Starting phenix.real_space_refine
on Wed Jul  1 22:09:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u3h_41862/07_2026/8u3h_41862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u3h_41862/07_2026/8u3h_41862.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u3h_41862/07_2026/8u3h_41862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u3h_41862/07_2026/8u3h_41862.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u3h_41862/07_2026/8u3h_41862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u3h_41862/07_2026/8u3h_41862.map"
  }
  resolution = 3.67
  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=   0.003 sd=   0.061
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      13      5.16       5
     C    2241      2.51       5
     N     521      2.21       5
     O     572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  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: 3347
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3321
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 406}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 26
          Unusual residues: {'VP1': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'VP1:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 0.73, per 1000 atoms: 0.22
  Number of scatterers: 3347
  At special positions: 0
  Unit cell: (54.78, 77.19, 81.34, 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      13     16.00
     O     572      8.00
     N     521      7.00
     C    2241      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 72.8 milliseconds
  

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  776

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      87.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 68
      removed outlier: 4.967A  pdb=" N   LEU A  60 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   SER A  61 " --> pdb=" O   ARG A  57 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   VAL A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   VAL A  65 " --> pdb=" O   SER A  61 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASP A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 122
      removed outlier: 4.835A  pdb=" N   PHE A 115 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   PHE A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   TYR A 117 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLY A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
    Processing helix  chain 'A' and resid 135 through 160
      removed outlier: 3.856A  pdb=" N   LEU A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
      Proline residue:  A 154  - end of helix
      removed outlier: 3.650A  pdb=" N   ASP A 158 " --> pdb=" O   PRO A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 176
    Processing helix  chain 'A' and resid 177 through 190
      removed outlier: 4.242A  pdb=" N   SER A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 224
      removed outlier: 4.187A  pdb=" N   GLY A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   ALA A 206 " --> pdb=" O   SER A 202 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   GLN A 207 " --> pdb=" O   TYR A 203 " (cutoff:3.500A)
      Proline residue:  A 215  - end of helix
    Processing helix  chain 'A' and resid 226 through 248
      removed outlier: 3.852A  pdb=" N   PHE A 230 " --> pdb=" O   TRP A 226 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   TRP A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL A 248 " --> pdb=" O   TRP A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 255
    Processing helix  chain 'A' and resid 259 through 275
      removed outlier: 4.357A  pdb=" N   ASN A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   GLN A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 310
      removed outlier: 3.724A  pdb=" N   TRP A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ILE A 294 " --> pdb=" O   PRO A 290 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 319
    Processing helix  chain 'A' and resid 323 through 332
      removed outlier: 3.715A  pdb=" N   SER A 332 " --> pdb=" O   GLY A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 356
      removed outlier: 3.783A  pdb=" N   LEU A 344 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY A 346 " --> pdb=" O   MET A 342 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLN A 347 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LYS A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 385
      removed outlier: 3.762A  pdb=" N   VAL A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG A 364 " --> pdb=" O   THR A 360 " (cutoff:3.500A)
      Proline residue:  A 375  - end of helix
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.574A  pdb=" N   ALA A 394 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
    Processing helix  chain 'A' and resid 412 through 417
    Processing helix  chain 'A' and resid 421 through 433
      removed outlier: 3.842A  pdb=" N   GLY A 427 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 448
      removed outlier: 3.544A  pdb=" N   MET A 438 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
      Proline residue:  A 441  - end of helix
    Processing helix  chain 'A' and resid 452 through 478

    244 hydrogen bonds defined for protein.
    726 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: 0.57

  Time building geometry restraints manager: 0.25 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: 492
        1.29 -     1.42: 1011
        1.42 -     1.55: 1926
        1.55 -     1.68: 1
        1.68 -     1.81: 20
  Bond restraints: 3450
  Sorted by residual:
  bond pdb=" C01 VP1 A 501 "
       pdb=" O03 VP1 A 501 "
    ideal  model  delta    sigma   weight residual
    1.304  1.437 -0.133 2.00e-02 2.50e+03 4.40e+01
  bond pdb=" C05 VP1 A 501 "
       pdb=" C12 VP1 A 501 "
    ideal  model  delta    sigma   weight residual
    1.510  1.445  0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" N   VAL A  53 "
       pdb=" CA  VAL A  53 "
    ideal  model  delta    sigma   weight residual
    1.462  1.499 -0.037 1.18e-02 7.18e+03 9.79e+00
  bond pdb=" C05 VP1 A 501 "
       pdb=" C06 VP1 A 501 "
    ideal  model  delta    sigma   weight residual
    1.511  1.456  0.055 2.00e-02 2.50e+03 7.68e+00
  bond pdb=" N   TYR A  54 "
       pdb=" CA  TYR A  54 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.030 1.28e-02 6.10e+03 5.38e+00
  ... (remaining 3445 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 4591
        2.06 -     4.12: 89
        4.12 -     6.18: 24
        6.18 -     8.24: 2
        8.24 -    10.30: 3
  Bond angle restraints: 4709
  Sorted by residual:
  angle pdb=" C   THR A 434 "
        pdb=" N   ILE A 435 "
        pdb=" CA  ILE A 435 "
      ideal   model   delta    sigma   weight residual
     120.24  123.23   -2.99 6.30e-01 2.52e+00 2.25e+01
  angle pdb=" CA  VAL A  53 "
        pdb=" C   VAL A  53 "
        pdb=" O   VAL A  53 "
      ideal   model   delta    sigma   weight residual
     121.29  117.59    3.70 1.07e+00 8.73e-01 1.20e+01
  angle pdb=" O02 VP1 A 501 "
        pdb=" C01 VP1 A 501 "
        pdb=" O03 VP1 A 501 "
      ideal   model   delta    sigma   weight residual
     128.83  118.53   10.30 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" C   PRO A 449 "
        pdb=" N   ASP A 450 "
        pdb=" CA  ASP A 450 "
      ideal   model   delta    sigma   weight residual
     122.17  117.50    4.67 1.54e+00 4.22e-01 9.19e+00
  angle pdb=" C05 VP1 A 501 "
        pdb=" C04 VP1 A 501 "
        pdb=" O03 VP1 A 501 "
      ideal   model   delta    sigma   weight residual
     107.36  116.35   -8.99 3.00e+00 1.11e-01 8.98e+00
  ... (remaining 4704 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.02: 1848
       27.02 -    54.05: 78
       54.05 -    81.07: 9
       81.07 -   108.10: 0
      108.10 -   135.12: 4
  Dihedral angle restraints: 1939
    sinusoidal: 720
      harmonic: 1219
  Sorted by residual:
  dihedral pdb=" C04 VP1 A 501 "
           pdb=" C05 VP1 A 501 "
           pdb=" C06 VP1 A 501 "
           pdb=" C11 VP1 A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     116.25 -108.63 -135.12     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" C04 VP1 A 501 "
           pdb=" C05 VP1 A 501 "
           pdb=" C06 VP1 A 501 "
           pdb=" C07 VP1 A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.13   67.95 -132.08     1      3.00e+01 1.11e-03 1.78e+01
  dihedral pdb=" C04 VP1 A 501 "
           pdb=" C05 VP1 A 501 "
           pdb=" C12 VP1 A 501 "
           pdb=" C17 VP1 A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     240.80  110.09  130.71     1      3.00e+01 1.11e-03 1.76e+01
  ... (remaining 1936 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.095: 533
       1.095 -    2.189: 0
       2.189 -    3.284: 0
       3.284 -    4.378: 0
       4.378 -    5.473: 1
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" C05 VP1 A 501 "
            pdb=" C04 VP1 A 501 "
            pdb=" C06 VP1 A 501 "
            pdb=" C12 VP1 A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74    2.73   -5.47 2.00e-01 2.50e+01 7.49e+02
  chirality pdb=" CA  VAL A 482 "
            pdb=" N   VAL A 482 "
            pdb=" C   VAL A 482 "
            pdb=" CB  VAL A 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.93e-01
  chirality pdb=" CA  VAL A  53 "
            pdb=" N   VAL A  53 "
            pdb=" C   VAL A  53 "
            pdb=" CB  VAL A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.16 2.00e-01 2.50e+01 6.74e-01
  ... (remaining 531 not shown)

  Planarity restraints: 569
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C05 VP1 A 501 "   -0.042 2.00e-02 2.50e+03   1.51e-02 7.39e+00
        pdb=" C06 VP1 A 501 "    0.013 2.00e-02 2.50e+03
        pdb=" C07 VP1 A 501 "    0.001 2.00e-02 2.50e+03
        pdb=" C08 VP1 A 501 "    0.006 2.00e-02 2.50e+03
        pdb=" C09 VP1 A 501 "   -0.004 2.00e-02 2.50e+03
        pdb=" C10 VP1 A 501 "   -0.002 2.00e-02 2.50e+03
        pdb=" C11 VP1 A 501 "    0.011 2.00e-02 2.50e+03
        pdb=" C12 VP1 A 501 "    0.017 2.00e-02 2.50e+03
        pdb=" C13 VP1 A 501 "    0.010 2.00e-02 2.50e+03
        pdb=" C14 VP1 A 501 "    0.010 2.00e-02 2.50e+03
        pdb=" C15 VP1 A 501 "   -0.004 2.00e-02 2.50e+03
        pdb=" C16 VP1 A 501 "   -0.018 2.00e-02 2.50e+03
        pdb=" C17 VP1 A 501 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 103 "    0.013 2.00e-02 2.50e+03   1.27e-02 4.01e+00
        pdb=" CG  TRP A 103 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 103 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 103 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 103 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 103 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 103 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 103 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 103 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 103 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 162 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.17e+00
        pdb=" N   PRO A 163 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 163 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 163 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 566 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 848
        2.79 -     3.32: 3422
        3.32 -     3.85: 5680
        3.85 -     4.37: 6380
        4.37 -     4.90: 11005
  Nonbonded interactions: 27335
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  40 "
            pdb=" OE2 GLU A 194 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OG1 THR A 304 "
            pdb=" OD1 ASN A 467 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   PRO A 419 "
            pdb=" OG  SER A 420 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" OG1 THR A 150 "
            pdb=" OE2 GLU A 171 "
     model   vdw
     2.465 3.040
  nonbonded pdb=" O   GLY A 209 "
            pdb=" OG  SER A 213 "
     model   vdw
     2.476 3.040
  ... (remaining 27330 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.090
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
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   0.133   3451  Z= 0.248
  Angle     :  0.766  10.302   4709  Z= 0.405
  Chirality :  0.241   5.473    534
  Planarity :  0.005   0.045    569
  Dihedral  : 15.851 135.119   1163
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.43 %
    Favored  : 86.57 %
  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:  0.06 (0.40), residues: 421
  helix:  0.50 (0.29), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.47 (0.57), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  57 
 TYR   0.010   0.001   TYR A 261 
 PHE   0.014   0.001   PHE A 410 
 TRP   0.032   0.002   TRP A 103 
 HIS   0.004   0.002   HIS A 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.23 ( 3450)
  covalent geometry    : angle       0.76635 /  0.40 ( 4709)
  hydrogen bonds       : bond        0.12582 /  8.00 (  244)
  hydrogen bonds       : angle       5.76166 /  4.10 (  726)
  Misc. bond           : bond        0.05438 /  2.86 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8229 (t0) cc_final: 0.8018 (t0)
REVERT: A  461 TYR cc_start: 0.8348 (m-80) cc_final: 0.8124 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0396
  time to fit residues: 2.1689
Evaluate side-chains
  38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0970
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0770
   chunk 37 optimal weight:    6.9990
   overall best weight:    0.4536

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.186809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.140808 restraints weight = 3802.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.140981 restraints weight = 3358.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.141796 restraints weight = 3006.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142171 restraints weight = 2756.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.142370 restraints weight = 2265.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3451  Z= 0.131
  Angle     :  0.610   5.626   4709  Z= 0.313
  Chirality :  0.043   0.156    534
  Planarity :  0.005   0.049    569
  Dihedral  :  6.076  63.550    462
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 14.29 %
    Favored  : 85.43 %
  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:  0.26 (0.40), residues: 421
  helix:  0.69 (0.28), residues: 343
  sheet:  None (None), residues: 0
  loop : -1.88 (0.56), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  57 
 TYR   0.011   0.001   TYR A 222 
 PHE   0.013   0.001   PHE A 116 
 TRP   0.016   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 3450)
  covalent geometry    : angle       0.60954 /  0.31 ( 4709)
  hydrogen bonds       : bond        0.04218 /  2.73 (  244)
  hydrogen bonds       : angle       4.57017 /  3.31 (  726)
  Misc. bond           : bond        0.00176 /  0.09 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  461 TYR cc_start: 0.8247 (m-80) cc_final: 0.7928 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 42
  average time/residue: 0.0453
  time to fit residues: 2.3874
Evaluate side-chains
  41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0970
   chunk 21 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.6378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.183739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.137457 restraints weight = 3765.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.137804 restraints weight = 3426.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.138410 restraints weight = 2781.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.138969 restraints weight = 2320.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.139510 restraints weight = 2041.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3451  Z= 0.131
  Angle     :  0.567   5.634   4709  Z= 0.294
  Chirality :  0.043   0.131    534
  Planarity :  0.005   0.049    569
  Dihedral  :  5.623  61.260    462
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.29 %
    Favored  : 84.57 %
  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:  0.50 (0.41), residues: 421
  helix:  0.84 (0.29), residues: 344
  sheet:  None (None), residues: 0
  loop : -1.74 (0.63), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.009   0.001   TYR A  54 
 PHE   0.012   0.001   PHE A 116 
 TRP   0.018   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 3450)
  covalent geometry    : angle       0.56734 /  0.29 ( 4709)
  hydrogen bonds       : bond        0.03905 /  2.52 (  244)
  hydrogen bonds       : angle       4.38343 /  3.14 (  726)
  Misc. bond           : bond        0.00077 /  0.04 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.066 
Fit side-chains
REVERT: A  461 TYR cc_start: 0.8207 (m-80) cc_final: 0.7850 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0399
  time to fit residues: 2.0943
Evaluate side-chains
  38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 ASN
A 483 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.182088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.135602 restraints weight = 3805.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.134897 restraints weight = 3927.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.136305 restraints weight = 3551.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.136800 restraints weight = 2685.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137415 restraints weight = 2320.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3451  Z= 0.144
  Angle     :  0.573   5.976   4709  Z= 0.297
  Chirality :  0.043   0.138    534
  Planarity :  0.005   0.050    569
  Dihedral  :  5.493  59.078    462
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 17.14 %
    Favored  : 81.71 %
  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:  0.39 (0.41), residues: 421
  helix:  0.77 (0.28), residues: 344
  sheet:  None (None), residues: 0
  loop : -1.78 (0.63), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.009   0.001   TYR A 335 
 PHE   0.013   0.001   PHE A 116 
 TRP   0.022   0.002   TRP A 103 
 HIS   0.003   0.001   HIS A 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.14 ( 3450)
  covalent geometry    : angle       0.57277 /  0.30 ( 4709)
  hydrogen bonds       : bond        0.03917 /  2.53 (  244)
  hydrogen bonds       : angle       4.37825 /  3.13 (  726)
  Misc. bond           : bond        0.00041 /  0.02 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  461 TYR cc_start: 0.8141 (m-80) cc_final: 0.7817 (m-80)
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.0579
  time to fit residues: 3.0577
Evaluate side-chains
  43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.181159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.136242 restraints weight = 3835.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.133213 restraints weight = 2828.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.133378 restraints weight = 2577.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.133750 restraints weight = 2415.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.133959 restraints weight = 2221.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3451  Z= 0.149
  Angle     :  0.573   6.042   4709  Z= 0.295
  Chirality :  0.043   0.132    534
  Planarity :  0.005   0.050    569
  Dihedral  :  5.443  58.764    462
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.86 %
    Favored  : 81.43 %
  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:  0.42 (0.41), residues: 421
  helix:  0.84 (0.28), residues: 342
  sheet:  None (None), residues: 0
  loop : -1.97 (0.62), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.010   0.001   TYR A 335 
 PHE   0.014   0.001   PHE A 116 
 TRP   0.022   0.002   TRP A 103 
 HIS   0.004   0.001   HIS A 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 3450)
  covalent geometry    : angle       0.57268 /  0.29 ( 4709)
  hydrogen bonds       : bond        0.03910 /  2.53 (  244)
  hydrogen bonds       : angle       4.41114 /  3.15 (  726)
  Misc. bond           : bond        0.00055 /  0.03 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.118 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 45
  average time/residue: 0.0555
  time to fit residues: 3.1925
Evaluate side-chains
  43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 23 optimal weight:    0.5980
   chunk 28 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.180028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.134128 restraints weight = 3833.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.132558 restraints weight = 3384.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.133436 restraints weight = 4019.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.134367 restraints weight = 2975.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.134622 restraints weight = 2511.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3451  Z= 0.157
  Angle     :  0.583   5.879   4709  Z= 0.302
  Chirality :  0.043   0.131    534
  Planarity :  0.005   0.051    569
  Dihedral  :  5.454  59.028    462
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.71 %
    Favored  : 80.86 %
  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:  0.38 (0.41), residues: 421
  helix:  0.84 (0.29), residues: 337
  sheet:  None (None), residues: 0
  loop : -1.97 (0.60), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.010   0.001   TYR A 335 
 PHE   0.014   0.001   PHE A 116 
 TRP   0.023   0.002   TRP A 103 
 HIS   0.004   0.001   HIS A 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 3450)
  covalent geometry    : angle       0.58323 /  0.30 ( 4709)
  hydrogen bonds       : bond        0.04021 /  2.60 (  244)
  hydrogen bonds       : angle       4.46143 /  3.19 (  726)
  Misc. bond           : bond        0.00056 /  0.03 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  175 GLU cc_start: 0.7924 (tp30) cc_final: 0.7490 (tp30)
REVERT: A  461 TYR cc_start: 0.8282 (m-80) cc_final: 0.8004 (m-80)
  outliers start: 5
  outliers final: 3
  residues processed: 42
  average time/residue: 0.0677
  time to fit residues: 3.5949
Evaluate side-chains
  41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  295 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.180739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.135042 restraints weight = 3887.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.134625 restraints weight = 3302.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.135595 restraints weight = 3548.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.136089 restraints weight = 2640.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.136386 restraints weight = 2323.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3451  Z= 0.143
  Angle     :  0.570   6.483   4709  Z= 0.295
  Chirality :  0.042   0.132    534
  Planarity :  0.005   0.051    569
  Dihedral  :  5.393  59.264    462
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.00 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.41), residues: 421
  helix:  0.92 (0.29), residues: 337
  sheet:  None (None), residues: 0
  loop : -1.95 (0.60), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.012   0.001   TYR A 222 
 PHE   0.013   0.001   PHE A 116 
 TRP   0.020   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 3450)
  covalent geometry    : angle       0.57022 /  0.30 ( 4709)
  hydrogen bonds       : bond        0.03914 /  2.53 (  244)
  hydrogen bonds       : angle       4.44607 /  3.17 (  726)
  Misc. bond           : bond        0.00048 /  0.03 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  175 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7583 (tp30)
REVERT: A  461 TYR cc_start: 0.8194 (m-80) cc_final: 0.7895 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 39
  average time/residue: 0.0694
  time to fit residues: 3.4092
Evaluate side-chains
  39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  175 GLU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 31 optimal weight:    0.3980
   chunk 29 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.182477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.136889 restraints weight = 3886.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.135962 restraints weight = 3379.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.136792 restraints weight = 3918.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.137570 restraints weight = 2820.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.138089 restraints weight = 2427.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3451  Z= 0.126
  Angle     :  0.551   6.478   4709  Z= 0.284
  Chirality :  0.041   0.132    534
  Planarity :  0.005   0.051    569
  Dihedral  :  5.482  67.198    462
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.14 %
    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 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:  0.62 (0.41), residues: 421
  helix:  1.01 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.95 (0.60), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.013   0.001   TYR A 222 
 PHE   0.013   0.001   PHE A 116 
 TRP   0.015   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 3450)
  covalent geometry    : angle       0.55076 /  0.28 ( 4709)
  hydrogen bonds       : bond        0.03740 /  2.40 (  244)
  hydrogen bonds       : angle       4.37183 /  3.12 (  726)
  Misc. bond           : bond        0.00041 /  0.02 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A  461 TYR cc_start: 0.8151 (m-80) cc_final: 0.7864 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0669
  time to fit residues: 3.4887
Evaluate side-chains
  37 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 ASN
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.180917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.135389 restraints weight = 3878.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.134914 restraints weight = 3348.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.135756 restraints weight = 3553.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.136415 restraints weight = 2687.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.136688 restraints weight = 2353.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3451  Z= 0.148
  Angle     :  0.588   8.483   4709  Z= 0.301
  Chirality :  0.042   0.132    534
  Planarity :  0.005   0.051    569
  Dihedral  :  5.409  63.678    462
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.29 %
    Favored  : 79.71 %
  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:  0.57 (0.41), residues: 421
  helix:  0.97 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.93 (0.60), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.011   0.001   TYR A 222 
 PHE   0.013   0.001   PHE A 116 
 TRP   0.015   0.001   TRP A 103 
 HIS   0.005   0.002   HIS A 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 ( 3450)
  covalent geometry    : angle       0.58823 /  0.30 ( 4709)
  hydrogen bonds       : bond        0.03917 /  2.53 (  244)
  hydrogen bonds       : angle       4.45106 /  3.18 (  726)
  Misc. bond           : bond        0.00062 /  0.03 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  461 TYR cc_start: 0.8136 (m-80) cc_final: 0.7851 (m-80)
  outliers start: 7
  outliers final: 6
  residues processed: 38
  average time/residue: 0.0746
  time to fit residues: 3.5392
Evaluate side-chains
  38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 PHE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 19 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.182526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.137068 restraints weight = 3826.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.135918 restraints weight = 3370.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.136712 restraints weight = 3901.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.137251 restraints weight = 2852.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.138061 restraints weight = 2499.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3451  Z= 0.132
  Angle     :  0.577   9.755   4709  Z= 0.295
  Chirality :  0.042   0.130    534
  Planarity :  0.005   0.052    569
  Dihedral  :  5.416  65.257    462
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.57 %
    Favored  : 79.43 %
  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:  0.62 (0.41), residues: 421
  helix:  1.01 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.97 (0.59), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.011   0.001   TYR A 222 
 PHE   0.013   0.001   PHE A 116 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 ( 3450)
  covalent geometry    : angle       0.57728 /  0.29 ( 4709)
  hydrogen bonds       : bond        0.03819 /  2.46 (  244)
  hydrogen bonds       : angle       4.41340 /  3.15 (  726)
  Misc. bond           : bond        0.00045 /  0.02 (    1)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  461 TYR cc_start: 0.8132 (m-80) cc_final: 0.7854 (m-80)
  outliers start: 7
  outliers final: 7
  residues processed: 38
  average time/residue: 0.0573
  time to fit residues: 2.7470
Evaluate side-chains
  39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 PHE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  342 MET
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    0.0870
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.183333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138424 restraints weight = 3927.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.138346 restraints weight = 3611.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.139096 restraints weight = 3528.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.139572 restraints weight = 2775.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.139989 restraints weight = 2378.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3451  Z= 0.127
  Angle     :  0.576  10.640   4709  Z= 0.294
  Chirality :  0.041   0.131    534
  Planarity :  0.005   0.051    569
  Dihedral  :  5.325  65.283    462
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 19.43 %
    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 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:  0.69 (0.41), residues: 421
  helix:  1.07 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.96 (0.58), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 168 
 TYR   0.010   0.001   TYR A 335 
 PHE   0.012   0.001   PHE A 116 
 TRP   0.013   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 3450)
  covalent geometry    : angle       0.57607 /  0.29 ( 4709)
  hydrogen bonds       : bond        0.03750 /  2.40 (  244)
  hydrogen bonds       : angle       4.39033 /  3.13 (  726)
  Misc. bond           : bond        0.00042 /  0.02 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 647.05 seconds
wall clock time: 11 minutes 50.06 seconds (710.06 seconds total)