Starting phenix.real_space_refine
on Wed Jul  1 22:59:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdo_37141/07_2026/8kdo_37141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdo_37141/07_2026/8kdo_37141.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdo_37141/07_2026/8kdo_37141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdo_37141/07_2026/8kdo_37141.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdo_37141/07_2026/8kdo_37141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdo_37141/07_2026/8kdo_37141.cif"
  }
  resolution = 4.12
  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=   0.002 sd=   0.010
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      22      5.16       5
     Cl      2      4.86       5
     C    2639      2.51       5
     N     616      2.21       5
     O     658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3937
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 409
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 2, 'TRANS': 49}
    Chain: "B"
      Number of atoms: 3509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3509
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 23, 'TRANS': 430}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'VUC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.09, per 1000 atoms: 0.28
  Number of scatterers: 3937
  At special positions: 0
  Unit cell: (78.2595, 84.3975, 81.3285, 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)
     Cl      2     17.00
     S      22     16.00
     O     658      8.00
     N     616      7.00
     C    2639      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.10

  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: 0.23
  Conformation dependent library (CDL) restraints added in 145.3 milliseconds
  

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      84.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 174
      removed outlier: 4.014A  pdb=" N   LYS A 171 " --> pdb=" O   GLU A 167 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 206
      removed outlier: 3.981A  pdb=" N   TRP A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
      removed outlier: 3.796A  pdb=" N   THR B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 71 through 80
      removed outlier: 4.298A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 111
      removed outlier: 3.714A  pdb=" N   LEU B  86 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ALA B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY B  93 " --> pdb=" O   TRP B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 122
      removed outlier: 3.995A  pdb=" N   MET B 120 " --> pdb=" O   ASP B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.517A  pdb=" N   LYS B 132 " --> pdb=" O   PRO B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 157
    Processing helix  chain 'B' and resid 158 through 161
    Processing helix  chain 'B' and resid 167 through 189
    Processing helix  chain 'B' and resid 189 through 222
      removed outlier: 3.696A  pdb=" N   ALA B 199 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LYS B 204 " --> pdb=" O   PHE B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 249
      removed outlier: 4.238A  pdb=" N   VAL B 244 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 254
      removed outlier: 4.275A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 267
      removed outlier: 6.140A  pdb=" N   GLU B 265 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 300
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
      removed outlier: 3.841A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 308
      removed outlier: 3.619A  pdb=" N   SER B 307 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.694A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B 349 " --> pdb=" O   THR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 392 through 400
      removed outlier: 4.078A  pdb=" N   ASN B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 422
      removed outlier: 4.019A  pdb=" N   ASN B 404 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 454
      removed outlier: 3.884A  pdb=" N   SER B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 467
      removed outlier: 3.885A  pdb=" N   GLY B 461 " --> pdb=" O   GLU B 457 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ILE B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.099A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501

    288 hydrogen bonds defined for protein.
    843 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: 0.36

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 661
        1.33 -     1.45: 1090
        1.45 -     1.58: 2256
        1.58 -     1.70: 0
        1.70 -     1.83: 33
  Bond restraints: 4040
  Sorted by residual:
  bond pdb=" C3  VUC B 601 "
       pdb=" N2  VUC B 601 "
    ideal  model  delta    sigma   weight residual
    1.436  1.366  0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C   LYS B 481 "
       pdb=" N   PRO B 482 "
    ideal  model  delta    sigma   weight residual
    1.333  1.367 -0.033 1.01e-02 9.80e+03 1.08e+01
  bond pdb=" CG  HIS B 367 "
       pdb=" CD2 HIS B 367 "
    ideal  model  delta    sigma   weight residual
    1.354  1.319  0.035 1.10e-02 8.26e+03 9.93e+00
  bond pdb=" C   HIS B 358 "
       pdb=" N   LEU B 359 "
    ideal  model  delta    sigma   weight residual
    1.326  1.358 -0.033 1.12e-02 7.97e+03 8.51e+00
  bond pdb=" CA  ALA A 207 "
       pdb=" CB  ALA A 207 "
    ideal  model  delta    sigma   weight residual
    1.537  1.497  0.040 1.38e-02 5.25e+03 8.46e+00
  ... (remaining 4035 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 4324
        1.95 -     3.90: 1016
        3.90 -     5.84: 147
        5.84 -     7.79: 23
        7.79 -     9.74: 4
  Bond angle restraints: 5514
  Sorted by residual:
  angle pdb=" CA  PHE B 399 "
        pdb=" CB  PHE B 399 "
        pdb=" CG  PHE B 399 "
      ideal   model   delta    sigma   weight residual
     113.80  123.54   -9.74 1.00e+00 1.00e+00 9.49e+01
  angle pdb=" CA  PHE B 262 "
        pdb=" CB  PHE B 262 "
        pdb=" CG  PHE B 262 "
      ideal   model   delta    sigma   weight residual
     113.80  119.37   -5.57 1.00e+00 1.00e+00 3.10e+01
  angle pdb=" CA  ASP B 239 "
        pdb=" CB  ASP B 239 "
        pdb=" CG  ASP B 239 "
      ideal   model   delta    sigma   weight residual
     112.60  118.01   -5.41 1.00e+00 1.00e+00 2.93e+01
  angle pdb=" N   TYR B 188 "
        pdb=" CA  TYR B 188 "
        pdb=" CB  TYR B 188 "
      ideal   model   delta    sigma   weight residual
     110.16  117.91   -7.75 1.48e+00 4.57e-01 2.74e+01
  angle pdb=" CA  PHE B 438 "
        pdb=" CB  PHE B 438 "
        pdb=" CG  PHE B 438 "
      ideal   model   delta    sigma   weight residual
     113.80  118.77   -4.97 1.00e+00 1.00e+00 2.47e+01
  ... (remaining 5509 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    16.81: 2146
       16.81 -    33.62: 152
       33.62 -    50.42: 33
       50.42 -    67.22: 5
       67.22 -    84.03: 2
  Dihedral angle restraints: 2338
    sinusoidal: 887
      harmonic: 1451
  Sorted by residual:
  dihedral pdb=" CA  LEU B 251 "
           pdb=" C   LEU B 251 "
           pdb=" N   PHE B 252 "
           pdb=" CA  PHE B 252 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.88   30.12     0      5.00e+00 4.00e-02 3.63e+01
  dihedral pdb=" CA  GLU B 457 "
           pdb=" C   GLU B 457 "
           pdb=" N   CYS B 458 "
           pdb=" CA  CYS B 458 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.31  -27.69     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CA  GLY B 125 "
           pdb=" C   GLY B 125 "
           pdb=" N   SER B 126 "
           pdb=" CA  SER B 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.08  -21.92     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 2335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 334
       0.054 -    0.107: 219
       0.107 -    0.160: 85
       0.160 -    0.213: 20
       0.213 -    0.267: 7
  Chirality restraints: 665
  Sorted by residual:
  chirality pdb=" CA  CYS B 176 "
            pdb=" N   CYS B 176 "
            pdb=" C   CYS B 176 "
            pdb=" CB  CYS B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CA  PHE B 399 "
            pdb=" N   PHE B 399 "
            pdb=" C   PHE B 399 "
            pdb=" CB  PHE B 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  TYR B 188 "
            pdb=" N   TYR B 188 "
            pdb=" C   TYR B 188 "
            pdb=" CB  TYR B 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 662 not shown)

  Planarity restraints: 661
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 348 "   -0.436 9.50e-02 1.11e+02   1.95e-01 2.35e+01
        pdb=" NE  ARG B 348 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 348 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 348 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 348 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 146 "   -0.045 2.00e-02 2.50e+03   2.26e-02 1.02e+01
        pdb=" CG  TYR B 146 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 146 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 146 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 146 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 146 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 146 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR B 146 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 417 "    0.032 2.00e-02 2.50e+03   1.66e-02 6.85e+00
        pdb=" CG  TRP B 417 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 417 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 417 "   -0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 417 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 417 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 417 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 417 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 417 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 417 "    0.027 2.00e-02 2.50e+03
  ... (remaining 658 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 2202
        3.03 -     3.50: 4345
        3.50 -     3.96: 6305
        3.96 -     4.43: 7148
        4.43 -     4.90: 11480
  Nonbonded interactions: 31480
  Sorted by model distance:
  nonbonded pdb=" O   GLY B  65 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.561 3.040
  nonbonded pdb=" O   ALA B 246 "
            pdb=" OG  SER B 249 "
     model   vdw
     2.561 3.040
  nonbonded pdb=" O   PHE B 344 "
            pdb=" OG  SER B 347 "
     model   vdw
     2.572 3.040
  nonbonded pdb=" O   PHE B 351 "
            pdb=" OG  SER B 354 "
     model   vdw
     2.611 3.040
  nonbonded pdb=" O   SER B 347 "
            pdb=" OG  SER B 376 "
     model   vdw
     2.614 3.040
  ... (remaining 31475 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.050
  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:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.730
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
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      :  0.011   0.075   4041  Z= 0.704
  Angle     :  1.694   9.741   5516  Z= 1.139
  Chirality :  0.079   0.267    665
  Planarity :  0.011   0.195    661
  Dihedral  : 12.731  84.028   1403
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 0.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  3.76 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.26 (0.31), residues: 500
  helix: -1.33 (0.21), residues: 378
  sheet:  None (None), residues: 0
  loop : -1.39 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 182 
 TYR   0.045   0.007   TYR B 146 
 PHE   0.027   0.005   PHE B 399 
 TRP   0.032   0.005   TRP B 417 
 HIS   0.005   0.002   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01094 /  0.70 ( 4040)
  covalent geometry    : angle       1.69130 /  1.14 ( 5514)
  SS BOND              : bond        0.06608 /  3.48 (    1)
  SS BOND              : angle       5.58721 /  2.54 (    2)
  hydrogen bonds       : bond        0.18865 / 12.42 (  288)
  hydrogen bonds       : angle       7.83629 /  5.69 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 199
  time to evaluate  : 0.142 
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: A  211 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8170 (ptt-90)
REVERT: A  212 GLU cc_start: 0.9328 (pt0) cc_final: 0.9095 (tm-30)
REVERT: B   54 ASN cc_start: 0.7474 (m-40) cc_final: 0.7016 (t0)
REVERT: B   60 VAL cc_start: 0.7067 (p) cc_final: 0.6813 (p)
REVERT: B  117 TYR cc_start: 0.7561 (t80) cc_final: 0.7103 (t80)
REVERT: B  251 LEU cc_start: 0.7899 (mt) cc_final: 0.7481 (mt)
REVERT: B  254 TYR cc_start: 0.8672 (m-80) cc_final: 0.8291 (m-80)
REVERT: B  261 ASN cc_start: 0.8044 (m110) cc_final: 0.7562 (t0)
REVERT: B  318 TYR cc_start: 0.8312 (t80) cc_final: 0.7990 (t80)
REVERT: B  358 HIS cc_start: 0.8199 (m90) cc_final: 0.7949 (m-70)
REVERT: B  369 GLN cc_start: 0.8917 (tp40) cc_final: 0.8504 (mp10)
REVERT: B  389 PHE cc_start: 0.7781 (p90) cc_final: 0.7269 (m-10)
REVERT: B  425 LEU cc_start: 0.7593 (mt) cc_final: 0.7316 (mp)
REVERT: B  477 TRP cc_start: 0.6909 (t60) cc_final: 0.6674 (t-100)
REVERT: B  478 TRP cc_start: 0.6377 (t-100) cc_final: 0.5980 (t-100)
  outliers start: 2
  outliers final: 2
  residues processed: 201
  average time/residue: 0.0660
  time to fit residues: 16.4151
Evaluate side-chains
  134 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  49 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.088790 restraints weight = 7190.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.091938 restraints weight = 3837.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.094001 restraints weight = 2531.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.095472 restraints weight = 1938.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.095995 restraints weight = 1629.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4041  Z= 0.164
  Angle     :  0.694   7.633   5516  Z= 0.356
  Chirality :  0.044   0.181    665
  Planarity :  0.005   0.042    661
  Dihedral  :  5.792  36.104    547
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  4.46 %
    Favored  : 95.07 %
  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:  0.55 (0.36), residues: 500
  helix:  0.72 (0.25), residues: 387
  sheet:  None (None), residues: 0
  loop : -0.56 (0.56), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 355 
 TYR   0.013   0.002   TYR B 472 
 PHE   0.038   0.002   PHE B 399 
 TRP   0.024   0.002   TRP B 417 
 HIS   0.003   0.001   HIS B 420 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.16 ( 4040)
  covalent geometry    : angle       0.69351 /  0.36 ( 5514)
  SS BOND              : bond        0.00334 /  0.18 (    1)
  SS BOND              : angle       1.49994 /  0.74 (    2)
  hydrogen bonds       : bond        0.05027 /  3.34 (  288)
  hydrogen bonds       : angle       4.65577 /  3.30 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 TRP cc_start: 0.6557 (t-100) cc_final: 0.6272 (t-100)
REVERT: B  178 CYS cc_start: 0.8501 (t) cc_final: 0.8268 (t)
REVERT: B  251 LEU cc_start: 0.8559 (mt) cc_final: 0.7943 (mt)
REVERT: B  273 ASN cc_start: 0.7973 (m-40) cc_final: 0.7495 (m110)
REVERT: B  323 MET cc_start: 0.7523 (mmm) cc_final: 0.7321 (mmt)
REVERT: B  358 HIS cc_start: 0.8376 (m90) cc_final: 0.7998 (m90)
REVERT: B  365 MET cc_start: 0.8552 (mmt) cc_final: 0.8026 (mmt)
REVERT: B  367 HIS cc_start: 0.8080 (t70) cc_final: 0.6597 (t-90)
REVERT: B  389 PHE cc_start: 0.7580 (p90) cc_final: 0.6983 (m-10)
REVERT: B  404 ASN cc_start: 0.7268 (t0) cc_final: 0.6982 (t0)
REVERT: B  425 LEU cc_start: 0.8094 (mt) cc_final: 0.7838 (mt)
REVERT: B  431 VAL cc_start: 0.7810 (p) cc_final: 0.7600 (p)
REVERT: B  483 LYS cc_start: 0.8244 (mptt) cc_final: 0.7841 (mmtt)
REVERT: B  485 LEU cc_start: 0.8459 (mt) cc_final: 0.8193 (mt)
REVERT: B  501 GLN cc_start: 0.7809 (tt0) cc_final: 0.7280 (tt0)
  outliers start: 2
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0381
  time to fit residues: 8.3619
Evaluate side-chains
  117 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN
B 367 HIS
B 487 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.107660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.085617 restraints weight = 7262.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.088544 restraints weight = 3873.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.090666 restraints weight = 2587.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.092046 restraints weight = 1985.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.092787 restraints weight = 1674.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4041  Z= 0.185
  Angle     :  0.712   6.721   5516  Z= 0.358
  Chirality :  0.044   0.153    665
  Planarity :  0.005   0.041    661
  Dihedral  :  5.420  32.545    547
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  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:  0.96 (0.37), residues: 500
  helix:  1.02 (0.26), residues: 393
  sheet:  None (None), residues: 0
  loop : -0.51 (0.60), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 348 
 TYR   0.016   0.002   TYR B 103 
 PHE   0.033   0.002   PHE B 399 
 TRP   0.017   0.002   TRP A 193 
 HIS   0.003   0.001   HIS B 420 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.18 ( 4040)
  covalent geometry    : angle       0.71082 /  0.36 ( 5514)
  SS BOND              : bond        0.00329 /  0.17 (    1)
  SS BOND              : angle       2.25900 /  1.05 (    2)
  hydrogen bonds       : bond        0.04750 /  3.14 (  288)
  hydrogen bonds       : angle       4.48714 /  3.16 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: B   54 ASN cc_start: 0.7134 (m-40) cc_final: 0.6831 (m-40)
REVERT: B   96 SER cc_start: 0.8609 (m) cc_final: 0.8406 (p)
REVERT: B  178 CYS cc_start: 0.8352 (t) cc_final: 0.8079 (t)
REVERT: B  197 GLN cc_start: 0.9136 (mm110) cc_final: 0.8883 (tp40)
REVERT: B  251 LEU cc_start: 0.8796 (mt) cc_final: 0.8178 (mt)
REVERT: B  273 ASN cc_start: 0.8014 (m-40) cc_final: 0.7477 (m110)
REVERT: B  358 HIS cc_start: 0.8330 (m90) cc_final: 0.7761 (m-70)
REVERT: B  367 HIS cc_start: 0.7684 (t-90) cc_final: 0.6830 (t-90)
REVERT: B  383 MET cc_start: 0.8495 (tpp) cc_final: 0.8176 (tpp)
REVERT: B  431 VAL cc_start: 0.7881 (p) cc_final: 0.7651 (p)
REVERT: B  483 LYS cc_start: 0.8265 (mptt) cc_final: 0.7930 (tttm)
REVERT: B  485 LEU cc_start: 0.8447 (mt) cc_final: 0.8207 (mt)
REVERT: B  487 GLN cc_start: 0.7700 (mp10) cc_final: 0.7404 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0442
  time to fit residues: 8.7953
Evaluate side-chains
  110 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0670
   chunk 46 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.5724

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 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 = 0.3289 r_free = 0.3289 target = 0.110188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.087530 restraints weight = 7081.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.090505 restraints weight = 3971.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.092592 restraints weight = 2696.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.093856 restraints weight = 2093.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.094875 restraints weight = 1793.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4041  Z= 0.149
  Angle     :  0.658   6.273   5516  Z= 0.331
  Chirality :  0.043   0.151    665
  Planarity :  0.004   0.030    661
  Dihedral  :  5.271  36.021    547
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.29 %
    Favored  : 96.48 %
  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:  1.34 (0.38), residues: 500
  helix:  1.29 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.19 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  48 
 TYR   0.021   0.002   TYR B 103 
 PHE   0.015   0.002   PHE B 315 
 TRP   0.013   0.002   TRP B 405 
 HIS   0.002   0.001   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 4040)
  covalent geometry    : angle       0.65711 /  0.33 ( 5514)
  SS BOND              : bond        0.00197 /  0.10 (    1)
  SS BOND              : angle       1.76088 /  0.84 (    2)
  hydrogen bonds       : bond        0.04266 /  2.85 (  288)
  hydrogen bonds       : angle       4.18299 /  2.96 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.147 
Fit side-chains
REVERT: B   54 ASN cc_start: 0.6927 (m-40) cc_final: 0.6673 (m-40)
REVERT: B  132 LYS cc_start: 0.8069 (tttp) cc_final: 0.7723 (tttm)
REVERT: B  178 CYS cc_start: 0.8426 (t) cc_final: 0.8048 (t)
REVERT: B  197 GLN cc_start: 0.9092 (mm110) cc_final: 0.8758 (tp40)
REVERT: B  251 LEU cc_start: 0.8601 (mt) cc_final: 0.8003 (mt)
REVERT: B  254 TYR cc_start: 0.8652 (m-80) cc_final: 0.7984 (m-80)
REVERT: B  273 ASN cc_start: 0.8295 (m-40) cc_final: 0.7736 (m110)
REVERT: B  283 PRO cc_start: 0.8843 (Cg_exo) cc_final: 0.8584 (Cg_endo)
REVERT: B  367 HIS cc_start: 0.7752 (t-90) cc_final: 0.6661 (t-90)
REVERT: B  385 LEU cc_start: 0.9339 (mm) cc_final: 0.9106 (mp)
REVERT: B  415 MET cc_start: 0.8472 (tmm) cc_final: 0.8245 (tmm)
REVERT: B  445 PHE cc_start: 0.6885 (t80) cc_final: 0.6663 (t80)
REVERT: B  483 LYS cc_start: 0.8171 (mptt) cc_final: 0.7854 (tttm)
REVERT: B  485 LEU cc_start: 0.8503 (mt) cc_final: 0.8221 (mt)
REVERT: B  486 LEU cc_start: 0.8468 (mt) cc_final: 0.8201 (mt)
REVERT: B  487 GLN cc_start: 0.7694 (mp10) cc_final: 0.7476 (mm110)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0526
  time to fit residues: 10.4171
Evaluate side-chains
  116 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  49 ASN
** B 501 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 = 0.3298 r_free = 0.3298 target = 0.110835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.088317 restraints weight = 7017.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.091059 restraints weight = 3958.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.093063 restraints weight = 2734.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.094288 restraints weight = 2148.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.094942 restraints weight = 1845.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4041  Z= 0.139
  Angle     :  0.633   7.286   5516  Z= 0.317
  Chirality :  0.042   0.158    665
  Planarity :  0.004   0.030    661
  Dihedral  :  5.069  35.276    547
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.58 %
    Favored  : 97.18 %
  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:  1.28 (0.38), residues: 500
  helix:  1.26 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop : -0.37 (0.60), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 182 
 TYR   0.012   0.001   TYR B 103 
 PHE   0.017   0.001   PHE B 399 
 TRP   0.013   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 4040)
  covalent geometry    : angle       0.63261 /  0.32 ( 5514)
  SS BOND              : bond        0.00103 /  0.05 (    1)
  SS BOND              : angle       1.59992 /  0.77 (    2)
  hydrogen bonds       : bond        0.04043 /  2.70 (  288)
  hydrogen bonds       : angle       4.11024 /  2.93 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 SER cc_start: 0.6374 (t) cc_final: 0.4148 (p)
REVERT: A  180 ARG cc_start: 0.7283 (mtp180) cc_final: 0.6743 (mtt180)
REVERT: A  212 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7057 (tm-30)
REVERT: B   54 ASN cc_start: 0.6871 (m-40) cc_final: 0.6546 (m-40)
REVERT: B  197 GLN cc_start: 0.9049 (mm110) cc_final: 0.8839 (mm110)
REVERT: B  243 ILE cc_start: 0.7156 (tp) cc_final: 0.6824 (pt)
REVERT: B  254 TYR cc_start: 0.8657 (m-80) cc_final: 0.8118 (m-80)
REVERT: B  273 ASN cc_start: 0.8319 (m-40) cc_final: 0.7700 (m110)
REVERT: B  358 HIS cc_start: 0.8213 (m-70) cc_final: 0.7705 (m-70)
REVERT: B  367 HIS cc_start: 0.7920 (t-90) cc_final: 0.6789 (t-90)
REVERT: B  406 LEU cc_start: 0.8130 (tp) cc_final: 0.7892 (tp)
REVERT: B  415 MET cc_start: 0.8432 (tmm) cc_final: 0.8022 (tmm)
REVERT: B  485 LEU cc_start: 0.8506 (mt) cc_final: 0.8164 (mt)
REVERT: B  486 LEU cc_start: 0.8397 (mt) cc_final: 0.8105 (mt)
REVERT: B  487 GLN cc_start: 0.7696 (mp10) cc_final: 0.7375 (mm-40)
REVERT: B  495 LEU cc_start: 0.8975 (mm) cc_final: 0.8755 (mm)
REVERT: B  500 MET cc_start: 0.7181 (mmm) cc_final: 0.6956 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0451
  time to fit residues: 9.3476
Evaluate side-chains
  118 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  49 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.111110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.089065 restraints weight = 7223.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.091926 restraints weight = 4022.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.094035 restraints weight = 2749.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.095364 restraints weight = 2123.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.096170 restraints weight = 1801.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.5261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4041  Z= 0.150
  Angle     :  0.643  11.207   5516  Z= 0.320
  Chirality :  0.042   0.134    665
  Planarity :  0.004   0.029    661
  Dihedral  :  5.118  34.455    547
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.17 %
    Favored  : 98.59 %
  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:  1.48 (0.38), residues: 500
  helix:  1.42 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.25 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 211 
 TYR   0.017   0.002   TYR B 472 
 PHE   0.026   0.002   PHE B 445 
 TRP   0.018   0.001   TRP B 257 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 4040)
  covalent geometry    : angle       0.64252 /  0.32 ( 5514)
  SS BOND              : bond        0.00104 /  0.05 (    1)
  SS BOND              : angle       1.52315 /  0.73 (    2)
  hydrogen bonds       : bond        0.04172 /  2.78 (  288)
  hydrogen bonds       : angle       3.99845 /  2.84 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6647 (mtt180)
REVERT: A  212 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6872 (tm-30)
REVERT: B   54 ASN cc_start: 0.6866 (m-40) cc_final: 0.6510 (m-40)
REVERT: B  181 LEU cc_start: 0.8937 (tp) cc_final: 0.8725 (tp)
REVERT: B  243 ILE cc_start: 0.7209 (tp) cc_final: 0.6891 (pt)
REVERT: B  254 TYR cc_start: 0.8551 (m-80) cc_final: 0.7348 (m-80)
REVERT: B  273 ASN cc_start: 0.7906 (m-40) cc_final: 0.7426 (m110)
REVERT: B  358 HIS cc_start: 0.8303 (m-70) cc_final: 0.7746 (m-70)
REVERT: B  367 HIS cc_start: 0.8278 (t-90) cc_final: 0.7161 (t-90)
REVERT: B  385 LEU cc_start: 0.8681 (mp) cc_final: 0.8473 (mp)
REVERT: B  406 LEU cc_start: 0.8072 (tp) cc_final: 0.7859 (tp)
REVERT: B  485 LEU cc_start: 0.8513 (mt) cc_final: 0.8169 (mt)
REVERT: B  500 MET cc_start: 0.7316 (mmm) cc_final: 0.7041 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 139
  average time/residue: 0.0469
  time to fit residues: 8.8716
Evaluate side-chains
  108 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0010
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0170
   chunk 29 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5626

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 487 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.113492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.091624 restraints weight = 7166.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.094611 restraints weight = 3952.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.096623 restraints weight = 2666.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.097628 restraints weight = 2063.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.098859 restraints weight = 1796.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4041  Z= 0.128
  Angle     :  0.621   5.918   5516  Z= 0.314
  Chirality :  0.042   0.166    665
  Planarity :  0.004   0.029    661
  Dihedral  :  4.985  35.034    547
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  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:  1.46 (0.38), residues: 500
  helix:  1.42 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.30 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 419 
 TYR   0.022   0.002   TYR B 103 
 PHE   0.032   0.002   PHE B 399 
 TRP   0.011   0.001   TRP B 257 
 HIS   0.003   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 4040)
  covalent geometry    : angle       0.62017 /  0.31 ( 5514)
  SS BOND              : bond        0.00100 /  0.05 (    1)
  SS BOND              : angle       1.26391 /  0.61 (    2)
  hydrogen bonds       : bond        0.03913 /  2.59 (  288)
  hydrogen bonds       : angle       4.01155 /  2.85 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.7141 (mtp180) cc_final: 0.6620 (mtt180)
REVERT: A  212 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6771 (tm-30)
REVERT: B   54 ASN cc_start: 0.7009 (m-40) cc_final: 0.6771 (m-40)
REVERT: B  103 TYR cc_start: 0.7827 (m-10) cc_final: 0.7504 (m-10)
REVERT: B  120 MET cc_start: 0.8339 (ptp) cc_final: 0.8121 (ptp)
REVERT: B  243 ILE cc_start: 0.7556 (tp) cc_final: 0.7266 (pt)
REVERT: B  273 ASN cc_start: 0.7857 (m-40) cc_final: 0.7436 (m110)
REVERT: B  358 HIS cc_start: 0.8107 (m-70) cc_final: 0.7672 (m-70)
REVERT: B  365 MET cc_start: 0.8146 (mmm) cc_final: 0.7178 (mtp)
REVERT: B  367 HIS cc_start: 0.8190 (t-90) cc_final: 0.7159 (t-90)
REVERT: B  404 ASN cc_start: 0.7387 (t0) cc_final: 0.7175 (t0)
REVERT: B  413 ILE cc_start: 0.8889 (mt) cc_final: 0.8583 (tt)
REVERT: B  455 PRO cc_start: 0.4743 (Cg_endo) cc_final: 0.4376 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0445
  time to fit residues: 8.5018
Evaluate side-chains
  113 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0670
   chunk 43 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    1.7724

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN
B 487 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.110526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.088130 restraints weight = 7324.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.091079 restraints weight = 4034.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.093021 restraints weight = 2722.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.094515 restraints weight = 2111.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.095379 restraints weight = 1778.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.5584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4041  Z= 0.155
  Angle     :  0.672   6.180   5516  Z= 0.340
  Chirality :  0.042   0.145    665
  Planarity :  0.004   0.028    661
  Dihedral  :  5.084  34.066    547
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  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 are not related in a simple way.
  whole:  1.37 (0.38), residues: 500
  helix:  1.37 (0.27), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.33 (0.56), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 211 
 TYR   0.032   0.002   TYR B 103 
 PHE   0.018   0.002   PHE B 445 
 TRP   0.011   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 ( 4040)
  covalent geometry    : angle       0.67149 /  0.34 ( 5514)
  SS BOND              : bond        0.00007 /  0.00 (    1)
  SS BOND              : angle       1.48890 /  0.70 (    2)
  hydrogen bonds       : bond        0.04241 /  2.84 (  288)
  hydrogen bonds       : angle       4.19287 /  2.98 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.7112 (mtp180) cc_final: 0.6847 (mtp85)
REVERT: A  212 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6744 (tm-30)
REVERT: B  103 TYR cc_start: 0.7976 (m-10) cc_final: 0.7458 (m-10)
REVERT: B  243 ILE cc_start: 0.7258 (tp) cc_final: 0.6661 (pt)
REVERT: B  247 LEU cc_start: 0.8480 (mm) cc_final: 0.8224 (mm)
REVERT: B  254 TYR cc_start: 0.8597 (m-80) cc_final: 0.8227 (m-80)
REVERT: B  273 ASN cc_start: 0.8034 (m-40) cc_final: 0.7595 (m110)
REVERT: B  358 HIS cc_start: 0.8192 (m-70) cc_final: 0.7718 (m-70)
REVERT: B  365 MET cc_start: 0.8082 (mmm) cc_final: 0.7153 (mtp)
REVERT: B  367 HIS cc_start: 0.8399 (t-90) cc_final: 0.7255 (t-90)
REVERT: B  369 GLN cc_start: 0.7578 (mp10) cc_final: 0.6866 (mp10)
REVERT: B  406 LEU cc_start: 0.8262 (tp) cc_final: 0.7788 (tp)
REVERT: B  412 ILE cc_start: 0.7982 (mm) cc_final: 0.7689 (mm)
REVERT: B  485 LEU cc_start: 0.8728 (mt) cc_final: 0.8312 (mt)
REVERT: B  486 LEU cc_start: 0.8146 (mt) cc_final: 0.7901 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0401
  time to fit residues: 7.3225
Evaluate side-chains
  114 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  54 ASN
B 261 ASN
B 487 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.114208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.092452 restraints weight = 7311.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.095396 restraints weight = 4045.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.097507 restraints weight = 2731.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.098900 restraints weight = 2101.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.099578 restraints weight = 1770.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.5782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4041  Z= 0.131
  Angle     :  0.653   8.192   5516  Z= 0.328
  Chirality :  0.042   0.145    665
  Planarity :  0.004   0.029    661
  Dihedral  :  5.004  35.012    547
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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:  1.25 (0.38), residues: 500
  helix:  1.30 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.53 (0.58), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 355 
 TYR   0.021   0.002   TYR B 103 
 PHE   0.020   0.002   PHE B 399 
 TRP   0.010   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 4040)
  covalent geometry    : angle       0.65318 /  0.33 ( 5514)
  SS BOND              : bond        0.00076 /  0.04 (    1)
  SS BOND              : angle       1.23546 /  0.59 (    2)
  hydrogen bonds       : bond        0.03932 /  2.63 (  288)
  hydrogen bonds       : angle       4.11551 /  2.93 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6845 (mtp180)
REVERT: B  103 TYR cc_start: 0.7829 (m-10) cc_final: 0.7026 (m-10)
REVERT: B  243 ILE cc_start: 0.7516 (tp) cc_final: 0.6907 (pt)
REVERT: B  247 LEU cc_start: 0.8477 (mm) cc_final: 0.8231 (mm)
REVERT: B  254 TYR cc_start: 0.8554 (m-80) cc_final: 0.7499 (m-80)
REVERT: B  273 ASN cc_start: 0.8021 (m-40) cc_final: 0.7544 (m110)
REVERT: B  358 HIS cc_start: 0.8169 (m-70) cc_final: 0.7682 (m-70)
REVERT: B  367 HIS cc_start: 0.8560 (t-90) cc_final: 0.7559 (t-90)
REVERT: B  369 GLN cc_start: 0.7326 (mp10) cc_final: 0.6606 (mp10)
REVERT: B  404 ASN cc_start: 0.7315 (t0) cc_final: 0.7010 (t0)
REVERT: B  406 LEU cc_start: 0.8276 (tp) cc_final: 0.7812 (tp)
REVERT: B  485 LEU cc_start: 0.8548 (mt) cc_final: 0.8300 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0387
  time to fit residues: 7.6289
Evaluate side-chains
  102 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN
B 487 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.113092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.090906 restraints weight = 7199.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.093875 restraints weight = 4019.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.095873 restraints weight = 2736.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.097120 restraints weight = 2129.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.098090 restraints weight = 1821.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.5795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4041  Z= 0.142
  Angle     :  0.677   8.364   5516  Z= 0.338
  Chirality :  0.043   0.187    665
  Planarity :  0.004   0.029    661
  Dihedral  :  4.992  34.594    547
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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:  1.20 (0.37), residues: 500
  helix:  1.28 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.61 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 141 
 TYR   0.038   0.003   TYR B 103 
 PHE   0.020   0.002   PHE B 399 
 TRP   0.010   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 4040)
  covalent geometry    : angle       0.67612 /  0.34 ( 5514)
  SS BOND              : bond        0.00002 /  0.00 (    1)
  SS BOND              : angle       1.43072 /  0.67 (    2)
  hydrogen bonds       : bond        0.04080 /  2.73 (  288)
  hydrogen bonds       : angle       4.13392 /  2.95 (  843)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6910 (mtp180)
REVERT: B  103 TYR cc_start: 0.8114 (m-10) cc_final: 0.7726 (m-10)
REVERT: B  120 MET cc_start: 0.8588 (ptp) cc_final: 0.8353 (ptp)
REVERT: B  243 ILE cc_start: 0.7365 (tp) cc_final: 0.6743 (pt)
REVERT: B  247 LEU cc_start: 0.8479 (mm) cc_final: 0.8242 (mm)
REVERT: B  254 TYR cc_start: 0.8625 (m-80) cc_final: 0.7161 (m-80)
REVERT: B  358 HIS cc_start: 0.8238 (m-70) cc_final: 0.7659 (m-70)
REVERT: B  367 HIS cc_start: 0.8616 (t-90) cc_final: 0.7568 (t-90)
REVERT: B  369 GLN cc_start: 0.7332 (mp10) cc_final: 0.6571 (mp10)
REVERT: B  406 LEU cc_start: 0.8259 (tp) cc_final: 0.7781 (tp)
REVERT: B  412 ILE cc_start: 0.7886 (mm) cc_final: 0.7651 (mm)
REVERT: B  485 LEU cc_start: 0.8525 (mt) cc_final: 0.8291 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0382
  time to fit residues: 7.3014
Evaluate side-chains
  98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 39 optimal weight:    0.4980
   chunk 35 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN
B 487 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.114402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.092150 restraints weight = 7168.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.095268 restraints weight = 3921.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.097196 restraints weight = 2622.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.098725 restraints weight = 2039.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.099638 restraints weight = 1711.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4041  Z= 0.131
  Angle     :  0.660   8.355   5516  Z= 0.329
  Chirality :  0.041   0.159    665
  Planarity :  0.005   0.029    661
  Dihedral  :  4.955  36.110    547
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.28 (0.38), residues: 500
  helix:  1.32 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.52 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 141 
 TYR   0.034   0.002   TYR B 103 
 PHE   0.020   0.002   PHE B 399 
 TRP   0.009   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 4040)
  covalent geometry    : angle       0.66000 /  0.33 ( 5514)
  SS BOND              : bond        0.00032 /  0.02 (    1)
  SS BOND              : angle       1.34138 /  0.63 (    2)
  hydrogen bonds       : bond        0.03867 /  2.60 (  288)
  hydrogen bonds       : angle       4.01641 /  2.85 (  843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 710.59 seconds
wall clock time: 12 minutes 58.98 seconds (778.98 seconds total)