Starting phenix.real_space_refine
on Fri Oct 10 16:50:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8izf_35863/10_2025/8izf_35863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8izf_35863/10_2025/8izf_35863.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8izf_35863/10_2025/8izf_35863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8izf_35863/10_2025/8izf_35863.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8izf_35863/10_2025/8izf_35863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8izf_35863/10_2025/8izf_35863.cif"
  }
  resolution = 3.85
  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=   0.004 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      38      5.16       5
     C    5088      2.51       5
     N    1202      2.21       5
     O    1264      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7594
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2670
          Classifications: {'peptide': 315}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1087
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'6PL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 12
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 2.27, per 1000 atoms: 0.30
  Number of scatterers: 7594
  At special positions: 0
  Unit cell: (110.416, 101.84, 100.768, 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      38     16.00
     P       2     15.00
     O    1264      8.00
     N    1202      7.00
     C    5088      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 102 " - pdb=" SG  CYS B 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 102 " - pdb=" SG  CYS D 142 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 455.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 2 sheets defined
      67.0% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 82
      removed outlier: 3.530A  pdb=" N   PHE A  75 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 100
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 130 through 162
      Proline residue:  A 157  - end of helix
    Processing helix  chain 'A' and resid 167 through 196
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 205 through 209
    Processing helix  chain 'A' and resid 217 through 241
    Processing helix  chain 'A' and resid 249 through 269
    Processing helix  chain 'A' and resid 275 through 298
      removed outlier: 3.786A  pdb=" N   LEU A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 335
      removed outlier: 3.947A  pdb=" N   TYR A 320 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 384
      removed outlier: 3.881A  pdb=" N   ILE A 356 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 47
    Processing helix  chain 'B' and resid 48 through 52
      removed outlier: 3.736A  pdb=" N   HIS B  52 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 48 through 52'
    Processing helix  chain 'B' and resid 76 through 92
      removed outlier: 3.541A  pdb=" N   TYR B  92 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 142
      removed outlier: 3.523A  pdb=" N   VAL B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 82
    Processing helix  chain 'C' and resid 84 through 100
    Processing helix  chain 'C' and resid 109 through 115
    Processing helix  chain 'C' and resid 130 through 162
      Proline residue:  C 157  - end of helix
    Processing helix  chain 'C' and resid 167 through 196
      Proline residue:  C 188  - end of helix
    Processing helix  chain 'C' and resid 205 through 209
    Processing helix  chain 'C' and resid 217 through 241
    Processing helix  chain 'C' and resid 249 through 269
    Processing helix  chain 'C' and resid 275 through 298
      removed outlier: 3.786A  pdb=" N   LEU C 288 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 335
      removed outlier: 3.946A  pdb=" N   TYR C 320 " --> pdb=" O   TYR C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 384
      removed outlier: 3.881A  pdb=" N   ILE C 356 " --> pdb=" O   ILE C 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 47
    Processing helix  chain 'D' and resid 48 through 52
      removed outlier: 3.736A  pdb=" N   HIS D  52 " --> pdb=" O   TYR D  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 48 through 52'
    Processing helix  chain 'D' and resid 76 through 92
      removed outlier: 3.541A  pdb=" N   TYR D  92 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 142
      removed outlier: 3.524A  pdb=" N   VAL D 138 " --> pdb=" O   ASP D 134 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 59
      removed outlier: 3.616A  pdb=" N   VAL B 129 " --> pdb=" O   ILE B  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 59
      removed outlier: 3.616A  pdb=" N   VAL D 129 " --> pdb=" O   ILE D  65 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1434 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: 1.17

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1096
        1.32 -     1.44: 2532
        1.44 -     1.57: 4158
        1.57 -     1.70: 2
        1.70 -     1.83: 58
  Bond restraints: 7846
  Sorted by residual:
  bond pdb=" C31 6PL D 201 "
       pdb=" O2  6PL D 201 "
    ideal  model  delta    sigma   weight residual
    1.330  1.430 -0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" C31 6PL B 201 "
       pdb=" O2  6PL B 201 "
    ideal  model  delta    sigma   weight residual
    1.330  1.430 -0.100 2.00e-02 2.50e+03 2.51e+01
  bond pdb=" C11 6PL D 201 "
       pdb=" O3  6PL D 201 "
    ideal  model  delta    sigma   weight residual
    1.327  1.426 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C11 6PL B 201 "
       pdb=" O3  6PL B 201 "
    ideal  model  delta    sigma   weight residual
    1.327  1.426 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" CA  PHE A 343 "
       pdb=" CB  PHE A 343 "
    ideal  model  delta    sigma   weight residual
    1.530  1.462  0.068 1.69e-02 3.50e+03 1.62e+01
  ... (remaining 7841 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.86: 10531
        3.86 -     7.73: 101
        7.73 -    11.59: 8
       11.59 -    15.46: 8
       15.46 -    19.32: 4
  Bond angle restraints: 10652
  Sorted by residual:
  angle pdb=" N   PHE C 343 "
        pdb=" CA  PHE C 343 "
        pdb=" C   PHE C 343 "
      ideal   model   delta    sigma   weight residual
     110.80  130.12  -19.32 2.13e+00 2.20e-01 8.23e+01
  angle pdb=" N   PHE A 343 "
        pdb=" CA  PHE A 343 "
        pdb=" C   PHE A 343 "
      ideal   model   delta    sigma   weight residual
     110.80  130.08  -19.28 2.13e+00 2.20e-01 8.20e+01
  angle pdb=" N   LYS C 247 "
        pdb=" CA  LYS C 247 "
        pdb=" C   LYS C 247 "
      ideal   model   delta    sigma   weight residual
     110.24   98.33   11.91 1.41e+00 5.03e-01 7.13e+01
  angle pdb=" N   LYS A 247 "
        pdb=" CA  LYS A 247 "
        pdb=" C   LYS A 247 "
      ideal   model   delta    sigma   weight residual
     110.24   98.35   11.89 1.41e+00 5.03e-01 7.11e+01
  angle pdb=" N   MET A 140 "
        pdb=" CA  MET A 140 "
        pdb=" C   MET A 140 "
      ideal   model   delta    sigma   weight residual
     111.36  103.42    7.94 1.09e+00 8.42e-01 5.31e+01
  ... (remaining 10647 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.05: 3954
       18.05 -    36.09: 412
       36.09 -    54.14: 100
       54.14 -    72.19: 16
       72.19 -    90.24: 16
  Dihedral angle restraints: 4498
    sinusoidal: 1834
      harmonic: 2664
  Sorted by residual:
  dihedral pdb=" CA  GLU D 118 "
           pdb=" C   GLU D 118 "
           pdb=" N   ASP D 119 "
           pdb=" CA  ASP D 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  GLU B 118 "
           pdb=" C   GLU B 118 "
           pdb=" N   ASP B 119 "
           pdb=" CA  ASP B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.70   21.30     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  CYS B  53 "
           pdb=" CB  CYS B  53 "
           pdb=" SG  CYS B  53 "
           pdb=" SG  CYS B  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    2.17  -75.17     1      2.00e+01 2.50e-03 1.79e+01
  ... (remaining 4495 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1107
       0.118 -    0.236: 27
       0.236 -    0.354: 2
       0.354 -    0.472: 0
       0.472 -    0.590: 2
  Chirality restraints: 1138
  Sorted by residual:
  chirality pdb=" CA  PHE C 343 "
            pdb=" N   PHE C 343 "
            pdb=" C   PHE C 343 "
            pdb=" CB  PHE C 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.59 2.00e-01 2.50e+01 8.71e+00
  chirality pdb=" CA  PHE A 343 "
            pdb=" N   PHE A 343 "
            pdb=" C   PHE A 343 "
            pdb=" CB  PHE A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.59 2.00e-01 2.50e+01 8.67e+00
  chirality pdb=" CA  LYS C 247 "
            pdb=" N   LYS C 247 "
            pdb=" C   LYS C 247 "
            pdb=" CB  LYS C 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.89e+00
  ... (remaining 1135 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 139 "   -0.019 2.00e-02 2.50e+03   3.87e-02 1.49e+01
        pdb=" C   TYR A 139 "    0.067 2.00e-02 2.50e+03
        pdb=" O   TYR A 139 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   MET A 140 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 139 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   TYR C 139 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   TYR C 139 "    0.026 2.00e-02 2.50e+03
        pdb=" N   MET C 140 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D  77 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   LYS D  77 "    0.057 2.00e-02 2.50e+03
        pdb=" O   LYS D  77 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ARG D  78 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 65
        2.54 -     3.13: 6462
        3.13 -     3.72: 12006
        3.72 -     4.31: 15506
        4.31 -     4.90: 25341
  Nonbonded interactions: 59380
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 103 "
            pdb=" OH  TYR D 148 "
     model   vdw
     1.945 3.040
  nonbonded pdb=" OH  TYR B 148 "
            pdb=" O   ILE D 103 "
     model   vdw
     1.952 3.040
  nonbonded pdb=" O   LYS A 244 "
            pdb=" O   PRO A 245 "
     model   vdw
     2.010 3.040
  nonbonded pdb=" O   LYS C 244 "
            pdb=" O   PRO C 245 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" OG  SER A 186 "
            pdb=" OD2 ASP A 283 "
     model   vdw
     2.168 3.040
  ... (remaining 59375 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             1.560
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.360
  Find NCS groups from input model:        0.050
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
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   0.100   7850  Z= 0.334
  Angle     :  1.097  19.322  10660  Z= 0.624
  Chirality :  0.057   0.590   1138
  Planarity :  0.006   0.063   1296
  Dihedral  : 16.149  90.235   2778
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  9.48 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  :  1.74 %
    Favored  : 95.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.27), residues: 886
  helix:  0.25 (0.20), residues: 562
  sheet: -1.68 (0.58), residues: 58
  loop : -3.81 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 156 
 TYR   0.032   0.002   TYR C 279 
 PHE   0.020   0.002   PHE A 271 
 TRP   0.020   0.002   TRP D  50 
 HIS   0.008   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 ( 7846)
  covalent geometry    : angle       1.09513 (10652)
  SS BOND              : bond        0.00184 (    4)
  SS BOND              : angle       2.55366 (    8)
  hydrogen bonds       : bond        0.13092 (  486)
  hydrogen bonds       : angle       6.44811 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 294
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8276 (p-90) cc_final: 0.7846 (p-90)
REVERT: A  168 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6197 (m90)
REVERT: A  174 MET cc_start: 0.8632 (mmt) cc_final: 0.8166 (mmt)
REVERT: A  182 TYR cc_start: 0.7918 (p90) cc_final: 0.7554 (t80)
REVERT: A  236 CYS cc_start: 0.8676 (p) cc_final: 0.8461 (p)
REVERT: A  251 GLU cc_start: 0.7857 (pm20) cc_final: 0.7458 (pm20)
REVERT: A  289 LEU cc_start: 0.8881 (tp) cc_final: 0.8584 (tt)
REVERT: A  334 ARG cc_start: 0.7006 (tmt170) cc_final: 0.6779 (tpt170)
REVERT: A  343 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7772 (t80)
REVERT: A  346 GLN cc_start: 0.8589 (mp10) cc_final: 0.8192 (mp10)
REVERT: B   80 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6841 (mt-10)
REVERT: C   84 TRP cc_start: 0.8268 (p-90) cc_final: 0.7829 (p-90)
REVERT: C  168 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6175 (m90)
REVERT: C  174 MET cc_start: 0.8753 (mmt) cc_final: 0.8272 (mmt)
REVERT: C  236 CYS cc_start: 0.8675 (p) cc_final: 0.8456 (p)
REVERT: C  251 GLU cc_start: 0.7866 (pm20) cc_final: 0.7507 (pm20)
REVERT: C  334 ARG cc_start: 0.6939 (tmt170) cc_final: 0.6227 (ttt180)
REVERT: C  343 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7797 (t80)
REVERT: C  346 GLN cc_start: 0.8577 (mp10) cc_final: 0.8163 (mp10)
REVERT: D   65 ILE cc_start: 0.9318 (pt) cc_final: 0.9085 (pt)
  outliers start: 22
  outliers final: 4
  residues processed: 306
  average time/residue: 0.0775
  time to fit residues: 33.0892
Evaluate side-chains
  207 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 199
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  364 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0170
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
A 332 GLN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS
C 332 GLN
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.137023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.116511 restraints weight = 16493.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.119169 restraints weight = 9498.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.120335 restraints weight = 6489.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.120976 restraints weight = 5426.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.121225 restraints weight = 5017.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7850  Z= 0.150
  Angle     :  0.728  12.973  10660  Z= 0.377
  Chirality :  0.042   0.134   1138
  Planarity :  0.005   0.056   1296
  Dihedral  :  9.776  56.469   1084
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 15.88 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.28), residues: 886
  helix:  0.88 (0.21), residues: 544
  sheet: -1.55 (0.56), residues: 58
  loop : -3.53 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  78 
 TYR   0.031   0.002   TYR A 182 
 PHE   0.043   0.002   PHE A 158 
 TRP   0.019   0.001   TRP B  68 
 HIS   0.006   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7846)
  covalent geometry    : angle       0.72672 (10652)
  SS BOND              : bond        0.00159 (    4)
  SS BOND              : angle       1.72204 (    8)
  hydrogen bonds       : bond        0.04955 (  486)
  hydrogen bonds       : angle       5.34634 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 250
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8186 (p-90) cc_final: 0.7828 (p-90)
REVERT: A  140 MET cc_start: 0.8558 (tpp) cc_final: 0.7943 (tpp)
REVERT: A  168 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.6526 (m90)
REVERT: A  203 ASN cc_start: 0.8411 (t0) cc_final: 0.8174 (t0)
REVERT: A  233 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8481 (tt0)
REVERT: A  332 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7582 (mt0)
REVERT: A  334 ARG cc_start: 0.6347 (tmt170) cc_final: 0.5643 (ttt180)
REVERT: A  343 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7890 (t80)
REVERT: A  357 VAL cc_start: 0.7679 (t) cc_final: 0.7449 (p)
REVERT: A  370 TYR cc_start: 0.7980 (t80) cc_final: 0.7774 (t80)
REVERT: B   80 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6852 (mt-10)
REVERT: B  148 TYR cc_start: 0.7699 (m-80) cc_final: 0.7407 (m-80)
REVERT: B  150 MET cc_start: 0.7302 (ttp) cc_final: 0.6959 (ptm)
REVERT: C   84 TRP cc_start: 0.8251 (p-90) cc_final: 0.7904 (p-90)
REVERT: C  139 TYR cc_start: 0.8256 (m-80) cc_final: 0.8007 (m-80)
REVERT: C  168 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6527 (m90)
REVERT: C  332 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7597 (mt0)
REVERT: C  334 ARG cc_start: 0.6305 (tmt170) cc_final: 0.5566 (ttt180)
REVERT: C  343 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7866 (t80)
REVERT: C  357 VAL cc_start: 0.7702 (t) cc_final: 0.7491 (p)
REVERT: C  370 TYR cc_start: 0.7980 (t80) cc_final: 0.7749 (t80)
REVERT: D   65 ILE cc_start: 0.9295 (pt) cc_final: 0.9081 (pt)
REVERT: D  150 MET cc_start: 0.7411 (ttp) cc_final: 0.7052 (ptm)
  outliers start: 36
  outliers final: 22
  residues processed: 270
  average time/residue: 0.0738
  time to fit residues: 28.0426
Evaluate side-chains
  227 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  175 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  175 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  237 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  332 GLN
Chi-restraints excluded: chain C residue  339 TYR
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue  126 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 75 optimal weight:    0.3980
   chunk 9 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 64 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
A 332 GLN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS
C 332 GLN
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.130684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.108322 restraints weight = 17108.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.111426 restraints weight = 10001.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.113557 restraints weight = 6990.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.114937 restraints weight = 5504.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.115830 restraints weight = 4687.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7850  Z= 0.146
  Angle     :  0.693   9.821  10660  Z= 0.360
  Chirality :  0.043   0.231   1138
  Planarity :  0.005   0.053   1296
  Dihedral  :  9.196  59.864   1082
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 19.73 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.27), residues: 886
  helix:  0.85 (0.21), residues: 558
  sheet: -0.79 (0.59), residues: 54
  loop : -3.52 (0.33), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  70 
 TYR   0.026   0.002   TYR C 279 
 PHE   0.035   0.002   PHE A 158 
 TRP   0.034   0.002   TRP C  72 
 HIS   0.008   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7846)
  covalent geometry    : angle       0.69184 (10652)
  SS BOND              : bond        0.00144 (    4)
  SS BOND              : angle       1.50131 (    8)
  hydrogen bonds       : bond        0.04687 (  486)
  hydrogen bonds       : angle       5.10555 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 236
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  140 MET cc_start: 0.8449 (tpp) cc_final: 0.8147 (tpp)
REVERT: A  168 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6770 (m90)
REVERT: A  203 ASN cc_start: 0.8454 (t0) cc_final: 0.8188 (t0)
REVERT: A  224 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7035 (t80)
REVERT: A  233 GLN cc_start: 0.8811 (tm-30) cc_final: 0.7977 (tm-30)
REVERT: A  248 ASP cc_start: 0.7525 (t70) cc_final: 0.6723 (t0)
REVERT: A  323 LEU cc_start: 0.8837 (mm) cc_final: 0.8615 (tp)
REVERT: A  334 ARG cc_start: 0.6535 (tmt170) cc_final: 0.5716 (ttt180)
REVERT: A  343 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7881 (t80)
REVERT: A  357 VAL cc_start: 0.7692 (t) cc_final: 0.7433 (p)
REVERT: B   28 PHE cc_start: 0.8609 (t80) cc_final: 0.8394 (t80)
REVERT: B   38 GLU cc_start: 0.8113 (tp30) cc_final: 0.7829 (tp30)
REVERT: B   80 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6909 (mt-10)
REVERT: B  148 TYR cc_start: 0.7991 (m-80) cc_final: 0.7611 (m-80)
REVERT: C  168 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6766 (m90)
REVERT: C  224 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7084 (t80)
REVERT: C  334 ARG cc_start: 0.6474 (tmt170) cc_final: 0.5677 (ttt180)
REVERT: C  343 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7832 (t80)
REVERT: C  357 VAL cc_start: 0.7643 (t) cc_final: 0.7405 (p)
REVERT: D   28 PHE cc_start: 0.8581 (t80) cc_final: 0.8371 (t80)
REVERT: D   80 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6728 (tt0)
REVERT: D   92 TYR cc_start: 0.8605 (m-10) cc_final: 0.8020 (m-10)
  outliers start: 41
  outliers final: 24
  residues processed: 259
  average time/residue: 0.0752
  time to fit residues: 27.6709
Evaluate side-chains
  243 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 213
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   67 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 113 HIS
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 113 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.118124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.096351 restraints weight = 18147.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.098139 restraints weight = 11018.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.098983 restraints weight = 8669.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.099498 restraints weight = 7271.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.100034 restraints weight = 6899.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   7850  Z= 0.238
  Angle     :  0.766  11.856  10660  Z= 0.395
  Chirality :  0.046   0.199   1138
  Planarity :  0.005   0.053   1296
  Dihedral  :  9.005  59.945   1082
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 20.84 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.27), residues: 886
  helix:  0.81 (0.21), residues: 552
  sheet: -0.85 (0.58), residues: 56
  loop : -3.67 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 156 
 TYR   0.022   0.002   TYR C 182 
 PHE   0.035   0.002   PHE C 158 
 TRP   0.017   0.002   TRP C  72 
 HIS   0.011   0.002   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 7846)
  covalent geometry    : angle       0.76381 (10652)
  SS BOND              : bond        0.00242 (    4)
  SS BOND              : angle       2.38504 (    8)
  hydrogen bonds       : bond        0.04972 (  486)
  hydrogen bonds       : angle       5.15794 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 215
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  168 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.6854 (m90)
REVERT: A  203 ASN cc_start: 0.8789 (t0) cc_final: 0.8403 (t0)
REVERT: A  224 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.6920 (t80)
REVERT: A  233 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8220 (tm-30)
REVERT: A  248 ASP cc_start: 0.7614 (t70) cc_final: 0.7108 (t0)
REVERT: A  251 GLU cc_start: 0.7711 (pm20) cc_final: 0.7433 (pm20)
REVERT: A  334 ARG cc_start: 0.6906 (tmt170) cc_final: 0.5902 (ttt180)
REVERT: A  343 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7831 (t80)
REVERT: A  346 GLN cc_start: 0.8895 (mp10) cc_final: 0.8595 (mp10)
REVERT: B   38 GLU cc_start: 0.8235 (tp30) cc_final: 0.7840 (tp30)
REVERT: B   67 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9020 (tt)
REVERT: B  149 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7413 (p90)
REVERT: C  168 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.6860 (m90)
REVERT: C  224 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.6895 (t80)
REVERT: C  248 ASP cc_start: 0.7715 (t0) cc_final: 0.7240 (t0)
REVERT: C  334 ARG cc_start: 0.6813 (tmt170) cc_final: 0.5815 (ttt180)
REVERT: C  343 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7867 (t80)
REVERT: C  346 GLN cc_start: 0.8879 (mp10) cc_final: 0.8654 (mp10)
REVERT: D   38 GLU cc_start: 0.8165 (tp30) cc_final: 0.7849 (tp30)
REVERT: D  149 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7316 (p90)
  outliers start: 54
  outliers final: 37
  residues processed: 247
  average time/residue: 0.0690
  time to fit residues: 24.7928
Evaluate side-chains
  258 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 212
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  237 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  325 ILE
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0470
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  52 HIS
** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  52 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.122436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.100846 restraints weight = 17899.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.102708 restraints weight = 11553.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.103832 restraints weight = 8715.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.104443 restraints weight = 7063.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.105073 restraints weight = 6603.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7850  Z= 0.132
  Angle     :  0.685   9.555  10660  Z= 0.351
  Chirality :  0.042   0.168   1138
  Planarity :  0.005   0.052   1296
  Dihedral  :  8.309  57.716   1082
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 25.06 %
    Favored  : 69.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.27), residues: 886
  helix:  0.93 (0.21), residues: 560
  sheet: -0.28 (0.60), residues: 52
  loop : -3.56 (0.31), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  90 
 TYR   0.020   0.001   TYR D  42 
 PHE   0.020   0.001   PHE A 158 
 TRP   0.013   0.001   TRP A  84 
 HIS   0.004   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7846)
  covalent geometry    : angle       0.68210 (10652)
  SS BOND              : bond        0.00179 (    4)
  SS BOND              : angle       2.31585 (    8)
  hydrogen bonds       : bond        0.04368 (  486)
  hydrogen bonds       : angle       4.89162 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 249
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.6982 (m90)
REVERT: A  203 ASN cc_start: 0.8583 (t0) cc_final: 0.8233 (t0)
REVERT: A  224 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.6767 (t80)
REVERT: A  233 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: A  248 ASP cc_start: 0.7460 (t70) cc_final: 0.6736 (t0)
REVERT: A  251 GLU cc_start: 0.7347 (pm20) cc_final: 0.6966 (pm20)
REVERT: A  332 GLN cc_start: 0.8419 (mt0) cc_final: 0.8099 (mt0)
REVERT: A  334 ARG cc_start: 0.6819 (tmt170) cc_final: 0.5762 (ttt180)
REVERT: A  342 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7624 (t0)
REVERT: A  343 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7843 (t80)
REVERT: A  357 VAL cc_start: 0.7668 (t) cc_final: 0.7467 (p)
REVERT: B   38 GLU cc_start: 0.8240 (tp30) cc_final: 0.7949 (tp30)
REVERT: B   80 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6725 (tt0)
REVERT: C  168 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.7011 (m90)
REVERT: C  224 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6889 (t80)
REVERT: C  233 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8001 (tt0)
REVERT: C  234 GLN cc_start: 0.8476 (mm110) cc_final: 0.8097 (mm-40)
REVERT: C  248 ASP cc_start: 0.7539 (t0) cc_final: 0.7247 (t0)
REVERT: C  332 GLN cc_start: 0.8374 (mt0) cc_final: 0.8049 (mt0)
REVERT: C  334 ARG cc_start: 0.6780 (tmt170) cc_final: 0.5745 (ttt180)
REVERT: C  343 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7841 (t80)
REVERT: C  357 VAL cc_start: 0.7682 (t) cc_final: 0.7479 (p)
REVERT: D   38 GLU cc_start: 0.8196 (tp30) cc_final: 0.7941 (tp30)
REVERT: D  149 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.7101 (p90)
  outliers start: 44
  outliers final: 23
  residues processed: 273
  average time/residue: 0.0658
  time to fit residues: 26.2138
Evaluate side-chains
  262 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 231
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 53 optimal weight:    6.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 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 = 0.3708 r_free = 0.3708 target = 0.120515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.098854 restraints weight = 18106.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.100646 restraints weight = 11307.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.101722 restraints weight = 8758.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.102197 restraints weight = 7267.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.102858 restraints weight = 6937.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7850  Z= 0.157
  Angle     :  0.717  10.953  10660  Z= 0.365
  Chirality :  0.043   0.142   1138
  Planarity :  0.005   0.052   1296
  Dihedral  :  8.088  59.888   1082
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 28.66 %
    Favored  : 66.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.28), residues: 886
  helix:  0.93 (0.21), residues: 564
  sheet: -0.55 (0.60), residues: 56
  loop : -3.45 (0.32), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  90 
 TYR   0.025   0.002   TYR C 182 
 PHE   0.022   0.001   PHE A 158 
 TRP   0.015   0.001   TRP A  84 
 HIS   0.003   0.001   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7846)
  covalent geometry    : angle       0.71431 (10652)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       2.17122 (    8)
  hydrogen bonds       : bond        0.04435 (  486)
  hydrogen bonds       : angle       4.82172 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 234
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 HIS cc_start: 0.7535 (m170) cc_final: 0.7048 (m90)
REVERT: A  203 ASN cc_start: 0.8581 (t0) cc_final: 0.8358 (t0)
REVERT: A  224 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.6802 (t80)
REVERT: A  233 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8672 (tm-30)
REVERT: A  332 GLN cc_start: 0.8517 (mt0) cc_final: 0.8311 (mt0)
REVERT: A  334 ARG cc_start: 0.6846 (tmt170) cc_final: 0.5746 (ttt180)
REVERT: B  149 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7184 (p90)
REVERT: C  140 MET cc_start: 0.8713 (tpp) cc_final: 0.8419 (tpp)
REVERT: C  224 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.6900 (t80)
REVERT: C  248 ASP cc_start: 0.7614 (t0) cc_final: 0.7165 (t0)
REVERT: C  251 GLU cc_start: 0.7755 (pm20) cc_final: 0.7275 (pm20)
REVERT: C  334 ARG cc_start: 0.6861 (tmt170) cc_final: 0.5787 (ttt180)
REVERT: D   89 THR cc_start: 0.8984 (t) cc_final: 0.8744 (t)
REVERT: D  149 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7127 (p90)
  outliers start: 42
  outliers final: 34
  residues processed: 258
  average time/residue: 0.0659
  time to fit residues: 25.0042
Evaluate side-chains
  262 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 224
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 79 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0670
   chunk 75 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 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 = 0.3737 r_free = 0.3737 target = 0.122566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.100941 restraints weight = 17711.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.102896 restraints weight = 11176.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.103913 restraints weight = 8547.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.104501 restraints weight = 6969.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.105104 restraints weight = 6567.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7850  Z= 0.138
  Angle     :  0.708   9.847  10660  Z= 0.361
  Chirality :  0.043   0.173   1138
  Planarity :  0.005   0.051   1296
  Dihedral  :  7.369  59.287   1074
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 28.41 %
    Favored  : 66.25 %
  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 aren not related in a simple way.
  whole: -0.48 (0.28), residues: 886
  helix:  1.03 (0.21), residues: 562
  sheet: -0.30 (0.64), residues: 56
  loop : -3.38 (0.32), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  70 
 TYR   0.020   0.001   TYR D  42 
 PHE   0.025   0.001   PHE C 158 
 TRP   0.017   0.001   TRP A  84 
 HIS   0.003   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7846)
  covalent geometry    : angle       0.70580 (10652)
  SS BOND              : bond        0.00171 (    4)
  SS BOND              : angle       2.02765 (    8)
  hydrogen bonds       : bond        0.04236 (  486)
  hydrogen bonds       : angle       4.77777 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 247
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8305 (p-90) cc_final: 0.8077 (p-90)
REVERT: A   91 LEU cc_start: 0.8231 (pp) cc_final: 0.7995 (pp)
REVERT: A  203 ASN cc_start: 0.8562 (t0) cc_final: 0.8305 (t0)
REVERT: A  224 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.6954 (t80)
REVERT: A  233 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8107 (tm-30)
REVERT: A  323 LEU cc_start: 0.8941 (mm) cc_final: 0.8719 (tp)
REVERT: A  332 GLN cc_start: 0.8465 (mt0) cc_final: 0.8240 (mt0)
REVERT: A  334 ARG cc_start: 0.6792 (tmt170) cc_final: 0.5762 (ttt180)
REVERT: A  342 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7616 (t0)
REVERT: B  149 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.6856 (p90)
REVERT: C   84 TRP cc_start: 0.8324 (p-90) cc_final: 0.8085 (p-90)
REVERT: C   91 LEU cc_start: 0.8224 (pp) cc_final: 0.7993 (pp)
REVERT: C  140 MET cc_start: 0.8623 (tpp) cc_final: 0.8319 (tpp)
REVERT: C  224 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.6881 (t80)
REVERT: C  248 ASP cc_start: 0.7516 (t0) cc_final: 0.7217 (t0)
REVERT: C  251 GLU cc_start: 0.7368 (pm20) cc_final: 0.7078 (pm20)
REVERT: C  334 ARG cc_start: 0.6783 (tmt170) cc_final: 0.5731 (ttt180)
  outliers start: 43
  outliers final: 32
  residues processed: 269
  average time/residue: 0.0696
  time to fit residues: 26.8795
Evaluate side-chains
  266 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 230
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  180 ILE
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  339 TYR
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   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 234 GLN
C 342 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.130488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107357 restraints weight = 17367.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.110373 restraints weight = 10198.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.112478 restraints weight = 7266.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.113805 restraints weight = 5789.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.114826 restraints weight = 5008.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7850  Z= 0.152
  Angle     :  0.739  10.250  10660  Z= 0.377
  Chirality :  0.044   0.184   1138
  Planarity :  0.005   0.051   1296
  Dihedral  :  7.279  59.389   1074
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 29.90 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.28), residues: 886
  helix:  1.04 (0.21), residues: 562
  sheet: -0.14 (0.67), residues: 56
  loop : -3.34 (0.32), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 156 
 TYR   0.028   0.002   TYR C 182 
 PHE   0.025   0.002   PHE C 220 
 TRP   0.013   0.001   TRP B  68 
 HIS   0.003   0.001   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7846)
  covalent geometry    : angle       0.73759 (10652)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       1.92317 (    8)
  hydrogen bonds       : bond        0.04319 (  486)
  hydrogen bonds       : angle       4.71918 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 232
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8304 (p-90) cc_final: 0.8082 (p-90)
REVERT: A   91 LEU cc_start: 0.8179 (pp) cc_final: 0.7944 (pp)
REVERT: A  140 MET cc_start: 0.8730 (tpp) cc_final: 0.8304 (tpp)
REVERT: A  203 ASN cc_start: 0.8404 (t0) cc_final: 0.8184 (t0)
REVERT: A  224 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7107 (t80)
REVERT: A  233 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8054 (tm-30)
REVERT: A  250 ASN cc_start: 0.7620 (p0) cc_final: 0.7396 (t0)
REVERT: A  332 GLN cc_start: 0.8441 (mt0) cc_final: 0.8210 (mt0)
REVERT: A  334 ARG cc_start: 0.6591 (tmt170) cc_final: 0.5646 (ttt180)
REVERT: A  342 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7661 (t0)
REVERT: B  118 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7631 (tm-30)
REVERT: B  149 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6616 (p90)
REVERT: C   84 TRP cc_start: 0.8317 (p-90) cc_final: 0.8090 (p-90)
REVERT: C   91 LEU cc_start: 0.8312 (pp) cc_final: 0.8069 (pp)
REVERT: C  224 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.6864 (t80)
REVERT: C  248 ASP cc_start: 0.7700 (t0) cc_final: 0.7419 (t0)
REVERT: C  251 GLU cc_start: 0.7472 (pm20) cc_final: 0.7094 (pm20)
REVERT: C  334 ARG cc_start: 0.6540 (tmt170) cc_final: 0.5612 (ttt180)
REVERT: D   78 ARG cc_start: 0.8777 (ttp-170) cc_final: 0.8398 (ptm160)
REVERT: D  118 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7694 (tm-30)
  outliers start: 40
  outliers final: 34
  residues processed: 251
  average time/residue: 0.0685
  time to fit residues: 24.8291
Evaluate side-chains
  262 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 224
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  180 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.129650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.107277 restraints weight = 17406.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.110144 restraints weight = 10482.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.112169 restraints weight = 7548.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.113407 restraints weight = 6050.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.114398 restraints weight = 5252.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7850  Z= 0.155
  Angle     :  0.748  10.362  10660  Z= 0.379
  Chirality :  0.044   0.178   1138
  Planarity :  0.005   0.055   1296
  Dihedral  :  7.173  59.102   1072
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 30.77 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.28), residues: 886
  helix:  1.08 (0.21), residues: 560
  sheet: -0.12 (0.66), residues: 56
  loop : -3.22 (0.33), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  70 
 TYR   0.022   0.002   TYR D  92 
 PHE   0.023   0.001   PHE C 158 
 TRP   0.014   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7846)
  covalent geometry    : angle       0.74661 (10652)
  SS BOND              : bond        0.00148 (    4)
  SS BOND              : angle       1.89029 (    8)
  hydrogen bonds       : bond        0.04349 (  486)
  hydrogen bonds       : angle       4.73885 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 231
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8272 (p-90) cc_final: 0.8067 (p-90)
REVERT: A   91 LEU cc_start: 0.8205 (pp) cc_final: 0.7981 (pp)
REVERT: A  140 MET cc_start: 0.8690 (tpp) cc_final: 0.8235 (tpp)
REVERT: A  224 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7210 (t80)
REVERT: A  233 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: A  250 ASN cc_start: 0.7589 (p0) cc_final: 0.7306 (t0)
REVERT: A  332 GLN cc_start: 0.8438 (mt0) cc_final: 0.8222 (mt0)
REVERT: A  334 ARG cc_start: 0.6560 (tmt170) cc_final: 0.5520 (ttm170)
REVERT: A  342 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7666 (t0)
REVERT: B  118 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: B  149 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6912 (p90)
REVERT: C   91 LEU cc_start: 0.8315 (pp) cc_final: 0.8090 (pp)
REVERT: C  334 ARG cc_start: 0.6497 (tmt170) cc_final: 0.5583 (ttt180)
  outliers start: 40
  outliers final: 34
  residues processed: 251
  average time/residue: 0.0704
  time to fit residues: 25.4539
Evaluate side-chains
  261 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 224
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  180 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  369 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0770
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8342

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

Flipped N/Q/H residues before XYZ refinement:
C  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.122055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.100661 restraints weight = 17911.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.102384 restraints weight = 11004.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.103394 restraints weight = 8559.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.103873 restraints weight = 7129.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.104549 restraints weight = 6828.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.4880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7850  Z= 0.154
  Angle     :  0.765  10.117  10660  Z= 0.390
  Chirality :  0.044   0.179   1138
  Planarity :  0.006   0.103   1296
  Dihedral  :  7.071  57.754   1070
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 31.89 %
    Favored  : 63.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.28), residues: 886
  helix:  1.12 (0.21), residues: 560
  sheet: -0.11 (0.66), residues: 56
  loop : -3.09 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B  78 
 TYR   0.034   0.002   TYR C 182 
 PHE   0.025   0.001   PHE C 158 
 TRP   0.012   0.001   TRP C  84 
 HIS   0.003   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7846)
  covalent geometry    : angle       0.76336 (10652)
  SS BOND              : bond        0.00136 (    4)
  SS BOND              : angle       1.87876 (    8)
  hydrogen bonds       : bond        0.04333 (  486)
  hydrogen bonds       : angle       4.71889 ( 1434)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 227
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8353 (p-90) cc_final: 0.8137 (p-90)
REVERT: A   91 LEU cc_start: 0.8251 (pp) cc_final: 0.8032 (pp)
REVERT: A  140 MET cc_start: 0.8727 (tpp) cc_final: 0.8273 (tpp)
REVERT: A  224 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7128 (t80)
REVERT: A  233 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: A  250 ASN cc_start: 0.7631 (p0) cc_final: 0.7146 (t0)
REVERT: A  332 GLN cc_start: 0.8621 (mt0) cc_final: 0.8339 (mt0)
REVERT: B  149 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.6861 (p90)
REVERT: C   91 LEU cc_start: 0.8459 (pp) cc_final: 0.8217 (pp)
REVERT: C  140 MET cc_start: 0.8633 (tpp) cc_final: 0.8350 (tpp)
REVERT: C  274 MET cc_start: 0.8251 (ptm) cc_final: 0.7987 (ppp)
REVERT: C  334 ARG cc_start: 0.6731 (tmt170) cc_final: 0.5661 (ttt180)
REVERT: D  150 MET cc_start: 0.7912 (ttp) cc_final: 0.7609 (ttp)
  outliers start: 37
  outliers final: 34
  residues processed: 246
  average time/residue: 0.0715
  time to fit residues: 25.5692
Evaluate side-chains
  257 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 221
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  180 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  369 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0970
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 342 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.122752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.101204 restraints weight = 17986.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.103044 restraints weight = 10906.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.104027 restraints weight = 8433.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.104566 restraints weight = 7051.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.105203 restraints weight = 6756.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.5008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7850  Z= 0.151
  Angle     :  0.770  10.104  10660  Z= 0.394
  Chirality :  0.045   0.225   1138
  Planarity :  0.005   0.051   1296
  Dihedral  :  6.896  56.016   1070
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 31.27 %
    Favored  : 63.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.28), residues: 886
  helix:  1.09 (0.21), residues: 564
  sheet: -0.07 (0.67), residues: 56
  loop : -3.19 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  78 
 TYR   0.026   0.002   TYR D  92 
 PHE   0.024   0.001   PHE C 158 
 TRP   0.013   0.001   TRP B  68 
 HIS   0.003   0.001   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7846)
  covalent geometry    : angle       0.76896 (10652)
  SS BOND              : bond        0.00119 (    4)
  SS BOND              : angle       1.91432 (    8)
  hydrogen bonds       : bond        0.04255 (  486)
  hydrogen bonds       : angle       4.69226 ( 1434)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1367.10 seconds
wall clock time: 24 minutes 28.26 seconds (1468.26 seconds total)