Starting phenix.real_space_refine
on Thu Jul  2 09:09:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vky_65146/07_2026/9vky_65146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vky_65146/07_2026/9vky_65146.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vky_65146/07_2026/9vky_65146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vky_65146/07_2026/9vky_65146.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vky_65146/07_2026/9vky_65146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vky_65146/07_2026/9vky_65146.map"
  }
  resolution = 2.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
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      52      5.16       5
     C    5051      2.51       5
     N    1287      2.21       5
     O    1394      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7784
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 519, 3878
          Classifications: {'peptide': 519}
          Link IDs: {'PTRANS': 21, 'TRANS': 497}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 3906
          Classifications: {'peptide': 523}
          Link IDs: {'PTRANS': 21, 'TRANS': 501}
          Chain breaks: 2
  Time building chain proxies: 1.64, per 1000 atoms: 0.21
  Number of scatterers: 7784
  At special positions: 0
  Unit cell: (89.06, 64.24, 129.94, 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      52     16.00
     O    1394      8.00
     N    1287      7.00
     C    5051      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 466.7 milliseconds
  

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1926

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      73.5% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 137
      removed outlier: 3.686A  pdb=" N   LEU A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      Proline residue:  A 128  - end of helix
      removed outlier: 3.545A  pdb=" N   ILE A 131 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 4.195A  pdb=" N   GLY A 144 " --> pdb=" O   PRO A 140 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU A 145 " --> pdb=" O   PRO A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.808A  pdb=" N   LEU A 153 " --> pdb=" O   PHE A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 184
      removed outlier: 3.512A  pdb=" N   GLN A 182 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ALA A 183 " --> pdb=" O   MET A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 214
    Processing helix  chain 'A' and resid 216 through 223
    Processing helix  chain 'A' and resid 224 through 243
    Processing helix  chain 'A' and resid 276 through 298
    Processing helix  chain 'A' and resid 301 through 307
      removed outlier: 4.227A  pdb=" N   SER A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 324
      removed outlier: 3.866A  pdb=" N   SER A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 383
    Processing helix  chain 'A' and resid 387 through 405
      removed outlier: 3.534A  pdb=" N   CYS A 404 " --> pdb=" O   MET A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 423
    Processing helix  chain 'A' and resid 428 through 444
      removed outlier: 3.856A  pdb=" N   ILE A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 453 through 469
      removed outlier: 4.001A  pdb=" N   LEU A 457 " --> pdb=" O   PRO A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 480
      removed outlier: 3.864A  pdb=" N   ALA A 474 " --> pdb=" O   ASP A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 498
    Processing helix  chain 'A' and resid 499 through 521
    Processing helix  chain 'A' and resid 564 through 583
      removed outlier: 3.704A  pdb=" N   GLY A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 622
      removed outlier: 3.677A  pdb=" N   ARG A 622 " --> pdb=" O   VAL A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 639
    Processing helix  chain 'A' and resid 642 through 648
    Processing helix  chain 'A' and resid 649 through 651
      No H-bonds generated for 'chain 'A' and resid 649 through 651'
    Processing helix  chain 'A' and resid 656 through 663
    Processing helix  chain 'B' and resid 113 through 137
      removed outlier: 4.021A  pdb=" N   LEU B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      Proline residue:  B 128  - end of helix
    Processing helix  chain 'B' and resid 140 through 147
      removed outlier: 4.139A  pdb=" N   GLY B 144 " --> pdb=" O   PRO B 140 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU B 145 " --> pdb=" O   PRO B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 159
      removed outlier: 3.712A  pdb=" N   LEU B 153 " --> pdb=" O   PHE B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 181
    Processing helix  chain 'B' and resid 189 through 214
    Processing helix  chain 'B' and resid 216 through 223
    Processing helix  chain 'B' and resid 224 through 244
    Processing helix  chain 'B' and resid 274 through 298
    Processing helix  chain 'B' and resid 302 through 307
    Processing helix  chain 'B' and resid 307 through 324
    Processing helix  chain 'B' and resid 342 through 346
      removed outlier: 3.897A  pdb=" N   LEU B 346 " --> pdb=" O   ALA B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 383
    Processing helix  chain 'B' and resid 387 through 405
    Processing helix  chain 'B' and resid 413 through 423
    Processing helix  chain 'B' and resid 428 through 445
      removed outlier: 3.953A  pdb=" N   ILE B 432 " --> pdb=" O   ALA B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 450
    Processing helix  chain 'B' and resid 453 through 469
      removed outlier: 4.013A  pdb=" N   LEU B 457 " --> pdb=" O   PRO B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 481
      removed outlier: 4.017A  pdb=" N   ALA B 474 " --> pdb=" O   ASP B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 497
    Processing helix  chain 'B' and resid 499 through 521
      removed outlier: 3.699A  pdb=" N   ILE B 515 " --> pdb=" O   SER B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 583
      removed outlier: 3.875A  pdb=" N   GLY B 569 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 621
    Processing helix  chain 'B' and resid 632 through 641
    Processing helix  chain 'B' and resid 642 through 649
    Processing helix  chain 'B' and resid 656 through 664
    Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167
    Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 538
      removed outlier: 4.388A  pdb=" N   VAL A 553 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
      removed outlier: 8.969A  pdb=" N   PHE A 654 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU A 628 " --> pdb=" O   PHE A 654 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 166 through 167
    Processing sheet with id=AA4, first strand: chain 'B' and resid 536 through 538
      removed outlier: 4.059A  pdb=" N   ASN B 523 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL B 553 " --> pdb=" O   LYS B 527 " (cutoff:3.500A)
      removed outlier: 9.331A  pdb=" N   VAL B 529 " --> pdb=" O   PHE B 551 " (cutoff:3.500A)
      removed outlier: 12.730A  pdb=" N   PHE B 551 " --> pdb=" O   VAL B 529 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL B 556 " --> pdb=" O   ASP B 597 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   SER B 599 " --> pdb=" O   VAL B 556 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ILE B 594 " --> pdb=" O   VAL B 627 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   ALA B 629 " --> pdb=" O   ILE B 594 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LEU B 596 " --> pdb=" O   ALA B 629 " (cutoff:3.500A)
      removed outlier: 8.967A  pdb=" N   PHE B 654 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU B 628 " --> pdb=" O   PHE B 654 " (cutoff:3.500A)

    569 hydrogen bonds defined for protein.
    1653 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1491
        1.33 -     1.45: 1741
        1.45 -     1.57: 4596
        1.57 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 7920
  Sorted by residual:
  bond pdb=" N   LEU A 158 "
       pdb=" CA  LEU A 158 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.16e-02 7.43e+03 9.55e+00
  bond pdb=" CA  PRO A 151 "
       pdb=" C   PRO A 151 "
    ideal  model  delta    sigma   weight residual
    1.517  1.545 -0.028 9.30e-03 1.16e+04 9.24e+00
  bond pdb=" N   ALA B 405 "
       pdb=" CA  ALA B 405 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.10e-02 8.26e+03 7.95e+00
  bond pdb=" C   GLY B 402 "
       pdb=" O   GLY B 402 "
    ideal  model  delta    sigma   weight residual
    1.234  1.208  0.026 1.19e-02 7.06e+03 4.74e+00
  bond pdb=" C   MET B 400 "
       pdb=" O   MET B 400 "
    ideal  model  delta    sigma   weight residual
    1.237  1.260 -0.024 1.19e-02 7.06e+03 3.93e+00
  ... (remaining 7915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 10606
        2.37 -     4.74: 144
        4.74 -     7.11: 7
        7.11 -     9.49: 0
        9.49 -    11.86: 1
  Bond angle restraints: 10758
  Sorted by residual:
  angle pdb=" N   LEU A 158 "
        pdb=" CA  LEU A 158 "
        pdb=" C   LEU A 158 "
      ideal   model   delta    sigma   weight residual
     112.59  117.25   -4.66 1.22e+00 6.72e-01 1.46e+01
  angle pdb=" N   SER B 403 "
        pdb=" CA  SER B 403 "
        pdb=" C   SER B 403 "
      ideal   model   delta    sigma   weight residual
     111.71  107.35    4.36 1.15e+00 7.56e-01 1.43e+01
  angle pdb=" CD  LYS A 482 "
        pdb=" CE  LYS A 482 "
        pdb=" NZ  LYS A 482 "
      ideal   model   delta    sigma   weight residual
     111.90  100.04   11.86 3.20e+00 9.77e-02 1.37e+01
  angle pdb=" N   SER A 156 "
        pdb=" CA  SER A 156 "
        pdb=" C   SER A 156 "
      ideal   model   delta    sigma   weight residual
     111.71  107.76    3.95 1.15e+00 7.56e-01 1.18e+01
  angle pdb=" N   ALA B 401 "
        pdb=" CA  ALA B 401 "
        pdb=" C   ALA B 401 "
      ideal   model   delta    sigma   weight residual
     111.28  107.66    3.62 1.09e+00 8.42e-01 1.11e+01
  ... (remaining 10753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.30: 4445
       16.30 -    32.59: 238
       32.59 -    48.89: 50
       48.89 -    65.18: 4
       65.18 -    81.48: 3
  Dihedral angle restraints: 4740
    sinusoidal: 1751
      harmonic: 2989
  Sorted by residual:
  dihedral pdb=" CA  TYR A 408 "
           pdb=" C   TYR A 408 "
           pdb=" N   VAL A 409 "
           pdb=" CA  VAL A 409 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.48  -16.52     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CG  ARG B 571 "
           pdb=" CD  ARG B 571 "
           pdb=" NE  ARG B 571 "
           pdb=" CZ  ARG B 571 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.16   42.84     2      1.50e+01 4.44e-03 9.86e+00
  dihedral pdb=" CB  MET B 573 "
           pdb=" CG  MET B 573 "
           pdb=" SD  MET B 573 "
           pdb=" CE  MET B 573 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.57  -57.57     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 4737 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 839
       0.034 -    0.068: 350
       0.068 -    0.102: 99
       0.102 -    0.136: 38
       0.136 -    0.170: 4
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" CA  VAL B 556 "
            pdb=" N   VAL B 556 "
            pdb=" C   VAL B 556 "
            pdb=" CB  VAL B 556 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CA  VAL B 548 "
            pdb=" N   VAL B 548 "
            pdb=" C   VAL B 548 "
            pdb=" CB  VAL B 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  VAL B 526 "
            pdb=" N   VAL B 526 "
            pdb=" C   VAL B 526 "
            pdb=" CB  VAL B 526 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 1327 not shown)

  Planarity restraints: 1330
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 428 "    0.015 2.00e-02 2.50e+03   2.87e-02 8.23e+00
        pdb=" C   ALA A 428 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ALA A 428 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 429 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 158 "    0.011 2.00e-02 2.50e+03   2.13e-02 4.53e+00
        pdb=" C   LEU A 158 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   LEU A 158 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY A 159 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 453 "    0.008 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   PRO A 453 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PRO A 453 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASN A 454 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1327 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 3885
        2.97 -     3.46: 8527
        3.46 -     3.94: 13252
        3.94 -     4.42: 15411
        4.42 -     4.90: 24589
  Nonbonded interactions: 65664
  Sorted by model distance:
  nonbonded pdb=" O   SER A 413 "
            pdb=" OG  SER A 417 "
     model   vdw
     2.493 3.040
  nonbonded pdb=" O   PRO A 549 "
            pdb=" OG  SER A 550 "
     model   vdw
     2.505 3.040
  nonbonded pdb=" O   VAL B 495 "
            pdb=" O   VAL B 498 "
     model   vdw
     2.559 3.040
  nonbonded pdb=" O   LEU A 153 "
            pdb=" OG  SER A 156 "
     model   vdw
     2.566 3.040
  nonbonded pdb=" O   MET B 400 "
            pdb=" OG  SER B 403 "
     model   vdw
     2.581 3.040
  ... (remaining 65659 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 112 through 666)
  selection = (chain 'B' and (resid 112 through 243 or resid 275 through 324 or resid 328 thro \ 
ugh 666))
}

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:             6.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.030
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
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      :  0.004   0.041   7920  Z= 0.209
  Angle     :  0.669  11.858  10758  Z= 0.365
  Chirality :  0.042   0.170   1330
  Planarity :  0.005   0.052   1330
  Dihedral  : 10.878  81.478   2814
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 0.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.26), residues: 1028
  helix:  0.85 (0.19), residues: 733
  sheet: -1.65 (0.57), residues: 41
  loop : -0.34 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 547 
 TYR   0.018   0.002   TYR B 408 
 PHE   0.023   0.002   PHE A 149 
 TRP   0.015   0.001   TRP A 478 
 HIS   0.003   0.001   HIS B 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.21 ( 7920)
  covalent geometry    : angle       0.66869 /  0.37 (10758)
  hydrogen bonds       : bond        0.11537 /  8.24 (  569)
  hydrogen bonds       : angle       5.71383 /  4.23 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  617 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7042 (mttt)
REVERT: A  620 GLU cc_start: 0.7683 (tt0) cc_final: 0.7395 (tp30)
REVERT: A  625 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7400 (mm-30)
REVERT: A  646 LYS cc_start: 0.7646 (mmtp) cc_final: 0.7440 (mmtm)
REVERT: B  215 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7829 (mmt180)
REVERT: B  225 LYS cc_start: 0.8051 (mttt) cc_final: 0.7558 (mmtt)
REVERT: B  414 PHE cc_start: 0.7777 (t80) cc_final: 0.7452 (t80)
REVERT: B  470 ASP cc_start: 0.8306 (t0) cc_final: 0.8084 (t0)
REVERT: B  518 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7342 (tm-30)
REVERT: B  546 MET cc_start: 0.7984 (ptt) cc_final: 0.7545 (mmm)
REVERT: B  592 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7014 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7461 (mttp) cc_final: 0.7066 (mttp)
REVERT: B  641 ASN cc_start: 0.7888 (m-40) cc_final: 0.7512 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.5231
  time to fit residues: 74.5761
Evaluate side-chains
  114 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 518 GLN
B 195 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.145982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.116195 restraints weight = 8707.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.79
r_work: 0.3260 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7920  Z= 0.190
  Angle     :  0.567   6.952  10758  Z= 0.294
  Chirality :  0.041   0.155   1330
  Planarity :  0.004   0.041   1330
  Dihedral  :  3.989  17.426   1108
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  5.55 %
    Favored  : 92.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.26), residues: 1028
  helix:  1.30 (0.19), residues: 737
  sheet: -1.08 (0.59), residues: 41
  loop : -0.21 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 652 
 TYR   0.020   0.002   TYR A 155 
 PHE   0.016   0.002   PHE B 378 
 TRP   0.006   0.001   TRP A 478 
 HIS   0.002   0.001   HIS A 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.19 ( 7920)
  covalent geometry    : angle       0.56726 /  0.29 (10758)
  hydrogen bonds       : bond        0.04805 /  3.26 (  569)
  hydrogen bonds       : angle       4.29374 /  3.22 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  385 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7850 (tp40)
REVERT: A  482 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.5072 (tptt)
REVERT: A  617 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7113 (mttt)
REVERT: A  620 GLU cc_start: 0.7842 (tt0) cc_final: 0.7432 (tp30)
REVERT: A  625 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7500 (mm-30)
REVERT: A  646 LYS cc_start: 0.7675 (mmtp) cc_final: 0.7311 (mmmm)
REVERT: B  181 ARG cc_start: 0.7704 (ttt180) cc_final: 0.7475 (ttm-80)
REVERT: B  189 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7818 (pt0)
REVERT: B  215 ARG cc_start: 0.8039 (mmt-90) cc_final: 0.7593 (mmt180)
REVERT: B  225 LYS cc_start: 0.7928 (mttt) cc_final: 0.7362 (mmtt)
REVERT: B  323 SER cc_start: 0.8714 (t) cc_final: 0.8448 (m)
REVERT: B  345 MET cc_start: 0.8422 (mtt) cc_final: 0.8064 (mtp)
REVERT: B  470 ASP cc_start: 0.8287 (t0) cc_final: 0.7741 (t0)
REVERT: B  518 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7398 (tm-30)
REVERT: B  546 MET cc_start: 0.7951 (ptt) cc_final: 0.7300 (mmm)
REVERT: B  592 ARG cc_start: 0.7704 (mtt180) cc_final: 0.6882 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7535 (mttp) cc_final: 0.7131 (mttp)
REVERT: B  641 ASN cc_start: 0.7828 (m-40) cc_final: 0.7404 (p0)
  outliers start: 13
  outliers final: 4
  residues processed: 116
  average time/residue: 0.5291
  time to fit residues: 64.9272
Evaluate side-chains
  114 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  598 MET
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  606 THR
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.145495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.115459 restraints weight = 8561.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.85
r_work: 0.3200 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7920  Z= 0.134
  Angle     :  0.499   5.999  10758  Z= 0.257
  Chirality :  0.039   0.142   1330
  Planarity :  0.004   0.043   1330
  Dihedral  :  3.821  16.679   1108
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  6.85 %
    Favored  : 91.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.26), residues: 1028
  helix:  1.66 (0.19), residues: 738
  sheet: -0.81 (0.60), residues: 41
  loop : -0.15 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 297 
 TYR   0.015   0.002   TYR A 155 
 PHE   0.013   0.001   PHE B 378 
 TRP   0.006   0.001   TRP A 478 
 HIS   0.002   0.000   HIS B 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 7920)
  covalent geometry    : angle       0.49876 /  0.26 (10758)
  hydrogen bonds       : bond        0.04097 /  2.79 (  569)
  hydrogen bonds       : angle       3.99415 /  3.02 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  482 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.4436 (pttt)
REVERT: A  617 LYS cc_start: 0.7423 (mtpt) cc_final: 0.6808 (mttt)
REVERT: A  620 GLU cc_start: 0.7862 (tt0) cc_final: 0.7380 (tp30)
REVERT: A  625 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7490 (mm-30)
REVERT: B  189 GLU cc_start: 0.8042 (pt0) cc_final: 0.7791 (pt0)
REVERT: B  215 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.7430 (mmt180)
REVERT: B  225 LYS cc_start: 0.7820 (mttt) cc_final: 0.7239 (mmtt)
REVERT: B  323 SER cc_start: 0.8649 (t) cc_final: 0.8399 (m)
REVERT: B  345 MET cc_start: 0.8262 (mtt) cc_final: 0.7932 (mtp)
REVERT: B  470 ASP cc_start: 0.8159 (t0) cc_final: 0.7915 (t0)
REVERT: B  518 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7090 (tm-30)
REVERT: B  546 MET cc_start: 0.7912 (ptt) cc_final: 0.7182 (mmm)
REVERT: B  579 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6329 (mp0)
REVERT: B  592 ARG cc_start: 0.7695 (mtt180) cc_final: 0.6736 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7430 (mttp) cc_final: 0.7151 (mttt)
REVERT: B  625 GLU cc_start: 0.7882 (tt0) cc_final: 0.7350 (mm-30)
REVERT: B  641 ASN cc_start: 0.7738 (m-40) cc_final: 0.7202 (p0)
  outliers start: 15
  outliers final: 6
  residues processed: 124
  average time/residue: 0.5040
  time to fit residues: 66.2378
Evaluate side-chains
  116 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 28 optimal weight:    0.2980
   chunk 4 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 91 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.146994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.117064 restraints weight = 8655.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.83
r_work: 0.3229 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7920  Z= 0.124
  Angle     :  0.481   5.770  10758  Z= 0.247
  Chirality :  0.038   0.140   1330
  Planarity :  0.004   0.043   1330
  Dihedral  :  3.728  16.897   1108
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  8.15 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.26), residues: 1028
  helix:  1.83 (0.19), residues: 740
  sheet: -0.47 (0.63), residues: 41
  loop : -0.00 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 652 
 TYR   0.014   0.001   TYR A 155 
 PHE   0.014   0.001   PHE B 378 
 TRP   0.005   0.000   TRP A 478 
 HIS   0.001   0.000   HIS A 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 ( 7920)
  covalent geometry    : angle       0.48107 /  0.25 (10758)
  hydrogen bonds       : bond        0.03830 /  2.59 (  569)
  hydrogen bonds       : angle       3.85469 /  2.92 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  385 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7704 (tp40)
REVERT: A  482 LYS cc_start: 0.6180 (OUTLIER) cc_final: 0.4467 (pttt)
REVERT: A  557 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8236 (mt-10)
REVERT: A  617 LYS cc_start: 0.7424 (mtpt) cc_final: 0.6874 (mttt)
REVERT: A  620 GLU cc_start: 0.7887 (tt0) cc_final: 0.7436 (tp30)
REVERT: A  625 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7472 (mm-30)
REVERT: B  189 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7733 (pt0)
REVERT: B  215 ARG cc_start: 0.7970 (mmt-90) cc_final: 0.7725 (mmt180)
REVERT: B  225 LYS cc_start: 0.7864 (mttt) cc_final: 0.7302 (mmtt)
REVERT: B  323 SER cc_start: 0.8674 (t) cc_final: 0.8404 (m)
REVERT: B  345 MET cc_start: 0.8214 (mtt) cc_final: 0.7847 (mtt)
REVERT: B  470 ASP cc_start: 0.8088 (t0) cc_final: 0.7839 (t0)
REVERT: B  518 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7021 (tm-30)
REVERT: B  546 MET cc_start: 0.7902 (ptt) cc_final: 0.7210 (mmm)
REVERT: B  579 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6369 (mp0)
REVERT: B  592 ARG cc_start: 0.7704 (mtt180) cc_final: 0.6794 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7448 (mttp) cc_final: 0.7076 (mttp)
REVERT: B  625 GLU cc_start: 0.7919 (tt0) cc_final: 0.7425 (mm-30)
REVERT: B  641 ASN cc_start: 0.7745 (m-40) cc_final: 0.7135 (p0)
  outliers start: 18
  outliers final: 7
  residues processed: 125
  average time/residue: 0.4700
  time to fit residues: 62.3193
Evaluate side-chains
  123 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  557 GLU
Chi-restraints excluded: chain A residue  598 MET
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 67 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0970
   chunk 56 optimal weight:    0.0980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.147945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.118114 restraints weight = 8618.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.84
r_work: 0.3241 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7920  Z= 0.112
  Angle     :  0.470   6.180  10758  Z= 0.240
  Chirality :  0.038   0.136   1330
  Planarity :  0.004   0.043   1330
  Dihedral  :  3.642  16.674   1108
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  :  8.50 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.27), residues: 1028
  helix:  2.01 (0.19), residues: 742
  sheet: -0.46 (0.61), residues: 41
  loop :  0.12 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 652 
 TYR   0.013   0.001   TYR A 155 
 PHE   0.013   0.001   PHE B 378 
 TRP   0.004   0.000   TRP A 478 
 HIS   0.001   0.000   HIS A 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 7920)
  covalent geometry    : angle       0.46972 /  0.24 (10758)
  hydrogen bonds       : bond        0.03612 /  2.45 (  569)
  hydrogen bonds       : angle       3.76659 /  2.87 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  385 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7698 (tp40)
REVERT: A  557 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8195 (mt-10)
REVERT: A  617 LYS cc_start: 0.7426 (mtpt) cc_final: 0.6869 (mttt)
REVERT: A  620 GLU cc_start: 0.7861 (tt0) cc_final: 0.7417 (tp30)
REVERT: A  625 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7439 (mm-30)
REVERT: B  215 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7728 (mmt180)
REVERT: B  225 LYS cc_start: 0.7834 (mttt) cc_final: 0.7280 (mmtt)
REVERT: B  323 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8397 (m)
REVERT: B  345 MET cc_start: 0.8168 (mtt) cc_final: 0.7789 (mtt)
REVERT: B  544 GLU cc_start: 0.7824 (pm20) cc_final: 0.7612 (pm20)
REVERT: B  546 MET cc_start: 0.7926 (ptt) cc_final: 0.7254 (mmm)
REVERT: B  579 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6336 (mp0)
REVERT: B  592 ARG cc_start: 0.7699 (mtt180) cc_final: 0.6791 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7429 (mttp) cc_final: 0.7049 (mttp)
REVERT: B  625 GLU cc_start: 0.7940 (tt0) cc_final: 0.7450 (mm-30)
REVERT: B  641 ASN cc_start: 0.7715 (m-40) cc_final: 0.7135 (p0)
  outliers start: 22
  outliers final: 8
  residues processed: 126
  average time/residue: 0.4734
  time to fit residues: 63.4078
Evaluate side-chains
  122 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  557 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 30 optimal weight:    0.2980
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.147039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.117135 restraints weight = 8604.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.83
r_work: 0.3241 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7920  Z= 0.127
  Angle     :  0.478   6.833  10758  Z= 0.245
  Chirality :  0.038   0.137   1330
  Planarity :  0.004   0.043   1330
  Dihedral  :  3.668  16.767   1108
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  9.45 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.26), residues: 1028
  helix:  2.01 (0.19), residues: 742
  sheet: -0.33 (0.64), residues: 43
  loop :  0.11 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 476 
 TYR   0.015   0.001   TYR A 155 
 PHE   0.015   0.001   PHE B 378 
 TRP   0.004   0.000   TRP A 478 
 HIS   0.001   0.000   HIS A 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 7920)
  covalent geometry    : angle       0.47829 /  0.24 (10758)
  hydrogen bonds       : bond        0.03747 /  2.53 (  569)
  hydrogen bonds       : angle       3.78557 /  2.88 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  385 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7716 (tp40)
REVERT: A  482 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.4617 (tttt)
REVERT: A  557 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8236 (mt-10)
REVERT: A  617 LYS cc_start: 0.7461 (mtpt) cc_final: 0.6896 (mttt)
REVERT: A  620 GLU cc_start: 0.7860 (tt0) cc_final: 0.7419 (tp30)
REVERT: A  625 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7449 (mm-30)
REVERT: B  215 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7756 (mmt180)
REVERT: B  225 LYS cc_start: 0.7856 (mttt) cc_final: 0.7305 (mmtt)
REVERT: B  323 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8398 (m)
REVERT: B  345 MET cc_start: 0.8204 (mtt) cc_final: 0.7853 (mtt)
REVERT: B  546 MET cc_start: 0.7930 (ptt) cc_final: 0.7269 (mmm)
REVERT: B  579 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6334 (mp0)
REVERT: B  592 ARG cc_start: 0.7730 (mtt180) cc_final: 0.6812 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7469 (mttp) cc_final: 0.7088 (mttp)
REVERT: B  625 GLU cc_start: 0.7973 (tt0) cc_final: 0.7495 (mm-30)
REVERT: B  641 ASN cc_start: 0.7694 (m-40) cc_final: 0.7051 (p0)
  outliers start: 19
  outliers final: 9
  residues processed: 125
  average time/residue: 0.5238
  time to fit residues: 69.4255
Evaluate side-chains
  124 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  557 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0570
   chunk 0 optimal weight:    6.9990
   chunk 74 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0470
   chunk 76 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0770
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.3954

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.148488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.118795 restraints weight = 8568.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.83
r_work: 0.3247 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7920  Z= 0.107
  Angle     :  0.460   7.392  10758  Z= 0.235
  Chirality :  0.038   0.132   1330
  Planarity :  0.004   0.043   1330
  Dihedral  :  3.567  16.303   1108
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  9.92 %
    Favored  : 88.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.27), residues: 1028
  helix:  2.17 (0.19), residues: 743
  sheet: -0.46 (0.63), residues: 44
  loop :  0.15 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 652 
 TYR   0.013   0.001   TYR A 155 
 PHE   0.013   0.001   PHE B 378 
 TRP   0.003   0.000   TRP A 478 
 HIS   0.001   0.000   HIS B 326 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 ( 7920)
  covalent geometry    : angle       0.45996 /  0.23 (10758)
  hydrogen bonds       : bond        0.03474 /  2.35 (  569)
  hydrogen bonds       : angle       3.70463 /  2.83 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  482 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.4621 (ttpt)
REVERT: A  557 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8184 (mt-10)
REVERT: A  617 LYS cc_start: 0.7427 (mtpt) cc_final: 0.6920 (mttt)
REVERT: A  620 GLU cc_start: 0.7859 (tt0) cc_final: 0.7395 (tp30)
REVERT: A  625 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7367 (tp30)
REVERT: B  215 ARG cc_start: 0.7959 (mmt-90) cc_final: 0.7701 (mmt180)
REVERT: B  225 LYS cc_start: 0.7844 (mttt) cc_final: 0.7302 (mmtt)
REVERT: B  323 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8389 (m)
REVERT: B  345 MET cc_start: 0.8150 (mtt) cc_final: 0.7800 (mtt)
REVERT: B  546 MET cc_start: 0.7921 (ptt) cc_final: 0.7254 (mmm)
REVERT: B  579 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6329 (mp0)
REVERT: B  592 ARG cc_start: 0.7724 (mtt180) cc_final: 0.6798 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7427 (mttp) cc_final: 0.7207 (mttt)
REVERT: B  625 GLU cc_start: 0.7953 (tt0) cc_final: 0.7480 (mm-30)
REVERT: B  641 ASN cc_start: 0.7671 (m-40) cc_final: 0.7075 (p0)
  outliers start: 16
  outliers final: 6
  residues processed: 121
  average time/residue: 0.4791
  time to fit residues: 61.5653
Evaluate side-chains
  120 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  557 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 100 optimal weight:    0.4980
   chunk 84 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 63 optimal weight:    0.7980
   chunk 94 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 195 GLN
B 358 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.147463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.117392 restraints weight = 8699.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.85
r_work: 0.3229 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7920  Z= 0.123
  Angle     :  0.478   9.096  10758  Z= 0.243
  Chirality :  0.038   0.136   1330
  Planarity :  0.004   0.043   1330
  Dihedral  :  3.613  16.652   1108
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.15 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.27), residues: 1028
  helix:  2.14 (0.19), residues: 741
  sheet: -0.40 (0.64), residues: 44
  loop :  0.17 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 652 
 TYR   0.014   0.001   TYR A 155 
 PHE   0.015   0.001   PHE B 378 
 TRP   0.004   0.000   TRP A 478 
 HIS   0.001   0.000   HIS A 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 ( 7920)
  covalent geometry    : angle       0.47814 /  0.24 (10758)
  hydrogen bonds       : bond        0.03635 /  2.46 (  569)
  hydrogen bonds       : angle       3.73801 /  2.85 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  385 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7687 (tp40)
REVERT: A  482 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.4638 (ttpt)
REVERT: A  557 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8237 (mt-10)
REVERT: A  617 LYS cc_start: 0.7434 (mtpt) cc_final: 0.6928 (mttt)
REVERT: A  620 GLU cc_start: 0.7863 (tt0) cc_final: 0.7422 (tp30)
REVERT: A  625 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7434 (tp30)
REVERT: B  215 ARG cc_start: 0.7988 (mmt-90) cc_final: 0.7718 (mmt180)
REVERT: B  225 LYS cc_start: 0.7839 (mttt) cc_final: 0.7288 (mmtt)
REVERT: B  323 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8388 (m)
REVERT: B  345 MET cc_start: 0.8169 (mtt) cc_final: 0.7822 (mtt)
REVERT: B  546 MET cc_start: 0.7917 (ptt) cc_final: 0.7251 (mmm)
REVERT: B  579 GLU cc_start: 0.6688 (mm-30) cc_final: 0.6360 (mp0)
REVERT: B  592 ARG cc_start: 0.7718 (mtt180) cc_final: 0.6784 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7447 (mttp) cc_final: 0.7228 (mttt)
REVERT: B  625 GLU cc_start: 0.7962 (tt0) cc_final: 0.7491 (mm-30)
REVERT: B  641 ASN cc_start: 0.7670 (m-40) cc_final: 0.7016 (p0)
  outliers start: 18
  outliers final: 8
  residues processed: 118
  average time/residue: 0.5770
  time to fit residues: 71.8840
Evaluate side-chains
  120 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  557 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 195 GLN
B 358 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.144382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.114102 restraints weight = 8585.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.88
r_work: 0.3193 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7920  Z= 0.156
  Angle     :  0.513   9.600  10758  Z= 0.262
  Chirality :  0.039   0.140   1330
  Planarity :  0.004   0.042   1330
  Dihedral  :  3.784  16.947   1108
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.39 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.26), residues: 1028
  helix:  1.98 (0.19), residues: 741
  sheet: -0.34 (0.64), residues: 43
  loop :  0.16 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 297 
 TYR   0.015   0.002   TYR A 155 
 PHE   0.018   0.001   PHE B 378 
 TRP   0.005   0.001   TRP A 478 
 HIS   0.002   0.001   HIS A 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 ( 7920)
  covalent geometry    : angle       0.51338 /  0.26 (10758)
  hydrogen bonds       : bond        0.04049 /  2.73 (  569)
  hydrogen bonds       : angle       3.86409 /  2.94 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  385 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7700 (tp40)
REVERT: A  482 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.4747 (ttpt)
REVERT: A  617 LYS cc_start: 0.7504 (mtpt) cc_final: 0.6874 (mttt)
REVERT: A  620 GLU cc_start: 0.7859 (tt0) cc_final: 0.7380 (tp30)
REVERT: A  625 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7357 (mm-30)
REVERT: B  215 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7670 (mmt180)
REVERT: B  225 LYS cc_start: 0.7795 (mttt) cc_final: 0.7215 (mmtt)
REVERT: B  323 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8406 (m)
REVERT: B  345 MET cc_start: 0.8236 (mtt) cc_final: 0.7923 (mtt)
REVERT: B  546 MET cc_start: 0.7909 (ptt) cc_final: 0.7210 (mmm)
REVERT: B  592 ARG cc_start: 0.7705 (mtt180) cc_final: 0.6789 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7443 (mttp) cc_final: 0.7063 (mttp)
REVERT: B  625 GLU cc_start: 0.8027 (tt0) cc_final: 0.7565 (mm-30)
REVERT: B  641 ASN cc_start: 0.7660 (m-40) cc_final: 0.6988 (p0)
  outliers start: 19
  outliers final: 7
  residues processed: 119
  average time/residue: 0.5457
  time to fit residues: 68.9005
Evaluate side-chains
  117 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 102 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 195 GLN
B 358 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.145540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.115475 restraints weight = 8527.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.85
r_work: 0.3213 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7920  Z= 0.129
  Angle     :  0.491   8.878  10758  Z= 0.250
  Chirality :  0.038   0.137   1330
  Planarity :  0.004   0.043   1330
  Dihedral  :  3.712  16.664   1108
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.57 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.27), residues: 1028
  helix:  2.08 (0.19), residues: 741
  sheet: -0.37 (0.63), residues: 43
  loop :  0.17 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 297 
 TYR   0.013   0.001   TYR A 155 
 PHE   0.014   0.001   PHE B 378 
 TRP   0.004   0.000   TRP A 478 
 HIS   0.001   0.000   HIS A 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 7920)
  covalent geometry    : angle       0.49053 /  0.25 (10758)
  hydrogen bonds       : bond        0.03778 /  2.55 (  569)
  hydrogen bonds       : angle       3.80496 /  2.90 ( 1653)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  385 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7699 (tp40)
REVERT: A  482 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.4758 (ttpt)
REVERT: A  617 LYS cc_start: 0.7442 (mtpt) cc_final: 0.6804 (mttt)
REVERT: A  620 GLU cc_start: 0.7846 (tt0) cc_final: 0.7369 (tp30)
REVERT: A  625 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7339 (mm-30)
REVERT: B  215 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.7679 (mmt180)
REVERT: B  225 LYS cc_start: 0.7823 (mttt) cc_final: 0.7241 (mmtt)
REVERT: B  323 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8400 (m)
REVERT: B  345 MET cc_start: 0.8187 (mtt) cc_final: 0.7871 (mtt)
REVERT: B  470 ASP cc_start: 0.7942 (t0) cc_final: 0.7715 (t0)
REVERT: B  546 MET cc_start: 0.7912 (ptt) cc_final: 0.7226 (mmm)
REVERT: B  592 ARG cc_start: 0.7705 (mtt180) cc_final: 0.6804 (mmp-170)
REVERT: B  617 LYS cc_start: 0.7433 (mttp) cc_final: 0.7055 (mttp)
REVERT: B  625 GLU cc_start: 0.8012 (tt0) cc_final: 0.7549 (mm-30)
REVERT: B  641 ASN cc_start: 0.7660 (m-40) cc_final: 0.6987 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 115
  average time/residue: 0.5684
  time to fit residues: 69.2355
Evaluate side-chains
  120 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  385 GLN
Chi-restraints excluded: chain A residue  446 MET
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  634 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 11 optimal weight:    0.1980
   chunk 44 optimal weight:    0.2980
   chunk 43 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.4780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.117692 restraints weight = 8571.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.84
r_work: 0.3247 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7920  Z= 0.115
  Angle     :  0.478   8.568  10758  Z= 0.243
  Chirality :  0.038   0.134   1330
  Planarity :  0.004   0.043   1330
  Dihedral  :  3.635  17.511   1108
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 11.81 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.27), residues: 1028
  helix:  2.16 (0.19), residues: 742
  sheet: -0.33 (0.63), residues: 43
  loop :  0.17 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 297 
 TYR   0.013   0.001   TYR A 155 
 PHE   0.013   0.001   PHE B 378 
 TRP   0.004   0.000   TRP A 478 
 HIS   0.001   0.000   HIS A 450 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.11 ( 7920)
  covalent geometry    : angle       0.47825 /  0.24 (10758)
  hydrogen bonds       : bond        0.03581 /  2.42 (  569)
  hydrogen bonds       : angle       3.73745 /  2.86 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2607.09 seconds
wall clock time: 45 minutes 5.16 seconds (2705.16 seconds total)