Starting phenix.real_space_refine
on Fri Aug 22 15:21:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr5_34046/08_2025/7yr5_34046.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr5_34046/08_2025/7yr5_34046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr5_34046/08_2025/7yr5_34046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr5_34046/08_2025/7yr5_34046.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr5_34046/08_2025/7yr5_34046.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr5_34046/08_2025/7yr5_34046.cif"
  }
  resolution = 3.63
  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=   0.015
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      35      5.16       5
     C    3164      2.51       5
     N     775      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 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4828
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1899
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 8, 'TRANS': 228}
    Chain: "A"
      Number of atoms: 2929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 2929
          Classifications: {'peptide': 385}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 367}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 0.90, per 1000 atoms: 0.19
  Number of scatterers: 4828
  At special positions: 0
  Unit cell: (73.08, 103.32, 123.48, 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      35     16.00
     O     854      8.00
     N     775      7.00
     C    3164      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  88 " - pdb=" SG  CYS B 142 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 180 " - pdb=" SG  CYS B 237 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 152.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1126

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 5 sheets defined
      61.7% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 257 through 290
      removed outlier: 4.103A  pdb=" N   LYS B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      Proline residue:  B 263  - end of helix
    Processing helix  chain 'A' and resid 19 through 40
      removed outlier: 4.237A  pdb=" N   PHE A  36 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
      Proline residue:  A  37  - end of helix
    Processing helix  chain 'A' and resid 40 through 51
      removed outlier: 4.150A  pdb=" N   LYS A  45 " --> pdb=" O   THR A  41 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   GLU A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLY A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A  50 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 72
      removed outlier: 5.085A  pdb=" N   ILE A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   SER A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 83
    Processing helix  chain 'A' and resid 84 through 104
    Processing helix  chain 'A' and resid 111 through 139
      removed outlier: 3.690A  pdb=" N   CYS A 115 " --> pdb=" O   GLN A 111 " (cutoff:3.500A)
      Proline residue:  A 130  - end of helix
    Processing helix  chain 'A' and resid 142 through 152
    Processing helix  chain 'A' and resid 152 through 162
      removed outlier: 4.313A  pdb=" N   VAL A 156 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 172
      removed outlier: 5.924A  pdb=" N   PHE A 169 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 188
      removed outlier: 3.519A  pdb=" N   ILE A 180 " --> pdb=" O   GLY A 176 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU A 181 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 194
    Processing helix  chain 'A' and resid 254 through 259
      removed outlier: 3.551A  pdb=" N   LEU A 257 " --> pdb=" O   ASP A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 291
      removed outlier: 4.491A  pdb=" N   PHE A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   GLY A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
      removed outlier: 5.279A  pdb=" N   SER A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   SER A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 322
      removed outlier: 3.590A  pdb=" N   LEU A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      Proline residue:  A 314  - end of helix
    Processing helix  chain 'A' and resid 323 through 326
    Processing helix  chain 'A' and resid 328 through 347
      removed outlier: 3.607A  pdb=" N   VAL A 338 " --> pdb=" O   ALA A 334 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA A 339 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN A 340 " --> pdb=" O   SER A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 374
      removed outlier: 3.859A  pdb=" N   TRP A 369 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   LEU A 370 " --> pdb=" O   ALA A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 382
    Processing helix  chain 'A' and resid 383 through 412
      removed outlier: 3.983A  pdb=" N   SER A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   SER A 389 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      Proline residue:  A 401  - end of helix
      Proline residue:  A 406  - end of helix
    Processing helix  chain 'A' and resid 418 through 420
      No H-bonds generated for 'chain 'A' and resid 418 through 420'
    Processing helix  chain 'A' and resid 421 through 448
      removed outlier: 3.934A  pdb=" N   ALA A 425 " --> pdb=" O   TYR A 421 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS A 426 " --> pdb=" O   THR A 422 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 61 through 64
      removed outlier: 5.621A  pdb=" N   ILE B  62 " --> pdb=" O   GLN B  89 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   THR B  91 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   LEU B  64 " --> pdb=" O   THR B  91 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 74
      removed outlier: 3.715A  pdb=" N   GLN B 150 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 169 through 171
    Processing sheet with id=AA4, first strand: chain 'B' and resid 191 through 194
    Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 213

    278 hydrogen bonds defined for protein.
    798 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: 0.52

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1472
        1.34 -     1.46: 1090
        1.46 -     1.58: 2336
        1.58 -     1.70: 0
        1.70 -     1.81: 51
  Bond restraints: 4949
  Sorted by residual:
  bond pdb=" N   VAL B  84 "
       pdb=" CA  VAL B  84 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.11e-02 8.12e+03 1.16e+01
  bond pdb=" N   ILE B  76 "
       pdb=" CA  ILE B  76 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.19e-02 7.06e+03 9.69e+00
  bond pdb=" N   VAL B 116 "
       pdb=" CA  VAL B 116 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.22e-02 6.72e+03 8.68e+00
  bond pdb=" N   VAL B  72 "
       pdb=" CA  VAL B  72 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.036 1.24e-02 6.50e+03 8.36e+00
  bond pdb=" N   LYS B 104 "
       pdb=" CA  LYS B 104 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.27e-02 6.20e+03 7.61e+00
  ... (remaining 4944 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 6220
        1.38 -     2.75: 367
        2.75 -     4.13: 89
        4.13 -     5.51: 33
        5.51 -     6.88: 6
  Bond angle restraints: 6715
  Sorted by residual:
  angle pdb=" C   ARG B 128 "
        pdb=" N   PHE B 129 "
        pdb=" CA  PHE B 129 "
      ideal   model   delta    sigma   weight residual
     122.77  117.48    5.29 1.33e+00 5.65e-01 1.58e+01
  angle pdb=" CA  PHE B 129 "
        pdb=" CB  PHE B 129 "
        pdb=" CG  PHE B 129 "
      ideal   model   delta    sigma   weight residual
     113.80  117.77   -3.97 1.00e+00 1.00e+00 1.58e+01
  angle pdb=" N   PHE B 154 "
        pdb=" CA  PHE B 154 "
        pdb=" C   PHE B 154 "
      ideal   model   delta    sigma   weight residual
     109.46  103.18    6.28 1.66e+00 3.63e-01 1.43e+01
  angle pdb=" C   CYS A 106 "
        pdb=" N   ASN A 107 "
        pdb=" CA  ASN A 107 "
      ideal   model   delta    sigma   weight residual
     122.61  128.02   -5.41 1.56e+00 4.11e-01 1.20e+01
  angle pdb=" C   CYS B  88 "
        pdb=" N   GLN B  89 "
        pdb=" CA  GLN B  89 "
      ideal   model   delta    sigma   weight residual
     123.05  118.23    4.82 1.40e+00 5.10e-01 1.18e+01
  ... (remaining 6710 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.54: 2481
       14.54 -    29.07: 292
       29.07 -    43.61: 82
       43.61 -    58.14: 13
       58.14 -    72.68: 7
  Dihedral angle restraints: 2875
    sinusoidal: 1101
      harmonic: 1774
  Sorted by residual:
  dihedral pdb=" CA  GLN A 166 "
           pdb=" C   GLN A 166 "
           pdb=" N   VAL A 167 "
           pdb=" CA  VAL A 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.92   26.08     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  LEU A 164 "
           pdb=" C   LEU A 164 "
           pdb=" N   ASN A 165 "
           pdb=" CA  ASN A 165 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.35   21.65     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  GLN A 110 "
           pdb=" C   GLN A 110 "
           pdb=" N   GLN A 111 "
           pdb=" CA  GLN A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.98   20.02     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 2872 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 571
       0.052 -    0.104: 141
       0.104 -    0.156: 34
       0.156 -    0.208: 12
       0.208 -    0.261: 4
  Chirality restraints: 762
  Sorted by residual:
  chirality pdb=" CA  PHE B 154 "
            pdb=" N   PHE B 154 "
            pdb=" C   PHE B 154 "
            pdb=" CB  PHE B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  CYS B  88 "
            pdb=" N   CYS B  88 "
            pdb=" C   CYS B  88 "
            pdb=" CB  CYS B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ILE B  62 "
            pdb=" N   ILE B  62 "
            pdb=" C   ILE B  62 "
            pdb=" CB  ILE B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 759 not shown)

  Planarity restraints: 834
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 253 "    0.021 2.00e-02 2.50e+03   4.20e-02 1.76e+01
        pdb=" C   VAL B 253 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   VAL B 253 "    0.027 2.00e-02 2.50e+03
        pdb=" N   VAL B 254 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  99 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.15e+00
        pdb=" C   VAL B  99 "    0.043 2.00e-02 2.50e+03
        pdb=" O   VAL B  99 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN B 100 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 114 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.42e+00
        pdb=" C   VAL A 114 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL A 114 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 115 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 831 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1062
        2.78 -     3.31: 4795
        3.31 -     3.84: 7906
        3.84 -     4.37: 9100
        4.37 -     4.90: 15390
  Nonbonded interactions: 38253
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  63 "
            pdb=" O   LEU A 403 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG  SER A  29 "
            pdb=" O   ASN A 127 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR A 138 "
            pdb=" O   ARG A 196 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OH  TYR B 210 "
            pdb=" OH  TYR B 235 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER B 134 "
            pdb=" O   GLU B 160 "
     model   vdw
     2.318 3.040
  ... (remaining 38248 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:             2.350
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.790
  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:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
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   0.042   4951  Z= 0.340
  Angle     :  0.807   6.881   6719  Z= 0.501
  Chirality :  0.054   0.261    762
  Planarity :  0.005   0.042    834
  Dihedral  : 13.919  72.678   1743
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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 aren not related in a simple way.
  whole: -0.05 (0.34), residues: 616
  helix:  0.65 (0.29), residues: 362
  sheet:  0.32 (0.53), residues: 102
  loop : -1.81 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 128 
 TYR   0.013   0.001   TYR A 445 
 PHE   0.017   0.001   PHE B 129 
 TRP   0.012   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 4949)
  covalent geometry    : angle       0.80756 ( 6715)
  SS BOND              : bond        0.00626 (    2)
  SS BOND              : angle       0.62855 (    4)
  hydrogen bonds       : bond        0.16864 (  278)
  hydrogen bonds       : angle       6.21610 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  151 MET cc_start: 0.8056 (ttm) cc_final: 0.7434 (ttp)
REVERT: A  416 TYR cc_start: 0.7273 (t80) cc_final: 0.6929 (t80)
REVERT: A  418 ASP cc_start: 0.7536 (t70) cc_final: 0.7060 (p0)
REVERT: A  446 ARG cc_start: 0.8201 (mmp80) cc_final: 0.7579 (mtp180)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0525
  time to fit residues: 7.9671
Evaluate side-chains
  84 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
A 129 ASN
A 165 ASN
A 260 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.166368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.121613 restraints weight = 7919.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.125107 restraints weight = 3759.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.127299 restraints weight = 2282.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.128427 restraints weight = 1653.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.129385 restraints weight = 1378.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4951  Z= 0.196
  Angle     :  0.670  10.048   6719  Z= 0.354
  Chirality :  0.044   0.157    762
  Planarity :  0.005   0.045    834
  Dihedral  :  5.040  25.592    665
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.33 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.34), residues: 616
  helix:  0.79 (0.29), residues: 362
  sheet: -0.03 (0.52), residues: 104
  loop : -1.50 (0.45), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  86 
 TYR   0.011   0.001   TYR A  83 
 PHE   0.022   0.002   PHE B 129 
 TRP   0.013   0.001   TRP A 369 
 HIS   0.006   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 4949)
  covalent geometry    : angle       0.67017 ( 6715)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       0.86721 (    4)
  hydrogen bonds       : bond        0.05107 (  278)
  hydrogen bonds       : angle       5.23959 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   83 TYR cc_start: 0.6922 (m-10) cc_final: 0.6708 (m-10)
REVERT: A  418 ASP cc_start: 0.7603 (t70) cc_final: 0.7223 (p0)
REVERT: A  438 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7768 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 92
  average time/residue: 0.0560
  time to fit residues: 7.3111
Evaluate side-chains
  90 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0050
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
A 127 ASN
A 129 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.170000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.125100 restraints weight = 7864.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.128721 restraints weight = 3709.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.131002 restraints weight = 2243.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.132324 restraints weight = 1617.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.133226 restraints weight = 1328.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4951  Z= 0.136
  Angle     :  0.615   8.680   6719  Z= 0.319
  Chirality :  0.042   0.144    762
  Planarity :  0.005   0.042    834
  Dihedral  :  4.851  22.715    665
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.41 %
    Favored  : 79.51 %
  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 aren not related in a simple way.
  whole:  0.24 (0.35), residues: 616
  helix:  0.92 (0.29), residues: 362
  sheet:  0.09 (0.53), residues: 104
  loop : -1.50 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 238 
 TYR   0.008   0.001   TYR B 124 
 PHE   0.018   0.001   PHE B 129 
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4949)
  covalent geometry    : angle       0.61478 ( 6715)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       0.72032 (    4)
  hydrogen bonds       : bond        0.04266 (  278)
  hydrogen bonds       : angle       4.88821 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7263 (tmmt)
REVERT: A  374 LEU cc_start: 0.9081 (tp) cc_final: 0.8872 (tp)
REVERT: A  416 TYR cc_start: 0.7528 (t80) cc_final: 0.6908 (t80)
REVERT: A  418 ASP cc_start: 0.7468 (t70) cc_final: 0.7265 (p0)
REVERT: A  420 LYS cc_start: 0.9071 (tmmt) cc_final: 0.8735 (tmmt)
REVERT: A  438 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7737 (t80)
  outliers start: 11
  outliers final: 7
  residues processed: 96
  average time/residue: 0.0597
  time to fit residues: 7.8766
Evaluate side-chains
  95 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0570
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.173277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.127984 restraints weight = 7921.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.131640 restraints weight = 3736.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.133943 restraints weight = 2253.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.135437 restraints weight = 1621.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.136179 restraints weight = 1317.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4951  Z= 0.127
  Angle     :  0.595   7.706   6719  Z= 0.308
  Chirality :  0.041   0.144    762
  Planarity :  0.004   0.039    834
  Dihedral  :  4.740  22.581    665
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 21.63 %
    Favored  : 76.28 %
  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 aren not related in a simple way.
  whole:  0.34 (0.36), residues: 616
  helix:  1.00 (0.29), residues: 362
  sheet:  0.06 (0.53), residues: 105
  loop : -1.40 (0.48), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 151 
 TYR   0.007   0.001   TYR B 210 
 PHE   0.017   0.001   PHE A 307 
 TRP   0.009   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4949)
  covalent geometry    : angle       0.59548 ( 6715)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.58892 (    4)
  hydrogen bonds       : bond        0.03938 (  278)
  hydrogen bonds       : angle       4.71096 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A  416 TYR cc_start: 0.7459 (t80) cc_final: 0.6892 (t80)
REVERT: A  418 ASP cc_start: 0.7350 (t70) cc_final: 0.7122 (p0)
REVERT: A  438 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7804 (t80)
  outliers start: 11
  outliers final: 6
  residues processed: 94
  average time/residue: 0.0597
  time to fit residues: 7.7371
Evaluate side-chains
  91 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 7 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN
A 291 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.170615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.125562 restraints weight = 7914.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.129112 restraints weight = 3760.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.131392 restraints weight = 2272.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.132759 restraints weight = 1632.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.133661 restraints weight = 1329.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4951  Z= 0.151
  Angle     :  0.606   8.422   6719  Z= 0.316
  Chirality :  0.042   0.148    762
  Planarity :  0.004   0.041    834
  Dihedral  :  4.797  22.660    665
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.01 %
    Favored  : 74.57 %
  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 aren not related in a simple way.
  whole:  0.32 (0.36), residues: 616
  helix:  0.97 (0.29), residues: 362
  sheet:  0.06 (0.54), residues: 105
  loop : -1.39 (0.48), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 151 
 TYR   0.016   0.001   TYR A 287 
 PHE   0.017   0.002   PHE A 307 
 TRP   0.009   0.001   TRP A 369 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4949)
  covalent geometry    : angle       0.60552 ( 6715)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       0.70313 (    4)
  hydrogen bonds       : bond        0.04255 (  278)
  hydrogen bonds       : angle       4.78484 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  416 TYR cc_start: 0.7457 (t80) cc_final: 0.6898 (t80)
REVERT: A  420 LYS cc_start: 0.9009 (tmmt) cc_final: 0.8700 (tmmt)
REVERT: A  438 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7781 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 100
  average time/residue: 0.0599
  time to fit residues: 8.1763
Evaluate side-chains
  103 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0980
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0000
   overall best weight:    1.2190

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.168405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.123268 restraints weight = 7950.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.126753 restraints weight = 3817.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128981 restraints weight = 2323.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.130214 restraints weight = 1679.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.131244 restraints weight = 1382.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4951  Z= 0.183
  Angle     :  0.650   9.507   6719  Z= 0.339
  Chirality :  0.043   0.153    762
  Planarity :  0.005   0.042    834
  Dihedral  :  4.909  23.640    665
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 23.15 %
    Favored  : 73.06 %
  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 aren not related in a simple way.
  whole:  0.24 (0.35), residues: 616
  helix:  0.92 (0.29), residues: 362
  sheet: -0.05 (0.54), residues: 105
  loop : -1.39 (0.47), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 238 
 TYR   0.020   0.001   TYR A 287 
 PHE   0.019   0.002   PHE B 129 
 TRP   0.011   0.001   TRP A 369 
 HIS   0.002   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 4949)
  covalent geometry    : angle       0.65009 ( 6715)
  SS BOND              : bond        0.00372 (    2)
  SS BOND              : angle       1.09885 (    4)
  hydrogen bonds       : bond        0.04598 (  278)
  hydrogen bonds       : angle       4.90356 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   48 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7215 (mm-30)
REVERT: A  374 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8844 (tt)
  outliers start: 20
  outliers final: 17
  residues processed: 99
  average time/residue: 0.0573
  time to fit residues: 7.9521
Evaluate side-chains
  99 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  374 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
B 113 ASN
A 129 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.169299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.124249 restraints weight = 7915.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.127861 restraints weight = 3792.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.130096 restraints weight = 2301.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.131496 restraints weight = 1663.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.132078 restraints weight = 1354.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4951  Z= 0.152
  Angle     :  0.627   8.550   6719  Z= 0.327
  Chirality :  0.042   0.146    762
  Planarity :  0.005   0.042    834
  Dihedral  :  4.894  22.616    665
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.53 %
    Favored  : 72.49 %
  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 aren not related in a simple way.
  whole:  0.27 (0.35), residues: 616
  helix:  0.96 (0.29), residues: 362
  sheet: -0.10 (0.54), residues: 104
  loop : -1.38 (0.47), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 238 
 TYR   0.017   0.001   TYR A 287 
 PHE   0.019   0.001   PHE B 129 
 TRP   0.011   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4949)
  covalent geometry    : angle       0.62508 ( 6715)
  SS BOND              : bond        0.00407 (    2)
  SS BOND              : angle       1.87017 (    4)
  hydrogen bonds       : bond        0.04320 (  278)
  hydrogen bonds       : angle       4.82347 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   48 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7135 (mm-30)
REVERT: A   65 MET cc_start: 0.8625 (tpp) cc_final: 0.8143 (ttm)
REVERT: A  416 TYR cc_start: 0.7576 (t80) cc_final: 0.6991 (t80)
REVERT: A  438 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7742 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 97
  average time/residue: 0.0573
  time to fit residues: 7.7428
Evaluate side-chains
  95 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 43 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0470
   chunk 60 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.170868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.125475 restraints weight = 7955.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.129181 restraints weight = 3829.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.131357 restraints weight = 2306.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.132901 restraints weight = 1664.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.133618 restraints weight = 1350.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4951  Z= 0.138
  Angle     :  0.620   9.450   6719  Z= 0.322
  Chirality :  0.041   0.144    762
  Planarity :  0.005   0.041    834
  Dihedral  :  4.846  22.210    665
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.72 %
    Favored  : 72.30 %
  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 aren not related in a simple way.
  whole:  0.30 (0.36), residues: 616
  helix:  1.01 (0.29), residues: 362
  sheet: -0.08 (0.53), residues: 104
  loop : -1.43 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 238 
 TYR   0.014   0.001   TYR A 287 
 PHE   0.022   0.002   PHE B 129 
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4949)
  covalent geometry    : angle       0.61921 ( 6715)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       1.21742 (    4)
  hydrogen bonds       : bond        0.04090 (  278)
  hydrogen bonds       : angle       4.75103 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   65 MET cc_start: 0.8544 (tpp) cc_final: 0.8215 (ttm)
REVERT: A  416 TYR cc_start: 0.7553 (t80) cc_final: 0.7044 (t80)
REVERT: A  438 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7745 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 98
  average time/residue: 0.0559
  time to fit residues: 7.6934
Evaluate side-chains
  99 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 0 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   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  89 GLN
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.171625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.126252 restraints weight = 7804.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.129868 restraints weight = 3764.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.132151 restraints weight = 2286.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133501 restraints weight = 1645.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.134456 restraints weight = 1339.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4951  Z= 0.140
  Angle     :  0.621   9.136   6719  Z= 0.323
  Chirality :  0.041   0.144    762
  Planarity :  0.004   0.040    834
  Dihedral  :  4.830  22.167    665
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.53 %
    Favored  : 72.30 %
  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 aren not related in a simple way.
  whole:  0.28 (0.36), residues: 616
  helix:  1.00 (0.29), residues: 362
  sheet: -0.14 (0.53), residues: 104
  loop : -1.42 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 238 
 TYR   0.014   0.001   TYR A 287 
 PHE   0.022   0.001   PHE B 129 
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4949)
  covalent geometry    : angle       0.61987 ( 6715)
  SS BOND              : bond        0.00395 (    2)
  SS BOND              : angle       1.41489 (    4)
  hydrogen bonds       : bond        0.04076 (  278)
  hydrogen bonds       : angle       4.73084 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B  193 TYR cc_start: 0.7358 (m-80) cc_final: 0.6953 (m-10)
REVERT: A   65 MET cc_start: 0.8498 (tpp) cc_final: 0.8274 (ttm)
REVERT: A  134 MET cc_start: 0.9007 (mmm) cc_final: 0.8806 (mmt)
REVERT: A  416 TYR cc_start: 0.7505 (t80) cc_final: 0.6985 (t80)
REVERT: A  438 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7762 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 98
  average time/residue: 0.0512
  time to fit residues: 7.1714
Evaluate side-chains
  98 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0770
   chunk 7 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.172009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.126731 restraints weight = 7904.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.130405 restraints weight = 3804.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.132727 restraints weight = 2306.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.134036 restraints weight = 1654.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.135017 restraints weight = 1352.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4951  Z= 0.139
  Angle     :  0.625   8.982   6719  Z= 0.325
  Chirality :  0.041   0.144    762
  Planarity :  0.004   0.039    834
  Dihedral  :  4.796  22.191    665
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 23.72 %
    Favored  : 72.68 %
  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 aren not related in a simple way.
  whole:  0.26 (0.36), residues: 616
  helix:  0.99 (0.29), residues: 362
  sheet: -0.17 (0.54), residues: 104
  loop : -1.43 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 238 
 TYR   0.014   0.001   TYR A 287 
 PHE   0.024   0.002   PHE A 307 
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4949)
  covalent geometry    : angle       0.62425 ( 6715)
  SS BOND              : bond        0.00526 (    2)
  SS BOND              : angle       1.50742 (    4)
  hydrogen bonds       : bond        0.04036 (  278)
  hydrogen bonds       : angle       4.70594 (  798)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.192 
Fit side-chains
REVERT: B  193 TYR cc_start: 0.7326 (m-80) cc_final: 0.6969 (m-10)
REVERT: A  134 MET cc_start: 0.8989 (mmm) cc_final: 0.8749 (mmt)
REVERT: A  416 TYR cc_start: 0.7482 (t80) cc_final: 0.6950 (t80)
REVERT: A  438 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7764 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 93
  average time/residue: 0.0549
  time to fit residues: 7.2239
Evaluate side-chains
  98 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 42 optimal weight:    0.2980
   chunk 52 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 14 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.170914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125634 restraints weight = 7863.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.129309 restraints weight = 3792.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.131616 restraints weight = 2299.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.132860 restraints weight = 1653.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.133993 restraints weight = 1361.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4951  Z= 0.139
  Angle     :  0.621   8.854   6719  Z= 0.322
  Chirality :  0.041   0.144    762
  Planarity :  0.004   0.039    834
  Dihedral  :  4.795  22.293    665
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 24.48 %
    Favored  : 72.11 %
  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 aren not related in a simple way.
  whole:  0.27 (0.36), residues: 616
  helix:  0.98 (0.29), residues: 362
  sheet: -0.14 (0.53), residues: 104
  loop : -1.40 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 238 
 TYR   0.014   0.001   TYR A 287 
 PHE   0.021   0.001   PHE B 129 
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4949)
  covalent geometry    : angle       0.62036 ( 6715)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       0.94332 (    4)
  hydrogen bonds       : bond        0.04031 (  278)
  hydrogen bonds       : angle       4.68792 (  798)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1113.69 seconds
wall clock time: 19 minutes 56.91 seconds (1196.91 seconds total)