Starting phenix.real_space_refine
on Tue Mar  3 12:55:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vu5_21387/03_2026/6vu5_21387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vu5_21387/03_2026/6vu5_21387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vu5_21387/03_2026/6vu5_21387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vu5_21387/03_2026/6vu5_21387.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vu5_21387/03_2026/6vu5_21387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vu5_21387/03_2026/6vu5_21387.map"
  }
  resolution = 3.5
  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=   0.006
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      25      5.16       5
     C    2961      2.51       5
     N     815      2.21       5
     O     854      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4657
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3454
          Classifications: {'peptide': 441}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 14, 'TRANS': 426}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 43
          Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 1, 'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "A"
      Number of atoms: 135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 135
          Classifications: {'peptide': 27}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'TRANS': 26}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'UNK:plan-1': 27}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 1068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1068
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 130}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 42
  Time building chain proxies: 1.18, per 1000 atoms: 0.25
  Number of scatterers: 4657
  At special positions: 0
  Unit cell: (109.06, 58.22, 83.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     P       2     15.00
     O     854      8.00
     N     815      7.00
     C    2961      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: 0.43
  Conformation dependent library (CDL) restraints added in 336.2 milliseconds
  

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1168

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 2 sheets defined
      58.3% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 12
      removed outlier: 3.771A  pdb=" N   ASP A   8 " --> pdb=" O   ARG A   4 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   THR A  12 " --> pdb=" O   ASP A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 29
      removed outlier: 4.285A  pdb=" N   ARG A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLU A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 38
      No H-bonds generated for 'chain 'A' and resid 36 through 38'
    Processing helix  chain 'A' and resid 39 through 57
      removed outlier: 3.740A  pdb=" N   GLN A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 74
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 6.287A  pdb=" N   SER A  78 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A  80 " --> pdb=" O   ARG A  77 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 75 through 80'
    Processing helix  chain 'A' and resid 85 through 96
      removed outlier: 3.759A  pdb=" N   LEU A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 127
    Processing helix  chain 'A' and resid 128 through 138
      removed outlier: 3.727A  pdb=" N   MET A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LEU A 134 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 150
      removed outlier: 4.474A  pdb=" N   GLU A 146 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 174
      removed outlier: 3.643A  pdb=" N   GLN A 161 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
      removed outlier: 3.592A  pdb=" N   LEU A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A 198 " --> pdb=" O   ASP A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 232
    Processing helix  chain 'A' and resid 242 through 260
      removed outlier: 4.121A  pdb=" N   MET A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 280
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.676A  pdb=" N   LEU A 286 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 320
    Processing helix  chain 'A' and resid 332 through 341
      removed outlier: 4.586A  pdb=" N   THR A 338 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 356
    Processing helix  chain 'A' and resid 371 through 380
    Processing helix  chain 'A' and resid 384 through 389
    Processing helix  chain 'A' and resid 389 through 398
      removed outlier: 4.516A  pdb=" N   LEU A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 411
    Processing helix  chain 'A' and resid 413 through 417
      removed outlier: 3.672A  pdb=" N   ALA A 416 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY A 417 " --> pdb=" O   ASN A 414 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 413 through 417'
    Processing helix  chain 'A' and resid 474 through 483
    Processing helix  chain 'B' and resid 246 through 255
    Processing helix  chain 'B' and resid 255 through 260
      removed outlier: 3.817A  pdb=" N   ILE B 259 " --> pdb=" O   PHE B 255 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   THR B 260 " --> pdb=" O   ARG B 256 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 255 through 260'
    Processing helix  chain 'B' and resid 275 through 279
    Processing helix  chain 'B' and resid 287 through 291
      removed outlier: 4.149A  pdb=" N   TYR B 291 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 315
    Processing helix  chain 'B' and resid 338 through 354
    Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 212
    Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 272
      removed outlier: 6.660A  pdb=" N   VAL B 269 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   HIS B 327 " --> pdb=" O   VAL B 269 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 271 " --> pdb=" O   HIS B 327 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    193 hydrogen bonds defined for protein.
    567 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: 0.50

  Time building geometry restraints manager: 0.53 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: 1329
        1.33 -     1.45: 735
        1.45 -     1.57: 2621
        1.57 -     1.69: 7
        1.69 -     1.81: 39
  Bond restraints: 4731
  Sorted by residual:
  bond pdb=" OG1 TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" O3P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.528  1.608 -0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" O2P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.528  1.608 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" O1P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.525  1.476  0.049 2.00e-02 2.50e+03 6.08e+00
  bond pdb=" CB  VAL A 275 "
       pdb=" CG1 VAL A 275 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.41e+00
  ... (remaining 4726 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 6213
        2.50 -     4.99: 166
        4.99 -     7.49: 21
        7.49 -     9.99: 9
        9.99 -    12.49: 1
  Bond angle restraints: 6410
  Sorted by residual:
  angle pdb=" CB  TPO A 440 "
        pdb=" OG1 TPO A 440 "
        pdb=" P   TPO A 440 "
      ideal   model   delta    sigma   weight residual
     119.31  106.82   12.49 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" C   VAL B 223 "
        pdb=" N   THR B 224 "
        pdb=" CA  THR B 224 "
      ideal   model   delta    sigma   weight residual
     121.54  128.71   -7.17 1.91e+00 2.74e-01 1.41e+01
  angle pdb=" OG1 TPO A 440 "
        pdb=" P   TPO A 440 "
        pdb=" O1P TPO A 440 "
      ideal   model   delta    sigma   weight residual
     100.43  109.19   -8.76 3.00e+00 1.11e-01 8.52e+00
  angle pdb=" CA  LEU A 278 "
        pdb=" CB  LEU A 278 "
        pdb=" CG  LEU A 278 "
      ideal   model   delta    sigma   weight residual
     116.30  126.28   -9.98 3.50e+00 8.16e-02 8.14e+00
  angle pdb=" C   ILE B 337 "
        pdb=" N   ARG B 338 "
        pdb=" CA  ARG B 338 "
      ideal   model   delta    sigma   weight residual
     122.61  126.88   -4.27 1.56e+00 4.11e-01 7.51e+00
  ... (remaining 6405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 2527
       17.08 -    34.16: 277
       34.16 -    51.24: 61
       51.24 -    68.32: 10
       68.32 -    85.40: 3
  Dihedral angle restraints: 2878
    sinusoidal: 1100
      harmonic: 1778
  Sorted by residual:
  dihedral pdb=" CA  PRO A 358 "
           pdb=" C   PRO A 358 "
           pdb=" N   LEU A 359 "
           pdb=" CA  LEU A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.71  -29.29     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  LEU A 395 "
           pdb=" C   LEU A 395 "
           pdb=" N   PHE A 396 "
           pdb=" CA  PHE A 396 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.40   25.60     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  LEU A 334 "
           pdb=" C   LEU A 334 "
           pdb=" N   SER A 335 "
           pdb=" CA  SER A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.04   24.96     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 2875 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 712
       0.100 -    0.199: 47
       0.199 -    0.299: 2
       0.299 -    0.399: 0
       0.399 -    0.499: 1
  Chirality restraints: 762
  Sorted by residual:
  chirality pdb=" CB  ILE B 337 "
            pdb=" CA  ILE B 337 "
            pdb=" CG1 ILE B 337 "
            pdb=" CG2 ILE B 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.15    0.50 2.00e-01 2.50e+01 6.22e+00
  chirality pdb=" CB  VAL A 288 "
            pdb=" CA  VAL A 288 "
            pdb=" CG1 VAL A 288 "
            pdb=" CG2 VAL A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  VAL A 355 "
            pdb=" CA  VAL A 355 "
            pdb=" CG1 VAL A 355 "
            pdb=" CG2 VAL A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 759 not shown)

  Planarity restraints: 818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 261 "    0.048 5.00e-02 4.00e+02   7.33e-02 8.59e+00
        pdb=" N   PRO B 262 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 262 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 262 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 156 "    0.038 5.00e-02 4.00e+02   5.78e-02 5.34e+00
        pdb=" N   PRO A 157 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 157 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 157 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 331 "   -0.037 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO A 332 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 815 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 839
        2.76 -     3.30: 4361
        3.30 -     3.83: 7693
        3.83 -     4.37: 8746
        4.37 -     4.90: 14932
  Nonbonded interactions: 36571
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 168 "
            pdb=" OG1 THR A 172 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   LEU A 227 "
            pdb=" OG1 THR A 231 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   PRO A 213 "
            pdb=" OG1 THR A 217 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   LEU A 281 "
            pdb=" NH2 ARG B 338 "
     model   vdw
     2.363 3.120
  nonbonded pdb=" ND2 ASN B 266 "
            pdb=" O   SER B 268 "
     model   vdw
     2.372 3.120
  ... (remaining 36566 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.380
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.240
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
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      :  0.007   0.109   4731  Z= 0.285
  Angle     :  0.990  12.485   6410  Z= 0.505
  Chirality :  0.056   0.499    762
  Planarity :  0.007   0.073    818
  Dihedral  : 15.263  85.402   1710
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  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: -4.94 (0.26), residues: 556
  helix: -3.14 (0.20), residues: 331
  sheet: -1.07 (1.45), residues: 12
  loop : -3.43 (0.34), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  43 
 TYR   0.013   0.002   TYR B 235 
 PHE   0.029   0.002   PHE A 270 
 TRP   0.008   0.002   TRP B 263 
 HIS   0.008   0.002   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00666 ( 4731)
  covalent geometry    : angle       0.98950 ( 6410)
  hydrogen bonds       : bond        0.13817 (  193)
  hydrogen bonds       : angle       6.59944 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7825 (mt) cc_final: 0.7516 (mt)
REVERT: A  150 LEU cc_start: 0.8718 (tp) cc_final: 0.8432 (tt)
REVERT: A  180 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6799 (mm110)
REVERT: A  257 CYS cc_start: 0.7732 (t) cc_final: 0.7320 (t)
REVERT: A  306 MET cc_start: 0.8405 (mmt) cc_final: 0.7748 (mmt)
REVERT: B  249 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6754 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0655
  time to fit residues: 10.3991
Evaluate side-chains
  79 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
A 180 GLN
A 184 GLN
A 414 ASN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.171707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.139762 restraints weight = 6835.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.144044 restraints weight = 4118.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.146918 restraints weight = 2959.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.148777 restraints weight = 2376.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.149815 restraints weight = 2052.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4731  Z= 0.141
  Angle     :  0.651   9.106   6410  Z= 0.326
  Chirality :  0.041   0.158    762
  Planarity :  0.005   0.045    818
  Dihedral  :  5.947  28.141    655
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 15.76 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.55 (0.31), residues: 556
  helix: -1.96 (0.25), residues: 331
  sheet:  None (None), residues: 0
  loop : -2.85 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 338 
 TYR   0.009   0.001   TYR B 261 
 PHE   0.020   0.002   PHE A 270 
 TRP   0.017   0.002   TRP B 263 
 HIS   0.019   0.002   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4731)
  covalent geometry    : angle       0.65126 ( 6410)
  hydrogen bonds       : bond        0.04115 (  193)
  hydrogen bonds       : angle       5.36221 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8669 (tp) cc_final: 0.8241 (tt)
REVERT: A  151 TYR cc_start: 0.6400 (m-10) cc_final: 0.5898 (m-10)
REVERT: A  302 MET cc_start: 0.7756 (ptt) cc_final: 0.7508 (ptt)
REVERT: A  306 MET cc_start: 0.8372 (mmt) cc_final: 0.7751 (mmt)
REVERT: B  249 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6761 (tm-30)
  outliers start: 17
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0654
  time to fit residues: 8.7030
Evaluate side-chains
  84 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  340 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 25 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.173490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.141843 restraints weight = 6750.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.145998 restraints weight = 4052.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148801 restraints weight = 2933.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.150696 restraints weight = 2364.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.151635 restraints weight = 2040.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4731  Z= 0.129
  Angle     :  0.623   9.713   6410  Z= 0.309
  Chirality :  0.040   0.186    762
  Planarity :  0.004   0.039    818
  Dihedral  :  5.502  28.417    655
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.44 %
    Favored  : 78.57 %
  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: -3.01 (0.33), residues: 556
  helix: -1.49 (0.27), residues: 337
  sheet:  None (None), residues: 0
  loop : -2.72 (0.38), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 345 
 TYR   0.015   0.001   TYR A 445 
 PHE   0.021   0.001   PHE A 270 
 TRP   0.022   0.002   TRP B 263 
 HIS   0.003   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4731)
  covalent geometry    : angle       0.62334 ( 6410)
  hydrogen bonds       : bond        0.03786 (  193)
  hydrogen bonds       : angle       5.06859 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.8628 (tp) cc_final: 0.8235 (tt)
REVERT: A  151 TYR cc_start: 0.6389 (m-10) cc_final: 0.5844 (m-10)
REVERT: A  306 MET cc_start: 0.8269 (mmt) cc_final: 0.7816 (mmt)
REVERT: B  249 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6754 (tm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 98
  average time/residue: 0.0596
  time to fit residues: 7.6370
Evaluate side-chains
  90 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0570
   chunk 44 optimal weight:   10.0000
   chunk 45 optimal weight:   20.0000
   overall best weight:    1.1300

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.172344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.140310 restraints weight = 6749.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.144473 restraints weight = 4087.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.147250 restraints weight = 2966.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148995 restraints weight = 2402.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.150405 restraints weight = 2089.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4731  Z= 0.152
  Angle     :  0.679  10.530   6410  Z= 0.325
  Chirality :  0.042   0.223    762
  Planarity :  0.004   0.031    818
  Dihedral  :  5.430  29.183    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 18.49 %
    Favored  : 77.73 %
  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: -2.84 (0.33), residues: 556
  helix: -1.29 (0.27), residues: 337
  sheet: -0.18 (1.54), residues: 14
  loop : -2.92 (0.37), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 345 
 TYR   0.033   0.002   TYR A  95 
 PHE   0.010   0.001   PHE A 163 
 TRP   0.019   0.002   TRP B 263 
 HIS   0.004   0.001   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4731)
  covalent geometry    : angle       0.67928 ( 6410)
  hydrogen bonds       : bond        0.03712 (  193)
  hydrogen bonds       : angle       5.03847 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8666 (tp) cc_final: 0.8274 (tt)
REVERT: A  151 TYR cc_start: 0.6374 (m-10) cc_final: 0.5846 (m-10)
REVERT: B  227 MET cc_start: 0.3684 (ppp) cc_final: 0.1690 (mtm)
REVERT: B  249 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6764 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 88
  average time/residue: 0.0667
  time to fit residues: 7.6464
Evaluate side-chains
  88 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0020
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
A 271 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.175715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.144727 restraints weight = 6698.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.148941 restraints weight = 3989.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.151771 restraints weight = 2853.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.153665 restraints weight = 2280.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.154589 restraints weight = 1963.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4731  Z= 0.122
  Angle     :  0.632  10.659   6410  Z= 0.303
  Chirality :  0.040   0.167    762
  Planarity :  0.004   0.031    818
  Dihedral  :  5.161  29.226    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.01 %
    Favored  : 75.42 %
  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: -2.51 (0.34), residues: 556
  helix: -0.98 (0.28), residues: 331
  sheet: -0.44 (1.46), residues: 14
  loop : -2.79 (0.38), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 345 
 TYR   0.015   0.001   TYR A  95 
 PHE   0.009   0.001   PHE A 163 
 TRP   0.018   0.003   TRP B 263 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4731)
  covalent geometry    : angle       0.63231 ( 6410)
  hydrogen bonds       : bond        0.03571 (  193)
  hydrogen bonds       : angle       4.91909 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.8641 (tp) cc_final: 0.8244 (tt)
REVERT: A  151 TYR cc_start: 0.6338 (m-10) cc_final: 0.5643 (m-10)
REVERT: A  164 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7610 (t0)
REVERT: A  197 GLU cc_start: 0.7600 (tp30) cc_final: 0.7390 (tp30)
REVERT: A  380 MET cc_start: 0.8269 (ttm) cc_final: 0.8004 (ttt)
REVERT: B  227 MET cc_start: 0.3775 (ppp) cc_final: 0.1220 (mtt)
  outliers start: 17
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0704
  time to fit residues: 8.6783
Evaluate side-chains
  92 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  164 ASP
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0670
   chunk 22 optimal weight:    0.4980
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    7.9990
   overall best weight:    0.5718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.177462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.147026 restraints weight = 6755.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.151271 restraints weight = 3978.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.154132 restraints weight = 2816.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.155814 restraints weight = 2229.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.157359 restraints weight = 1912.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4731  Z= 0.118
  Angle     :  0.643  12.106   6410  Z= 0.305
  Chirality :  0.039   0.143    762
  Planarity :  0.004   0.032    818
  Dihedral  :  4.986  28.357    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.48 %
    Favored  : 73.74 %
  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: -2.32 (0.34), residues: 556
  helix: -0.77 (0.28), residues: 331
  sheet: -0.55 (1.46), residues: 14
  loop : -2.81 (0.38), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 345 
 TYR   0.011   0.001   TYR A  95 
 PHE   0.022   0.001   PHE A 270 
 TRP   0.017   0.003   TRP B 263 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4731)
  covalent geometry    : angle       0.64261 ( 6410)
  hydrogen bonds       : bond        0.03413 (  193)
  hydrogen bonds       : angle       4.82210 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.8642 (tp) cc_final: 0.8402 (tt)
REVERT: A  151 TYR cc_start: 0.6334 (m-10) cc_final: 0.5702 (m-10)
REVERT: A  164 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7629 (t0)
  outliers start: 18
  outliers final: 15
  residues processed: 93
  average time/residue: 0.0705
  time to fit residues: 8.4559
Evaluate side-chains
  92 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  164 ASP
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 36 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 47 optimal weight:    0.3980
   chunk 44 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0870
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 1 optimal weight:    8.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
B 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.178973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.149055 restraints weight = 6600.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.153256 restraints weight = 3898.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.156130 restraints weight = 2758.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.157951 restraints weight = 2177.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.159374 restraints weight = 1855.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4731  Z= 0.114
  Angle     :  0.646  11.452   6410  Z= 0.307
  Chirality :  0.039   0.142    762
  Planarity :  0.004   0.032    818
  Dihedral  :  4.806  27.752    655
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.69 %
    Favored  : 73.74 %
  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 (0.34), residues: 556
  helix: -0.66 (0.29), residues: 334
  sheet: -0.71 (1.42), residues: 14
  loop : -2.76 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 345 
 TYR   0.011   0.001   TYR A  95 
 PHE   0.020   0.001   PHE A 270 
 TRP   0.017   0.003   TRP B 263 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4731)
  covalent geometry    : angle       0.64583 ( 6410)
  hydrogen bonds       : bond        0.03405 (  193)
  hydrogen bonds       : angle       4.77604 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.8650 (tp) cc_final: 0.8392 (tt)
REVERT: A  151 TYR cc_start: 0.6382 (m-10) cc_final: 0.5726 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0745
  time to fit residues: 8.9004
Evaluate side-chains
  90 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 45 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0870
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** 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 = 0.4210 r_free = 0.4210 target = 0.178367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.148046 restraints weight = 6790.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.152198 restraints weight = 4045.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.155033 restraints weight = 2870.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.156890 restraints weight = 2278.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.157842 restraints weight = 1945.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4731  Z= 0.122
  Angle     :  0.666  13.443   6410  Z= 0.314
  Chirality :  0.040   0.211    762
  Planarity :  0.004   0.033    818
  Dihedral  :  4.778  28.734    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.64 %
    Favored  : 74.16 %
  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: -2.07 (0.35), residues: 556
  helix: -0.60 (0.29), residues: 333
  sheet:  0.06 (1.91), residues: 10
  loop : -2.66 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 345 
 TYR   0.011   0.001   TYR B 325 
 PHE   0.019   0.001   PHE A 270 
 TRP   0.017   0.002   TRP B 263 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4731)
  covalent geometry    : angle       0.66631 ( 6410)
  hydrogen bonds       : bond        0.03392 (  193)
  hydrogen bonds       : angle       4.80192 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8661 (tp) cc_final: 0.8400 (tt)
REVERT: A  151 TYR cc_start: 0.6415 (m-10) cc_final: 0.5724 (m-10)
REVERT: A  283 LEU cc_start: 0.8395 (mp) cc_final: 0.8192 (mp)
REVERT: B  249 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6674 (tm-30)
  outliers start: 20
  outliers final: 17
  residues processed: 91
  average time/residue: 0.0733
  time to fit residues: 8.5552
Evaluate side-chains
  92 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  343 MET
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 25 optimal weight:    0.2980
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 2 optimal weight:    4.9990
   chunk 45 optimal weight:   20.0000
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** 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 = 0.4180 r_free = 0.4180 target = 0.175460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.144663 restraints weight = 6635.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.148471 restraints weight = 4096.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.151078 restraints weight = 3004.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.152800 restraints weight = 2438.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.154030 restraints weight = 2115.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4731  Z= 0.155
  Angle     :  0.681  12.936   6410  Z= 0.327
  Chirality :  0.042   0.189    762
  Planarity :  0.004   0.033    818
  Dihedral  :  4.967  30.165    655
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.27 %
    Favored  : 73.95 %
  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: -2.14 (0.34), residues: 556
  helix: -0.66 (0.29), residues: 332
  sheet: -0.48 (1.47), residues: 14
  loop : -2.69 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  77 
 TYR   0.011   0.002   TYR A  95 
 PHE   0.019   0.001   PHE A 270 
 TRP   0.018   0.002   TRP B 263 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4731)
  covalent geometry    : angle       0.68146 ( 6410)
  hydrogen bonds       : bond        0.03597 (  193)
  hydrogen bonds       : angle       4.86325 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.8687 (tp) cc_final: 0.8446 (tt)
REVERT: A  151 TYR cc_start: 0.6395 (m-10) cc_final: 0.5720 (m-10)
REVERT: A  283 LEU cc_start: 0.8320 (mp) cc_final: 0.8119 (mp)
REVERT: A  302 MET cc_start: 0.7781 (ptt) cc_final: 0.7562 (ptt)
REVERT: A  324 HIS cc_start: 0.7288 (p90) cc_final: 0.6919 (p-80)
  outliers start: 18
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0631
  time to fit residues: 7.1459
Evaluate side-chains
  89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  343 MET
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0670
   chunk 54 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0270
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
A 414 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.179938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.149622 restraints weight = 6662.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.153681 restraints weight = 3986.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.156507 restraints weight = 2821.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.158182 restraints weight = 2231.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.159612 restraints weight = 1917.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4731  Z= 0.118
  Angle     :  0.663  13.013   6410  Z= 0.317
  Chirality :  0.040   0.163    762
  Planarity :  0.004   0.034    818
  Dihedral  :  4.767  29.046    655
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 23.74 %
    Favored  : 72.90 %
  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: -1.93 (0.35), residues: 556
  helix: -0.54 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -2.38 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  77 
 TYR   0.012   0.001   TYR A  95 
 PHE   0.018   0.001   PHE A 270 
 TRP   0.018   0.002   TRP B 263 
 HIS   0.022   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4731)
  covalent geometry    : angle       0.66315 ( 6410)
  hydrogen bonds       : bond        0.03407 (  193)
  hydrogen bonds       : angle       4.80008 (  567)

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8651 (tp) cc_final: 0.8408 (tt)
REVERT: A  151 TYR cc_start: 0.6401 (m-10) cc_final: 0.5717 (m-10)
REVERT: B  292 PHE cc_start: 0.6725 (m-10) cc_final: 0.6483 (m-10)
  outliers start: 16
  outliers final: 15
  residues processed: 85
  average time/residue: 0.0650
  time to fit residues: 7.3512
Evaluate side-chains
  88 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.179214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.149073 restraints weight = 6648.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.153124 restraints weight = 3953.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.155845 restraints weight = 2817.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.157671 restraints weight = 2246.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.158894 restraints weight = 1921.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   4731  Z= 0.127
  Angle     :  0.665  13.179   6410  Z= 0.320
  Chirality :  0.040   0.157    762
  Planarity :  0.004   0.035    818
  Dihedral  :  4.785  29.667    655
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 23.11 %
    Favored  : 73.53 %
  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: -1.80 (0.35), residues: 556
  helix: -0.54 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -2.11 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  77 
 TYR   0.012   0.001   TYR A  95 
 PHE   0.018   0.001   PHE A 270 
 TRP   0.017   0.002   TRP B 263 
 HIS   0.021   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4731)
  covalent geometry    : angle       0.66537 ( 6410)
  hydrogen bonds       : bond        0.03423 (  193)
  hydrogen bonds       : angle       4.84448 (  567)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 957.30 seconds
wall clock time: 17 minutes 9.61 seconds (1029.61 seconds total)