Starting phenix.real_space_refine
on Thu Sep 10 23:38:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6up7_20836/09_2026/6up7_20836.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6up7_20836/09_2026/6up7_20836.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6up7_20836/09_2026/6up7_20836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6up7_20836/09_2026/6up7_20836.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6up7_20836/09_2026/6up7_20836.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6up7_20836/09_2026/6up7_20836.cif"
  }
  resolution = 4.2
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1653 atoms to isotropic.
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       3      5.49       5
     S       4      5.16       5
     C    2632      2.51       5
     N     756      2.21       5
     O     771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4166
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 48
          Classifications: {'peptide': 6}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2063
          Classifications: {'peptide': 348}
          Incomplete info: {'truncation_to_alanine': 202}
          Link IDs: {'PTRANS': 24, 'TRANS': 323}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 715
          Unresolved non-hydrogen angles: 909
          Unresolved non-hydrogen dihedrals: 569
          Unresolved non-hydrogen chiralities: 72
          Planarities with less than four sites: {'ASN:plan1': 12, 'TYR:plan': 7, 'ASP:plan': 21, 'HIS:plan': 6, 'GLU:plan': 23, 'ARG:plan': 13, 'PHE:plan': 5, 'GLN:plan1': 5}
          Unresolved non-hydrogen planarities: 385
    Chain: "R"
      Number of atoms: 1970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 1970
          Classifications: {'peptide': 322}
          Incomplete info: {'truncation_to_alanine': 183}
          Link IDs: {'PTRANS': 10, 'TRANS': 311}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 599
          Unresolved non-hydrogen angles: 771
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 86
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 9, 'TYR:plan': 4, 'ARG:plan': 10, 'GLN:plan1': 8, 'HIS:plan': 6, 'PHE:plan': 7, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 266
    Chain: "V"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 45
          Classifications: {'peptide': 9}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'UNK:plan-1': 9}
          Unresolved non-hydrogen planarities: 9
    Chain: "R"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'PIO': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
  Time building chain proxies: 0.94, per 1000 atoms: 0.23
  Number of scatterers: 4166
  At special positions: 0
  Unit cell: (72.08, 87.98, 121.9, 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       4     16.00
     P       3     15.00
     O     771      8.00
     N     756      7.00
     C    2632      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.02

  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: 0.30
  Conformation dependent library (CDL) restraints added in 192.3 milliseconds
  

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1310

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 9 sheets defined
      40.7% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'B' and resid 67 through 71
      removed outlier: 4.036A  pdb=" N   VAL B  70 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 107
    Processing helix  chain 'R' and resid 51 through 55
      removed outlier: 3.505A  pdb=" N   LEU R  54 " --> pdb=" O   SER R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 93
    Processing helix  chain 'R' and resid 101 through 129
      Proline residue:  R 121  - end of helix
      removed outlier: 3.996A  pdb=" N   PHE R 127 " --> pdb=" O   GLU R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 172
      removed outlier: 3.769A  pdb=" N   ILE R 170 " --> pdb=" O   ARG R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 180
    Processing helix  chain 'R' and resid 181 through 200
      removed outlier: 3.795A  pdb=" N   ALA R 200 " --> pdb=" O   SER R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 200 through 205
      removed outlier: 3.811A  pdb=" N   LEU R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 270
      removed outlier: 5.856A  pdb=" N   PHE R 247 " --> pdb=" O   MET R 243 " (cutoff:3.500A)
      Proline residue:  R 248  - end of helix
    Processing helix  chain 'R' and resid 295 through 328
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 365
      removed outlier: 3.897A  pdb=" N   TYR R 339 " --> pdb=" O   THR R 335 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ASN R 360 " --> pdb=" O   SER R 356 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 369 through 383
      removed outlier: 3.646A  pdb=" N   CYS R 383 " --> pdb=" O   LEU R 379 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 27
    Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 37
    Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85
    Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 185
    Processing sheet with id=AA6, first strand: chain 'B' and resid 214 through 215
    Processing sheet with id=AA7, first strand: chain 'B' and resid 249 through 252
      removed outlier: 3.966A  pdb=" N   ALA B 239 " --> pdb=" O   TYR B 249 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU B 256 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 252
      removed outlier: 3.966A  pdb=" N   ALA B 239 " --> pdb=" O   TYR B 249 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL B 345 " --> pdb=" O   VAL B 325 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 210 through 211

    263 hydrogen bonds defined for protein.
    741 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: 0.48

  Time building geometry restraints manager: 0.35 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: 1402
        1.34 -     1.46: 815
        1.46 -     1.57: 2021
        1.57 -     1.69: 4
        1.69 -     1.81: 4
  Bond restraints: 4246
  Sorted by residual:
  bond pdb=" C1B PIO R 400 "
       pdb=" O3C PIO R 400 "
    ideal  model  delta    sigma   weight residual
    1.331  1.457 -0.126 2.00e-02 2.50e+03 3.94e+01
  bond pdb=" C1A PIO R 400 "
       pdb=" O2C PIO R 400 "
    ideal  model  delta    sigma   weight residual
    1.332  1.455 -0.123 2.00e-02 2.50e+03 3.81e+01
  bond pdb=" O4  PIO R 400 "
       pdb=" P4  PIO R 400 "
    ideal  model  delta    sigma   weight residual
    1.710  1.612  0.098 2.00e-02 2.50e+03 2.40e+01
  bond pdb=" O5  PIO R 400 "
       pdb=" P5  PIO R 400 "
    ideal  model  delta    sigma   weight residual
    1.699  1.611  0.088 2.00e-02 2.50e+03 1.92e+01
  bond pdb=" C   GLU R 291 "
       pdb=" N   PRO R 292 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.030 1.25e-02 6.40e+03 5.91e+00
  ... (remaining 4241 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 5550
        2.00 -     4.00: 260
        4.00 -     6.01: 44
        6.01 -     8.01: 17
        8.01 -    10.01: 9
  Bond angle restraints: 5880
  Sorted by residual:
  angle pdb=" N   GLN R 333 "
        pdb=" CA  GLN R 333 "
        pdb=" C   GLN R 333 "
      ideal   model   delta    sigma   weight residual
     111.28  116.35   -5.07 1.09e+00 8.42e-01 2.16e+01
  angle pdb=" N   TRP R 334 "
        pdb=" CA  TRP R 334 "
        pdb=" C   TRP R 334 "
      ideal   model   delta    sigma   weight residual
     109.07  115.86   -6.79 1.61e+00 3.86e-01 1.78e+01
  angle pdb=" N   ARG R 182 "
        pdb=" CA  ARG R 182 "
        pdb=" C   ARG R 182 "
      ideal   model   delta    sigma   weight residual
     111.36  106.79    4.57 1.09e+00 8.42e-01 1.76e+01
  angle pdb=" N   LYS B  95 "
        pdb=" CA  LYS B  95 "
        pdb=" C   LYS B  95 "
      ideal   model   delta    sigma   weight residual
     109.81  118.49   -8.68 2.21e+00 2.05e-01 1.54e+01
  angle pdb=" N   ASN R 360 "
        pdb=" CA  ASN R 360 "
        pdb=" C   ASN R 360 "
      ideal   model   delta    sigma   weight residual
     109.81  117.99   -8.18 2.21e+00 2.05e-01 1.37e+01
  ... (remaining 5875 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.99: 2325
       14.99 -    29.99: 108
       29.99 -    44.98: 16
       44.98 -    59.97: 5
       59.97 -    74.97: 3
  Dihedral angle restraints: 2457
    sinusoidal: 448
      harmonic: 2009
  Sorted by residual:
  dihedral pdb=" CA  ILE B 241 "
           pdb=" C   ILE B 241 "
           pdb=" N   VAL B 242 "
           pdb=" CA  VAL B 242 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.99  -28.01     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  LYS B 226 "
           pdb=" C   LYS B 226 "
           pdb=" N   THR B 227 "
           pdb=" CA  THR B 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.51   27.49     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  GLN R  95 "
           pdb=" C   GLN R  95 "
           pdb=" N   SER R  96 "
           pdb=" CA  SER R  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.88   26.12     0      5.00e+00 4.00e-02 2.73e+01
  ... (remaining 2454 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 588
       0.070 -    0.141: 118
       0.141 -    0.211: 21
       0.211 -    0.282: 3
       0.282 -    0.352: 2
  Chirality restraints: 732
  Sorted by residual:
  chirality pdb=" CB  ILE B 317 "
            pdb=" CA  ILE B 317 "
            pdb=" CG1 ILE B 317 "
            pdb=" CG2 ILE B 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.35 2.00e-01 2.50e+01 3.10e+00
  chirality pdb=" CB  ILE B 241 "
            pdb=" CA  ILE B 241 "
            pdb=" CG1 ILE B 241 "
            pdb=" CG2 ILE B 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  TRP R 316 "
            pdb=" N   TRP R 316 "
            pdb=" C   TRP R 316 "
            pdb=" CB  TRP R 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 729 not shown)

  Planarity restraints: 786
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R 134 "    0.013 2.00e-02 2.50e+03   2.68e-02 7.18e+00
        pdb=" C   TRP R 134 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   TRP R 134 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA R 135 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 247 "    0.042 5.00e-02 4.00e+02   6.26e-02 6.28e+00
        pdb=" N   PRO R 248 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO R 248 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 248 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 242 "   -0.011 2.00e-02 2.50e+03   2.23e-02 4.98e+00
        pdb=" C   PHE R 242 "    0.039 2.00e-02 2.50e+03
        pdb=" O   PHE R 242 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET R 243 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 783 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 697
        2.75 -     3.29: 4206
        3.29 -     3.83: 6817
        3.83 -     4.36: 6651
        4.36 -     4.90: 11819
  Nonbonded interactions: 30190
  Sorted by model distance:
  nonbonded pdb=" O   PRO C  10 "
            pdb=" CE1 PHE R 326 "
     model   vdw
     2.216 3.340
  nonbonded pdb=" O   ALA B 301 "
            pdb=" OH  TYR B 321 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   VAL R  83 "
            pdb=" OG1 THR R  87 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER R 213 "
            pdb=" O   ASP R 215 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   LEU R 108 "
            pdb=" OG  SER R 111 "
     model   vdw
     2.310 3.040
  ... (remaining 30185 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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.010
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
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      :  0.009   0.126   4247  Z= 0.430
  Angle     :  1.078  10.010   5882  Z= 0.592
  Chirality :  0.061   0.352    732
  Planarity :  0.008   0.063    786
  Dihedral  : 10.401  74.968   1144
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.17 %
    Favored  : 86.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  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 are not related in a simple way.
  whole: -5.14 (0.26), residues: 668
  helix: -1.80 (0.26), residues: 242
  sheet: -4.64 (0.31), residues: 133
  loop : -4.19 (0.30), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.002   ARG R 323 
 TYR   0.013   0.003   TYR B 272 
 PHE   0.020   0.003   PHE R 345 
 TRP   0.025   0.006   TRP R 134 
 HIS   0.014   0.004   HIS R 320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00850 /  0.43 ( 4246)
  covalent geometry    : angle       1.07786 /  0.59 ( 5880)
  SS BOND              : bond        0.00840 /  0.44 (    1)
  SS BOND              : angle       0.87858 /  0.49 (    2)
  hydrogen bonds       : bond        0.17933 / 11.43 (  260)
  hydrogen bonds       : angle       8.78474 /  5.89 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.157 
Fit side-chains
REVERT: B   76 ARG cc_start: 0.9053 (ppp-140) cc_final: 0.8792 (ptm-80)
REVERT: B  236 ARG cc_start: 0.8197 (mpp80) cc_final: 0.7600 (mtp85)
REVERT: B  250 LYS cc_start: 0.8873 (ttpp) cc_final: 0.7837 (tttt)
REVERT: R   88 LEU cc_start: 0.9423 (tt) cc_final: 0.8952 (tt)
REVERT: R  102 HIS cc_start: 0.6599 (t-90) cc_final: 0.6108 (t-90)
REVERT: R  104 HIS cc_start: 0.9020 (m90) cc_final: 0.8445 (m-70)
REVERT: R  148 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8173 (ttp80)
REVERT: R  190 SER cc_start: 0.9426 (m) cc_final: 0.9075 (p)
REVERT: R  315 CYS cc_start: 0.8333 (p) cc_final: 0.7878 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0729
  time to fit residues: 8.2971
Evaluate side-chains
  77 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:   30.0000
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 237 GLN
R 373 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.079698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.065203 restraints weight = 19519.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.066453 restraints weight = 13736.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.067336 restraints weight = 10780.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.067857 restraints weight = 9087.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.068277 restraints weight = 8167.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4247  Z= 0.134
  Angle     :  0.638   8.217   5882  Z= 0.327
  Chirality :  0.045   0.237    732
  Planarity :  0.005   0.036    786
  Dihedral  :  7.114  79.846    721
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  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 are not related in a simple way.
  whole: -3.50 (0.30), residues: 668
  helix:  0.21 (0.30), residues: 264
  sheet: -4.29 (0.33), residues: 136
  loop : -3.89 (0.32), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG R 323 
 TYR   0.028   0.002   TYR R 153 
 PHE   0.008   0.001   PHE B 117 
 TRP   0.021   0.002   TRP R 316 
 HIS   0.008   0.002   HIS R 373 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.13 ( 4246)
  covalent geometry    : angle       0.63758 /  0.33 ( 5880)
  SS BOND              : bond        0.00301 /  0.16 (    1)
  SS BOND              : angle       0.55728 /  0.30 (    2)
  hydrogen bonds       : bond        0.04381 /  3.26 (  260)
  hydrogen bonds       : angle       5.78992 /  3.87 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.094 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.8048 (t80) cc_final: 0.7789 (t80)
REVERT: B  217 ASN cc_start: 0.9386 (t0) cc_final: 0.9154 (t0)
REVERT: B  236 ARG cc_start: 0.8032 (mpp80) cc_final: 0.7638 (mtp85)
REVERT: B  250 LYS cc_start: 0.9063 (ttpp) cc_final: 0.7842 (ttmt)
REVERT: B  285 ARG cc_start: 0.7953 (mtp85) cc_final: 0.7644 (ttm170)
REVERT: B  346 GLU cc_start: 0.7914 (mp0) cc_final: 0.7697 (mp0)
REVERT: R   88 LEU cc_start: 0.9492 (tt) cc_final: 0.8906 (tt)
REVERT: R   98 GLN cc_start: 0.7624 (mt0) cc_final: 0.7366 (mt0)
REVERT: R  102 HIS cc_start: 0.6941 (t-90) cc_final: 0.6184 (t-90)
REVERT: R  190 SER cc_start: 0.9346 (m) cc_final: 0.8982 (p)
REVERT: R  233 VAL cc_start: 0.9554 (m) cc_final: 0.9317 (p)
REVERT: R  344 TYR cc_start: 0.8460 (m-80) cc_final: 0.8110 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0641
  time to fit residues: 7.4862
Evaluate side-chains
  83 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0000
   chunk 48 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0030
   chunk 54 optimal weight:    0.4980
   chunk 5 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    1.6998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 237 GLN
R 104 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.078112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.063666 restraints weight = 19539.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.064882 restraints weight = 13831.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.065682 restraints weight = 10950.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.066018 restraints weight = 9345.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.066611 restraints weight = 8582.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4247  Z= 0.181
  Angle     :  0.628   7.514   5882  Z= 0.329
  Chirality :  0.044   0.155    732
  Planarity :  0.004   0.033    786
  Dihedral  :  6.553  73.405    721
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.63 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  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: -2.67 (0.32), residues: 668
  helix:  1.07 (0.32), residues: 261
  sheet: -4.08 (0.34), residues: 138
  loop : -3.41 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 182 
 TYR   0.010   0.001   TYR B  63 
 PHE   0.011   0.002   PHE R 127 
 TRP   0.013   0.002   TRP R 134 
 HIS   0.005   0.002   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.18 ( 4246)
  covalent geometry    : angle       0.62801 /  0.33 ( 5880)
  SS BOND              : bond        0.00355 /  0.19 (    1)
  SS BOND              : angle       0.75639 /  0.40 (    2)
  hydrogen bonds       : bond        0.04413 /  3.29 (  260)
  hydrogen bonds       : angle       5.53819 /  3.68 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.111 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.7925 (t80) cc_final: 0.7383 (t80)
REVERT: B  202 SER cc_start: 0.8947 (p) cc_final: 0.8187 (t)
REVERT: B  217 ASN cc_start: 0.9380 (t0) cc_final: 0.8938 (p0)
REVERT: B  236 ARG cc_start: 0.8009 (mpp80) cc_final: 0.7134 (mtp85)
REVERT: B  244 PHE cc_start: 0.7611 (t80) cc_final: 0.7009 (t80)
REVERT: B  250 LYS cc_start: 0.9231 (ttpp) cc_final: 0.8008 (tttt)
REVERT: B  346 GLU cc_start: 0.7902 (mp0) cc_final: 0.7677 (mp0)
REVERT: R   88 LEU cc_start: 0.9622 (tt) cc_final: 0.9031 (tt)
REVERT: R   98 GLN cc_start: 0.7373 (mt0) cc_final: 0.7052 (tt0)
REVERT: R  102 HIS cc_start: 0.7192 (t-90) cc_final: 0.6427 (t-90)
REVERT: R  190 SER cc_start: 0.9325 (m) cc_final: 0.8951 (p)
REVERT: R  233 VAL cc_start: 0.9540 (m) cc_final: 0.9269 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0598
  time to fit residues: 6.5565
Evaluate side-chains
  78 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 66 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    2.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 237 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.076951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.062533 restraints weight = 19671.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.063502 restraints weight = 14057.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.064407 restraints weight = 11393.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.064928 restraints weight = 9722.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.065224 restraints weight = 8767.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4247  Z= 0.225
  Angle     :  0.643   7.225   5882  Z= 0.341
  Chirality :  0.045   0.140    732
  Planarity :  0.004   0.030    786
  Dihedral  :  6.252  51.630    721
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.38 %
    Favored  : 88.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  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: -2.52 (0.33), residues: 668
  helix:  1.11 (0.32), residues: 263
  sheet: -3.98 (0.35), residues: 139
  loop : -3.26 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 148 
 TYR   0.011   0.002   TYR C  11 
 PHE   0.013   0.002   PHE R 326 
 TRP   0.013   0.002   TRP R 134 
 HIS   0.007   0.002   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00448 /  0.22 ( 4246)
  covalent geometry    : angle       0.64324 /  0.34 ( 5880)
  SS BOND              : bond        0.00395 /  0.21 (    1)
  SS BOND              : angle       0.85400 /  0.45 (    2)
  hydrogen bonds       : bond        0.04565 /  3.44 (  260)
  hydrogen bonds       : angle       5.56196 /  3.68 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.166 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.7975 (t80) cc_final: 0.7250 (t80)
REVERT: B  202 SER cc_start: 0.8934 (p) cc_final: 0.8365 (t)
REVERT: B  217 ASN cc_start: 0.9354 (t0) cc_final: 0.8963 (p0)
REVERT: B  236 ARG cc_start: 0.7944 (mpp80) cc_final: 0.7274 (mtp85)
REVERT: B  244 PHE cc_start: 0.7728 (t80) cc_final: 0.6908 (t80)
REVERT: B  250 LYS cc_start: 0.9207 (ttpp) cc_final: 0.8423 (ttpp)
REVERT: R   88 LEU cc_start: 0.9612 (tt) cc_final: 0.8901 (tt)
REVERT: R  102 HIS cc_start: 0.7087 (t-90) cc_final: 0.6167 (t-90)
REVERT: R  144 TYR cc_start: 0.8713 (t80) cc_final: 0.8377 (t80)
REVERT: R  190 SER cc_start: 0.9320 (m) cc_final: 0.8975 (p)
REVERT: R  233 VAL cc_start: 0.9576 (m) cc_final: 0.9305 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0663
  time to fit residues: 6.9240
Evaluate side-chains
  74 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0270
   chunk 44 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 64 optimal weight:    0.5980
   chunk 51 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 9 optimal weight:    0.3980
   chunk 39 optimal weight:    8.9990
   overall best weight:    0.6038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 237 GLN
R 104 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.080588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.066256 restraints weight = 19378.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.067409 restraints weight = 14166.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.068211 restraints weight = 11399.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.068774 restraints weight = 9799.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.069029 restraints weight = 8821.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4247  Z= 0.113
  Angle     :  0.560   6.233   5882  Z= 0.283
  Chirality :  0.043   0.188    732
  Planarity :  0.003   0.026    786
  Dihedral  :  5.677  67.125    721
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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: -2.00 (0.33), residues: 668
  helix:  1.47 (0.31), residues: 269
  sheet: -3.60 (0.37), residues: 139
  loop : -3.06 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  65 
 TYR   0.013   0.002   TYR R 342 
 PHE   0.014   0.001   PHE R 247 
 TRP   0.017   0.002   TRP R 316 
 HIS   0.006   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00223 /  0.11 ( 4246)
  covalent geometry    : angle       0.55987 /  0.28 ( 5880)
  SS BOND              : bond        0.00194 /  0.10 (    1)
  SS BOND              : angle       0.29513 /  0.16 (    2)
  hydrogen bonds       : bond        0.03711 /  2.78 (  260)
  hydrogen bonds       : angle       4.75442 /  3.16 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.093 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.7715 (t80) cc_final: 0.7102 (t80)
REVERT: B  202 SER cc_start: 0.8976 (p) cc_final: 0.8514 (t)
REVERT: B  217 ASN cc_start: 0.9375 (t0) cc_final: 0.8973 (p0)
REVERT: B  236 ARG cc_start: 0.7800 (mpp80) cc_final: 0.7301 (mtp85)
REVERT: B  244 PHE cc_start: 0.7925 (t80) cc_final: 0.7267 (t80)
REVERT: B  250 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8666 (ttmt)
REVERT: R   88 LEU cc_start: 0.9583 (tt) cc_final: 0.8783 (tt)
REVERT: R  102 HIS cc_start: 0.7047 (t-90) cc_final: 0.6053 (t-90)
REVERT: R  190 SER cc_start: 0.9244 (m) cc_final: 0.8891 (p)
REVERT: R  233 VAL cc_start: 0.9532 (m) cc_final: 0.9324 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0558
  time to fit residues: 6.4035
Evaluate side-chains
  80 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 18 optimal weight:   30.0000
   chunk 37 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 19 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   overall best weight:    4.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.074417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.060169 restraints weight = 20740.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.061193 restraints weight = 14680.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.062145 restraints weight = 11715.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.062586 restraints weight = 9906.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.063026 restraints weight = 8987.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   4247  Z= 0.353
  Angle     :  0.761   7.107   5882  Z= 0.415
  Chirality :  0.048   0.192    732
  Planarity :  0.005   0.026    786
  Dihedral  :  6.681  63.104    721
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.77 %
    Favored  : 86.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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: -2.70 (0.32), residues: 668
  helix:  0.63 (0.31), residues: 257
  sheet: -3.81 (0.34), residues: 139
  loop : -3.07 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG R 148 
 TYR   0.020   0.003   TYR R 153 
 PHE   0.020   0.003   PHE R 326 
 TRP   0.018   0.003   TRP R 134 
 HIS   0.010   0.003   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00705 /  0.35 ( 4246)
  covalent geometry    : angle       0.76051 /  0.41 ( 5880)
  SS BOND              : bond        0.00032 /  0.02 (    1)
  SS BOND              : angle       1.77989 /  0.94 (    2)
  hydrogen bonds       : bond        0.05395 /  4.05 (  260)
  hydrogen bonds       : angle       6.21425 /  4.13 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
REVERT: B   63 TYR cc_start: 0.8178 (t80) cc_final: 0.7627 (t80)
REVERT: B  236 ARG cc_start: 0.8057 (mpp80) cc_final: 0.7844 (mtp85)
REVERT: B  250 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8602 (ttmt)
REVERT: R   88 LEU cc_start: 0.9593 (tt) cc_final: 0.8808 (tt)
REVERT: R  102 HIS cc_start: 0.7158 (t-90) cc_final: 0.6377 (t-90)
REVERT: R  190 SER cc_start: 0.9377 (m) cc_final: 0.9066 (p)
REVERT: R  344 TYR cc_start: 0.8489 (m-80) cc_final: 0.8017 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0642
  time to fit residues: 6.3841
Evaluate side-chains
  69 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 237 GLN
R 104 HIS
R 373 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.077978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.063546 restraints weight = 19908.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.064790 restraints weight = 14049.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.065671 restraints weight = 11021.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.066075 restraints weight = 9320.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.066539 restraints weight = 8473.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4247  Z= 0.154
  Angle     :  0.621   7.082   5882  Z= 0.317
  Chirality :  0.045   0.144    732
  Planarity :  0.004   0.027    786
  Dihedral  :  6.021  72.751    721
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  2.93 %
    Favored  : 96.59 %
  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 (0.33), residues: 668
  helix:  1.27 (0.32), residues: 263
  sheet: -3.56 (0.35), residues: 145
  loop : -2.83 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  65 
 TYR   0.016   0.002   TYR R 342 
 PHE   0.012   0.001   PHE R 247 
 TRP   0.011   0.002   TRP R 316 
 HIS   0.009   0.002   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.15 ( 4246)
  covalent geometry    : angle       0.62087 /  0.32 ( 5880)
  SS BOND              : bond        0.00255 /  0.13 (    1)
  SS BOND              : angle       1.18480 /  0.63 (    2)
  hydrogen bonds       : bond        0.04195 /  3.15 (  260)
  hydrogen bonds       : angle       5.13962 /  3.41 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.178 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.8011 (t80) cc_final: 0.7221 (t80)
REVERT: B  236 ARG cc_start: 0.8066 (mpp80) cc_final: 0.7406 (mtp85)
REVERT: B  250 LYS cc_start: 0.9196 (ttpp) cc_final: 0.8644 (tttt)
REVERT: R   88 LEU cc_start: 0.9592 (tt) cc_final: 0.8850 (tt)
REVERT: R  102 HIS cc_start: 0.7147 (t-90) cc_final: 0.6417 (t-90)
REVERT: R  148 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8563 (ttm-80)
REVERT: R  190 SER cc_start: 0.9349 (m) cc_final: 0.9045 (p)
REVERT: R  233 VAL cc_start: 0.9531 (m) cc_final: 0.9295 (p)
REVERT: R  344 TYR cc_start: 0.8422 (m-80) cc_final: 0.7985 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0730
  time to fit residues: 7.6139
Evaluate side-chains
  75 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0670
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.8126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 237 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 = 0.3327 r_free = 0.3327 target = 0.075940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.061848 restraints weight = 20078.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.062985 restraints weight = 14273.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.063832 restraints weight = 11275.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.064226 restraints weight = 9558.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.064607 restraints weight = 8670.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   4247  Z= 0.256
  Angle     :  0.669   6.617   5882  Z= 0.355
  Chirality :  0.046   0.189    732
  Planarity :  0.004   0.032    786
  Dihedral  :  6.349  74.029    721
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.38 %
    Favored  : 88.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.10 (0.33), residues: 668
  helix:  1.13 (0.31), residues: 262
  sheet: -3.49 (0.37), residues: 136
  loop : -2.82 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 236 
 TYR   0.009   0.001   TYR B 321 
 PHE   0.017   0.002   PHE R 245 
 TRP   0.013   0.002   TRP R 134 
 HIS   0.009   0.002   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00517 /  0.26 ( 4246)
  covalent geometry    : angle       0.66907 /  0.36 ( 5880)
  SS BOND              : bond        0.00337 /  0.18 (    1)
  SS BOND              : angle       0.83416 /  0.45 (    2)
  hydrogen bonds       : bond        0.04698 /  3.56 (  260)
  hydrogen bonds       : angle       5.53145 /  3.67 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.161 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.8121 (t80) cc_final: 0.7473 (t80)
REVERT: B  250 LYS cc_start: 0.9292 (ttpp) cc_final: 0.8812 (tttt)
REVERT: R   88 LEU cc_start: 0.9586 (tt) cc_final: 0.8795 (tt)
REVERT: R  102 HIS cc_start: 0.7084 (t-90) cc_final: 0.6309 (t-90)
REVERT: R  144 TYR cc_start: 0.8664 (t80) cc_final: 0.8381 (t80)
REVERT: R  190 SER cc_start: 0.9364 (m) cc_final: 0.9048 (p)
REVERT: R  233 VAL cc_start: 0.9533 (m) cc_final: 0.9271 (p)
REVERT: R  323 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8446 (mtm180)
REVERT: R  344 TYR cc_start: 0.8384 (m-80) cc_final: 0.8067 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0666
  time to fit residues: 6.8452
Evaluate side-chains
  73 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 5 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 237 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 = 0.3379 r_free = 0.3379 target = 0.078288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.063913 restraints weight = 19948.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.065146 restraints weight = 14012.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.065936 restraints weight = 10978.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.066447 restraints weight = 9334.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.066447 restraints weight = 8407.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4247  Z= 0.150
  Angle     :  0.612   6.749   5882  Z= 0.311
  Chirality :  0.044   0.152    732
  Planarity :  0.004   0.027    786
  Dihedral  :  6.071  78.643    721
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.34), residues: 668
  helix:  1.53 (0.31), residues: 263
  sheet: -3.21 (0.37), residues: 142
  loop : -2.75 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  65 
 TYR   0.020   0.002   TYR R 342 
 PHE   0.028   0.001   PHE B 268 
 TRP   0.010   0.002   TRP R 316 
 HIS   0.007   0.001   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.15 ( 4246)
  covalent geometry    : angle       0.61207 /  0.31 ( 5880)
  SS BOND              : bond        0.00356 /  0.19 (    1)
  SS BOND              : angle       0.69276 /  0.36 (    2)
  hydrogen bonds       : bond        0.04119 /  3.09 (  260)
  hydrogen bonds       : angle       5.07628 /  3.39 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.176 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.8006 (t80) cc_final: 0.6955 (t80)
REVERT: B  244 PHE cc_start: 0.7883 (t80) cc_final: 0.7043 (t80)
REVERT: B  324 LYS cc_start: 0.9111 (tttt) cc_final: 0.8875 (tttt)
REVERT: R   88 LEU cc_start: 0.9570 (tt) cc_final: 0.8801 (tt)
REVERT: R  102 HIS cc_start: 0.7063 (t-90) cc_final: 0.6292 (t-90)
REVERT: R  103 TYR cc_start: 0.8578 (m-80) cc_final: 0.8201 (m-80)
REVERT: R  190 SER cc_start: 0.9297 (m) cc_final: 0.8983 (p)
REVERT: R  233 VAL cc_start: 0.9527 (m) cc_final: 0.9293 (p)
REVERT: R  344 TYR cc_start: 0.8373 (m-80) cc_final: 0.8167 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0776
  time to fit residues: 8.4768
Evaluate side-chains
  76 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 33 optimal weight:   30.0000
   chunk 24 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 237 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 = 0.3372 r_free = 0.3372 target = 0.078019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.063760 restraints weight = 19652.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.064973 restraints weight = 13985.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.065740 restraints weight = 11071.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.065740 restraints weight = 9477.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.065740 restraints weight = 9477.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4247  Z= 0.166
  Angle     :  0.612   6.903   5882  Z= 0.311
  Chirality :  0.044   0.159    732
  Planarity :  0.004   0.029    786
  Dihedral  :  5.917  81.101    721
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.34), residues: 668
  helix:  1.64 (0.31), residues: 263
  sheet: -3.04 (0.38), residues: 142
  loop : -2.69 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  76 
 TYR   0.009   0.001   TYR B  63 
 PHE   0.039   0.002   PHE R 245 
 TRP   0.011   0.002   TRP R 316 
 HIS   0.007   0.002   HIS R 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.17 ( 4246)
  covalent geometry    : angle       0.61239 /  0.31 ( 5880)
  SS BOND              : bond        0.00223 /  0.12 (    1)
  SS BOND              : angle       0.58589 /  0.32 (    2)
  hydrogen bonds       : bond        0.04135 /  3.13 (  260)
  hydrogen bonds       : angle       5.05357 /  3.35 (  741)

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

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

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1336 Ramachandran restraints generated.
    668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.138 
Fit side-chains
REVERT: B   63 TYR cc_start: 0.8001 (t80) cc_final: 0.6931 (t80)
REVERT: B  244 PHE cc_start: 0.8014 (t80) cc_final: 0.7131 (t80)
REVERT: B  250 LYS cc_start: 0.8814 (tttt) cc_final: 0.8599 (tttt)
REVERT: B  324 LYS cc_start: 0.9166 (tttt) cc_final: 0.8523 (ttpt)
REVERT: R   88 LEU cc_start: 0.9600 (tt) cc_final: 0.8827 (tt)
REVERT: R  102 HIS cc_start: 0.7167 (t-90) cc_final: 0.6398 (t-90)
REVERT: R  144 TYR cc_start: 0.8634 (t80) cc_final: 0.8359 (t80)
REVERT: R  190 SER cc_start: 0.9354 (m) cc_final: 0.9053 (p)
REVERT: R  233 VAL cc_start: 0.9517 (m) cc_final: 0.9270 (p)
REVERT: R  344 TYR cc_start: 0.8370 (m-80) cc_final: 0.8161 (m-80)
REVERT: R  373 HIS cc_start: 0.9126 (t-90) cc_final: 0.8904 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0588
  time to fit residues: 6.5912
Evaluate side-chains
  79 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 237 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 = 0.3332 r_free = 0.3332 target = 0.076091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.061765 restraints weight = 20125.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.062979 restraints weight = 14180.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.063604 restraints weight = 11164.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.064322 restraints weight = 9658.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.064573 restraints weight = 8575.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4247  Z= 0.254
  Angle     :  0.659   6.778   5882  Z= 0.349
  Chirality :  0.045   0.148    732
  Planarity :  0.004   0.027    786
  Dihedral  :  6.263  85.942    721
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.23 %
    Favored  : 88.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.34), residues: 668
  helix:  1.30 (0.31), residues: 262
  sheet: -3.09 (0.38), residues: 146
  loop : -2.64 (0.40), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  76 
 TYR   0.021   0.002   TYR R 342 
 PHE   0.027   0.002   PHE B 268 
 TRP   0.012   0.002   TRP R 134 
 HIS   0.009   0.002   HIS R 320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00514 /  0.25 ( 4246)
  covalent geometry    : angle       0.65851 /  0.35 ( 5880)
  SS BOND              : bond        0.00349 /  0.18 (    1)
  SS BOND              : angle       0.82811 /  0.44 (    2)
  hydrogen bonds       : bond        0.04670 /  3.52 (  260)
  hydrogen bonds       : angle       5.47296 /  3.64 (  741)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 751.48 seconds
wall clock time: 14 minutes 4.93 seconds (844.93 seconds total)