Starting phenix.real_space_refine
on Tue Mar  3 11:52:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dep_27394/03_2026/8dep_27394.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dep_27394/03_2026/8dep_27394.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dep_27394/03_2026/8dep_27394.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dep_27394/03_2026/8dep_27394.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dep_27394/03_2026/8dep_27394.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dep_27394/03_2026/8dep_27394.cif"
  }
  resolution = 3.6
  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=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       7      5.16       5
     C    2175      2.51       5
     N     489      2.21       5
     O     552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3223
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3062
          Classifications: {'peptide': 398}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 13, 'TRANS': 384}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 77
    Chain: "A"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 161
          Unusual residues: {'AJP': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 196
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 422
          Unresolved non-hydrogen chiralities: 81
  Time building chain proxies: 1.04, per 1000 atoms: 0.32
  Number of scatterers: 3223
  At special positions: 0
  Unit cell: (74.52, 69.12, 79.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       7     16.00
     O     552      8.00
     N     489      7.00
     C    2175      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: 0.29
  Conformation dependent library (CDL) restraints added in 121.1 milliseconds
  

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  752

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      87.7% 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 23 through 40
      removed outlier: 4.147A  pdb=" N   HIS A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   CYS A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 67 through 90
      removed outlier: 4.010A  pdb=" N   VAL A  71 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
    Processing helix  chain 'A' and resid 91 through 113
      removed outlier: 4.063A  pdb=" N   VAL A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.620A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 144
      removed outlier: 3.681A  pdb=" N   SER A 138 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 179
      removed outlier: 3.922A  pdb=" N   SER A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 169 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 203
      removed outlier: 3.616A  pdb=" N   ALA A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LEU A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 263
      removed outlier: 3.714A  pdb=" N   ARG A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 296
      removed outlier: 4.090A  pdb=" N   ARG A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   TRP A 270 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER A 278 " --> pdb=" O   TRP A 274 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 327
      removed outlier: 3.680A  pdb=" N   GLY A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 327 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 356
      removed outlier: 3.548A  pdb=" N   THR A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 391
      removed outlier: 3.710A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A 380 " --> pdb=" O   TYR A 376 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
      removed outlier: 4.683A  pdb=" N   SER A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   LEU A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 419
      removed outlier: 3.965A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   LEU A 398 " --> pdb=" O   GLU A 394 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN A 403 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 459
      removed outlier: 3.561A  pdb=" N   VAL A 437 " --> pdb=" O   GLN A 433 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)

    238 hydrogen bonds defined for protein.
    714 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: 0.52

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 911
        1.35 -     1.46: 916
        1.46 -     1.58: 1491
        1.58 -     1.69: 4
        1.69 -     1.81: 11
  Bond restraints: 3333
  Sorted by residual:
  bond pdb=" C23 AJP A 703 "
       pdb=" C24 AJP A 703 "
    ideal  model  delta    sigma   weight residual
    1.522  1.610 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" C23 AJP A 702 "
       pdb=" C24 AJP A 702 "
    ideal  model  delta    sigma   weight residual
    1.522  1.609 -0.087 2.00e-02 2.50e+03 1.91e+01
  bond pdb=" C05 AJP A 704 "
       pdb=" C06 AJP A 704 "
    ideal  model  delta    sigma   weight residual
    1.534  1.449  0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C23 AJP A 701 "
       pdb=" C24 AJP A 701 "
    ideal  model  delta    sigma   weight residual
    1.522  1.607 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C23 AJP A 704 "
       pdb=" C24 AJP A 704 "
    ideal  model  delta    sigma   weight residual
    1.522  1.606 -0.084 2.00e-02 2.50e+03 1.77e+01
  ... (remaining 3328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 4364
        1.38 -     2.75: 155
        2.75 -     4.13: 64
        4.13 -     5.51: 26
        5.51 -     6.88: 6
  Bond angle restraints: 4615
  Sorted by residual:
  angle pdb=" N   LEU A  80 "
        pdb=" CA  LEU A  80 "
        pdb=" C   LEU A  80 "
      ideal   model   delta    sigma   weight residual
     111.02  114.67   -3.65 1.22e+00 6.72e-01 8.95e+00
  angle pdb=" N   ILE A  41 "
        pdb=" CA  ILE A  41 "
        pdb=" C   ILE A  41 "
      ideal   model   delta    sigma   weight residual
     106.55  110.75   -4.20 1.45e+00 4.76e-01 8.40e+00
  angle pdb=" C   ILE A  41 "
        pdb=" CA  ILE A  41 "
        pdb=" CB  ILE A  41 "
      ideal   model   delta    sigma   weight residual
     112.68  109.72    2.96 1.14e+00 7.69e-01 6.74e+00
  angle pdb=" C07 AJP A 701 "
        pdb=" C06 AJP A 701 "
        pdb=" C83 AJP A 701 "
      ideal   model   delta    sigma   weight residual
     114.76  107.88    6.88 3.00e+00 1.11e-01 5.26e+00
  angle pdb=" N   PHE A 202 "
        pdb=" CA  PHE A 202 "
        pdb=" C   PHE A 202 "
      ideal   model   delta    sigma   weight residual
     111.82  114.30   -2.48 1.16e+00 7.43e-01 4.59e+00
  ... (remaining 4610 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.18: 2153
       32.18 -    64.37: 52
       64.37 -    96.55: 20
       96.55 -   128.73: 13
      128.73 -   160.91: 2
  Dihedral angle restraints: 2240
    sinusoidal: 1069
      harmonic: 1171
  Sorted by residual:
  dihedral pdb=" O31 AJP A 702 "
           pdb=" C30 AJP A 702 "
           pdb=" C32 AJP A 702 "
           pdb=" O33 AJP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.28  -21.81 -160.91     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" C29 AJP A 702 "
           pdb=" C30 AJP A 702 "
           pdb=" C32 AJP A 702 "
           pdb=" O33 AJP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.96   98.67 -159.63     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" C02 AJP A 703 "
           pdb=" C85 AJP A 703 "
           pdb=" O84 AJP A 703 "
           pdb=" C05 AJP A 703 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.60   62.65 -120.25     1      3.00e+01 1.11e-03 1.60e+01
  ... (remaining 2237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 512
       0.070 -    0.140: 39
       0.140 -    0.210: 15
       0.210 -    0.280: 11
       0.280 -    0.350: 9
  Chirality restraints: 586
  Sorted by residual:
  chirality pdb=" C11 AJP A 702 "
            pdb=" C10 AJP A 702 "
            pdb=" C12 AJP A 702 "
            pdb=" C16 AJP A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.55   -0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" C19 AJP A 702 "
            pdb=" C18 AJP A 702 "
            pdb=" C20 AJP A 702 "
            pdb=" C24 AJP A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" C23 AJP A 703 "
            pdb=" C22 AJP A 703 "
            pdb=" C24 AJP A 703 "
            pdb=" O25 AJP A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.81    0.31 2.00e-01 2.50e+01 2.33e+00
  ... (remaining 583 not shown)

  Planarity restraints: 521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  93 "   -0.042 5.00e-02 4.00e+02   6.47e-02 6.70e+00
        pdb=" N   PRO A  94 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A  94 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  94 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  81 "   -0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO A  82 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  42 "    0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO A  43 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.021 5.00e-02 4.00e+02
  ... (remaining 518 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 287
        2.74 -     3.28: 3597
        3.28 -     3.82: 5361
        3.82 -     4.36: 5566
        4.36 -     4.90: 9822
  Nonbonded interactions: 24633
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 135 "
            pdb=" OG  SER A 138 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O33 AJP A 701 "
            pdb=" O77 AJP A 701 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   LEU A 124 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   GLN A 433 "
            pdb=" OG  SER A 436 "
     model   vdw
     2.410 3.040
  nonbonded pdb=" OE1 GLN A 172 "
            pdb=" OG1 THR A 176 "
     model   vdw
     2.424 3.040
  ... (remaining 24628 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.310
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.370
  Find NCS groups from input model:        0.020
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
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   0.088   3333  Z= 0.401
  Angle     :  0.764   6.883   4615  Z= 0.347
  Chirality :  0.067   0.350    586
  Planarity :  0.005   0.065    521
  Dihedral  : 19.701 160.914   1488
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  8.09 %
    Favored  : 91.26 %
  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:  3.03 (0.41), residues: 394
  helix:  2.57 (0.27), residues: 317
  sheet:  None (None), residues: 0
  loop : -0.49 (0.73), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 268 
 TYR   0.009   0.001   TYR A  35 
 PHE   0.008   0.001   PHE A 326 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00794 ( 3333)
  covalent geometry    : angle       0.76372 ( 4615)
  hydrogen bonds       : bond        0.15026 (  238)
  hydrogen bonds       : angle       5.61415 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8175 (tt0) cc_final: 0.7965 (tt0)
REVERT: A   75 SER cc_start: 0.9174 (m) cc_final: 0.8962 (t)
REVERT: A  287 TYR cc_start: 0.8051 (m-80) cc_final: 0.7787 (m-10)
REVERT: A  293 ASN cc_start: 0.8596 (t0) cc_final: 0.8340 (t0)
REVERT: A  294 GLU cc_start: 0.7821 (tp30) cc_final: 0.7325 (tp30)
REVERT: A  306 ASN cc_start: 0.8570 (m-40) cc_final: 0.8218 (t0)
REVERT: A  310 ASP cc_start: 0.9019 (t0) cc_final: 0.8749 (t70)
REVERT: A  316 LEU cc_start: 0.8900 (tp) cc_final: 0.8699 (tt)
REVERT: A  346 GLN cc_start: 0.8607 (mt0) cc_final: 0.8370 (mt0)
REVERT: A  361 SER cc_start: 0.8810 (m) cc_final: 0.8588 (t)
REVERT: A  412 THR cc_start: 0.8790 (m) cc_final: 0.8457 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0531
  time to fit residues: 7.9581
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   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 277 ASN
A 355 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.122498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.108571 restraints weight = 5620.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.112168 restraints weight = 2403.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.114518 restraints weight = 1319.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.115976 restraints weight = 847.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.117070 restraints weight = 617.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3333  Z= 0.152
  Angle     :  0.665   7.343   4615  Z= 0.308
  Chirality :  0.040   0.222    586
  Planarity :  0.004   0.052    521
  Dihedral  : 12.647 127.672    892
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.42 %
    Favored  : 77.35 %
  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:  3.66 (0.42), residues: 394
  helix:  2.88 (0.27), residues: 327
  sheet:  None (None), residues: 0
  loop : -0.03 (0.87), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 148 
 TYR   0.017   0.002   TYR A 149 
 PHE   0.023   0.001   PHE A 141 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.008   0.002   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3333)
  covalent geometry    : angle       0.66505 ( 4615)
  hydrogen bonds       : bond        0.05529 (  238)
  hydrogen bonds       : angle       4.26131 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8268 (tt0) cc_final: 0.8032 (tt0)
REVERT: A  123 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8008 (mm-30)
REVERT: A  181 SER cc_start: 0.8860 (m) cc_final: 0.8272 (p)
REVERT: A  293 ASN cc_start: 0.8533 (t0) cc_final: 0.8095 (t0)
REVERT: A  306 ASN cc_start: 0.8338 (m-40) cc_final: 0.7807 (t0)
REVERT: A  310 ASP cc_start: 0.9014 (t0) cc_final: 0.8768 (t70)
REVERT: A  346 GLN cc_start: 0.8691 (mt0) cc_final: 0.8146 (mt0)
REVERT: A  361 SER cc_start: 0.8809 (m) cc_final: 0.8440 (t)
  outliers start: 10
  outliers final: 7
  residues processed: 105
  average time/residue: 0.0515
  time to fit residues: 6.6702
Evaluate side-chains
  92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0050
   chunk 26 optimal weight:    0.0770
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.4352

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
** A 431 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 = 0.3488 r_free = 0.3488 target = 0.123550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.109161 restraints weight = 5598.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.112812 restraints weight = 2397.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.115137 restraints weight = 1314.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.116809 restraints weight = 851.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.117783 restraints weight = 602.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3333  Z= 0.127
  Angle     :  0.603   6.770   4615  Z= 0.282
  Chirality :  0.035   0.162    586
  Planarity :  0.004   0.047    521
  Dihedral  : 10.417 127.050    892
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 25.57 %
    Favored  : 71.84 %
  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:  3.68 (0.43), residues: 394
  helix:  2.95 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -0.22 (0.84), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 133 
 TYR   0.023   0.002   TYR A 287 
 PHE   0.017   0.001   PHE A 141 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3333)
  covalent geometry    : angle       0.60274 ( 4615)
  hydrogen bonds       : bond        0.04626 (  238)
  hydrogen bonds       : angle       3.85631 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8297 (tt0) cc_final: 0.8028 (tt0)
REVERT: A  123 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8067 (mm-30)
REVERT: A  172 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: A  181 SER cc_start: 0.8806 (m) cc_final: 0.8223 (p)
REVERT: A  277 ASN cc_start: 0.8670 (m-40) cc_final: 0.8384 (m-40)
REVERT: A  293 ASN cc_start: 0.8447 (t0) cc_final: 0.8199 (t0)
REVERT: A  306 ASN cc_start: 0.8377 (m-40) cc_final: 0.7824 (t0)
REVERT: A  310 ASP cc_start: 0.9119 (t0) cc_final: 0.8829 (t70)
REVERT: A  346 GLN cc_start: 0.8626 (mt0) cc_final: 0.8129 (mt0)
REVERT: A  393 LYS cc_start: 0.8611 (tppt) cc_final: 0.8292 (tptp)
  outliers start: 8
  outliers final: 4
  residues processed: 97
  average time/residue: 0.0514
  time to fit residues: 6.3443
Evaluate side-chains
  86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  430 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** 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 = 0.3452 r_free = 0.3452 target = 0.121075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.107024 restraints weight = 5591.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110610 restraints weight = 2411.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.112831 restraints weight = 1331.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.114450 restraints weight = 873.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.115442 restraints weight = 622.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3333  Z= 0.134
  Angle     :  0.572   6.856   4615  Z= 0.270
  Chirality :  0.035   0.136    586
  Planarity :  0.004   0.044    521
  Dihedral  :  8.119 110.746    892
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 26.54 %
    Favored  : 67.64 %
  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:  3.49 (0.43), residues: 394
  helix:  2.80 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.26 (0.82), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 133 
 TYR   0.017   0.002   TYR A 366 
 PHE   0.011   0.001   PHE A 141 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3333)
  covalent geometry    : angle       0.57168 ( 4615)
  hydrogen bonds       : bond        0.04404 (  238)
  hydrogen bonds       : angle       3.83360 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8325 (tt0) cc_final: 0.8076 (tt0)
REVERT: A  123 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8011 (mm-30)
REVERT: A  172 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: A  181 SER cc_start: 0.8886 (m) cc_final: 0.8319 (p)
REVERT: A  277 ASN cc_start: 0.8735 (m-40) cc_final: 0.8388 (m110)
REVERT: A  287 TYR cc_start: 0.7910 (m-10) cc_final: 0.7692 (m-10)
REVERT: A  293 ASN cc_start: 0.8382 (t0) cc_final: 0.8066 (t0)
REVERT: A  306 ASN cc_start: 0.8418 (m-40) cc_final: 0.7826 (t0)
REVERT: A  310 ASP cc_start: 0.9139 (t0) cc_final: 0.8832 (t0)
REVERT: A  346 GLN cc_start: 0.8675 (mt0) cc_final: 0.8160 (mt0)
REVERT: A  393 LYS cc_start: 0.8650 (tppt) cc_final: 0.8326 (tptp)
REVERT: A  412 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8802 (t)
REVERT: A  435 TYR cc_start: 0.9096 (m-80) cc_final: 0.8781 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 103
  average time/residue: 0.0517
  time to fit residues: 6.8312
Evaluate side-chains
  94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0050
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0070
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4612

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.123065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.109057 restraints weight = 5568.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.112708 restraints weight = 2387.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.115024 restraints weight = 1304.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.116586 restraints weight = 833.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.117569 restraints weight = 591.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3333  Z= 0.118
  Angle     :  0.559   7.133   4615  Z= 0.264
  Chirality :  0.034   0.186    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.714  55.235    892
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 28.48 %
    Favored  : 67.64 %
  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:  3.42 (0.43), residues: 394
  helix:  2.80 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.53 (0.79), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 133 
 TYR   0.022   0.002   TYR A 366 
 PHE   0.010   0.001   PHE A 141 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 3333)
  covalent geometry    : angle       0.55867 ( 4615)
  hydrogen bonds       : bond        0.04014 (  238)
  hydrogen bonds       : angle       3.74012 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8299 (tt0) cc_final: 0.8039 (tt0)
REVERT: A  181 SER cc_start: 0.8905 (m) cc_final: 0.8306 (p)
REVERT: A  277 ASN cc_start: 0.8676 (m-40) cc_final: 0.8394 (m110)
REVERT: A  287 TYR cc_start: 0.7699 (m-10) cc_final: 0.7445 (m-10)
REVERT: A  293 ASN cc_start: 0.8360 (t0) cc_final: 0.8145 (t0)
REVERT: A  294 GLU cc_start: 0.7978 (tp30) cc_final: 0.7199 (tp30)
REVERT: A  306 ASN cc_start: 0.8425 (m-40) cc_final: 0.7919 (t0)
REVERT: A  310 ASP cc_start: 0.9121 (t0) cc_final: 0.8851 (t0)
REVERT: A  313 SER cc_start: 0.9309 (p) cc_final: 0.8989 (p)
REVERT: A  346 GLN cc_start: 0.8679 (mt0) cc_final: 0.8175 (mt0)
REVERT: A  411 LYS cc_start: 0.8724 (tttt) cc_final: 0.8441 (tttp)
REVERT: A  412 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8762 (t)
  outliers start: 12
  outliers final: 6
  residues processed: 91
  average time/residue: 0.0441
  time to fit residues: 5.2206
Evaluate side-chains
  89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  430 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.0770
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0040
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4750

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** 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 = 0.3481 r_free = 0.3481 target = 0.123895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.109762 restraints weight = 5597.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.113451 restraints weight = 2387.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.115730 restraints weight = 1301.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117295 restraints weight = 842.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.118461 restraints weight = 602.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3333  Z= 0.116
  Angle     :  0.540   6.903   4615  Z= 0.257
  Chirality :  0.033   0.112    586
  Planarity :  0.004   0.043    521
  Dihedral  :  5.195  54.476    892
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 27.83 %
    Favored  : 67.64 %
  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:  3.44 (0.43), residues: 394
  helix:  2.84 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.68 (0.76), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 133 
 TYR   0.022   0.002   TYR A 366 
 PHE   0.006   0.001   PHE A  59 
 TRP   0.008   0.001   TRP A 363 
 HIS   0.002   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 3333)
  covalent geometry    : angle       0.54025 ( 4615)
  hydrogen bonds       : bond        0.03901 (  238)
  hydrogen bonds       : angle       3.71298 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8312 (tt0) cc_final: 0.8063 (tt0)
REVERT: A  181 SER cc_start: 0.8931 (m) cc_final: 0.8321 (p)
REVERT: A  277 ASN cc_start: 0.8604 (m-40) cc_final: 0.8332 (m110)
REVERT: A  287 TYR cc_start: 0.7667 (m-10) cc_final: 0.7414 (m-10)
REVERT: A  293 ASN cc_start: 0.8329 (t0) cc_final: 0.8106 (t0)
REVERT: A  294 GLU cc_start: 0.7937 (tp30) cc_final: 0.7287 (tp30)
REVERT: A  306 ASN cc_start: 0.8374 (m-40) cc_final: 0.7851 (t0)
REVERT: A  310 ASP cc_start: 0.9127 (t0) cc_final: 0.8828 (t0)
REVERT: A  346 GLN cc_start: 0.8661 (mt0) cc_final: 0.8149 (mt0)
  outliers start: 14
  outliers final: 10
  residues processed: 92
  average time/residue: 0.0462
  time to fit residues: 5.5202
Evaluate side-chains
  94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** 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 = 0.3447 r_free = 0.3447 target = 0.121380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.107297 restraints weight = 5776.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.110887 restraints weight = 2455.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.113257 restraints weight = 1347.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.114755 restraints weight = 857.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.115832 restraints weight = 618.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3333  Z= 0.137
  Angle     :  0.556   8.622   4615  Z= 0.270
  Chirality :  0.034   0.115    586
  Planarity :  0.004   0.043    521
  Dihedral  :  5.219  53.983    892
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 28.16 %
    Favored  : 67.96 %
  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:  3.40 (0.43), residues: 394
  helix:  2.83 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -0.76 (0.74), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 133 
 TYR   0.023   0.002   TYR A 149 
 PHE   0.006   0.001   PHE A 416 
 TRP   0.009   0.001   TRP A 363 
 HIS   0.002   0.000   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3333)
  covalent geometry    : angle       0.55639 ( 4615)
  hydrogen bonds       : bond        0.04117 (  238)
  hydrogen bonds       : angle       3.75147 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8306 (tt0) cc_final: 0.8009 (tt0)
REVERT: A  179 ARG cc_start: 0.7160 (mtt180) cc_final: 0.6946 (mtt180)
REVERT: A  277 ASN cc_start: 0.8637 (m-40) cc_final: 0.8383 (m110)
REVERT: A  293 ASN cc_start: 0.8303 (t0) cc_final: 0.8057 (t0)
REVERT: A  294 GLU cc_start: 0.7994 (tp30) cc_final: 0.7551 (tp30)
REVERT: A  306 ASN cc_start: 0.8399 (m-40) cc_final: 0.7847 (t0)
REVERT: A  310 ASP cc_start: 0.9144 (t0) cc_final: 0.8860 (t0)
REVERT: A  313 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9028 (p)
REVERT: A  346 GLN cc_start: 0.8676 (mt0) cc_final: 0.8244 (mt0)
REVERT: A  393 LYS cc_start: 0.8547 (tppt) cc_final: 0.8236 (tppt)
REVERT: A  411 LYS cc_start: 0.8560 (tttp) cc_final: 0.8348 (tttp)
  outliers start: 12
  outliers final: 11
  residues processed: 93
  average time/residue: 0.0519
  time to fit residues: 6.1626
Evaluate side-chains
  101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** 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 = 0.3423 r_free = 0.3423 target = 0.118921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.104778 restraints weight = 5783.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.108305 restraints weight = 2428.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.110621 restraints weight = 1328.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.112093 restraints weight = 850.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.113192 restraints weight = 619.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3333  Z= 0.161
  Angle     :  0.581   8.116   4615  Z= 0.285
  Chirality :  0.036   0.122    586
  Planarity :  0.004   0.043    521
  Dihedral  :  5.388  53.560    892
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 28.16 %
    Favored  : 66.99 %
  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:  3.17 (0.43), residues: 394
  helix:  2.72 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.98 (0.72), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 133 
 TYR   0.021   0.002   TYR A 366 
 PHE   0.008   0.001   PHE A 416 
 TRP   0.011   0.001   TRP A 363 
 HIS   0.002   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3333)
  covalent geometry    : angle       0.58066 ( 4615)
  hydrogen bonds       : bond        0.04372 (  238)
  hydrogen bonds       : angle       3.91465 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8359 (tt0) cc_final: 0.8087 (tt0)
REVERT: A  141 PHE cc_start: 0.8871 (t80) cc_final: 0.7910 (t80)
REVERT: A  179 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6952 (mtt180)
REVERT: A  277 ASN cc_start: 0.8644 (m-40) cc_final: 0.8410 (m110)
REVERT: A  293 ASN cc_start: 0.8363 (t0) cc_final: 0.8008 (t0)
REVERT: A  294 GLU cc_start: 0.8078 (tp30) cc_final: 0.7572 (tp30)
REVERT: A  306 ASN cc_start: 0.8444 (m-40) cc_final: 0.7882 (t0)
REVERT: A  310 ASP cc_start: 0.9143 (t0) cc_final: 0.8835 (t0)
REVERT: A  313 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9037 (p)
REVERT: A  336 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7259 (mmtt)
REVERT: A  346 GLN cc_start: 0.8722 (mt0) cc_final: 0.8316 (mt0)
REVERT: A  393 LYS cc_start: 0.8559 (tppt) cc_final: 0.8159 (tppt)
REVERT: A  411 LYS cc_start: 0.8566 (tttp) cc_final: 0.8343 (tttm)
  outliers start: 15
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0500
  time to fit residues: 5.9394
Evaluate side-chains
  96 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   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 277 ASN ** 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 = 0.3429 r_free = 0.3429 target = 0.120020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.106008 restraints weight = 5789.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.109543 restraints weight = 2445.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111864 restraints weight = 1342.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.113297 restraints weight = 858.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.114390 restraints weight = 624.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.4137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3333  Z= 0.146
  Angle     :  0.602   8.923   4615  Z= 0.285
  Chirality :  0.036   0.144    586
  Planarity :  0.004   0.043    521
  Dihedral  :  5.370  54.021    892
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 29.13 %
    Favored  : 66.67 %
  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:  3.13 (0.43), residues: 394
  helix:  2.68 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.91 (0.73), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 133 
 TYR   0.023   0.002   TYR A 149 
 PHE   0.009   0.001   PHE A 125 
 TRP   0.013   0.001   TRP A 363 
 HIS   0.002   0.000   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3333)
  covalent geometry    : angle       0.60178 ( 4615)
  hydrogen bonds       : bond        0.04282 (  238)
  hydrogen bonds       : angle       3.89285 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8335 (tt0) cc_final: 0.8080 (tt0)
REVERT: A  141 PHE cc_start: 0.8755 (t80) cc_final: 0.7958 (t80)
REVERT: A  179 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6967 (mtt180)
REVERT: A  277 ASN cc_start: 0.8613 (m-40) cc_final: 0.8392 (m110)
REVERT: A  293 ASN cc_start: 0.8345 (t0) cc_final: 0.7987 (t0)
REVERT: A  294 GLU cc_start: 0.8086 (tp30) cc_final: 0.7583 (tp30)
REVERT: A  306 ASN cc_start: 0.8428 (m-40) cc_final: 0.7867 (t0)
REVERT: A  310 ASP cc_start: 0.9132 (t0) cc_final: 0.8831 (t0)
REVERT: A  313 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9068 (p)
REVERT: A  336 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7371 (mmtt)
REVERT: A  346 GLN cc_start: 0.8702 (mt0) cc_final: 0.8260 (mt0)
REVERT: A  393 LYS cc_start: 0.8504 (tppt) cc_final: 0.8155 (tppt)
REVERT: A  411 LYS cc_start: 0.8576 (tttp) cc_final: 0.8329 (tttm)
  outliers start: 13
  outliers final: 11
  residues processed: 93
  average time/residue: 0.0460
  time to fit residues: 5.4974
Evaluate side-chains
  99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** 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 = 0.3457 r_free = 0.3457 target = 0.121752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.108046 restraints weight = 5742.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111518 restraints weight = 2445.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.113717 restraints weight = 1340.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.115251 restraints weight = 869.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.116266 restraints weight = 621.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3333  Z= 0.128
  Angle     :  0.588   8.681   4615  Z= 0.280
  Chirality :  0.035   0.137    586
  Planarity :  0.004   0.043    521
  Dihedral  :  5.324  54.501    892
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 29.13 %
    Favored  : 66.99 %
  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:  3.17 (0.43), residues: 394
  helix:  2.70 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.86 (0.73), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 133 
 TYR   0.021   0.002   TYR A 366 
 PHE   0.006   0.001   PHE A 103 
 TRP   0.022   0.001   TRP A 363 
 HIS   0.002   0.000   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3333)
  covalent geometry    : angle       0.58817 ( 4615)
  hydrogen bonds       : bond        0.04009 (  238)
  hydrogen bonds       : angle       3.82908 (  714)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8310 (tt0) cc_final: 0.8081 (tt0)
REVERT: A  125 PHE cc_start: 0.8860 (m-80) cc_final: 0.8610 (m-80)
REVERT: A  141 PHE cc_start: 0.8794 (t80) cc_final: 0.7678 (t80)
REVERT: A  293 ASN cc_start: 0.8314 (t0) cc_final: 0.8050 (t0)
REVERT: A  294 GLU cc_start: 0.8048 (tp30) cc_final: 0.7583 (tp30)
REVERT: A  306 ASN cc_start: 0.8448 (m-40) cc_final: 0.7902 (t0)
REVERT: A  310 ASP cc_start: 0.9110 (t0) cc_final: 0.8818 (t0)
REVERT: A  313 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.9048 (p)
REVERT: A  336 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7253 (mmtt)
REVERT: A  346 GLN cc_start: 0.8717 (mt0) cc_final: 0.8306 (mt0)
REVERT: A  393 LYS cc_start: 0.8369 (tppt) cc_final: 0.7979 (tppt)
REVERT: A  411 LYS cc_start: 0.8520 (tttp) cc_final: 0.8277 (tttm)
  outliers start: 12
  outliers final: 8
  residues processed: 91
  average time/residue: 0.0397
  time to fit residues: 4.8323
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.121233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.107460 restraints weight = 5876.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111027 restraints weight = 2483.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.113257 restraints weight = 1358.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.114779 restraints weight = 883.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.115890 restraints weight = 636.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.4390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3333  Z= 0.150
  Angle     :  0.619   9.043   4615  Z= 0.293
  Chirality :  0.036   0.169    586
  Planarity :  0.004   0.042    521
  Dihedral  :  5.345  53.979    892
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 29.45 %
    Favored  : 66.99 %
  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:  3.10 (0.43), residues: 394
  helix:  2.65 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.88 (0.73), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 133 
 TYR   0.021   0.002   TYR A 366 
 PHE   0.006   0.001   PHE A 141 
 TRP   0.022   0.001   TRP A 363 
 HIS   0.002   0.000   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3333)
  covalent geometry    : angle       0.61874 ( 4615)
  hydrogen bonds       : bond        0.04195 (  238)
  hydrogen bonds       : angle       3.87454 (  714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 680.02 seconds
wall clock time: 12 minutes 18.52 seconds (738.52 seconds total)