Starting phenix.real_space_refine
on Tue Mar  3 11:30:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pqg_13593/03_2026/7pqg_13593.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pqg_13593/03_2026/7pqg_13593.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pqg_13593/03_2026/7pqg_13593.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pqg_13593/03_2026/7pqg_13593.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pqg_13593/03_2026/7pqg_13593.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pqg_13593/03_2026/7pqg_13593.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    2134      2.51       5
     N     522      2.21       5
     O     564      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3251
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 955
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "A"
      Number of atoms: 2296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2296
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 16, 'TRANS': 282}
  Time building chain proxies: 0.92, per 1000 atoms: 0.28
  Number of scatterers: 3251
  At special positions: 0
  Unit cell: (61.488, 75.6, 99.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O     564      8.00
     N     522      7.00
     C    2134      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " 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: 0.27
  Conformation dependent library (CDL) restraints added in 129.3 milliseconds
  

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 3 sheets defined
      67.8% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'B' and resid 62 through 65
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.715A  pdb=" N   ASP B  90 " --> pdb=" O   LYS B  87 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 87 through 91'
    Processing helix  chain 'B' and resid 109 through 113
      removed outlier: 3.610A  pdb=" N   TYR B 113 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 44
      removed outlier: 4.031A  pdb=" N   ASP A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 55
      removed outlier: 3.588A  pdb=" N   ALA A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 83
      removed outlier: 3.686A  pdb=" N   MET A  72 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 86 through 98
    Processing helix  chain 'A' and resid 102 through 113
    Processing helix  chain 'A' and resid 115 through 143
      removed outlier: 3.970A  pdb=" N   SER A 119 " --> pdb=" O   ASP A 115 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 131 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   GLY A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      Proline residue:  A 135  - end of helix
      removed outlier: 3.785A  pdb=" N   ARG A 143 " --> pdb=" O   TYR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 153
      removed outlier: 4.475A  pdb=" N   ASP A 152 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 179
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 183 through 210
      removed outlier: 3.590A  pdb=" N   VAL A 187 " --> pdb=" O   TYR A 183 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE A 188 " --> pdb=" O   MET A 184 " (cutoff:3.500A)
      removed outlier: 5.388A  pdb=" N   LYS A 189 " --> pdb=" O   ARG A 185 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLY A 190 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 218
      removed outlier: 4.281A  pdb=" N   MET A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 244
      Proline residue:  A 230  - end of helix
    Processing helix  chain 'A' and resid 247 through 260
      removed outlier: 3.568A  pdb=" N   CYS A 260 " --> pdb=" O   MET A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 274
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 284 through 310
      removed outlier: 3.535A  pdb=" N   LEU A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS A 309 " --> pdb=" O   TRP A 305 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE A 310 " --> pdb=" O   CYS A 306 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4
      removed outlier: 3.800A  pdb=" N   MET B  83 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU B  20 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60
      removed outlier: 3.933A  pdb=" N   ALA B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA B  98 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TYR B 115 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 93
      removed outlier: 3.707A  pdb=" N   VAL B 122 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)

    199 hydrogen bonds defined for protein.
    567 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.48

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 863
        1.33 -     1.45: 598
        1.45 -     1.57: 1814
        1.57 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 3324
  Sorted by residual:
  bond pdb=" CG  GLN A 293 "
       pdb=" CD  GLN A 293 "
    ideal  model  delta    sigma   weight residual
    1.516  1.466  0.050 2.50e-02 1.60e+03 4.06e+00
  bond pdb=" N   LYS A 189 "
       pdb=" CA  LYS A 189 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.016 1.29e-02 6.01e+03 1.58e+00
  bond pdb=" C   VAL A 187 "
       pdb=" N   ILE A 188 "
    ideal  model  delta    sigma   weight residual
    1.335  1.321  0.014 1.26e-02 6.30e+03 1.21e+00
  bond pdb=" CB  CYS A 125 "
       pdb=" SG  CYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.808  1.773  0.035 3.30e-02 9.18e+02 1.11e+00
  bond pdb=" N   THR A  13 "
       pdb=" CA  THR A  13 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.94e-01
  ... (remaining 3319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 4194
        1.58 -     3.17: 244
        3.17 -     4.75: 49
        4.75 -     6.33: 17
        6.33 -     7.91: 2
  Bond angle restraints: 4506
  Sorted by residual:
  angle pdb=" N   VAL A 187 "
        pdb=" CA  VAL A 187 "
        pdb=" C   VAL A 187 "
      ideal   model   delta    sigma   weight residual
     110.62  114.37   -3.75 1.02e+00 9.61e-01 1.35e+01
  angle pdb=" N   GLN A 293 "
        pdb=" CA  GLN A 293 "
        pdb=" CB  GLN A 293 "
      ideal   model   delta    sigma   weight residual
     110.28  115.50   -5.22 1.55e+00 4.16e-01 1.14e+01
  angle pdb=" N   ILE A 188 "
        pdb=" CA  ILE A 188 "
        pdb=" C   ILE A 188 "
      ideal   model   delta    sigma   weight residual
     110.62  114.01   -3.39 1.02e+00 9.61e-01 1.10e+01
  angle pdb=" N   GLN A 261 "
        pdb=" CA  GLN A 261 "
        pdb=" C   GLN A 261 "
      ideal   model   delta    sigma   weight residual
     109.96  114.98   -5.02 1.58e+00 4.01e-01 1.01e+01
  angle pdb=" N   TYR A 186 "
        pdb=" CA  TYR A 186 "
        pdb=" C   TYR A 186 "
      ideal   model   delta    sigma   weight residual
     113.50  109.63    3.87 1.23e+00 6.61e-01 9.89e+00
  ... (remaining 4501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 1809
       17.01 -    34.02: 131
       34.02 -    51.03: 22
       51.03 -    68.04: 3
       68.04 -    85.05: 3
  Dihedral angle restraints: 1968
    sinusoidal: 758
      harmonic: 1210
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.83  -71.83     1      1.00e+01 1.00e-02 6.61e+01
  dihedral pdb=" CA  LYS A 309 "
           pdb=" C   LYS A 309 "
           pdb=" N   PHE A 310 "
           pdb=" CA  PHE A 310 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.01  -21.99     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  GLU B  89 "
           pdb=" C   GLU B  89 "
           pdb=" N   ASP B  90 "
           pdb=" CA  ASP B  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.48  -21.52     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 1965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 335
       0.037 -    0.074: 120
       0.074 -    0.112: 50
       0.112 -    0.149: 19
       0.149 -    0.186: 3
  Chirality restraints: 527
  Sorted by residual:
  chirality pdb=" CB  ILE A  88 "
            pdb=" CA  ILE A  88 "
            pdb=" CG1 ILE A  88 "
            pdb=" CG2 ILE A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.65e-01
  chirality pdb=" CA  MET A 229 "
            pdb=" N   MET A 229 "
            pdb=" C   MET A 229 "
            pdb=" CB  MET A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.85e-01
  chirality pdb=" CG  LEU A  79 "
            pdb=" CB  LEU A  79 "
            pdb=" CD1 LEU A  79 "
            pdb=" CD2 LEU A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.18e-01
  ... (remaining 524 not shown)

  Planarity restraints: 551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 109 "    0.033 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO B 110 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 110 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 110 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 289 "    0.009 2.00e-02 2.50e+03   1.90e-02 3.62e+00
        pdb=" C   TYR A 289 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   TYR A 289 "    0.012 2.00e-02 2.50e+03
        pdb=" N   MET A 290 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  36 "   -0.011 2.00e-02 2.50e+03   1.33e-02 3.08e+00
        pdb=" CG  PHE A  36 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  36 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  36 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  36 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  36 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 548 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 389
        2.74 -     3.28: 3900
        3.28 -     3.82: 5577
        3.82 -     4.36: 6655
        4.36 -     4.90: 10332
  Nonbonded interactions: 26853
  Sorted by model distance:
  nonbonded pdb=" O   THR A 124 "
            pdb=" OG1 THR A 127 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   TRP B  53 "
            pdb=" NH2 ARG B  72 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   LYS A 113 "
            pdb=" NH2 ARG A 249 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG  SER B   7 "
            pdb=" OG  SER B  21 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ILE A 168 "
            pdb=" OG1 THR A 171 "
     model   vdw
     2.252 3.040
  ... (remaining 26848 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.990
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.240
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
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      :  0.004   0.050   3325  Z= 0.199
  Angle     :  0.880   7.914   4508  Z= 0.481
  Chirality :  0.049   0.186    527
  Planarity :  0.006   0.049    551
  Dihedral  : 12.564  85.048   1195
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 28.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.28 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.41), residues: 419
  helix:  0.44 (0.32), residues: 241
  sheet: -3.49 (0.73), residues: 34
  loop : -1.44 (0.53), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG B  38 
 TYR   0.018   0.002   TYR A  69 
 PHE   0.031   0.003   PHE A  36 
 TRP   0.016   0.002   TRP B 116 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 3324)
  covalent geometry    : angle       0.88012 ( 4506)
  SS BOND              : bond        0.00041 (    1)
  SS BOND              : angle       1.42286 (    2)
  hydrogen bonds       : bond        0.17443 (  199)
  hydrogen bonds       : angle       6.78926 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7405 (mmm160)
REVERT: B   93 LEU cc_start: 0.8568 (tp) cc_final: 0.8307 (tp)
REVERT: A   36 PHE cc_start: 0.8694 (m-80) cc_final: 0.8482 (m-80)
REVERT: A   52 LYS cc_start: 0.8498 (mtmm) cc_final: 0.7612 (tppt)
REVERT: A  108 PHE cc_start: 0.9052 (m-80) cc_final: 0.8737 (m-80)
REVERT: A  129 LEU cc_start: 0.8905 (mm) cc_final: 0.8299 (mm)
REVERT: A  133 MET cc_start: 0.8119 (mpp) cc_final: 0.7717 (mpp)
REVERT: A  215 MET cc_start: 0.8917 (mpp) cc_final: 0.8577 (mpp)
REVERT: A  234 PHE cc_start: 0.8544 (m-80) cc_final: 0.8227 (m-80)
REVERT: A  288 LEU cc_start: 0.9296 (mt) cc_final: 0.8966 (mt)
REVERT: A  290 MET cc_start: 0.8966 (tmm) cc_final: 0.8709 (tmm)
REVERT: A  291 ILE cc_start: 0.9399 (pt) cc_final: 0.8850 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0639
  time to fit residues: 11.0327
Evaluate side-chains
  119 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B   1 GLN
B  39 GLN
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  82 GLN
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 GLN
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** 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 = 0.3692 r_free = 0.3692 target = 0.076191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.063721 restraints weight = 13734.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.065583 restraints weight = 9481.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.066947 restraints weight = 7080.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.067922 restraints weight = 5602.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.068734 restraints weight = 4648.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3325  Z= 0.191
  Angle     :  0.892  10.212   4508  Z= 0.464
  Chirality :  0.052   0.207    527
  Planarity :  0.006   0.049    551
  Dihedral  :  5.715  19.967    454
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 27.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.17 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.41), residues: 419
  helix:  0.48 (0.32), residues: 250
  sheet: -2.25 (0.88), residues: 35
  loop : -1.98 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  72 
 TYR   0.020   0.002   TYR A 289 
 PHE   0.027   0.003   PHE A 128 
 TRP   0.009   0.002   TRP B  36 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 3324)
  covalent geometry    : angle       0.89168 ( 4506)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       1.88308 (    2)
  hydrogen bonds       : bond        0.05359 (  199)
  hydrogen bonds       : angle       5.52266 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 GLU cc_start: 0.8545 (pm20) cc_final: 0.8299 (pm20)
REVERT: B   45 ARG cc_start: 0.6982 (tmm-80) cc_final: 0.6214 (tmm-80)
REVERT: B   80 TYR cc_start: 0.8085 (t80) cc_final: 0.7806 (t80)
REVERT: A   34 MET cc_start: 0.9117 (ptp) cc_final: 0.8850 (ptp)
REVERT: A   36 PHE cc_start: 0.8643 (m-80) cc_final: 0.8429 (m-80)
REVERT: A   83 PHE cc_start: 0.7664 (m-80) cc_final: 0.7291 (m-80)
REVERT: A  108 PHE cc_start: 0.9089 (m-80) cc_final: 0.8655 (m-80)
REVERT: A  129 LEU cc_start: 0.8927 (mm) cc_final: 0.8109 (mm)
REVERT: A  133 MET cc_start: 0.8181 (mpp) cc_final: 0.7870 (mpp)
REVERT: A  215 MET cc_start: 0.8816 (mpp) cc_final: 0.8415 (mpp)
REVERT: A  221 HIS cc_start: 0.8523 (m-70) cc_final: 0.7939 (m-70)
REVERT: A  291 ILE cc_start: 0.9428 (pt) cc_final: 0.8747 (pt)
  outliers start: 8
  outliers final: 4
  residues processed: 132
  average time/residue: 0.0672
  time to fit residues: 10.6495
Evaluate side-chains
  117 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 GLN
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  117 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.0060
   chunk 18 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 39 optimal weight:    0.3980
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
B   1 GLN
B  39 GLN
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.077264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.064711 restraints weight = 14320.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.066613 restraints weight = 9853.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.067997 restraints weight = 7343.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.069077 restraints weight = 5832.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.069854 restraints weight = 4811.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3325  Z= 0.175
  Angle     :  0.874   9.058   4508  Z= 0.458
  Chirality :  0.053   0.325    527
  Planarity :  0.005   0.033    551
  Dihedral  :  5.491  19.853    454
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 26.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.37 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.42), residues: 419
  helix:  0.36 (0.32), residues: 252
  sheet: -2.47 (0.79), residues: 44
  loop : -1.75 (0.58), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 252 
 TYR   0.026   0.002   TYR B  32 
 PHE   0.024   0.002   PHE A 128 
 TRP   0.007   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3324)
  covalent geometry    : angle       0.87343 ( 4506)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       1.07965 (    2)
  hydrogen bonds       : bond        0.05323 (  199)
  hydrogen bonds       : angle       5.37662 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6010 (tmm-80)
REVERT: B   76 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8341 (tptp)
REVERT: B   83 MET cc_start: 0.7434 (ppp) cc_final: 0.7166 (ppp)
REVERT: B   93 LEU cc_start: 0.8926 (tp) cc_final: 0.8723 (tt)
REVERT: A   34 MET cc_start: 0.9098 (ptp) cc_final: 0.8774 (ptp)
REVERT: A   36 PHE cc_start: 0.8598 (m-80) cc_final: 0.8333 (m-80)
REVERT: A  104 LEU cc_start: 0.8537 (pt) cc_final: 0.7426 (pp)
REVERT: A  108 PHE cc_start: 0.9094 (m-80) cc_final: 0.8540 (m-80)
REVERT: A  112 MET cc_start: 0.7385 (ppp) cc_final: 0.6316 (ppp)
REVERT: A  147 ASP cc_start: 0.8586 (m-30) cc_final: 0.8177 (p0)
REVERT: A  182 GLN cc_start: 0.8834 (mm110) cc_final: 0.8525 (mm-40)
REVERT: A  215 MET cc_start: 0.8649 (mpp) cc_final: 0.8331 (mpp)
REVERT: A  221 HIS cc_start: 0.8663 (m-70) cc_final: 0.8132 (m-70)
REVERT: A  234 PHE cc_start: 0.8819 (m-80) cc_final: 0.8350 (m-80)
REVERT: A  290 MET cc_start: 0.8997 (tmm) cc_final: 0.8772 (tmm)
REVERT: A  291 ILE cc_start: 0.9229 (pt) cc_final: 0.9008 (pt)
REVERT: A  296 GLU cc_start: 0.9024 (pt0) cc_final: 0.8639 (pt0)
  outliers start: 10
  outliers final: 5
  residues processed: 130
  average time/residue: 0.0662
  time to fit residues: 10.4171
Evaluate side-chains
  121 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   45 ARG
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  293 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.0020
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 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 = 0.3725 r_free = 0.3725 target = 0.077632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.064528 restraints weight = 14026.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.066418 restraints weight = 9720.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.067813 restraints weight = 7317.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.068823 restraints weight = 5833.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.069674 restraints weight = 4891.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3325  Z= 0.166
  Angle     :  0.849   8.870   4508  Z= 0.439
  Chirality :  0.052   0.257    527
  Planarity :  0.005   0.033    551
  Dihedral  :  5.414  22.905    454
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 24.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 21.57 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.41), residues: 419
  helix:  0.29 (0.32), residues: 252
  sheet: -2.55 (0.77), residues: 44
  loop : -1.91 (0.57), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  45 
 TYR   0.026   0.002   TYR B  32 
 PHE   0.024   0.002   PHE A 128 
 TRP   0.007   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3324)
  covalent geometry    : angle       0.84919 ( 4506)
  SS BOND              : bond        0.00174 (    1)
  SS BOND              : angle       1.15055 (    2)
  hydrogen bonds       : bond        0.05008 (  199)
  hydrogen bonds       : angle       5.25094 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8388 (tptp)
REVERT: B   83 MET cc_start: 0.7840 (ppp) cc_final: 0.7319 (ppp)
REVERT: A   34 MET cc_start: 0.9149 (ptp) cc_final: 0.8878 (ptp)
REVERT: A   36 PHE cc_start: 0.8588 (m-80) cc_final: 0.8346 (m-80)
REVERT: A  104 LEU cc_start: 0.8649 (pt) cc_final: 0.7510 (pp)
REVERT: A  108 PHE cc_start: 0.9114 (m-80) cc_final: 0.8571 (m-80)
REVERT: A  112 MET cc_start: 0.7343 (ppp) cc_final: 0.6073 (ppp)
REVERT: A  133 MET cc_start: 0.8169 (mpp) cc_final: 0.7953 (mpp)
REVERT: A  147 ASP cc_start: 0.8629 (m-30) cc_final: 0.8112 (p0)
REVERT: A  182 GLN cc_start: 0.8825 (mm110) cc_final: 0.8530 (mm-40)
REVERT: A  215 MET cc_start: 0.8587 (mpp) cc_final: 0.8262 (mpp)
REVERT: A  234 PHE cc_start: 0.8851 (m-80) cc_final: 0.8383 (m-80)
REVERT: A  290 MET cc_start: 0.9089 (tmm) cc_final: 0.8767 (tmm)
REVERT: A  291 ILE cc_start: 0.9245 (pt) cc_final: 0.8928 (pt)
REVERT: A  296 GLU cc_start: 0.8999 (pt0) cc_final: 0.8650 (pt0)
  outliers start: 14
  outliers final: 6
  residues processed: 125
  average time/residue: 0.0618
  time to fit residues: 9.4673
Evaluate side-chains
  118 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   45 ARG
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  293 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.077350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.064583 restraints weight = 14553.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.066422 restraints weight = 10199.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.067765 restraints weight = 7698.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.068788 restraints weight = 6158.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.069493 restraints weight = 5130.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3325  Z= 0.178
  Angle     :  0.872   9.909   4508  Z= 0.447
  Chirality :  0.052   0.373    527
  Planarity :  0.005   0.039    551
  Dihedral  :  5.409  20.823    454
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 26.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.69 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.42), residues: 419
  helix:  0.33 (0.33), residues: 251
  sheet: -2.47 (0.77), residues: 44
  loop : -1.96 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  45 
 TYR   0.028   0.002   TYR B  32 
 PHE   0.025   0.002   PHE A 128 
 TRP   0.007   0.001   TRP B 105 
 HIS   0.003   0.002   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 3324)
  covalent geometry    : angle       0.87219 ( 4506)
  SS BOND              : bond        0.00197 (    1)
  SS BOND              : angle       1.05016 (    2)
  hydrogen bonds       : bond        0.04844 (  199)
  hydrogen bonds       : angle       5.24132 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7610 (mmm-85)
REVERT: B   76 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8428 (tptp)
REVERT: B   83 MET cc_start: 0.7777 (ppp) cc_final: 0.6628 (ppp)
REVERT: A   34 MET cc_start: 0.9208 (ptp) cc_final: 0.8997 (ptp)
REVERT: A   36 PHE cc_start: 0.8612 (m-80) cc_final: 0.8374 (m-80)
REVERT: A  108 PHE cc_start: 0.9148 (m-80) cc_final: 0.8727 (m-80)
REVERT: A  112 MET cc_start: 0.7528 (ppp) cc_final: 0.6338 (ppp)
REVERT: A  147 ASP cc_start: 0.8592 (m-30) cc_final: 0.8124 (p0)
REVERT: A  215 MET cc_start: 0.8633 (mpp) cc_final: 0.8161 (mpp)
REVERT: A  234 PHE cc_start: 0.8825 (m-80) cc_final: 0.8359 (m-80)
REVERT: A  293 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8818 (mp10)
REVERT: A  296 GLU cc_start: 0.9030 (pt0) cc_final: 0.8656 (pt0)
  outliers start: 14
  outliers final: 8
  residues processed: 126
  average time/residue: 0.0612
  time to fit residues: 9.5135
Evaluate side-chains
  122 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   45 ARG
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  293 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    0.1980
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.077595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.064511 restraints weight = 14209.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.066474 restraints weight = 9878.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.067890 restraints weight = 7380.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.068915 restraints weight = 5847.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.069758 restraints weight = 4869.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3325  Z= 0.186
  Angle     :  0.909  10.749   4508  Z= 0.462
  Chirality :  0.053   0.301    527
  Planarity :  0.005   0.037    551
  Dihedral  :  5.459  21.402    454
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 28.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 26.89 %
    Favored  : 69.19 %
  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 are not related in a simple way.
  whole: -1.16 (0.41), residues: 419
  helix:  0.13 (0.32), residues: 255
  sheet: -1.96 (0.91), residues: 35
  loop : -2.10 (0.56), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  45 
 TYR   0.029   0.002   TYR B  32 
 PHE   0.023   0.002   PHE A 128 
 TRP   0.007   0.001   TRP B 105 
 HIS   0.003   0.002   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 3324)
  covalent geometry    : angle       0.90913 ( 4506)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       1.24915 (    2)
  hydrogen bonds       : bond        0.04981 (  199)
  hydrogen bonds       : angle       5.32456 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   68 PHE cc_start: 0.8709 (m-10) cc_final: 0.8496 (m-10)
REVERT: B   76 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8444 (tptp)
REVERT: B   80 TYR cc_start: 0.8236 (t80) cc_final: 0.7773 (t80)
REVERT: B   93 LEU cc_start: 0.9048 (tp) cc_final: 0.8838 (tp)
REVERT: A   36 PHE cc_start: 0.8586 (m-80) cc_final: 0.8345 (m-80)
REVERT: A  104 LEU cc_start: 0.8613 (pt) cc_final: 0.7317 (pp)
REVERT: A  108 PHE cc_start: 0.9122 (m-80) cc_final: 0.8573 (m-80)
REVERT: A  112 MET cc_start: 0.7507 (ppp) cc_final: 0.7152 (ppp)
REVERT: A  134 MET cc_start: 0.8556 (mmm) cc_final: 0.8327 (mmm)
REVERT: A  147 ASP cc_start: 0.8613 (m-30) cc_final: 0.8110 (p0)
REVERT: A  215 MET cc_start: 0.8577 (mpp) cc_final: 0.8089 (mpp)
REVERT: A  234 PHE cc_start: 0.8799 (m-80) cc_final: 0.8350 (m-80)
REVERT: A  243 LEU cc_start: 0.8592 (mt) cc_final: 0.8288 (mm)
REVERT: A  290 MET cc_start: 0.8806 (tpp) cc_final: 0.8568 (tpp)
  outliers start: 14
  outliers final: 11
  residues processed: 128
  average time/residue: 0.0734
  time to fit residues: 11.2781
Evaluate side-chains
  125 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   45 ARG
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  293 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0040
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.4392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.079051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.065832 restraints weight = 14276.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.067747 restraints weight = 9975.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.069180 restraints weight = 7520.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.070211 restraints weight = 5991.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.071013 restraints weight = 4989.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3325  Z= 0.173
  Angle     :  0.946  11.182   4508  Z= 0.481
  Chirality :  0.055   0.312    527
  Planarity :  0.005   0.039    551
  Dihedral  :  5.431  20.405    454
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 26.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 28.29 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.41), residues: 419
  helix:  0.16 (0.32), residues: 255
  sheet: -1.85 (0.92), residues: 35
  loop : -2.08 (0.56), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  45 
 TYR   0.031   0.002   TYR B  32 
 PHE   0.025   0.002   PHE A 128 
 TRP   0.007   0.001   TRP B 105 
 HIS   0.005   0.002   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3324)
  covalent geometry    : angle       0.94583 ( 4506)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       0.95241 (    2)
  hydrogen bonds       : bond        0.04960 (  199)
  hydrogen bonds       : angle       5.27284 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.6101 (ttp80)
REVERT: B   76 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8391 (tptp)
REVERT: B   80 TYR cc_start: 0.8141 (t80) cc_final: 0.7807 (t80)
REVERT: B   93 LEU cc_start: 0.8979 (tp) cc_final: 0.8494 (tp)
REVERT: A   36 PHE cc_start: 0.8510 (m-80) cc_final: 0.8281 (m-80)
REVERT: A  108 PHE cc_start: 0.9060 (m-80) cc_final: 0.8787 (m-80)
REVERT: A  147 ASP cc_start: 0.8489 (m-30) cc_final: 0.8041 (p0)
REVERT: A  182 GLN cc_start: 0.8750 (mm110) cc_final: 0.8449 (mm-40)
REVERT: A  215 MET cc_start: 0.8561 (mpp) cc_final: 0.8118 (mpp)
REVERT: A  221 HIS cc_start: 0.8553 (m-70) cc_final: 0.8305 (m90)
REVERT: A  234 PHE cc_start: 0.8789 (m-80) cc_final: 0.8393 (m-80)
REVERT: A  243 LEU cc_start: 0.8617 (mt) cc_final: 0.8315 (mm)
REVERT: A  290 MET cc_start: 0.8700 (tpp) cc_final: 0.8426 (tpp)
  outliers start: 13
  outliers final: 8
  residues processed: 131
  average time/residue: 0.0644
  time to fit residues: 10.1914
Evaluate side-chains
  128 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   45 ARG
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  293 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 4 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 3 optimal weight:    0.1980
   chunk 15 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0000
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
B  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.078461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.064966 restraints weight = 14512.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.066901 restraints weight = 10143.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.068332 restraints weight = 7684.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.069354 restraints weight = 6148.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.070159 restraints weight = 5167.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3325  Z= 0.178
  Angle     :  0.978  11.005   4508  Z= 0.495
  Chirality :  0.056   0.309    527
  Planarity :  0.006   0.044    551
  Dihedral  :  5.505  20.664    454
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 26.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 30.25 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.41), residues: 419
  helix:  0.15 (0.32), residues: 255
  sheet: -1.75 (0.93), residues: 35
  loop : -2.11 (0.55), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  38 
 TYR   0.027   0.002   TYR B  32 
 PHE   0.022   0.002   PHE A 128 
 TRP   0.008   0.001   TRP B 105 
 HIS   0.001   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3324)
  covalent geometry    : angle       0.97792 ( 4506)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       1.13825 (    2)
  hydrogen bonds       : bond        0.04891 (  199)
  hydrogen bonds       : angle       5.40084 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8381 (tptp)
REVERT: B   80 TYR cc_start: 0.8126 (t80) cc_final: 0.7787 (t80)
REVERT: A   36 PHE cc_start: 0.8505 (m-80) cc_final: 0.8287 (m-80)
REVERT: A   46 MET cc_start: 0.8203 (tmm) cc_final: 0.6016 (mtt)
REVERT: A   47 GLU cc_start: 0.9031 (pm20) cc_final: 0.8430 (pm20)
REVERT: A  108 PHE cc_start: 0.9102 (m-80) cc_final: 0.8711 (m-80)
REVERT: A  112 MET cc_start: 0.7168 (ppp) cc_final: 0.5604 (ppp)
REVERT: A  147 ASP cc_start: 0.8564 (m-30) cc_final: 0.8044 (p0)
REVERT: A  182 GLN cc_start: 0.8794 (mm110) cc_final: 0.8428 (mm-40)
REVERT: A  215 MET cc_start: 0.8605 (mpp) cc_final: 0.8287 (mpp)
REVERT: A  221 HIS cc_start: 0.8571 (m-70) cc_final: 0.8360 (m90)
REVERT: A  234 PHE cc_start: 0.8810 (m-80) cc_final: 0.8399 (m-80)
REVERT: A  243 LEU cc_start: 0.8608 (mt) cc_final: 0.8311 (mm)
REVERT: A  274 PHE cc_start: 0.8322 (m-80) cc_final: 0.7704 (t80)
REVERT: A  290 MET cc_start: 0.8666 (tpp) cc_final: 0.8370 (tpp)
  outliers start: 11
  outliers final: 10
  residues processed: 129
  average time/residue: 0.0599
  time to fit residues: 9.4875
Evaluate side-chains
  130 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   45 ARG
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  293 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0870
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.6358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.079253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.066009 restraints weight = 14244.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.067879 restraints weight = 10090.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.069248 restraints weight = 7680.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.070229 restraints weight = 6161.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.071047 restraints weight = 5195.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3325  Z= 0.183
  Angle     :  1.026  13.081   4508  Z= 0.515
  Chirality :  0.058   0.312    527
  Planarity :  0.006   0.045    551
  Dihedral  :  5.497  20.579    454
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 26.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 31.65 %
    Favored  : 65.27 %
  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 are not related in a simple way.
  whole: -1.10 (0.41), residues: 419
  helix:  0.21 (0.32), residues: 255
  sheet: -1.87 (0.91), residues: 35
  loop : -2.19 (0.54), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  45 
 TYR   0.033   0.002   TYR B  32 
 PHE   0.023   0.002   PHE A 128 
 TRP   0.008   0.001   TRP B 105 
 HIS   0.001   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 3324)
  covalent geometry    : angle       1.02637 ( 4506)
  SS BOND              : bond        0.00173 (    1)
  SS BOND              : angle       0.75249 (    2)
  hydrogen bonds       : bond        0.04878 (  199)
  hydrogen bonds       : angle       5.48693 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8404 (tptp)
REVERT: B   80 TYR cc_start: 0.8132 (t80) cc_final: 0.7715 (t80)
REVERT: B   93 LEU cc_start: 0.9101 (tp) cc_final: 0.8841 (tp)
REVERT: A   36 PHE cc_start: 0.8494 (m-80) cc_final: 0.8285 (m-80)
REVERT: A   46 MET cc_start: 0.8156 (tmm) cc_final: 0.5904 (mtt)
REVERT: A   47 GLU cc_start: 0.9001 (pm20) cc_final: 0.8417 (pm20)
REVERT: A  108 PHE cc_start: 0.9080 (m-80) cc_final: 0.8688 (m-80)
REVERT: A  112 MET cc_start: 0.7200 (ppp) cc_final: 0.5699 (ppp)
REVERT: A  147 ASP cc_start: 0.8506 (m-30) cc_final: 0.8007 (p0)
REVERT: A  182 GLN cc_start: 0.8766 (mm110) cc_final: 0.8426 (mm-40)
REVERT: A  215 MET cc_start: 0.8571 (mpp) cc_final: 0.8247 (mpp)
REVERT: A  234 PHE cc_start: 0.8751 (m-80) cc_final: 0.8377 (m-80)
REVERT: A  243 LEU cc_start: 0.8580 (mt) cc_final: 0.8271 (mm)
REVERT: A  274 PHE cc_start: 0.8273 (m-80) cc_final: 0.7658 (t80)
REVERT: A  290 MET cc_start: 0.8627 (tpp) cc_final: 0.8320 (tpp)
  outliers start: 11
  outliers final: 10
  residues processed: 128
  average time/residue: 0.0627
  time to fit residues: 9.8560
Evaluate side-chains
  130 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   45 ARG
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  293 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 221 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.079159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.065804 restraints weight = 14146.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.067711 restraints weight = 10017.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.069135 restraints weight = 7629.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.070178 restraints weight = 6119.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.070789 restraints weight = 5134.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.4404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3325  Z= 0.191
  Angle     :  1.081  13.381   4508  Z= 0.543
  Chirality :  0.060   0.357    527
  Planarity :  0.006   0.049    551
  Dihedral  :  5.624  21.447    454
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 27.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 33.33 %
    Favored  : 63.59 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.41), residues: 419
  helix:  0.28 (0.32), residues: 254
  sheet: -1.96 (0.79), residues: 41
  loop : -2.10 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  38 
 TYR   0.032   0.002   TYR B  32 
 PHE   0.022   0.003   PHE A 128 
 TRP   0.007   0.001   TRP B 105 
 HIS   0.009   0.003   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 3324)
  covalent geometry    : angle       1.08099 ( 4506)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.86299 (    2)
  hydrogen bonds       : bond        0.05002 (  199)
  hydrogen bonds       : angle       5.68188 (  567)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8471 (tptp)
REVERT: B   80 TYR cc_start: 0.8133 (t80) cc_final: 0.7760 (t80)
REVERT: B   93 LEU cc_start: 0.9164 (tp) cc_final: 0.8915 (tp)
REVERT: A   36 PHE cc_start: 0.8533 (m-80) cc_final: 0.8294 (m-80)
REVERT: A   46 MET cc_start: 0.8201 (tmm) cc_final: 0.5964 (mtt)
REVERT: A   47 GLU cc_start: 0.9089 (pm20) cc_final: 0.8521 (pm20)
REVERT: A  108 PHE cc_start: 0.9129 (m-80) cc_final: 0.8722 (m-80)
REVERT: A  112 MET cc_start: 0.7230 (ppp) cc_final: 0.5779 (ppp)
REVERT: A  147 ASP cc_start: 0.8535 (m-30) cc_final: 0.8016 (p0)
REVERT: A  215 MET cc_start: 0.8660 (mpp) cc_final: 0.8293 (mpp)
REVERT: A  234 PHE cc_start: 0.8803 (m-80) cc_final: 0.8420 (m-80)
REVERT: A  243 LEU cc_start: 0.8616 (mt) cc_final: 0.8311 (mm)
REVERT: A  274 PHE cc_start: 0.8285 (m-80) cc_final: 0.7643 (t80)
REVERT: A  290 MET cc_start: 0.8686 (tpp) cc_final: 0.8375 (tpp)
  outliers start: 11
  outliers final: 10
  residues processed: 123
  average time/residue: 0.0587
  time to fit residues: 8.7877
Evaluate side-chains
  126 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   45 ARG
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  293 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0070
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.080031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.066522 restraints weight = 14006.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.068401 restraints weight = 9937.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.069840 restraints weight = 7553.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.070844 restraints weight = 6050.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.071657 restraints weight = 5084.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3325  Z= 0.188
  Angle     :  1.115  17.076   4508  Z= 0.551
  Chirality :  0.060   0.349    527
  Planarity :  0.006   0.042    551
  Dihedral  :  5.678  22.510    454
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 27.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 34.45 %
    Favored  : 63.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.41), residues: 419
  helix:  0.12 (0.32), residues: 254
  sheet: -2.09 (0.77), residues: 41
  loop : -2.15 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  45 
 TYR   0.030   0.002   TYR B  32 
 PHE   0.024   0.002   PHE A 128 
 TRP   0.004   0.001   TRP B 116 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 3324)
  covalent geometry    : angle       1.11494 ( 4506)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       0.89043 (    2)
  hydrogen bonds       : bond        0.05177 (  199)
  hydrogen bonds       : angle       5.71739 (  567)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 825.06 seconds
wall clock time: 14 minutes 51.45 seconds (891.45 seconds total)