Starting phenix.real_space_refine
on Sat May 10 03:34:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j3o_61121/05_2025/9j3o_61121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j3o_61121/05_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_61121/05_2025/9j3o_61121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j3o_61121/05_2025/9j3o_61121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j3o_61121/05_2025/9j3o_61121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j3o_61121/05_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-5687/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: 3.21, per 1000 atoms: 0.66
  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: 1.06
  Conformation dependent library (CDL) restraints added in 554.2 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: 0.53
  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: 1.35

  Time building geometry restraints manager: 1.26 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:             0.870
  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:                     14.610
  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:12.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.440
-------------------------------------------------------------------------------
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  : 0.455 
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: 0.7850
  time to fit residues: 97.8335
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  : 0.460 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4080 r_free = 0.4080 target = 0.176610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.142675 restraints weight = 5574.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.55
r_work: 0.3555 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.1472

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= 0.175
  Angle     :  0.684   8.889   6749  Z= 0.349
  Chirality :  0.044   0.170    770
  Planarity :  0.005   0.049    824
  Dihedral  :  5.859  33.002    668
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  8.77 %
    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: -2.18 (0.34), residues: 613
  helix: -0.74 (0.26), residues: 378
  sheet: -3.30 (0.77), residues: 36
  loop : -2.24 (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 B 103 
 PHE   0.022   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        0.04654 (  286)
  hydrogen bonds       : angle       6.05687 (  831)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.28032 (    2)
  covalent geometry    : bond        0.00401 ( 4971)
  covalent geometry    : angle       0.68448 ( 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: 12
    poor density    : 117
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A  161 SER cc_start: 0.8285 (m) cc_final: 0.7815 (p)
REVERT: A  255 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.5444 (p90)
REVERT: A  269 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7814 (tttm)
REVERT: A  283 ARG cc_start: 0.7411 (mtm110) cc_final: 0.6975 (mtm180)
REVERT: A  333 THR cc_start: 0.8500 (t) cc_final: 0.8047 (m)
REVERT: A  339 LEU cc_start: 0.8320 (mt) cc_final: 0.8061 (mm)
REVERT: A  342 LEU cc_start: 0.8108 (mt) cc_final: 0.7833 (mp)
REVERT: A  395 MET cc_start: 0.8411 (tpp) cc_final: 0.8178 (tpp)
REVERT: A  406 ILE cc_start: 0.8410 (tt) cc_final: 0.8144 (tt)
REVERT: B   34 MET cc_start: 0.8673 (mmp) cc_final: 0.8444 (mmp)
REVERT: B   45 ARG cc_start: 0.7359 (ttm170) cc_final: 0.5279 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8192 (mttt) cc_final: 0.7917 (mttt)
REVERT: B   82 GLN cc_start: 0.8305 (tp40) cc_final: 0.7717 (tm-30)
REVERT: B   94 TYR cc_start: 0.8338 (m-80) cc_final: 0.7958 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 119
  average time/residue: 0.8090
  time to fit residues: 102.3302
Evaluate side-chains
  119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 PHE
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:    0.0000
   chunk 42 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 56 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0980
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4384

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.181153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.148155 restraints weight = 5638.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.55
r_work: 0.3621 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   4972  Z= 0.147
  Angle     :  0.608   9.011   6749  Z= 0.310
  Chirality :  0.042   0.162    770
  Planarity :  0.004   0.037    824
  Dihedral  :  5.072  20.297    662
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 13.06 %
    Favored  : 83.24 %
  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: -1.51 (0.35), residues: 613
  helix: -0.28 (0.27), residues: 380
  sheet: -3.13 (0.78), residues: 36
  loop : -1.79 (0.49), 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   0.019   0.002   PHE B  29 
 TYR   0.013   0.001   TYR A 153 
 ARG   0.003   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04172 (  286)
  hydrogen bonds       : angle       5.65132 (  831)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       0.12507 (    2)
  covalent geometry    : bond        0.00328 ( 4971)
  covalent geometry    : angle       0.60816 ( 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
  136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A  161 SER cc_start: 0.8347 (m) cc_final: 0.7914 (p)
REVERT: A  255 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.5630 (p90)
REVERT: A  269 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7748 (tttm)
REVERT: A  283 ARG cc_start: 0.7327 (mtm110) cc_final: 0.6896 (mtm180)
REVERT: A  326 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8095 (mmm)
REVERT: A  342 LEU cc_start: 0.8246 (mt) cc_final: 0.8032 (mp)
REVERT: A  406 ILE cc_start: 0.8451 (tt) cc_final: 0.8189 (tt)
REVERT: A  501 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7281 (mmtt)
REVERT: B   34 MET cc_start: 0.8655 (mmp) cc_final: 0.8430 (mmp)
REVERT: B   45 ARG cc_start: 0.7313 (ttm170) cc_final: 0.5293 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8215 (mttt) cc_final: 0.7885 (mttt)
REVERT: B   82 GLN cc_start: 0.8147 (tp40) cc_final: 0.7750 (tm-30)
REVERT: B   94 TYR cc_start: 0.8297 (m-80) cc_final: 0.7865 (m-80)
  outliers start: 19
  outliers final: 9
  residues processed: 119
  average time/residue: 0.9214
  time to fit residues: 115.6179
Evaluate side-chains
  122 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.179897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.146718 restraints weight = 5715.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.55
r_work: 0.3597 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2346

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= 0.164
  Angle     :  0.605   8.364   6749  Z= 0.309
  Chirality :  0.042   0.160    770
  Planarity :  0.004   0.035    824
  Dihedral  :  4.875  20.444    662
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 15.20 %
    Favored  : 80.70 %
  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: -1.37 (0.35), residues: 613
  helix: -0.17 (0.26), residues: 391
  sheet: -2.98 (0.80), residues: 36
  loop : -1.83 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 159 
 HIS   0.004   0.001   HIS A 121 
 PHE   0.012   0.002   PHE B  29 
 TYR   0.010   0.001   TYR B  53 
 ARG   0.004   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04047 (  286)
  hydrogen bonds       : angle       5.44448 (  831)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.07618 (    2)
  covalent geometry    : bond        0.00376 ( 4971)
  covalent geometry    : angle       0.60474 ( 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
  143 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7817 (mtm) cc_final: 0.7615 (mtm)
REVERT: A   67 LYS cc_start: 0.7281 (mtpt) cc_final: 0.6339 (tttm)
REVERT: A  161 SER cc_start: 0.8424 (m) cc_final: 0.8002 (p)
REVERT: A  255 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.5749 (p90)
REVERT: A  283 ARG cc_start: 0.7364 (mtm110) cc_final: 0.6908 (mtm180)
REVERT: A  326 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8264 (mmm)
REVERT: A  351 LYS cc_start: 0.6763 (ptpt) cc_final: 0.6227 (tppt)
REVERT: A  406 ILE cc_start: 0.8449 (tt) cc_final: 0.8163 (tt)
REVERT: A  498 SER cc_start: 0.8562 (t) cc_final: 0.8349 (m)
REVERT: B   45 ARG cc_start: 0.7373 (ttm170) cc_final: 0.5249 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8225 (mttt) cc_final: 0.7836 (mttt)
REVERT: B   82 GLN cc_start: 0.8116 (tp40) cc_final: 0.7720 (tm-30)
REVERT: B   94 TYR cc_start: 0.8295 (m-80) cc_final: 0.7844 (m-80)
  outliers start: 21
  outliers final: 11
  residues processed: 128
  average time/residue: 0.7422
  time to fit residues: 100.8633
Evaluate side-chains
  130 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
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  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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 54 optimal weight:    0.1980
   chunk 56 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4154 r_free = 0.4154 target = 0.180023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.146846 restraints weight = 5788.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.60
r_work: 0.3601 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4972  Z= 0.154
  Angle     :  0.596   8.724   6749  Z= 0.303
  Chirality :  0.042   0.164    770
  Planarity :  0.004   0.032    824
  Dihedral  :  4.779  20.216    662
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.35 %
    Favored  : 79.14 %
  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: -1.12 (0.35), residues: 613
  helix:  0.04 (0.26), residues: 397
  sheet: -2.79 (0.83), residues: 36
  loop : -1.86 (0.50), residues: 180

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   0.020   0.002   PHE B  68 
 TYR   0.009   0.001   TYR A 424 
 ARG   0.004   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04002 (  286)
  hydrogen bonds       : angle       5.30062 (  831)
  SS BOND              : bond        0.00055 (    1)
  SS BOND              : angle       0.09540 (    2)
  covalent geometry    : bond        0.00354 ( 4971)
  covalent geometry    : angle       0.59563 ( 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
  134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7861 (mtm) cc_final: 0.7629 (mtm)
REVERT: A   67 LYS cc_start: 0.7369 (mtpt) cc_final: 0.6432 (tttm)
REVERT: A   84 LYS cc_start: 0.7573 (tppt) cc_final: 0.6853 (tppt)
REVERT: A  149 PHE cc_start: 0.7986 (m-10) cc_final: 0.7542 (m-10)
REVERT: A  161 SER cc_start: 0.8442 (m) cc_final: 0.8028 (p)
REVERT: A  220 TRP cc_start: 0.8385 (m100) cc_final: 0.8142 (m100)
REVERT: A  255 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.5843 (p90)
REVERT: A  269 LYS cc_start: 0.7995 (ttpm) cc_final: 0.7760 (tttm)
REVERT: A  283 ARG cc_start: 0.7362 (mtm110) cc_final: 0.6923 (mtm180)
REVERT: A  326 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8348 (mmp)
REVERT: A  351 LYS cc_start: 0.6812 (ptpt) cc_final: 0.6252 (tppt)
REVERT: A  406 ILE cc_start: 0.8449 (tt) cc_final: 0.8187 (tt)
REVERT: B   45 ARG cc_start: 0.7384 (ttm170) cc_final: 0.5242 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8207 (mttt) cc_final: 0.7832 (mttt)
REVERT: B   82 GLN cc_start: 0.8209 (tp40) cc_final: 0.7812 (tm-30)
REVERT: B   94 TYR cc_start: 0.8287 (m-80) cc_final: 0.7859 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 123
  average time/residue: 0.7882
  time to fit residues: 102.5567
Evaluate side-chains
  127 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0020
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.179257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.145963 restraints weight = 5842.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 2.61
r_work: 0.3591 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4972  Z= 0.162
  Angle     :  0.602   8.656   6749  Z= 0.306
  Chirality :  0.042   0.163    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.747  19.991    662
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 17.54 %
    Favored  : 77.78 %
  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: -0.96 (0.35), residues: 613
  helix:  0.14 (0.26), residues: 399
  sheet: -2.80 (0.83), residues: 36
  loop : -1.72 (0.51), 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   0.029   0.002   PHE B  68 
 TYR   0.009   0.001   TYR A 424 
 ARG   0.003   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  286)
  hydrogen bonds       : angle       5.24272 (  831)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.12300 (    2)
  covalent geometry    : bond        0.00371 ( 4971)
  covalent geometry    : angle       0.60221 ( 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
  140 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7876 (mtm) cc_final: 0.7619 (mtm)
REVERT: A   67 LYS cc_start: 0.7353 (mtpt) cc_final: 0.6483 (tttm)
REVERT: A   84 LYS cc_start: 0.7575 (tppt) cc_final: 0.6850 (tppt)
REVERT: A  149 PHE cc_start: 0.7923 (m-10) cc_final: 0.7553 (m-10)
REVERT: A  161 SER cc_start: 0.8483 (m) cc_final: 0.8081 (p)
REVERT: A  220 TRP cc_start: 0.8374 (m100) cc_final: 0.8045 (m100)
REVERT: A  255 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.5840 (p90)
REVERT: A  283 ARG cc_start: 0.7401 (mtm110) cc_final: 0.6958 (mtm180)
REVERT: A  326 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8378 (mmp)
REVERT: A  342 LEU cc_start: 0.8300 (mt) cc_final: 0.8080 (mt)
REVERT: A  351 LYS cc_start: 0.6888 (ptpt) cc_final: 0.6322 (tppt)
REVERT: B   45 ARG cc_start: 0.7447 (ttm170) cc_final: 0.5244 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8144 (mttt) cc_final: 0.7807 (mttt)
REVERT: B   82 GLN cc_start: 0.8264 (tp40) cc_final: 0.7422 (tm-30)
REVERT: B   94 TYR cc_start: 0.8277 (m-80) cc_final: 0.7839 (m-80)
  outliers start: 24
  outliers final: 13
  residues processed: 125
  average time/residue: 0.7632
  time to fit residues: 100.8287
Evaluate side-chains
  130 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0030
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.6990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.178864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.146010 restraints weight = 5726.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.52
r_work: 0.3590 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.2888

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= 0.167
  Angle     :  0.615   8.774   6749  Z= 0.312
  Chirality :  0.042   0.172    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.744  19.938    662
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.91 %
    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: -0.83 (0.35), residues: 613
  helix:  0.23 (0.26), residues: 398
  sheet: -2.90 (0.81), residues: 36
  loop : -1.63 (0.52), residues: 179

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   0.036   0.002   PHE B  68 
 TYR   0.011   0.001   TYR A 286 
 ARG   0.003   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03988 (  286)
  hydrogen bonds       : angle       5.20346 (  831)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.09610 (    2)
  covalent geometry    : bond        0.00384 ( 4971)
  covalent geometry    : angle       0.61554 ( 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
  134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7863 (mtm) cc_final: 0.7593 (mtm)
REVERT: A   67 LYS cc_start: 0.7433 (mtpt) cc_final: 0.6561 (tttm)
REVERT: A  149 PHE cc_start: 0.7909 (m-10) cc_final: 0.7542 (m-10)
REVERT: A  157 GLU cc_start: 0.8358 (tp30) cc_final: 0.7571 (tp30)
REVERT: A  161 SER cc_start: 0.8480 (m) cc_final: 0.8063 (p)
REVERT: A  255 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.5908 (p90)
REVERT: A  283 ARG cc_start: 0.7362 (mtm110) cc_final: 0.6865 (mtm180)
REVERT: A  326 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8372 (mmp)
REVERT: A  342 LEU cc_start: 0.8287 (mt) cc_final: 0.8086 (mt)
REVERT: A  351 LYS cc_start: 0.6946 (ptpt) cc_final: 0.6362 (tppt)
REVERT: A  406 ILE cc_start: 0.8406 (tt) cc_final: 0.8100 (tt)
REVERT: B   34 MET cc_start: 0.8544 (mmp) cc_final: 0.8304 (mmp)
REVERT: B   45 ARG cc_start: 0.7450 (ttm170) cc_final: 0.5225 (ptt-90)
REVERT: B   82 GLN cc_start: 0.8259 (tp40) cc_final: 0.7726 (tm-30)
REVERT: B   94 TYR cc_start: 0.8256 (m-80) cc_final: 0.7665 (m-80)
  outliers start: 18
  outliers final: 11
  residues processed: 122
  average time/residue: 0.7287
  time to fit residues: 94.4504
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  : 0.467 
-------------------------------------------------------------------------------
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0670
   chunk 30 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6320

-------------------------------------------------------------------------------
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 = 0.179117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.145750 restraints weight = 5805.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.61
r_work: 0.3590 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4972  Z= 0.161
  Angle     :  0.618   9.076   6749  Z= 0.313
  Chirality :  0.042   0.169    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.709  19.762    662
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 19.30 %
    Favored  : 76.61 %
  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: -0.76 (0.35), residues: 613
  helix:  0.25 (0.26), residues: 400
  sheet: -2.98 (0.79), residues: 36
  loop : -1.49 (0.53), residues: 177

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   0.018   0.002   PHE B  68 
 TYR   0.016   0.001   TYR A 242 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  286)
  hydrogen bonds       : angle       5.18641 (  831)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.10323 (    2)
  covalent geometry    : bond        0.00371 ( 4971)
  covalent geometry    : angle       0.61812 ( 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
  138 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.7442 (mtpt) cc_final: 0.6629 (tttm)
REVERT: A  149 PHE cc_start: 0.7888 (m-10) cc_final: 0.7531 (m-10)
REVERT: A  157 GLU cc_start: 0.8377 (tp30) cc_final: 0.7612 (tp30)
REVERT: A  161 SER cc_start: 0.8494 (m) cc_final: 0.8086 (p)
REVERT: A  255 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.5887 (p90)
REVERT: A  283 ARG cc_start: 0.7395 (mtm110) cc_final: 0.6884 (mtm180)
REVERT: A  326 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8360 (mmp)
REVERT: A  342 LEU cc_start: 0.8331 (mt) cc_final: 0.7919 (mp)
REVERT: A  351 LYS cc_start: 0.6958 (ptpt) cc_final: 0.6379 (tppt)
REVERT: A  388 MET cc_start: 0.8494 (tpp) cc_final: 0.8047 (tpp)
REVERT: A  406 ILE cc_start: 0.8418 (tt) cc_final: 0.8129 (tt)
REVERT: A  412 LYS cc_start: 0.7707 (tttm) cc_final: 0.7370 (tttm)
REVERT: B   45 ARG cc_start: 0.7416 (ttm170) cc_final: 0.5218 (ptt-90)
REVERT: B   82 GLN cc_start: 0.8295 (tp40) cc_final: 0.7485 (tm-30)
REVERT: B   94 TYR cc_start: 0.8254 (m-80) cc_final: 0.7691 (m-80)
  outliers start: 21
  outliers final: 13
  residues processed: 125
  average time/residue: 0.7910
  time to fit residues: 105.0146
Evaluate side-chains
  131 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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    7 SER
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=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:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   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 = 0.4118 r_free = 0.4118 target = 0.177521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.143945 restraints weight = 5796.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.61
r_work: 0.3570 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4972  Z= 0.191
  Angle     :  0.645  10.389   6749  Z= 0.325
  Chirality :  0.043   0.169    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.771  21.288    662
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.27 %
    Favored  : 76.02 %
  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: -0.78 (0.35), residues: 613
  helix:  0.24 (0.26), residues: 398
  sheet: -3.00 (0.78), residues: 36
  loop : -1.49 (0.52), residues: 179

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   0.021   0.002   PHE B  68 
 TYR   0.025   0.002   TYR A 242 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  286)
  hydrogen bonds       : angle       5.22605 (  831)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.14065 (    2)
  covalent geometry    : bond        0.00446 ( 4971)
  covalent geometry    : angle       0.64542 ( 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
  134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.547 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7903 (mtm) cc_final: 0.7656 (mtm)
REVERT: A   67 LYS cc_start: 0.7475 (mtpt) cc_final: 0.6645 (tttm)
REVERT: A  149 PHE cc_start: 0.7935 (m-10) cc_final: 0.7565 (m-10)
REVERT: A  157 GLU cc_start: 0.8376 (tp30) cc_final: 0.7598 (tp30)
REVERT: A  161 SER cc_start: 0.8511 (m) cc_final: 0.8089 (p)
REVERT: A  255 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.5904 (p90)
REVERT: A  283 ARG cc_start: 0.7432 (mtm110) cc_final: 0.6896 (mtm180)
REVERT: A  326 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8371 (mmm)
REVERT: A  351 LYS cc_start: 0.6995 (ptpt) cc_final: 0.6434 (tppt)
REVERT: A  388 MET cc_start: 0.8538 (tpp) cc_final: 0.8030 (tpp)
REVERT: A  406 ILE cc_start: 0.8459 (tt) cc_final: 0.8178 (tt)
REVERT: A  412 LYS cc_start: 0.7760 (tttm) cc_final: 0.7439 (tttm)
REVERT: B   45 ARG cc_start: 0.7450 (ttm170) cc_final: 0.5254 (ptt-90)
REVERT: B   65 LYS cc_start: 0.8011 (mttt) cc_final: 0.7802 (mttt)
REVERT: B   82 GLN cc_start: 0.8345 (tp40) cc_final: 0.7912 (tp-100)
REVERT: B   94 TYR cc_start: 0.8265 (m-80) cc_final: 0.7807 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 121
  average time/residue: 0.8366
  time to fit residues: 106.9172
Evaluate side-chains
  130 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
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    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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:   20.0000
   chunk 35 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4073 r_free = 0.4073 target = 0.176052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.141325 restraints weight = 5667.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.67
r_work: 0.3533 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4972  Z= 0.172
  Angle     :  0.657  11.711   6749  Z= 0.328
  Chirality :  0.043   0.170    770
  Planarity :  0.004   0.031    824
  Dihedral  :  4.769  21.514    662
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.66 %
    Favored  : 76.02 %
  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: -0.73 (0.35), residues: 613
  helix:  0.19 (0.26), residues: 402
  sheet: -2.71 (0.81), residues: 35
  loop : -1.34 (0.53), residues: 176

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   0.011   0.002   PHE A 278 
 TYR   0.030   0.002   TYR A 242 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  286)
  hydrogen bonds       : angle       5.21665 (  831)
  SS BOND              : bond        0.00245 (    1)
  SS BOND              : angle       0.10464 (    2)
  covalent geometry    : bond        0.00400 ( 4971)
  covalent geometry    : angle       0.65700 ( 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
  132 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.531 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7759 (mtm) cc_final: 0.7473 (mtm)
REVERT: A   67 LYS cc_start: 0.7399 (mtpt) cc_final: 0.6621 (tttm)
REVERT: A  149 PHE cc_start: 0.7842 (m-10) cc_final: 0.7487 (m-10)
REVERT: A  157 GLU cc_start: 0.8364 (tp30) cc_final: 0.7584 (tp30)
REVERT: A  161 SER cc_start: 0.8444 (m) cc_final: 0.7994 (p)
REVERT: A  255 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.5718 (p90)
REVERT: A  283 ARG cc_start: 0.7344 (mtm110) cc_final: 0.6825 (mtm180)
REVERT: A  326 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8365 (mmp)
REVERT: A  341 MET cc_start: 0.8645 (mtt) cc_final: 0.8179 (mtt)
REVERT: A  351 LYS cc_start: 0.6938 (ptpt) cc_final: 0.6369 (tppt)
REVERT: A  388 MET cc_start: 0.8407 (tpp) cc_final: 0.7996 (tpp)
REVERT: A  406 ILE cc_start: 0.8402 (tt) cc_final: 0.8122 (tt)
REVERT: A  412 LYS cc_start: 0.7600 (tttm) cc_final: 0.7268 (tttm)
REVERT: B   45 ARG cc_start: 0.7454 (ttm170) cc_final: 0.5188 (ptt-90)
REVERT: B   82 GLN cc_start: 0.8354 (tp40) cc_final: 0.7890 (tp-100)
REVERT: B   94 TYR cc_start: 0.8270 (m-80) cc_final: 0.7769 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 120
  average time/residue: 0.8390
  time to fit residues: 106.5302
Evaluate side-chains
  127 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
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    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:    0.7980
   chunk 55 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4079 r_free = 0.4079 target = 0.176657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.142037 restraints weight = 5640.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.66
r_work: 0.3538 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4972  Z= 0.163
  Angle     :  0.655  11.439   6749  Z= 0.326
  Chirality :  0.043   0.188    770
  Planarity :  0.004   0.032    824
  Dihedral  :  4.731  20.830    662
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.05 %
    Favored  : 76.02 %
  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: -0.71 (0.35), residues: 613
  helix:  0.19 (0.26), residues: 403
  sheet: -2.98 (0.77), residues: 37
  loop : -1.21 (0.55), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  36 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.014   0.002   PHE B  68 
 TYR   0.036   0.002   TYR A 242 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04056 (  286)
  hydrogen bonds       : angle       5.24735 (  831)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.26506 (    2)
  covalent geometry    : bond        0.00379 ( 4971)
  covalent geometry    : angle       0.65514 ( 6747)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3561.85 seconds
wall clock time: 62 minutes 39.52 seconds (3759.52 seconds total)