Starting phenix.real_space_refine
on Thu Jun  5 02:17:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j3o_61121/06_2025/9j3o_61121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j3o_61121/06_2025/9j3o_61121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j3o_61121/06_2025/9j3o_61121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j3o_61121/06_2025/9j3o_61121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j3o_61121/06_2025/9j3o_61121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j3o_61121/06_2025/9j3o_61121.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.067
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      27      5.16       5
     C    3207      2.51       5
     N     783      2.21       5
     O     828      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4845
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 3896
          Classifications: {'peptide': 496}
          Link IDs: {'PTRANS': 21, 'TRANS': 474}
    Chain: "B"
      Number of atoms: 949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 949
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
  Time building chain proxies: 3.14, per 1000 atoms: 0.65
  Number of scatterers: 4845
  At special positions: 0
  Unit cell: (81.88, 96.6, 111.32, 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      27     16.00
     O     828      8.00
     N     783      7.00
     C    3207      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 530.0 milliseconds
  

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1138

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      70.0% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 17
    Processing helix  chain 'A' and resid 21 through 25
      removed outlier: 3.841A  pdb=" N   LEU A  24 " --> pdb=" O   THR A  21 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LYS A  25 " --> pdb=" O   HIS A  22 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 21 through 25'
    Processing helix  chain 'A' and resid 26 through 52
      removed outlier: 3.823A  pdb=" N   MET A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR A  50 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 70
    Processing helix  chain 'A' and resid 70 through 89
      removed outlier: 3.844A  pdb=" N   ASN A  87 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 112
      Proline residue:  A 101  - end of helix
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 127 through 133
      removed outlier: 3.528A  pdb=" N   ILE A 132 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU A 133 " --> pdb=" O   GLN A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 146
      removed outlier: 3.715A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 164
      removed outlier: 4.279A  pdb=" N   GLY A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER A 161 " --> pdb=" O   GLU A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 176
    Processing helix  chain 'A' and resid 177 through 185
      removed outlier: 3.789A  pdb=" N   ARG A 183 " --> pdb=" O   HIS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 210
      removed outlier: 3.746A  pdb=" N   ALA A 192 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 248
    Processing helix  chain 'A' and resid 257 through 266
      removed outlier: 3.644A  pdb=" N   MET A 261 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLN A 262 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LYS A 263 " --> pdb=" O   GLU A 259 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLY A 264 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 281
    Processing helix  chain 'A' and resid 284 through 307
    Processing helix  chain 'A' and resid 307 through 316
      removed outlier: 3.669A  pdb=" N   GLN A 311 " --> pdb=" O   THR A 307 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   LYS A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 343
      removed outlier: 4.025A  pdb=" N   GLY A 334 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   MET A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 352
      removed outlier: 3.747A  pdb=" N   ASN A 347 " --> pdb=" O   PHE A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 377
      removed outlier: 3.673A  pdb=" N   GLY A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   THR A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 379 through 383
      removed outlier: 3.702A  pdb=" N   SER A 383 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 3.672A  pdb=" N   GLY A 390 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 407
    Processing helix  chain 'A' and resid 415 through 424
      removed outlier: 3.694A  pdb=" N   TYR A 424 " --> pdb=" O   LYS A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 433
    Processing helix  chain 'A' and resid 433 through 442
    Processing helix  chain 'A' and resid 444 through 460
      removed outlier: 3.615A  pdb=" N   LYS A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ALA A 452 " --> pdb=" O   LYS A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 467
    Processing helix  chain 'A' and resid 468 through 501
      removed outlier: 3.686A  pdb=" N   VAL A 474 " --> pdb=" O   PRO A 470 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS A 492 " --> pdb=" O   THR A 488 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 493 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA A 499 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LYS A 501 " --> pdb=" O   GLN A 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 30
      No H-bonds generated for 'chain 'B' and resid 28 through 30'
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.510A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7
      removed outlier: 4.070A  pdb=" N   SER B  21 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  83 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU B  81 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   CYS B  22 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR B  78 " --> pdb=" O   ASP B  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.505A  pdb=" N   THR B 115 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   THR B 112 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.575A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   THR B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   MET B  34 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY B  35 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    831 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: 1.47

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 730
        1.29 -     1.42: 1357
        1.42 -     1.55: 2833
        1.55 -     1.68: 3
        1.68 -     1.81: 48
  Bond restraints: 4971
  Sorted by residual:
  bond pdb=" CA  TYR A 286 "
       pdb=" C   TYR A 286 "
    ideal  model  delta    sigma   weight residual
    1.524  1.435  0.089 1.26e-02 6.30e+03 4.93e+01
  bond pdb=" C   TYR A 286 "
       pdb=" O   TYR A 286 "
    ideal  model  delta    sigma   weight residual
    1.237  1.162  0.074 1.16e-02 7.43e+03 4.08e+01
  bond pdb=" CA  PHE A  68 "
       pdb=" C   PHE A  68 "
    ideal  model  delta    sigma   weight residual
    1.519  1.453  0.066 1.22e-02 6.72e+03 2.94e+01
  bond pdb=" N   TYR A 286 "
       pdb=" CA  TYR A 286 "
    ideal  model  delta    sigma   weight residual
    1.459  1.509 -0.050 1.20e-02 6.94e+03 1.72e+01
  bond pdb=" C   PHE A  68 "
       pdb=" N   TRP A  69 "
    ideal  model  delta    sigma   weight residual
    1.333  1.285  0.048 1.55e-02 4.16e+03 9.68e+00
  ... (remaining 4966 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 6528
        1.94 -     3.88: 164
        3.88 -     5.82: 42
        5.82 -     7.76: 9
        7.76 -     9.70: 4
  Bond angle restraints: 6747
  Sorted by residual:
  angle pdb=" N   LYS A 265 "
        pdb=" CA  LYS A 265 "
        pdb=" C   LYS A 265 "
      ideal   model   delta    sigma   weight residual
     111.82  102.12    9.70 1.16e+00 7.43e-01 6.99e+01
  angle pdb=" N   THR A 123 "
        pdb=" CA  THR A 123 "
        pdb=" C   THR A 123 "
      ideal   model   delta    sigma   weight residual
     110.64  102.65    7.99 1.48e+00 4.57e-01 2.91e+01
  angle pdb=" N   GLY A 267 "
        pdb=" CA  GLY A 267 "
        pdb=" C   GLY A 267 "
      ideal   model   delta    sigma   weight residual
     111.12  116.44   -5.32 1.49e+00 4.50e-01 1.28e+01
  angle pdb=" C   LYS A 309 "
        pdb=" N   SER A 310 "
        pdb=" CA  SER A 310 "
      ideal   model   delta    sigma   weight residual
     121.54  128.31   -6.77 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" C   TYR A 286 "
        pdb=" CA  TYR A 286 "
        pdb=" CB  TYR A 286 "
      ideal   model   delta    sigma   weight residual
     110.90  105.37    5.53 1.58e+00 4.01e-01 1.23e+01
  ... (remaining 6742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 2672
       17.75 -    35.51: 199
       35.51 -    53.26: 20
       53.26 -    71.01: 3
       71.01 -    88.76: 2
  Dihedral angle restraints: 2896
    sinusoidal: 1117
      harmonic: 1779
  Sorted by residual:
  dihedral pdb=" CA  SER A 337 "
           pdb=" C   SER A 337 "
           pdb=" N   VAL A 338 "
           pdb=" CA  VAL A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.35   26.65     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  THR A 123 "
           pdb=" C   THR A 123 "
           pdb=" N   GLU A 124 "
           pdb=" CA  GLU A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.30  -21.70     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  ASN A 257 "
           pdb=" C   ASN A 257 "
           pdb=" N   PRO A 258 "
           pdb=" CA  PRO A 258 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.62  -21.38     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 2893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 488
       0.038 -    0.077: 216
       0.077 -    0.115: 56
       0.115 -    0.154: 4
       0.154 -    0.192: 6
  Chirality restraints: 770
  Sorted by residual:
  chirality pdb=" CG  LEU A 342 "
            pdb=" CB  LEU A 342 "
            pdb=" CD1 LEU A 342 "
            pdb=" CD2 LEU A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.19 2.00e-01 2.50e+01 9.21e-01
  chirality pdb=" CA  TRP A  69 "
            pdb=" N   TRP A  69 "
            pdb=" C   TRP A  69 "
            pdb=" CB  TRP A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.86e-01
  chirality pdb=" CA  THR A 361 "
            pdb=" N   THR A 361 "
            pdb=" C   THR A 361 "
            pdb=" CB  THR A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 7.04e-01
  ... (remaining 767 not shown)

  Planarity restraints: 824
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 252 "   -0.040 5.00e-02 4.00e+02   6.15e-02 6.06e+00
        pdb=" N   PRO A 253 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 253 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 253 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  53 "   -0.018 2.00e-02 2.50e+03   1.45e-02 4.18e+00
        pdb=" CG  TYR B  53 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  53 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  53 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  53 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  53 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  67 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" C   LYS A  67 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   LYS A  67 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PHE A  68 "    0.012 2.00e-02 2.50e+03
  ... (remaining 821 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 572
        2.75 -     3.29: 5148
        3.29 -     3.82: 8199
        3.82 -     4.36: 10164
        4.36 -     4.90: 16757
  Nonbonded interactions: 40840
  Sorted by model distance:
  nonbonded pdb=" O   THR B  28 "
            pdb=" OG1 THR B  32 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE B  29 "
            pdb=" NH2 ARG B  72 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" NZ  LYS A  48 "
            pdb=" OD1 ASP A  49 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" O   LEU A 415 "
            pdb=" OG1 THR A 419 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   PHE A 343 "
            pdb=" ND2 ASN A 347 "
     model   vdw
     2.270 3.120
  ... (remaining 40835 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.260
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:23.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
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      :  0.005   0.089   4972  Z= 0.271
  Angle     :  0.812   9.698   6749  Z= 0.431
  Chirality :  0.045   0.192    770
  Planarity :  0.005   0.062    824
  Dihedral  : 12.356  88.763   1755
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  0.19 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.32), residues: 613
  helix: -1.72 (0.24), residues: 380
  sheet: -3.52 (0.76), residues: 36
  loop : -2.61 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 332 
 HIS   0.007   0.001   HIS A 121 
 PHE   0.029   0.002   PHE A 255 
 TYR   0.031   0.002   TYR B  53 
 ARG   0.007   0.001   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22006 (  286)
  hydrogen bonds       : angle       9.85994 (  831)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.24932 (    2)
  covalent geometry    : bond        0.00474 ( 4971)
  covalent geometry    : angle       0.81189 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.7466 (tppt) cc_final: 0.6862 (tppt)
REVERT: A  149 PHE cc_start: 0.7967 (m-10) cc_final: 0.7655 (m-10)
REVERT: A  269 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7837 (tttm)
REVERT: A  333 THR cc_start: 0.8871 (t) cc_final: 0.8578 (m)
REVERT: A  406 ILE cc_start: 0.8250 (tt) cc_final: 0.7909 (tt)
REVERT: B   45 ARG cc_start: 0.7297 (ttm170) cc_final: 0.5302 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8167 (mttt) cc_final: 0.7931 (mttt)
REVERT: B   82 GLN cc_start: 0.8186 (tp40) cc_final: 0.7685 (tm-30)
REVERT: B   94 TYR cc_start: 0.8195 (m-80) cc_final: 0.7583 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 118
  average time/residue: 1.0009
  time to fit residues: 124.3589
Evaluate side-chains
  111 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain A residue  266 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 429 GLN
B  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.176723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.142988 restraints weight = 5570.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.54
r_work: 0.3556 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4972  Z= 0.174
  Angle     :  0.681   8.875   6749  Z= 0.348
  Chirality :  0.044   0.171    770
  Planarity :  0.005   0.048    824
  Dihedral  :  5.887  33.868    668
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  8.58 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.34), residues: 613
  helix: -0.76 (0.26), residues: 378
  sheet: -3.33 (0.76), residues: 36
  loop : -2.26 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 332 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.021   0.002   PHE B  29 
 TYR   0.018   0.001   TYR B  53 
 ARG   0.005   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04692 (  286)
  hydrogen bonds       : angle       6.08622 (  831)
  SS BOND              : bond        0.00142 (    1)
  SS BOND              : angle       0.32252 (    2)
  covalent geometry    : bond        0.00399 ( 4971)
  covalent geometry    : angle       0.68143 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  161 SER cc_start: 0.8283 (m) cc_final: 0.7813 (p)
REVERT: A  255 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.5399 (p90)
REVERT: A  269 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7814 (tttm)
REVERT: A  283 ARG cc_start: 0.7410 (mtm110) cc_final: 0.6975 (mtm180)
REVERT: A  333 THR cc_start: 0.8504 (t) cc_final: 0.8067 (m)
REVERT: A  339 LEU cc_start: 0.8362 (mt) cc_final: 0.8111 (mm)
REVERT: A  342 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7850 (mp)
REVERT: A  406 ILE cc_start: 0.8405 (tt) cc_final: 0.8144 (tt)
REVERT: B   34 MET cc_start: 0.8697 (mmp) cc_final: 0.8482 (mmp)
REVERT: B   45 ARG cc_start: 0.7354 (ttm170) cc_final: 0.5281 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8195 (mttt) cc_final: 0.7921 (mttt)
REVERT: B   82 GLN cc_start: 0.8308 (tp40) cc_final: 0.7705 (tm-30)
REVERT: B   94 TYR cc_start: 0.8336 (m-80) cc_final: 0.7963 (m-80)
  outliers start: 13
  outliers final: 6
  residues processed: 118
  average time/residue: 1.1230
  time to fit residues: 140.3648
Evaluate side-chains
  121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 56 optimal weight:    0.3980
   chunk 55 optimal weight:    0.0370
   chunk 60 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.4157 r_free = 0.4157 target = 0.180131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.147183 restraints weight = 5637.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.54
r_work: 0.3607 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4972  Z= 0.153
  Angle     :  0.611   8.956   6749  Z= 0.311
  Chirality :  0.042   0.162    770
  Planarity :  0.004   0.037    824
  Dihedral  :  5.128  20.475    662
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 13.26 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.35), residues: 613
  helix: -0.32 (0.27), residues: 380
  sheet: -3.10 (0.80), residues: 36
  loop : -1.83 (0.48), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 332 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.021   0.002   PHE B  29 
 TYR   0.011   0.001   TYR B  53 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04224 (  286)
  hydrogen bonds       : angle       5.68242 (  831)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       0.04500 (    2)
  covalent geometry    : bond        0.00346 ( 4971)
  covalent geometry    : angle       0.61102 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.556 
Fit side-chains
REVERT: A  161 SER cc_start: 0.8357 (m) cc_final: 0.7922 (p)
REVERT: A  255 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.5537 (p90)
REVERT: A  269 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7736 (tttm)
REVERT: A  283 ARG cc_start: 0.7345 (mtm110) cc_final: 0.6919 (mtm180)
REVERT: A  326 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8248 (mmm)
REVERT: A  342 LEU cc_start: 0.8182 (mt) cc_final: 0.7970 (mp)
REVERT: A  351 LYS cc_start: 0.6880 (ptpt) cc_final: 0.6347 (tppt)
REVERT: A  406 ILE cc_start: 0.8447 (tt) cc_final: 0.8188 (tt)
REVERT: A  501 LYS cc_start: 0.7519 (mmmt) cc_final: 0.7304 (mmtt)
REVERT: B   34 MET cc_start: 0.8673 (mmp) cc_final: 0.8463 (mmp)
REVERT: B   45 ARG cc_start: 0.7336 (ttm170) cc_final: 0.5300 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8221 (mttt) cc_final: 0.7901 (mttt)
REVERT: B   82 GLN cc_start: 0.8267 (tp40) cc_final: 0.7748 (tm-30)
REVERT: B   94 TYR cc_start: 0.8310 (m-80) cc_final: 0.7863 (m-80)
  outliers start: 21
  outliers final: 9
  residues processed: 122
  average time/residue: 1.3623
  time to fit residues: 174.7006
Evaluate side-chains
  121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B 103 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.172011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.136940 restraints weight = 5712.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.64
r_work: 0.3477 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   4972  Z= 0.244
  Angle     :  0.661   8.711   6749  Z= 0.341
  Chirality :  0.045   0.168    770
  Planarity :  0.004   0.036    824
  Dihedral  :  5.045  20.856    662
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.98 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.34), residues: 613
  helix: -0.34 (0.26), residues: 391
  sheet: -3.22 (0.77), residues: 36
  loop : -1.93 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 332 
 HIS   0.004   0.001   HIS A 121 
 PHE   0.015   0.002   PHE B  29 
 TYR   0.016   0.002   TYR B  53 
 ARG   0.005   0.001   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04410 (  286)
  hydrogen bonds       : angle       5.61430 (  831)
  SS BOND              : bond        0.00118 (    1)
  SS BOND              : angle       0.32277 (    2)
  covalent geometry    : bond        0.00569 ( 4971)
  covalent geometry    : angle       0.66138 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A  255 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.5782 (p90)
REVERT: A  283 ARG cc_start: 0.7422 (mtm110) cc_final: 0.6921 (mtm180)
REVERT: A  326 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8324 (mmp)
REVERT: A  351 LYS cc_start: 0.6799 (ptpt) cc_final: 0.6203 (tppt)
REVERT: A  406 ILE cc_start: 0.8424 (tt) cc_final: 0.8150 (tt)
REVERT: A  498 SER cc_start: 0.8640 (t) cc_final: 0.8354 (m)
REVERT: B   34 MET cc_start: 0.8609 (mmp) cc_final: 0.8385 (tpp)
REVERT: B   45 ARG cc_start: 0.7540 (ttm170) cc_final: 0.5247 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8219 (mttt) cc_final: 0.7834 (mttt)
REVERT: B   82 GLN cc_start: 0.8257 (tp40) cc_final: 0.7829 (tm-30)
REVERT: B   94 TYR cc_start: 0.8303 (m-80) cc_final: 0.7810 (m-80)
  outliers start: 19
  outliers final: 10
  residues processed: 131
  average time/residue: 0.7445
  time to fit residues: 103.5659
Evaluate side-chains
  130 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0370
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4058

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.179566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.146538 restraints weight = 5776.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 2.57
r_work: 0.3591 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4972  Z= 0.136
  Angle     :  0.581   9.240   6749  Z= 0.299
  Chirality :  0.041   0.168    770
  Planarity :  0.004   0.032    824
  Dihedral  :  4.823  20.029    662
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.96 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.35), residues: 613
  helix: -0.04 (0.26), residues: 399
  sheet: -3.03 (0.81), residues: 36
  loop : -1.83 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 159 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.018   0.002   PHE B  68 
 TYR   0.009   0.001   TYR B  53 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03970 (  286)
  hydrogen bonds       : angle       5.31334 (  831)
  SS BOND              : bond        0.00280 (    1)
  SS BOND              : angle       0.32553 (    2)
  covalent geometry    : bond        0.00303 ( 4971)
  covalent geometry    : angle       0.58135 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.7504 (mtpt) cc_final: 0.6529 (tttm)
REVERT: A  149 PHE cc_start: 0.7914 (m-10) cc_final: 0.7554 (m-10)
REVERT: A  161 SER cc_start: 0.8362 (m) cc_final: 0.7969 (p)
REVERT: A  255 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.5810 (p90)
REVERT: A  269 LYS cc_start: 0.7953 (ttpm) cc_final: 0.7715 (tttm)
REVERT: A  283 ARG cc_start: 0.7359 (mtm110) cc_final: 0.6857 (mtm180)
REVERT: A  326 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8372 (mmp)
REVERT: A  350 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.8207 (mtm180)
REVERT: A  351 LYS cc_start: 0.6864 (ptpt) cc_final: 0.6261 (tppt)
REVERT: A  406 ILE cc_start: 0.8443 (tt) cc_final: 0.8076 (tt)
REVERT: B   45 ARG cc_start: 0.7373 (ttm170) cc_final: 0.5238 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8138 (mttt) cc_final: 0.7876 (mttt)
REVERT: B   82 GLN cc_start: 0.8293 (tp40) cc_final: 0.7796 (tm-30)
REVERT: B   94 TYR cc_start: 0.8276 (m-80) cc_final: 0.7811 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 132
  average time/residue: 0.9946
  time to fit residues: 139.1582
Evaluate side-chains
  134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0980
   chunk 52 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.178480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.145242 restraints weight = 5825.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.55
r_work: 0.3577 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4972  Z= 0.156
  Angle     :  0.598   9.039   6749  Z= 0.307
  Chirality :  0.042   0.174    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.751  19.858    662
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 18.32 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.35), residues: 613
  helix:  0.16 (0.26), residues: 393
  sheet: -2.99 (0.80), residues: 36
  loop : -1.74 (0.51), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 159 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.030   0.002   PHE B  68 
 TYR   0.010   0.001   TYR A 424 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03985 (  286)
  hydrogen bonds       : angle       5.22653 (  831)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.11440 (    2)
  covalent geometry    : bond        0.00354 ( 4971)
  covalent geometry    : angle       0.59833 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.7431 (mtpt) cc_final: 0.6530 (tttm)
REVERT: A   92 GLN cc_start: 0.8269 (mp10) cc_final: 0.7857 (mp10)
REVERT: A  149 PHE cc_start: 0.7918 (m-10) cc_final: 0.7539 (m-10)
REVERT: A  157 GLU cc_start: 0.8345 (tp30) cc_final: 0.7575 (tp30)
REVERT: A  161 SER cc_start: 0.8413 (m) cc_final: 0.8036 (p)
REVERT: A  255 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.5909 (p90)
REVERT: A  283 ARG cc_start: 0.7360 (mtm110) cc_final: 0.6854 (mtm180)
REVERT: A  326 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8372 (mmp)
REVERT: A  351 LYS cc_start: 0.6912 (ptpt) cc_final: 0.6352 (tppt)
REVERT: A  381 GLN cc_start: 0.8537 (pt0) cc_final: 0.7983 (tm-30)
REVERT: A  406 ILE cc_start: 0.8380 (tt) cc_final: 0.8073 (tt)
REVERT: A  456 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6704 (tm-30)
REVERT: B   45 ARG cc_start: 0.7419 (ttm170) cc_final: 0.5229 (ptt-90)
REVERT: B   82 GLN cc_start: 0.8303 (tp40) cc_final: 0.7827 (tm-30)
REVERT: B   94 TYR cc_start: 0.8270 (m-80) cc_final: 0.7845 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 134
  average time/residue: 0.8752
  time to fit residues: 123.3289
Evaluate side-chains
  141 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0030
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN
A 173 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.179182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.145620 restraints weight = 5704.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.55
r_work: 0.3586 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4972  Z= 0.153
  Angle     :  0.608   9.149   6749  Z= 0.309
  Chirality :  0.042   0.169    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.741  19.948    662
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.88 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.35), residues: 613
  helix:  0.20 (0.26), residues: 399
  sheet: -2.86 (0.82), residues: 36
  loop : -1.62 (0.52), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 159 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.035   0.002   PHE B  68 
 TYR   0.010   0.001   TYR A 242 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  286)
  hydrogen bonds       : angle       5.17144 (  831)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       0.13327 (    2)
  covalent geometry    : bond        0.00350 ( 4971)
  covalent geometry    : angle       0.60786 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.7411 (mtpt) cc_final: 0.6536 (tttm)
REVERT: A  149 PHE cc_start: 0.7872 (m-10) cc_final: 0.7508 (m-10)
REVERT: A  157 GLU cc_start: 0.8383 (tp30) cc_final: 0.7628 (tp30)
REVERT: A  161 SER cc_start: 0.8407 (m) cc_final: 0.8026 (p)
REVERT: A  255 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.5914 (p90)
REVERT: A  283 ARG cc_start: 0.7352 (mtm110) cc_final: 0.6836 (mtm180)
REVERT: A  326 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8348 (mmp)
REVERT: A  342 LEU cc_start: 0.8302 (mt) cc_final: 0.8080 (mt)
REVERT: A  351 LYS cc_start: 0.6958 (ptpt) cc_final: 0.6397 (tppt)
REVERT: A  406 ILE cc_start: 0.8377 (tt) cc_final: 0.8086 (tt)
REVERT: B   34 MET cc_start: 0.8569 (mmp) cc_final: 0.8315 (mmp)
REVERT: B   45 ARG cc_start: 0.7423 (ttm170) cc_final: 0.5221 (ptt-90)
REVERT: B   82 GLN cc_start: 0.8281 (tp40) cc_final: 0.7663 (tm-30)
REVERT: B   94 TYR cc_start: 0.8256 (m-80) cc_final: 0.7849 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 126
  average time/residue: 0.7980
  time to fit residues: 106.2608
Evaluate side-chains
  132 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0870
   chunk 57 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.8762

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.177257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.143610 restraints weight = 5760.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.54
r_work: 0.3562 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4972  Z= 0.194
  Angle     :  0.644  10.076   6749  Z= 0.327
  Chirality :  0.044   0.169    770
  Planarity :  0.004   0.032    824
  Dihedral  :  4.794  20.862    662
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 20.47 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.35), residues: 613
  helix:  0.15 (0.26), residues: 400
  sheet: -3.00 (0.79), residues: 36
  loop : -1.51 (0.52), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 159 
 HIS   0.002   0.001   HIS A 121 
 PHE   0.027   0.002   PHE B  68 
 TYR   0.026   0.002   TYR A 242 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04117 (  286)
  hydrogen bonds       : angle       5.21963 (  831)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       0.13570 (    2)
  covalent geometry    : bond        0.00452 ( 4971)
  covalent geometry    : angle       0.64365 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.7509 (mtpt) cc_final: 0.6671 (tttm)
REVERT: A  149 PHE cc_start: 0.7921 (m-10) cc_final: 0.7550 (m-10)
REVERT: A  157 GLU cc_start: 0.8393 (tp30) cc_final: 0.7631 (tp30)
REVERT: A  161 SER cc_start: 0.8434 (m) cc_final: 0.8044 (p)
REVERT: A  255 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.5995 (p90)
REVERT: A  283 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6878 (mtm180)
REVERT: A  326 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8376 (mmp)
REVERT: A  351 LYS cc_start: 0.7000 (ptpt) cc_final: 0.6419 (tppt)
REVERT: A  406 ILE cc_start: 0.8440 (tt) cc_final: 0.8153 (tt)
REVERT: A  412 LYS cc_start: 0.7727 (tttm) cc_final: 0.7398 (tttm)
REVERT: B   45 ARG cc_start: 0.7471 (ttm170) cc_final: 0.5252 (ptt-90)
REVERT: B   82 GLN cc_start: 0.8315 (tp40) cc_final: 0.7495 (tm-30)
REVERT: B   94 TYR cc_start: 0.8270 (m-80) cc_final: 0.7806 (m-80)
  outliers start: 20
  outliers final: 12
  residues processed: 124
  average time/residue: 0.7648
  time to fit residues: 100.6707
Evaluate side-chains
  129 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 49 optimal weight:    0.4980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4160 r_free = 0.4160 target = 0.180341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.147184 restraints weight = 5711.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.53
r_work: 0.3604 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4972  Z= 0.148
  Angle     :  0.635  11.527   6749  Z= 0.318
  Chirality :  0.042   0.172    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.742  21.369    662
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.64 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.35), residues: 613
  helix:  0.21 (0.26), residues: 402
  sheet: -2.98 (0.77), residues: 36
  loop : -1.34 (0.54), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 159 
 HIS   0.002   0.001   HIS A 121 
 PHE   0.015   0.002   PHE B  68 
 TYR   0.030   0.001   TYR A 242 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03942 (  286)
  hydrogen bonds       : angle       5.16498 (  831)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       0.26764 (    2)
  covalent geometry    : bond        0.00341 ( 4971)
  covalent geometry    : angle       0.63542 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.7464 (mtpt) cc_final: 0.6607 (tttm)
REVERT: A  149 PHE cc_start: 0.7855 (m-10) cc_final: 0.7511 (m-10)
REVERT: A  157 GLU cc_start: 0.8377 (tp30) cc_final: 0.7634 (tp30)
REVERT: A  161 SER cc_start: 0.8404 (m) cc_final: 0.8024 (p)
REVERT: A  255 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.5770 (p90)
REVERT: A  283 ARG cc_start: 0.7347 (mtm110) cc_final: 0.6831 (mtm180)
REVERT: A  326 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8245 (mmm)
REVERT: A  351 LYS cc_start: 0.6978 (ptpt) cc_final: 0.6409 (tppt)
REVERT: A  406 ILE cc_start: 0.8418 (tt) cc_final: 0.8135 (tt)
REVERT: A  412 LYS cc_start: 0.7674 (tttm) cc_final: 0.7363 (tttm)
REVERT: B   34 MET cc_start: 0.8538 (mmp) cc_final: 0.8152 (tpp)
REVERT: B   45 ARG cc_start: 0.7361 (ttm170) cc_final: 0.5232 (ptt-90)
REVERT: B   82 GLN cc_start: 0.8300 (tp40) cc_final: 0.7554 (tm-30)
REVERT: B   94 TYR cc_start: 0.8238 (m-80) cc_final: 0.7743 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 121
  average time/residue: 0.8258
  time to fit residues: 106.2304
Evaluate side-chains
  126 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 35 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4081 r_free = 0.4081 target = 0.176622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.141493 restraints weight = 5623.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.66
r_work: 0.3534 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4972  Z= 0.167
  Angle     :  0.662  12.056   6749  Z= 0.329
  Chirality :  0.043   0.173    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.738  20.746    662
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.25 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.36), residues: 613
  helix:  0.22 (0.26), residues: 402
  sheet: -2.85 (0.79), residues: 36
  loop : -1.23 (0.54), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 159 
 HIS   0.002   0.001   HIS A 121 
 PHE   0.010   0.001   PHE A 416 
 TYR   0.036   0.002   TYR A 242 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04069 (  286)
  hydrogen bonds       : angle       5.17678 (  831)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       0.18729 (    2)
  covalent geometry    : bond        0.00389 ( 4971)
  covalent geometry    : angle       0.66178 ( 6747)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.7422 (mtpt) cc_final: 0.6587 (tttm)
REVERT: A  149 PHE cc_start: 0.7829 (m-10) cc_final: 0.7485 (m-10)
REVERT: A  157 GLU cc_start: 0.8354 (tp30) cc_final: 0.7581 (tp30)
REVERT: A  161 SER cc_start: 0.8371 (m) cc_final: 0.7963 (p)
REVERT: A  255 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.5683 (p90)
REVERT: A  283 ARG cc_start: 0.7318 (mtm110) cc_final: 0.6797 (mtm180)
REVERT: A  326 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8375 (mmp)
REVERT: A  351 LYS cc_start: 0.6952 (ptpt) cc_final: 0.6365 (tppt)
REVERT: A  406 ILE cc_start: 0.8401 (tt) cc_final: 0.8126 (tt)
REVERT: B   45 ARG cc_start: 0.7420 (ttm170) cc_final: 0.5201 (ptt-90)
REVERT: B   82 GLN cc_start: 0.8390 (tp40) cc_final: 0.8019 (tp-100)
REVERT: B   94 TYR cc_start: 0.8277 (m-80) cc_final: 0.7738 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 118
  average time/residue: 0.9292
  time to fit residues: 116.6361
Evaluate side-chains
  125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0370
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.5258

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.177971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.142800 restraints weight = 5628.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.68
r_work: 0.3546 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4972  Z= 0.150
  Angle     :  0.648  12.252   6749  Z= 0.322
  Chirality :  0.043   0.185    770
  Planarity :  0.004   0.032    824
  Dihedral  :  4.676  20.389    662
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.64 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.36), residues: 613
  helix:  0.24 (0.26), residues: 402
  sheet: -2.70 (0.81), residues: 37
  loop : -1.17 (0.55), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 159 
 HIS   0.002   0.001   HIS A 121 
 PHE   0.011   0.001   PHE A 106 
 TYR   0.036   0.002   TYR A 242 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  286)
  hydrogen bonds       : angle       5.15400 (  831)
  SS BOND              : bond        0.00348 (    1)
  SS BOND              : angle       0.09850 (    2)
  covalent geometry    : bond        0.00344 ( 4971)
  covalent geometry    : angle       0.64840 ( 6747)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4193.09 seconds
wall clock time: 76 minutes 10.82 seconds (4570.82 seconds total)