195 (mm-40)
REVERT: A  181 PHE cc_start: 0.8555 (m-80) cc_final: 0.8305 (m-80)
REVERT: A  263 SER cc_start: 0.8044 (t) cc_final: 0.7554 (m)
REVERT: A  264 SER cc_start: 0.8442 (m) cc_final: 0.8132 (p)
REVERT: A  328 LYS cc_start: 0.8249 (tttt) cc_final: 0.8019 (tttm)
REVERT: A  389 LYS cc_start: 0.8456 (tttt) cc_final: 0.8189 (tttm)
REVERT: A  391 TYR cc_start: 0.8151 (m-80) cc_final: 0.7388 (m-80)
REVERT: B  116 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7573 (tt)
REVERT: B  127 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8185 (mmtp)
REVERT: B  133 GLN cc_start: 0.8325 (mt0) cc_final: 0.7450 (mm-40)
REVERT: B  166 ARG cc_start: 0.7355 (mtt-85) cc_final: 0.6701 (mmt180)
REVERT: B  263 SER cc_start: 0.8032 (t) cc_final: 0.7547 (m)
REVERT: B  264 SER cc_start: 0.8453 (m) cc_final: 0.8157 (p)
REVERT: B  328 LYS cc_start: 0.8228 (tttt) cc_final: 0.7988 (tttm)
REVERT: B  389 LYS cc_start: 0.8510 (tttt) cc_final: 0.8254 (tttm)
REVERT: B  391 TYR cc_start: 0.8170 (m-80) cc_final: 0.7408 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 113
  average time/residue: 0.0766
  time to fit residues: 11.4904
Evaluate side-chains
  115 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain B residue   11 THR
Chi-restraints excluded: chain B residue   74 MET
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  311 MET
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  394 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.153663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.130422 restraints weight = 7602.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.83
r_work: 0.3344 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6396  Z= 0.169
  Angle     :  0.570   5.545   8706  Z= 0.289
  Chirality :  0.040   0.146    984
  Planarity :  0.005   0.053   1064
  Dihedral  :  3.999  17.024    866
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.87 %
    Favored  : 83.23 %
  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 are not related in a simple way.
  whole:  2.90 (0.30), residues: 806
  helix:  2.15 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop :  0.88 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 166 
 TYR   0.013   0.001   TYR A  24 
 PHE   0.017   0.002   PHE B 103 
 TRP   0.013   0.002   TRP B 227 
 HIS   0.001   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6396)
  covalent geometry    : angle       0.56958 ( 8706)
  hydrogen bonds       : bond        0.04593 (  534)
  hydrogen bonds       : angle       4.19335 ( 1596)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1456.50 seconds
wall clock time: 25 minutes 42.77 seconds (1542.77 seconds total)