Starting phenix.real_space_refine
on Tue Mar  3 12:27:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f3u_31441/03_2026/7f3u_31441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f3u_31441/03_2026/7f3u_31441.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f3u_31441/03_2026/7f3u_31441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f3u_31441/03_2026/7f3u_31441.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f3u_31441/03_2026/7f3u_31441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f3u_31441/03_2026/7f3u_31441.cif"
  }
  resolution = 4.0
  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=   1.000
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      18      5.16       5
     C    2716      2.51       5
     N     740      2.21       5
     O     800      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4274
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2137
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 153}
          Link IDs: {'PTRANS': 8, 'TRANS': 319}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 653
          Unresolved non-hydrogen angles: 828
          Unresolved non-hydrogen dihedrals: 568
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 11, 'TRP:plan': 5, 'GLU:plan': 12, 'GLN:plan1': 16, 'PHE:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 6, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 397
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.45, per 1000 atoms: 0.34
  Number of scatterers: 4274
  At special positions: 0
  Unit cell: (71.34, 113.98, 88.56, 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      18     16.00
     O     800      8.00
     N     740      7.00
     C    2716      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.26
  Conformation dependent library (CDL) restraints added in 189.0 milliseconds
  

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1244

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      85.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 72
      Proline residue:  A  70  - end of helix
    Processing helix  chain 'A' and resid 73 through 99
      removed outlier: 4.186A  pdb=" N   ALA A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 113
    Processing helix  chain 'A' and resid 122 through 154
    Processing helix  chain 'A' and resid 157 through 186
      removed outlier: 3.623A  pdb=" N   ASP A 161 " --> pdb=" O   SER A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 209
    Processing helix  chain 'A' and resid 213 through 252
      removed outlier: 4.526A  pdb=" N   ASN A 221 " --> pdb=" O   GLN A 217 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   GLN A 222 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 297
      Proline residue:  A 277  - end of helix
    Processing helix  chain 'A' and resid 306 through 334
      Proline residue:  A 313  - end of helix
    Processing helix  chain 'B' and resid 8 through 72
      Proline residue:  B  70  - end of helix
    Processing helix  chain 'B' and resid 73 through 99
      removed outlier: 4.185A  pdb=" N   ALA B  79 " --> pdb=" O   GLU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 113
    Processing helix  chain 'B' and resid 122 through 154
    Processing helix  chain 'B' and resid 157 through 186
      removed outlier: 3.623A  pdb=" N   ASP B 161 " --> pdb=" O   SER B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 209
    Processing helix  chain 'B' and resid 213 through 252
      removed outlier: 4.527A  pdb=" N   ASN B 221 " --> pdb=" O   GLN B 217 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   GLN B 222 " --> pdb=" O   LYS B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 297
      Proline residue:  B 277  - end of helix
    Processing helix  chain 'B' and resid 306 through 334
      Proline residue:  B 313  - end of helix

    461 hydrogen bonds defined for protein.
    1383 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: 0.69

  Time building geometry restraints manager: 0.37 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: 1428
        1.34 -     1.45: 646
        1.45 -     1.57: 2258
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 4356
  Sorted by residual:
  bond pdb=" CG  ARG A 178 "
       pdb=" CD  ARG A 178 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.80e+00
  bond pdb=" CG  ARG B 178 "
       pdb=" CD  ARG B 178 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.79e+00
  bond pdb=" CA  VAL A 233 "
       pdb=" CB  VAL A 233 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.015 1.25e-02 6.40e+03 1.51e+00
  bond pdb=" CB  TRP A 170 "
       pdb=" CG  TRP A 170 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.49e+00
  bond pdb=" CA  ILE B 145 "
       pdb=" CB  ILE B 145 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.014 1.17e-02 7.31e+03 1.49e+00
  ... (remaining 4351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 5828
        2.26 -     4.51: 126
        4.51 -     6.77: 32
        6.77 -     9.02: 6
        9.02 -    11.28: 2
  Bond angle restraints: 5994
  Sorted by residual:
  angle pdb=" N   PRO B   8 "
        pdb=" CA  PRO B   8 "
        pdb=" CB  PRO B   8 "
      ideal   model   delta    sigma   weight residual
     103.39  110.08   -6.69 1.08e+00 8.57e-01 3.84e+01
  angle pdb=" N   PRO A   8 "
        pdb=" CA  PRO A   8 "
        pdb=" CB  PRO A   8 "
      ideal   model   delta    sigma   weight residual
     103.39  110.07   -6.68 1.08e+00 8.57e-01 3.83e+01
  angle pdb=" NE  ARG B 178 "
        pdb=" CZ  ARG B 178 "
        pdb=" NH1 ARG B 178 "
      ideal   model   delta    sigma   weight residual
     121.50  117.42    4.08 1.00e+00 1.00e+00 1.66e+01
  angle pdb=" NE  ARG A 178 "
        pdb=" CZ  ARG A 178 "
        pdb=" NH1 ARG A 178 "
      ideal   model   delta    sigma   weight residual
     121.50  117.52    3.98 1.00e+00 1.00e+00 1.58e+01
  angle pdb=" CB  MET A  87 "
        pdb=" CG  MET A  87 "
        pdb=" SD  MET A  87 "
      ideal   model   delta    sigma   weight residual
     112.70  123.98  -11.28 3.00e+00 1.11e-01 1.41e+01
  ... (remaining 5989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.29: 2272
       12.29 -    24.58: 152
       24.58 -    36.86: 74
       36.86 -    49.15: 6
       49.15 -    61.44: 6
  Dihedral angle restraints: 2510
    sinusoidal: 586
      harmonic: 1924
  Sorted by residual:
  dihedral pdb=" CA  LEU B 154 "
           pdb=" C   LEU B 154 "
           pdb=" N   LEU B 155 "
           pdb=" CA  LEU B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.52  -26.48     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  LEU A 154 "
           pdb=" C   LEU A 154 "
           pdb=" N   LEU A 155 "
           pdb=" CA  LEU A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.53  -26.47     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  GLY A 106 "
           pdb=" C   GLY A 106 "
           pdb=" N   LEU A 107 "
           pdb=" CA  LEU A 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.77   25.23     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 2507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 524
       0.046 -    0.093: 174
       0.093 -    0.139: 17
       0.139 -    0.185: 7
       0.185 -    0.231: 2
  Chirality restraints: 724
  Sorted by residual:
  chirality pdb=" CA  PRO A   8 "
            pdb=" N   PRO A   8 "
            pdb=" C   PRO A   8 "
            pdb=" CB  PRO A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  PRO B   8 "
            pdb=" N   PRO B   8 "
            pdb=" C   PRO B   8 "
            pdb=" CB  PRO B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CG  LEU B 140 "
            pdb=" CB  LEU B 140 "
            pdb=" CD1 LEU B 140 "
            pdb=" CD2 LEU B 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.10e-01
  ... (remaining 721 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 139 "    0.016 2.00e-02 2.50e+03   1.39e-02 3.84e+00
        pdb=" CG  TYR B 139 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 139 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 139 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 139 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 139 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 139 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 139 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 139 "   -0.016 2.00e-02 2.50e+03   1.38e-02 3.79e+00
        pdb=" CG  TYR A 139 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 139 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 139 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 139 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 139 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 139 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 139 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 238 "    0.016 2.00e-02 2.50e+03   9.75e-03 1.90e+00
        pdb=" CG  TYR A 238 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 238 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 238 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 238 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 238 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 238 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR A 238 "    0.000 2.00e-02 2.50e+03
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1454
        2.82 -     3.34: 5127
        3.34 -     3.86: 7295
        3.86 -     4.38: 7293
        4.38 -     4.90: 11642
  Nonbonded interactions: 32811
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 105 "
            pdb=" O   ASN A 115 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND2 ASN B 105 "
            pdb=" O   ASN B 115 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND2 ASN B 165 "
            pdb=" OG  SER B 204 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" ND2 ASN A 165 "
            pdb=" OG  SER A 204 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   MET A 228 "
            pdb=" OG  SER A 231 "
     model   vdw
     2.324 3.040
  ... (remaining 32806 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=0.00 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:             1.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.280
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
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      :  0.006   0.050   4356  Z= 0.307
  Angle     :  0.885  11.280   5994  Z= 0.512
  Chirality :  0.045   0.231    724
  Planarity :  0.004   0.029    790
  Dihedral  : 11.591  61.439   1266
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 21.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.22 (0.33), residues: 652
  helix:  2.47 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -3.11 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 152 
 TYR   0.034   0.003   TYR B 139 
 PHE   0.021   0.002   PHE A 153 
 TRP   0.014   0.002   TRP A 210 
 HIS   0.009   0.003   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 ( 4356)
  covalent geometry    : angle       0.88521 ( 5994)
  hydrogen bonds       : bond        0.09859 (  461)
  hydrogen bonds       : angle       4.75288 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.8931 (mmmm) cc_final: 0.7947 (mmmm)
REVERT: A  139 TYR cc_start: 0.7886 (m-80) cc_final: 0.7335 (m-80)
REVERT: B  135 LYS cc_start: 0.8908 (mmmm) cc_final: 0.7930 (mmmm)
REVERT: B  136 PHE cc_start: 0.8158 (t80) cc_final: 0.7954 (t80)
REVERT: B  139 TYR cc_start: 0.7900 (m-80) cc_final: 0.7287 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0613
  time to fit residues: 13.2220
Evaluate side-chains
  120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:   30.0000
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.099605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.080487 restraints weight = 15889.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.082674 restraints weight = 9591.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.084164 restraints weight = 6718.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.085071 restraints weight = 5184.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.085792 restraints weight = 4391.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4356  Z= 0.159
  Angle     :  0.730  10.181   5994  Z= 0.381
  Chirality :  0.041   0.144    724
  Planarity :  0.004   0.023    790
  Dihedral  :  4.785  22.403    690
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  7.29 %
    Allowed  : 20.14 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.28 (0.34), residues: 652
  helix:  3.17 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -3.17 (0.54), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  90 
 TYR   0.021   0.002   TYR B 139 
 PHE   0.018   0.001   PHE A 153 
 TRP   0.015   0.001   TRP A 210 
 HIS   0.003   0.002   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4356)
  covalent geometry    : angle       0.72978 ( 5994)
  hydrogen bonds       : bond        0.04918 (  461)
  hydrogen bonds       : angle       3.80570 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8309 (mmmm)
REVERT: A  139 TYR cc_start: 0.8077 (m-80) cc_final: 0.7542 (m-80)
REVERT: A  153 PHE cc_start: 0.8516 (m-80) cc_final: 0.8110 (m-80)
REVERT: A  245 LEU cc_start: 0.8074 (mm) cc_final: 0.7872 (mm)
REVERT: B  135 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8283 (mmmm)
REVERT: B  139 TYR cc_start: 0.8021 (m-80) cc_final: 0.7497 (m-80)
REVERT: B  153 PHE cc_start: 0.8494 (m-80) cc_final: 0.8082 (m-80)
  outliers start: 21
  outliers final: 14
  residues processed: 166
  average time/residue: 0.0596
  time to fit residues: 12.6582
Evaluate side-chains
  156 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  232 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 25 optimal weight:   40.0000
   chunk 12 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 32 optimal weight:    8.9990
   chunk 24 optimal weight:   30.0000
   chunk 14 optimal weight:    6.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 165 ASN
A 185 ASN
A 196 HIS
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 165 ASN
B 185 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.094063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.075914 restraints weight = 16496.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.077102 restraints weight = 11643.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.077978 restraints weight = 9174.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.078465 restraints weight = 7723.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.078841 restraints weight = 6977.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   4356  Z= 0.302
  Angle     :  0.843   8.647   5994  Z= 0.465
  Chirality :  0.044   0.163    724
  Planarity :  0.004   0.025    790
  Dihedral  :  5.133  24.549    690
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  9.72 %
    Allowed  : 30.90 %
    Favored  : 59.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.33), residues: 652
  helix:  2.76 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -3.22 (0.54), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 178 
 TYR   0.025   0.003   TYR A 133 
 PHE   0.015   0.002   PHE A 235 
 TRP   0.008   0.002   TRP B 170 
 HIS   0.010   0.003   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 4356)
  covalent geometry    : angle       0.84276 ( 5994)
  hydrogen bonds       : bond        0.05762 (  461)
  hydrogen bonds       : angle       4.48499 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  153 PHE cc_start: 0.8842 (m-80) cc_final: 0.8471 (m-80)
REVERT: A  175 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9246 (tt)
REVERT: B  153 PHE cc_start: 0.8839 (m-80) cc_final: 0.8425 (m-80)
REVERT: B  175 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9230 (tt)
  outliers start: 28
  outliers final: 22
  residues processed: 135
  average time/residue: 0.0538
  time to fit residues: 9.6088
Evaluate side-chains
  142 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0270
   chunk 15 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 20 optimal weight:    0.3980
   chunk 63 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    2.6844

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 ASN
A 237 GLN
B 185 ASN
B 237 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.097647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.078434 restraints weight = 15780.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.080484 restraints weight = 9661.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.081864 restraints weight = 6856.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.082838 restraints weight = 5377.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.083428 restraints weight = 4529.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4356  Z= 0.170
  Angle     :  0.729   8.500   5994  Z= 0.385
  Chirality :  0.041   0.163    724
  Planarity :  0.003   0.022    790
  Dihedral  :  4.692  21.625    690
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers : 10.07 %
    Allowed  : 29.86 %
    Favored  : 60.07 %
  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:  3.35 (0.33), residues: 652
  helix:  3.19 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -3.10 (0.54), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 247 
 TYR   0.020   0.002   TYR A 171 
 PHE   0.020   0.001   PHE A 219 
 TRP   0.010   0.001   TRP B 210 
 HIS   0.002   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4356)
  covalent geometry    : angle       0.72934 ( 5994)
  hydrogen bonds       : bond        0.04882 (  461)
  hydrogen bonds       : angle       3.86325 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.134 
Fit side-chains
REVERT: B  153 PHE cc_start: 0.8771 (m-80) cc_final: 0.8554 (m-80)
  outliers start: 29
  outliers final: 22
  residues processed: 153
  average time/residue: 0.0649
  time to fit residues: 12.7247
Evaluate side-chains
  156 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 24 optimal weight:   30.0000
   chunk 34 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:   20.0000
   chunk 38 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 ASN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.096852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.078969 restraints weight = 16232.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.080431 restraints weight = 11249.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.081471 restraints weight = 8617.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.082153 restraints weight = 7102.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.082401 restraints weight = 6200.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4356  Z= 0.177
  Angle     :  0.775  10.559   5994  Z= 0.400
  Chirality :  0.043   0.224    724
  Planarity :  0.003   0.020    790
  Dihedral  :  4.603  21.597    690
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers : 10.42 %
    Allowed  : 30.56 %
    Favored  : 59.03 %
  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:  3.34 (0.33), residues: 652
  helix:  3.23 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop : -3.14 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 152 
 TYR   0.019   0.002   TYR A 171 
 PHE   0.015   0.001   PHE A 219 
 TRP   0.020   0.002   TRP A 210 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4356)
  covalent geometry    : angle       0.77503 ( 5994)
  hydrogen bonds       : bond        0.04827 (  461)
  hydrogen bonds       : angle       3.87807 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  153 PHE cc_start: 0.8690 (m-10) cc_final: 0.8310 (m-80)
  outliers start: 30
  outliers final: 30
  residues processed: 153
  average time/residue: 0.0610
  time to fit residues: 11.8669
Evaluate side-chains
  167 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  210 TRP
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0270
   chunk 27 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.9042

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.100571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.081352 restraints weight = 15673.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.083501 restraints weight = 9642.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.084897 restraints weight = 6805.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.085948 restraints weight = 5328.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.086673 restraints weight = 4448.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4356  Z= 0.141
  Angle     :  0.741   9.677   5994  Z= 0.371
  Chirality :  0.042   0.294    724
  Planarity :  0.003   0.019    790
  Dihedral  :  4.399  19.959    690
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  9.72 %
    Allowed  : 34.03 %
    Favored  : 56.25 %
  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:  3.60 (0.34), residues: 652
  helix:  3.41 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop : -3.07 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 220 
 TYR   0.022   0.002   TYR A 171 
 PHE   0.021   0.001   PHE B 136 
 TRP   0.022   0.001   TRP A 210 
 HIS   0.002   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4356)
  covalent geometry    : angle       0.74098 ( 5994)
  hydrogen bonds       : bond        0.04316 (  461)
  hydrogen bonds       : angle       3.57834 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   87 MET cc_start: 0.7975 (mmt) cc_final: 0.7759 (mmt)
REVERT: B  153 PHE cc_start: 0.8471 (m-10) cc_final: 0.8149 (m-80)
REVERT: B  314 PHE cc_start: 0.9056 (m-80) cc_final: 0.8706 (m-80)
  outliers start: 28
  outliers final: 24
  residues processed: 159
  average time/residue: 0.0661
  time to fit residues: 13.1828
Evaluate side-chains
  167 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  210 TRP
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0670
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0980
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.6324

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN
B 217 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.100152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.080928 restraints weight = 15656.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.083081 restraints weight = 9714.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.084538 restraints weight = 6914.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.085393 restraints weight = 5387.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.086256 restraints weight = 4577.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4356  Z= 0.148
  Angle     :  0.776  10.562   5994  Z= 0.392
  Chirality :  0.043   0.314    724
  Planarity :  0.003   0.022    790
  Dihedral  :  4.353  19.741    690
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 35.42 %
    Favored  : 55.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.55 (0.34), residues: 652
  helix:  3.37 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop : -3.01 (0.57), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  90 
 TYR   0.015   0.001   TYR B 238 
 PHE   0.023   0.001   PHE B 136 
 TRP   0.020   0.001   TRP B 210 
 HIS   0.002   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4356)
  covalent geometry    : angle       0.77603 ( 5994)
  hydrogen bonds       : bond        0.04315 (  461)
  hydrogen bonds       : angle       3.67320 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.167 
Fit side-chains
REVERT: B  153 PHE cc_start: 0.8584 (m-10) cc_final: 0.8246 (m-80)
  outliers start: 26
  outliers final: 25
  residues processed: 148
  average time/residue: 0.0621
  time to fit residues: 11.6906
Evaluate side-chains
  163 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  210 TRP
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:   40.0000
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.101107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.081922 restraints weight = 15485.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.084048 restraints weight = 9718.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.085474 restraints weight = 7005.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.086422 restraints weight = 5469.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.087200 restraints weight = 4617.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4356  Z= 0.143
  Angle     :  0.775  11.677   5994  Z= 0.390
  Chirality :  0.043   0.334    724
  Planarity :  0.003   0.022    790
  Dihedral  :  4.309  18.969    690
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  7.99 %
    Allowed  : 36.11 %
    Favored  : 55.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.31 (0.34), residues: 652
  helix:  3.24 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.79 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 220 
 TYR   0.024   0.002   TYR A 171 
 PHE   0.024   0.001   PHE A 136 
 TRP   0.020   0.001   TRP B 210 
 HIS   0.002   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4356)
  covalent geometry    : angle       0.77526 ( 5994)
  hydrogen bonds       : bond        0.04136 (  461)
  hydrogen bonds       : angle       3.64786 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  314 PHE cc_start: 0.9055 (m-80) cc_final: 0.8716 (m-80)
REVERT: B  108 TYR cc_start: 0.8576 (t80) cc_final: 0.8288 (t80)
REVERT: B  153 PHE cc_start: 0.8555 (m-10) cc_final: 0.8260 (m-80)
  outliers start: 23
  outliers final: 21
  residues processed: 152
  average time/residue: 0.0621
  time to fit residues: 12.0639
Evaluate side-chains
  162 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  210 TRP
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 25 optimal weight:   30.0000
   chunk 49 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.099599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.080179 restraints weight = 16046.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.082307 restraints weight = 10007.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.083749 restraints weight = 7163.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.084746 restraints weight = 5582.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.085525 restraints weight = 4689.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4356  Z= 0.152
  Angle     :  0.793  11.543   5994  Z= 0.404
  Chirality :  0.044   0.341    724
  Planarity :  0.003   0.024    790
  Dihedral  :  4.324  19.902    690
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 35.76 %
    Favored  : 55.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.29 (0.34), residues: 652
  helix:  3.22 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.76 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 220 
 TYR   0.015   0.002   TYR A 108 
 PHE   0.024   0.001   PHE A 136 
 TRP   0.018   0.001   TRP A 210 
 HIS   0.002   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4356)
  covalent geometry    : angle       0.79339 ( 5994)
  hydrogen bonds       : bond        0.04187 (  461)
  hydrogen bonds       : angle       3.74096 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 22
  residues processed: 150
  average time/residue: 0.0587
  time to fit residues: 11.2758
Evaluate side-chains
  157 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  210 TRP
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.100130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.081013 restraints weight = 15608.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.083119 restraints weight = 9812.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.084544 restraints weight = 7017.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.085614 restraints weight = 5527.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.086349 restraints weight = 4609.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4356  Z= 0.149
  Angle     :  0.793  11.874   5994  Z= 0.405
  Chirality :  0.044   0.349    724
  Planarity :  0.003   0.023    790
  Dihedral  :  4.310  19.513    690
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  7.99 %
    Allowed  : 36.81 %
    Favored  : 55.21 %
  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:  3.24 (0.34), residues: 652
  helix:  3.19 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.79 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 178 
 TYR   0.028   0.002   TYR B  33 
 PHE   0.025   0.001   PHE B 136 
 TRP   0.019   0.001   TRP A 210 
 HIS   0.002   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4356)
  covalent geometry    : angle       0.79324 ( 5994)
  hydrogen bonds       : bond        0.04196 (  461)
  hydrogen bonds       : angle       3.72946 ( 1383)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 PHE cc_start: 0.9022 (m-80) cc_final: 0.8747 (m-80)
REVERT: B  153 PHE cc_start: 0.8654 (m-10) cc_final: 0.8367 (m-80)
  outliers start: 23
  outliers final: 23
  residues processed: 151
  average time/residue: 0.0638
  time to fit residues: 12.2429
Evaluate side-chains
  158 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  210 TRP
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 38 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.100459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.081192 restraints weight = 15755.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.083279 restraints weight = 9833.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.084762 restraints weight = 7044.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.085602 restraints weight = 5498.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.086425 restraints weight = 4688.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4356  Z= 0.149
  Angle     :  0.803  11.858   5994  Z= 0.408
  Chirality :  0.044   0.356    724
  Planarity :  0.003   0.023    790
  Dihedral  :  4.304  19.580    690
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 35.76 %
    Favored  : 55.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.27 (0.34), residues: 652
  helix:  3.20 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.73 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 178 
 TYR   0.026   0.002   TYR B  33 
 PHE   0.024   0.001   PHE B 136 
 TRP   0.018   0.001   TRP A 210 
 HIS   0.002   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4356)
  covalent geometry    : angle       0.80255 ( 5994)
  hydrogen bonds       : bond        0.04165 (  461)
  hydrogen bonds       : angle       3.70863 ( 1383)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 861.54 seconds
wall clock time: 15 minutes 26.79 seconds (926.79 seconds total)