Starting phenix.real_space_refine
on Mon Feb 10 23:42:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pqg_13593/02_2025/7pqg_13593.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pqg_13593/02_2025/7pqg_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pqg_13593/02_2025/7pqg_13593.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pqg_13593/02_2025/7pqg_13593.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pqg_13593/02_2025/7pqg_13593.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pqg_13593/02_2025/7pqg_13593.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 2.92, per 1000 atoms: 0.90
  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: 0.84
  Conformation dependent library (CDL) restraints added in 388.6 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: 0.34
  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: 0.86

  Time building geometry restraints manager: 0.99 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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.720
  Find NCS groups from input model:        0.030
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.060
-------------------------------------------------------------------------------
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   3324  Z= 0.271
  Angle     :  0.880   7.914   4506  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.016   0.002   TRP B 116 
 HIS   0.003   0.001   HIS A  54 
 PHE   0.031   0.003   PHE A  36 
 TYR   0.018   0.002   TYR A  69 
 ARG   0.013   0.002   ARG B  38 

*********************** 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  : 0.365 
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: 0.8474 (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: 0.8918 (mpp) cc_final: 0.8576 (mpp)
REVERT: A  234 PHE cc_start: 0.8544 (m-80) cc_final: 0.8226 (m-80)
REVERT: A  288 LEU cc_start: 0.9295 (mt) cc_final: 0.8965 (mt)
REVERT: A  290 MET cc_start: 0.8966 (tmm) cc_final: 0.8710 (tmm)
REVERT: A  291 ILE cc_start: 0.9400 (pt) cc_final: 0.8852 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1631
  time to fit residues: 27.7899
Evaluate side-chains
  118 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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  82 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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.074189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.062245 restraints weight = 14141.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.064052 restraints weight = 9678.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.065369 restraints weight = 7195.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3324  Z= 0.309
  Angle     :  0.882   8.706   4506  Z= 0.466
  Chirality :  0.052   0.200    527
  Planarity :  0.006   0.054    551
  Dihedral  :  5.799  20.337    454
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 30.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.45 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.41), residues: 419
  helix:  0.33 (0.32), residues: 251
  sheet: -2.64 (0.73), residues: 44
  loop : -1.86 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  36 
 HIS   0.003   0.002   HIS A  54 
 PHE   0.027   0.003   PHE A 128 
 TYR   0.020   0.002   TYR B  59 
 ARG   0.005   0.001   ARG B  72 

*********************** 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
  141 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 GLU cc_start: 0.8564 (pm20) cc_final: 0.8361 (pm20)
REVERT: B   45 ARG cc_start: 0.7128 (tmm-80) cc_final: 0.6121 (tmm-80)
REVERT: A   36 PHE cc_start: 0.8722 (m-80) cc_final: 0.8505 (m-80)
REVERT: A   38 ILE cc_start: 0.9697 (pt) cc_final: 0.9494 (pt)
REVERT: A   83 PHE cc_start: 0.7690 (m-80) cc_final: 0.7489 (m-80)
REVERT: A  104 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.7707 (pp)
REVERT: A  108 PHE cc_start: 0.9197 (m-80) cc_final: 0.8612 (m-80)
REVERT: A  112 MET cc_start: 0.7743 (ppp) cc_final: 0.6370 (ppp)
REVERT: A  129 LEU cc_start: 0.8968 (mm) cc_final: 0.8191 (mm)
REVERT: A  133 MET cc_start: 0.8332 (mpp) cc_final: 0.8008 (mpp)
REVERT: A  215 MET cc_start: 0.8863 (mpp) cc_final: 0.8531 (mpp)
REVERT: A  221 HIS cc_start: 0.8470 (m-70) cc_final: 0.7967 (m-70)
REVERT: A  264 GLN cc_start: 0.9007 (mp10) cc_final: 0.8685 (mp10)
REVERT: A  290 MET cc_start: 0.9032 (tmm) cc_final: 0.8698 (tmm)
REVERT: A  291 ILE cc_start: 0.9462 (pt) cc_final: 0.8779 (pt)
  outliers start: 8
  outliers final: 5
  residues processed: 137
  average time/residue: 0.1589
  time to fit residues: 25.8929
Evaluate side-chains
  120 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
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  104 LEU
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  229 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    0.4980
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B   1 GLN
B  39 GLN
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 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 = 0.3695 r_free = 0.3695 target = 0.075377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.063348 restraints weight = 14352.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.065215 restraints weight = 9799.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.066525 restraints weight = 7262.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3324  Z= 0.249
  Angle     :  0.871  11.568   4506  Z= 0.449
  Chirality :  0.053   0.314    527
  Planarity :  0.005   0.054    551
  Dihedral  :  5.592  20.316    454
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 26.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.41), residues: 419
  helix:  0.35 (0.32), residues: 251
  sheet: -2.35 (0.77), residues: 44
  loop : -1.83 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A  54 
 PHE   0.025   0.002   PHE A 128 
 TYR   0.026   0.002   TYR B  32 
 ARG   0.010   0.001   ARG A 252 

*********************** 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
  137 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8364 (tptp)
REVERT: B   83 MET cc_start: 0.7701 (ppp) cc_final: 0.7204 (ppp)
REVERT: B   93 LEU cc_start: 0.8897 (tp) cc_final: 0.8361 (tp)
REVERT: A   35 LEU cc_start: 0.9433 (mt) cc_final: 0.9175 (mt)
REVERT: A   36 PHE cc_start: 0.8658 (m-80) cc_final: 0.8438 (m-80)
REVERT: A  104 LEU cc_start: 0.8704 (pt) cc_final: 0.7648 (pp)
REVERT: A  108 PHE cc_start: 0.9167 (m-80) cc_final: 0.8574 (m-80)
REVERT: A  112 MET cc_start: 0.7619 (ppp) cc_final: 0.6076 (ppp)
REVERT: A  182 GLN cc_start: 0.8738 (mm110) cc_final: 0.8524 (mm-40)
REVERT: A  215 MET cc_start: 0.8700 (mpp) cc_final: 0.8381 (mpp)
REVERT: A  221 HIS cc_start: 0.8519 (m-70) cc_final: 0.8090 (m-70)
REVERT: A  234 PHE cc_start: 0.8805 (m-80) cc_final: 0.8362 (m-80)
REVERT: A  290 MET cc_start: 0.9020 (tmm) cc_final: 0.8797 (tmm)
REVERT: A  291 ILE cc_start: 0.9389 (pt) cc_final: 0.8685 (pt)
  outliers start: 12
  outliers final: 8
  residues processed: 131
  average time/residue: 0.1434
  time to fit residues: 22.8031
Evaluate side-chains
  125 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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 B residue  123 THR
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  231 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 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 = 0.3704 r_free = 0.3704 target = 0.075956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.063233 restraints weight = 13927.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.065071 restraints weight = 9689.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.066445 restraints weight = 7285.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3324  Z= 0.241
  Angle     :  0.868   9.175   4506  Z= 0.442
  Chirality :  0.052   0.329    527
  Planarity :  0.005   0.039    551
  Dihedral  :  5.528  20.461    454
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 28.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.01 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.41), residues: 419
  helix:  0.38 (0.32), residues: 250
  sheet: -2.48 (0.77), residues: 44
  loop : -1.90 (0.57), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A  54 
 PHE   0.024   0.002   PHE A 128 
 TYR   0.027   0.002   TYR B  32 
 ARG   0.005   0.001   ARG B  45 

*********************** 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
  134 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.7986 (ttm-80)
REVERT: B   76 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8399 (tptp)
REVERT: B   83 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7290 (ppp)
REVERT: B   93 LEU cc_start: 0.8899 (tp) cc_final: 0.8377 (tp)
REVERT: A   36 PHE cc_start: 0.8697 (m-80) cc_final: 0.8456 (m-80)
REVERT: A  104 LEU cc_start: 0.8612 (pt) cc_final: 0.7501 (pp)
REVERT: A  108 PHE cc_start: 0.9188 (m-80) cc_final: 0.8626 (m-80)
REVERT: A  112 MET cc_start: 0.7537 (ppp) cc_final: 0.6105 (ppp)
REVERT: A  133 MET cc_start: 0.8306 (mpp) cc_final: 0.7958 (mpp)
REVERT: A  147 ASP cc_start: 0.8668 (m-30) cc_final: 0.8167 (p0)
REVERT: A  182 GLN cc_start: 0.8711 (mm110) cc_final: 0.8295 (mm-40)
REVERT: A  215 MET cc_start: 0.8650 (mpp) cc_final: 0.8338 (mpp)
REVERT: A  221 HIS cc_start: 0.8693 (m-70) cc_final: 0.8322 (m170)
REVERT: A  234 PHE cc_start: 0.8816 (m-80) cc_final: 0.8434 (m-80)
REVERT: A  291 ILE cc_start: 0.9411 (pt) cc_final: 0.8672 (pt)
  outliers start: 13
  outliers final: 6
  residues processed: 126
  average time/residue: 0.1584
  time to fit residues: 23.9112
Evaluate side-chains
  123 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
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   83 MET
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.3980
   chunk 1 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.076880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.064029 restraints weight = 14088.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.065858 restraints weight = 9821.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.067197 restraints weight = 7434.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3324  Z= 0.251
  Angle     :  0.910  10.751   4506  Z= 0.459
  Chirality :  0.054   0.342    527
  Planarity :  0.005   0.044    551
  Dihedral  :  5.564  19.993    454
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 28.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.97 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.41), residues: 419
  helix:  0.28 (0.32), residues: 251
  sheet: -2.51 (0.76), residues: 44
  loop : -1.95 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A  54 
 PHE   0.024   0.002   PHE A 128 
 TYR   0.028   0.002   TYR B  32 
 ARG   0.009   0.001   ARG B  45 

*********************** 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
  145 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7548 (mmm-85)
REVERT: B   45 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6674 (tmm-80)
REVERT: B   76 LYS cc_start: 0.8850 (mtmm) cc_final: 0.8417 (tptp)
REVERT: B   83 MET cc_start: 0.7683 (ppp) cc_final: 0.7351 (ppp)
REVERT: B   93 LEU cc_start: 0.8964 (tp) cc_final: 0.8189 (tp)
REVERT: A   36 PHE cc_start: 0.8644 (m-80) cc_final: 0.8413 (m-80)
REVERT: A  108 PHE cc_start: 0.9148 (m-80) cc_final: 0.8665 (m-80)
REVERT: A  112 MET cc_start: 0.7526 (ppp) cc_final: 0.5724 (ppp)
REVERT: A  133 MET cc_start: 0.8299 (mpp) cc_final: 0.8016 (mpp)
REVERT: A  147 ASP cc_start: 0.8596 (m-30) cc_final: 0.8146 (p0)
REVERT: A  182 GLN cc_start: 0.8704 (mm110) cc_final: 0.8325 (mm-40)
REVERT: A  215 MET cc_start: 0.8666 (mpp) cc_final: 0.8179 (mpp)
REVERT: A  221 HIS cc_start: 0.8700 (m-70) cc_final: 0.8449 (m170)
REVERT: A  234 PHE cc_start: 0.8793 (m-80) cc_final: 0.8382 (m-80)
  outliers start: 15
  outliers final: 6
  residues processed: 136
  average time/residue: 0.1719
  time to fit residues: 27.4707
Evaluate side-chains
  126 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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 B residue  123 THR
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  231 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0980
   chunk 36 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3719 r_free = 0.3719 target = 0.076640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.063319 restraints weight = 14829.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.065280 restraints weight = 10303.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.066695 restraints weight = 7709.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3324  Z= 0.257
  Angle     :  0.963  11.254   4506  Z= 0.484
  Chirality :  0.054   0.356    527
  Planarity :  0.005   0.040    551
  Dihedral  :  5.610  21.118    454
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 27.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 27.73 %
    Favored  : 68.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.41), residues: 419
  helix:  0.13 (0.32), residues: 254
  sheet: -2.99 (0.65), residues: 50
  loop : -1.82 (0.60), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A  54 
 PHE   0.021   0.002   PHE A 128 
 TYR   0.029   0.002   TYR B  32 
 ARG   0.008   0.001   ARG B  45 

*********************** 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
  136 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6710 (tmm-80)
REVERT: B   76 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8386 (tptp)
REVERT: B   83 MET cc_start: 0.7805 (ppp) cc_final: 0.7009 (ppp)
REVERT: B   93 LEU cc_start: 0.8903 (tp) cc_final: 0.8385 (tp)
REVERT: A   36 PHE cc_start: 0.8630 (m-80) cc_final: 0.8357 (m-80)
REVERT: A   47 GLU cc_start: 0.9174 (pm20) cc_final: 0.8630 (pm20)
REVERT: A  108 PHE cc_start: 0.9183 (m-80) cc_final: 0.8775 (m-80)
REVERT: A  112 MET cc_start: 0.7521 (ppp) cc_final: 0.5941 (ppp)
REVERT: A  147 ASP cc_start: 0.8593 (m-30) cc_final: 0.8118 (p0)
REVERT: A  182 GLN cc_start: 0.8746 (mm110) cc_final: 0.8368 (mm-40)
REVERT: A  215 MET cc_start: 0.8600 (mpp) cc_final: 0.8158 (mpp)
REVERT: A  221 HIS cc_start: 0.8692 (m-70) cc_final: 0.8446 (m170)
REVERT: A  234 PHE cc_start: 0.8802 (m-80) cc_final: 0.8377 (m-80)
  outliers start: 12
  outliers final: 7
  residues processed: 128
  average time/residue: 0.1599
  time to fit residues: 24.5412
Evaluate side-chains
  123 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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  123 THR
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  244 PHE
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 11 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0770
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6940

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.077424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.064440 restraints weight = 14219.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.066361 restraints weight = 9853.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.067755 restraints weight = 7364.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3324  Z= 0.250
  Angle     :  0.994  11.918   4506  Z= 0.493
  Chirality :  0.057   0.377    527
  Planarity :  0.006   0.047    551
  Dihedral  :  5.612  22.286    454
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 27.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 29.69 %
    Favored  : 67.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.41), residues: 419
  helix:  0.17 (0.32), residues: 255
  sheet: -2.91 (0.65), residues: 50
  loop : -1.90 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 105 
 HIS   0.001   0.001   HIS A  54 
 PHE   0.023   0.002   PHE A 128 
 TYR   0.025   0.002   TYR B  32 
 ARG   0.008   0.001   ARG B  45 

*********************** 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
  131 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 TYR cc_start: 0.7378 (p90) cc_final: 0.7094 (p90)
REVERT: B   76 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8428 (tptp)
REVERT: B   93 LEU cc_start: 0.8895 (tp) cc_final: 0.8416 (tp)
REVERT: A   36 PHE cc_start: 0.8624 (m-80) cc_final: 0.8328 (m-80)
REVERT: A   47 GLU cc_start: 0.9107 (pm20) cc_final: 0.8635 (pm20)
REVERT: A  108 PHE cc_start: 0.9116 (m-80) cc_final: 0.8734 (m-80)
REVERT: A  112 MET cc_start: 0.7531 (ppp) cc_final: 0.7322 (ppp)
REVERT: A  133 MET cc_start: 0.8133 (mpp) cc_final: 0.7907 (ptp)
REVERT: A  147 ASP cc_start: 0.8549 (m-30) cc_final: 0.8102 (p0)
REVERT: A  182 GLN cc_start: 0.8646 (mm110) cc_final: 0.8294 (mm-40)
REVERT: A  215 MET cc_start: 0.8602 (mpp) cc_final: 0.8161 (mpp)
REVERT: A  221 HIS cc_start: 0.8701 (m-70) cc_final: 0.8457 (m170)
REVERT: A  234 PHE cc_start: 0.8781 (m-80) cc_final: 0.8344 (m-80)
REVERT: A  274 PHE cc_start: 0.8302 (m-80) cc_final: 0.8080 (m-80)
REVERT: A  289 TYR cc_start: 0.8270 (t80) cc_final: 0.8014 (t80)
  outliers start: 11
  outliers final: 8
  residues processed: 124
  average time/residue: 0.1681
  time to fit residues: 24.9008
Evaluate side-chains
  120 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
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  244 PHE
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 7 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0770
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3745 r_free = 0.3745 target = 0.078406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.065373 restraints weight = 14402.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.067262 restraints weight = 10044.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.068659 restraints weight = 7547.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   3324  Z= 0.265
  Angle     :  1.037  13.031   4506  Z= 0.520
  Chirality :  0.057   0.374    527
  Planarity :  0.006   0.074    551
  Dihedral  :  5.641  22.038    454
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 29.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 30.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.41), residues: 419
  helix:  0.26 (0.32), residues: 255
  sheet: -2.45 (0.71), residues: 44
  loop : -1.91 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 105 
 HIS   0.001   0.000   HIS A  54 
 PHE   0.021   0.002   PHE A 128 
 TYR   0.023   0.002   TYR B  32 
 ARG   0.004   0.001   ARG B  27 

*********************** 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
  128 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 TYR cc_start: 0.7452 (p90) cc_final: 0.7102 (p90)
REVERT: B   76 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8369 (tptp)
REVERT: B   80 TYR cc_start: 0.8189 (t80) cc_final: 0.7423 (t80)
REVERT: B   93 LEU cc_start: 0.8838 (tp) cc_final: 0.8367 (tp)
REVERT: A   36 PHE cc_start: 0.8608 (m-80) cc_final: 0.8361 (m-80)
REVERT: A   47 GLU cc_start: 0.9073 (pm20) cc_final: 0.8597 (pm20)
REVERT: A  108 PHE cc_start: 0.9142 (m-80) cc_final: 0.8826 (m-80)
REVERT: A  112 MET cc_start: 0.7474 (ppp) cc_final: 0.7248 (ppp)
REVERT: A  147 ASP cc_start: 0.8550 (m-30) cc_final: 0.8069 (p0)
REVERT: A  182 GLN cc_start: 0.8630 (mm110) cc_final: 0.8272 (mm-40)
REVERT: A  215 MET cc_start: 0.8590 (mpp) cc_final: 0.8180 (mpp)
REVERT: A  234 PHE cc_start: 0.8760 (m-80) cc_final: 0.8315 (m-80)
REVERT: A  274 PHE cc_start: 0.8341 (m-80) cc_final: 0.8128 (m-80)
REVERT: A  289 TYR cc_start: 0.8255 (t80) cc_final: 0.8026 (t80)
  outliers start: 9
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1637
  time to fit residues: 23.7895
Evaluate side-chains
  123 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
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  244 PHE
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 18 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0000
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3749 r_free = 0.3749 target = 0.078775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.065596 restraints weight = 14352.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.067540 restraints weight = 9907.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.068699 restraints weight = 7427.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   3324  Z= 0.279
  Angle     :  1.111  13.598   4506  Z= 0.551
  Chirality :  0.058   0.346    527
  Planarity :  0.006   0.067    551
  Dihedral  :  5.614  21.632    454
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 29.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 32.21 %
    Favored  : 64.99 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.41), residues: 419
  helix:  0.35 (0.32), residues: 255
  sheet: -2.41 (0.71), residues: 44
  loop : -2.02 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 105 
 HIS   0.001   0.001   HIS A 221 
 PHE   0.019   0.002   PHE A 128 
 TYR   0.022   0.002   TYR B  32 
 ARG   0.004   0.001   ARG B  27 

*********************** 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
  127 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7293 (mmm160)
REVERT: B   32 TYR cc_start: 0.7476 (p90) cc_final: 0.7098 (p90)
REVERT: B   76 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8414 (tptp)
REVERT: B   80 TYR cc_start: 0.8138 (t80) cc_final: 0.7596 (t80)
REVERT: B   93 LEU cc_start: 0.8842 (tp) cc_final: 0.8591 (tp)
REVERT: A   36 PHE cc_start: 0.8595 (m-80) cc_final: 0.8341 (m-80)
REVERT: A   47 GLU cc_start: 0.9081 (pm20) cc_final: 0.8653 (pm20)
REVERT: A  108 PHE cc_start: 0.9183 (m-80) cc_final: 0.8747 (m-80)
REVERT: A  112 MET cc_start: 0.7542 (ppp) cc_final: 0.6068 (ppp)
REVERT: A  147 ASP cc_start: 0.8488 (m-30) cc_final: 0.8035 (p0)
REVERT: A  182 GLN cc_start: 0.8634 (mm110) cc_final: 0.8246 (mm-40)
REVERT: A  215 MET cc_start: 0.8592 (mpp) cc_final: 0.8253 (mpp)
REVERT: A  234 PHE cc_start: 0.8785 (m-80) cc_final: 0.8344 (m-80)
REVERT: A  274 PHE cc_start: 0.8374 (m-80) cc_final: 0.8163 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 121
  average time/residue: 0.1612
  time to fit residues: 23.4732
Evaluate side-chains
  120 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
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  219 THR
Chi-restraints excluded: chain A residue  244 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.3736 r_free = 0.3736 target = 0.077933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.065151 restraints weight = 14468.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.067022 restraints weight = 10114.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.068378 restraints weight = 7627.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   3324  Z= 0.291
  Angle     :  1.146  14.195   4506  Z= 0.573
  Chirality :  0.061   0.350    527
  Planarity :  0.006   0.061    551
  Dihedral  :  5.645  21.825    454
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 30.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 32.21 %
    Favored  : 64.99 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.41), residues: 419
  helix:  0.33 (0.33), residues: 254
  sheet: -2.64 (0.66), residues: 50
  loop : -2.10 (0.57), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  36 
 HIS   0.001   0.001   HIS A 221 
 PHE   0.021   0.002   PHE A 128 
 TYR   0.021   0.002   TYR B  32 
 ARG   0.006   0.001   ARG B  45 

********************** 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
  125 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.7465 (mmm160) cc_final: 0.7117 (mmm160)
REVERT: B   32 TYR cc_start: 0.7549 (p90) cc_final: 0.7146 (p90)
REVERT: B   44 GLU cc_start: 0.8774 (tp30) cc_final: 0.8324 (pm20)
REVERT: B   76 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8395 (tptp)
REVERT: B   80 TYR cc_start: 0.8147 (t80) cc_final: 0.7596 (t80)
REVERT: B   83 MET cc_start: 0.7600 (ptm) cc_final: 0.7320 (ppp)
REVERT: A   36 PHE cc_start: 0.8457 (m-80) cc_final: 0.8228 (m-80)
REVERT: A   47 GLU cc_start: 0.9058 (pm20) cc_final: 0.8644 (pm20)
REVERT: A  108 PHE cc_start: 0.9130 (m-80) cc_final: 0.8733 (m-80)
REVERT: A  112 MET cc_start: 0.7536 (ppp) cc_final: 0.6010 (ppp)
REVERT: A  147 ASP cc_start: 0.8507 (m-30) cc_final: 0.8053 (p0)
REVERT: A  182 GLN cc_start: 0.8622 (mm110) cc_final: 0.8246 (mm-40)
REVERT: A  215 MET cc_start: 0.8593 (mpp) cc_final: 0.8269 (mpp)
REVERT: A  234 PHE cc_start: 0.8785 (m-80) cc_final: 0.8326 (m-80)
REVERT: A  274 PHE cc_start: 0.8313 (m-80) cc_final: 0.8091 (m-80)
  outliers start: 10
  outliers final: 9
  residues processed: 119
  average time/residue: 0.1616
  time to fit residues: 23.2837
Evaluate side-chains
  120 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 VAL
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  244 PHE
Chi-restraints excluded: chain A residue  285 PHE
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 23 optimal weight:    0.1980
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 221 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.078848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.065813 restraints weight = 14582.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.067676 restraints weight = 10153.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.069063 restraints weight = 7657.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   3324  Z= 0.298
  Angle     :  1.187  17.071   4506  Z= 0.584
  Chirality :  0.060   0.337    527
  Planarity :  0.006   0.053    551
  Dihedral  :  5.713  22.614    454
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 30.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 32.49 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.52 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.41), residues: 419
  helix:  0.20 (0.33), residues: 254
  sheet: -2.58 (0.66), residues: 50
  loop : -2.10 (0.55), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  36 
 HIS   0.016   0.006   HIS A 221 
 PHE   0.023   0.002   PHE A 128 
 TYR   0.021   0.002   TYR B  32 
 ARG   0.007   0.001   ARG B  45 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1486.39 seconds
wall clock time: 27 minutes 32.69 seconds (1652.69 seconds total)