Starting phenix.real_space_refine
on Wed Jul 23 17:53:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jj2_61515/07_2025/9jj2_61515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jj2_61515/07_2025/9jj2_61515.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jj2_61515/07_2025/9jj2_61515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jj2_61515/07_2025/9jj2_61515.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jj2_61515/07_2025/9jj2_61515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jj2_61515/07_2025/9jj2_61515.cif"
  }
  resolution = 3.0
  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=  -0.001 sd=   0.004
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      28      5.16       5
     C    2540      2.51       5
     N     650      2.21       5
     O     698      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3916
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1958
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 8, 'TRANS': 249}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1958
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 8, 'TRANS': 249}
          Chain breaks: 1
  Time building chain proxies: 3.36, per 1000 atoms: 0.86
  Number of scatterers: 3916
  At special positions: 0
  Unit cell: (51.46, 82.17, 100.43, 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      28     16.00
     O     698      8.00
     N     650      7.00
     C    2540      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 642.8 milliseconds
  

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  964

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 4 sheets defined
      71.3% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 98
      removed outlier: 5.232A  pdb=" N   VAL A  85 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE A  86 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 127
    Processing helix  chain 'A' and resid 140 through 170
      removed outlier: 3.593A  pdb=" N   LEU A 169 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 199
      removed outlier: 3.821A  pdb=" N   MET A 180 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   LEU A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 259
    Processing helix  chain 'A' and resid 264 through 294
      removed outlier: 3.602A  pdb=" N   ILE A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
    Processing helix  chain 'A' and resid 301 through 311
    Processing helix  chain 'A' and resid 344 through 361
    Processing helix  chain 'B' and resid 81 through 98
      removed outlier: 3.879A  pdb=" N   VAL B  85 " --> pdb=" O   ALA B  81 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY B  89 " --> pdb=" O   VAL B  85 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLU B  90 " --> pdb=" O   PHE B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 127
      removed outlier: 4.036A  pdb=" N   THR B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 170
      removed outlier: 3.600A  pdb=" N   LEU B 169 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 199
      removed outlier: 3.868A  pdb=" N   MET B 180 " --> pdb=" O   GLU B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 259
    Processing helix  chain 'B' and resid 264 through 294
      removed outlier: 3.640A  pdb=" N   ILE B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 311
    Processing helix  chain 'B' and resid 344 through 361
    Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 317
      removed outlier: 6.852A  pdb=" N   ALA A 338 " --> pdb=" O   ARG A 316 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE A 339 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 325
      removed outlier: 7.049A  pdb=" N   HIS A 331 " --> pdb=" O   SER A 364 " (cutoff:3.500A)
      removed outlier: 8.789A  pdb=" N   THR A 366 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA A 333 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 315 through 317
      removed outlier: 3.675A  pdb=" N   ALA B 317 " --> pdb=" O   ALA B 338 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE B 339 " --> pdb=" O   GLU B 370 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 325
      removed outlier: 7.078A  pdb=" N   HIS B 331 " --> pdb=" O   SER B 364 " (cutoff:3.500A)
      removed outlier: 8.812A  pdb=" N   THR B 366 " --> pdb=" O   HIS B 331 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ALA B 333 " --> pdb=" O   THR B 366 " (cutoff:3.500A)

    295 hydrogen bonds defined for protein.
    876 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1226
        1.34 -     1.46: 822
        1.46 -     1.58: 1914
        1.58 -     1.70: 0
        1.70 -     1.82: 46
  Bond restraints: 4008
  Sorted by residual:
  bond pdb=" C   HIS B 238 "
       pdb=" O   HIS B 238 "
    ideal  model  delta    sigma   weight residual
    1.236  1.219  0.016 1.29e-02 6.01e+03 1.63e+00
  bond pdb=" CB  ASP B 112 "
       pdb=" CG  ASP B 112 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.41e+00
  bond pdb=" CG1 ILE B 254 "
       pdb=" CD1 ILE B 254 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.29e+00
  bond pdb=" CB  ASP A 344 "
       pdb=" CG  ASP A 344 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.18e+00
  bond pdb=" CB  ASP B 344 "
       pdb=" CG  ASP B 344 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.13e+00
  ... (remaining 4003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 5302
        1.90 -     3.80: 111
        3.80 -     5.70: 31
        5.70 -     7.60: 11
        7.60 -     9.51: 9
  Bond angle restraints: 5464
  Sorted by residual:
  angle pdb=" C   SER A 115 "
        pdb=" N   MET A 116 "
        pdb=" CA  MET A 116 "
      ideal   model   delta    sigma   weight residual
     121.66  114.51    7.15 1.76e+00 3.23e-01 1.65e+01
  angle pdb=" CA  GLU B 176 "
        pdb=" CB  GLU B 176 "
        pdb=" CG  GLU B 176 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" CA  GLU A 142 "
        pdb=" CB  GLU A 142 "
        pdb=" CG  GLU A 142 "
      ideal   model   delta    sigma   weight residual
     114.10  119.94   -5.84 2.00e+00 2.50e-01 8.53e+00
  angle pdb=" CB  MET B 117 "
        pdb=" CG  MET B 117 "
        pdb=" SD  MET B 117 "
      ideal   model   delta    sigma   weight residual
     112.70  121.06   -8.36 3.00e+00 1.11e-01 7.77e+00
  angle pdb=" CB  GLU B 176 "
        pdb=" CG  GLU B 176 "
        pdb=" CD  GLU B 176 "
      ideal   model   delta    sigma   weight residual
     112.60  117.29   -4.69 1.70e+00 3.46e-01 7.62e+00
  ... (remaining 5459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.34: 1847
       12.34 -    24.69: 235
       24.69 -    37.03: 157
       37.03 -    49.37: 64
       49.37 -    61.71: 19
  Dihedral angle restraints: 2322
    sinusoidal: 830
      harmonic: 1492
  Sorted by residual:
  dihedral pdb=" CA  ASP A 340 "
           pdb=" CB  ASP A 340 "
           pdb=" CG  ASP A 340 "
           pdb=" OD1 ASP A 340 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.75   55.75     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  MET A 117 "
           pdb=" CB  MET A 117 "
           pdb=" CG  MET A 117 "
           pdb=" SD  MET A 117 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.69   59.69     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LEU A 310 "
           pdb=" CB  LEU A 310 "
           pdb=" CG  LEU A 310 "
           pdb=" CD1 LEU A 310 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.65   59.35     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 2319 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 451
       0.036 -    0.072: 143
       0.072 -    0.107: 49
       0.107 -    0.143: 15
       0.143 -    0.179: 4
  Chirality restraints: 662
  Sorted by residual:
  chirality pdb=" CG  LEU B 182 "
            pdb=" CB  LEU B 182 "
            pdb=" CD1 LEU B 182 "
            pdb=" CD2 LEU B 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.01e-01
  chirality pdb=" CA  MET A 116 "
            pdb=" N   MET A 116 "
            pdb=" C   MET A 116 "
            pdb=" CB  MET A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CB  VAL B 237 "
            pdb=" CA  VAL B 237 "
            pdb=" CG1 VAL B 237 "
            pdb=" CG2 VAL B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.17e-01
  ... (remaining 659 not shown)

  Planarity restraints: 670
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 132 "    0.126 9.50e-02 1.11e+02   5.70e-02 2.64e+00
        pdb=" NE  ARG A 132 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 132 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 132 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 132 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 112 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" CG  ASP A 112 "   -0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 112 "    0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 112 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 116 "    0.006 2.00e-02 2.50e+03   1.20e-02 1.44e+00
        pdb=" C   MET A 116 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   MET A 116 "    0.008 2.00e-02 2.50e+03
        pdb=" N   MET A 117 "    0.007 2.00e-02 2.50e+03
  ... (remaining 667 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 2010
        2.97 -     3.45: 4221
        3.45 -     3.93: 6472
        3.93 -     4.42: 7163
        4.42 -     4.90: 11504
  Nonbonded interactions: 31370
  Sorted by model distance:
  nonbonded pdb=" O   THR B 342 "
            pdb=" OG1 THR B 342 "
     model   vdw
     2.484 3.040
  nonbonded pdb=" N   GLU B 176 "
            pdb=" OE1 GLU B 176 "
     model   vdw
     2.504 3.120
  nonbonded pdb=" N   ASP B 172 "
            pdb=" OD1 ASP B 172 "
     model   vdw
     2.528 3.120
  nonbonded pdb=" N   ASP A 172 "
            pdb=" OD1 ASP A 172 "
     model   vdw
     2.533 3.120
  nonbonded pdb=" N   GLU A 142 "
            pdb=" OE1 GLU A 142 "
     model   vdw
     2.540 3.120
  ... (remaining 31365 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.700
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.500
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
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   0.044   4008  Z= 0.168
  Angle     :  0.795   9.505   5464  Z= 0.378
  Chirality :  0.043   0.179    662
  Planarity :  0.004   0.057    670
  Dihedral  : 17.558  61.715   1358
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 46.15 %
    Favored  : 52.40 %
  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:  2.59 (0.38), residues: 508
  helix:  2.80 (0.26), residues: 344
  sheet: -1.08 (0.80), residues: 52
  loop : -0.37 (0.61), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 324 
 HIS   0.004   0.001   HIS B 108 
 PHE   0.007   0.001   PHE A 302 
 TYR   0.014   0.001   TYR B  95 
 ARG   0.014   0.001   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11674 (  295)
  hydrogen bonds       : angle       6.29828 (  876)
  covalent geometry    : bond        0.00367 ( 4008)
  covalent geometry    : angle       0.79525 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  351 GLU cc_start: 0.8745 (tp30) cc_final: 0.8234 (tp30)
REVERT: B  116 MET cc_start: 0.4244 (mtp) cc_final: 0.3930 (mtt)
REVERT: B  351 GLU cc_start: 0.8476 (tp30) cc_final: 0.8114 (tp30)
  outliers start: 6
  outliers final: 5
  residues processed: 105
  average time/residue: 0.6095
  time to fit residues: 67.7426
Evaluate side-chains
  109 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  191 ASN
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  291 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0010
   chunk 12 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.7992

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.117897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.093315 restraints weight = 7349.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.90
r_work: 0.3119 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4008  Z= 0.138
  Angle     :  0.641   8.465   5464  Z= 0.296
  Chirality :  0.040   0.140    662
  Planarity :  0.004   0.028    670
  Dihedral  :  6.017  57.552    562
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 34.86 %
    Favored  : 57.45 %
  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:  2.91 (0.39), residues: 508
  helix:  3.06 (0.26), residues: 348
  sheet: -1.23 (0.82), residues: 52
  loop : -0.31 (0.64), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 324 
 HIS   0.003   0.001   HIS B 108 
 PHE   0.010   0.001   PHE B 196 
 TYR   0.006   0.001   TYR B  95 
 ARG   0.007   0.001   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04224 (  295)
  hydrogen bonds       : angle       4.50504 (  876)
  covalent geometry    : bond        0.00300 ( 4008)
  covalent geometry    : angle       0.64100 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A  132 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.8290 (mtp180)
REVERT: A  263 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7943 (ttpt)
REVERT: A  351 GLU cc_start: 0.8791 (tp30) cc_final: 0.8290 (tp30)
REVERT: B  116 MET cc_start: 0.4321 (mtp) cc_final: 0.4005 (mtt)
REVERT: B  180 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8037 (mtm)
REVERT: B  254 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8813 (mp)
REVERT: B  351 GLU cc_start: 0.8651 (tp30) cc_final: 0.8197 (tp30)
  outliers start: 32
  outliers final: 16
  residues processed: 132
  average time/residue: 0.6559
  time to fit residues: 91.3456
Evaluate side-chains
  125 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  344 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  372 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   chunk 3 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0040
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.119462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.095121 restraints weight = 7442.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.90
r_work: 0.3141 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4008  Z= 0.124
  Angle     :  0.640   8.099   5464  Z= 0.294
  Chirality :  0.039   0.145    662
  Planarity :  0.003   0.028    670
  Dihedral  :  4.793  54.626    555
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 34.38 %
    Favored  : 58.89 %
  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:  2.90 (0.38), residues: 508
  helix:  3.05 (0.26), residues: 348
  sheet: -1.26 (0.82), residues: 52
  loop : -0.29 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 324 
 HIS   0.003   0.001   HIS B 108 
 PHE   0.010   0.001   PHE B 196 
 TYR   0.011   0.001   TYR B  95 
 ARG   0.009   0.001   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  295)
  hydrogen bonds       : angle       4.32989 (  876)
  covalent geometry    : bond        0.00264 ( 4008)
  covalent geometry    : angle       0.64010 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A  112 ASP cc_start: 0.8311 (t0) cc_final: 0.8091 (t0)
REVERT: A  132 ARG cc_start: 0.8513 (mtp-110) cc_final: 0.8305 (mtp180)
REVERT: A  263 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7911 (ttpt)
REVERT: A  340 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8299 (m-30)
REVERT: A  351 GLU cc_start: 0.8777 (tp30) cc_final: 0.8259 (tp30)
REVERT: B  180 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8036 (mtm)
REVERT: B  250 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8002 (tm)
REVERT: B  254 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8843 (mp)
REVERT: B  351 GLU cc_start: 0.8732 (tp30) cc_final: 0.8241 (tp30)
  outliers start: 28
  outliers final: 11
  residues processed: 130
  average time/residue: 0.6589
  time to fit residues: 90.6459
Evaluate side-chains
  125 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  372 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0270
   chunk 2 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.120122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.095790 restraints weight = 7439.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.89
r_work: 0.3134 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4008  Z= 0.123
  Angle     :  0.648   8.525   5464  Z= 0.290
  Chirality :  0.039   0.135    662
  Planarity :  0.003   0.028    670
  Dihedral  :  4.821  57.014    555
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 35.10 %
    Favored  : 57.93 %
  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:  2.86 (0.38), residues: 508
  helix:  3.03 (0.26), residues: 348
  sheet: -1.36 (0.81), residues: 52
  loop : -0.31 (0.61), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 324 
 HIS   0.002   0.000   HIS B 108 
 PHE   0.007   0.001   PHE B 196 
 TYR   0.004   0.001   TYR A  95 
 ARG   0.005   0.000   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  295)
  hydrogen bonds       : angle       4.25479 (  876)
  covalent geometry    : bond        0.00265 ( 4008)
  covalent geometry    : angle       0.64789 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A  132 ARG cc_start: 0.8506 (mtp-110) cc_final: 0.8268 (mtp180)
REVERT: A  239 VAL cc_start: 0.8332 (t) cc_final: 0.8103 (t)
REVERT: A  263 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7912 (ttpt)
REVERT: A  340 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8277 (m-30)
REVERT: A  351 GLU cc_start: 0.8801 (tp30) cc_final: 0.8298 (tp30)
REVERT: B  180 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8139 (mtm)
REVERT: B  250 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7989 (tm)
REVERT: B  254 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8823 (mp)
REVERT: B  340 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7960 (m-30)
REVERT: B  351 GLU cc_start: 0.8764 (tp30) cc_final: 0.8268 (tp30)
  outliers start: 29
  outliers final: 12
  residues processed: 130
  average time/residue: 0.8766
  time to fit residues: 120.1154
Evaluate side-chains
  123 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  344 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN
B 191 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.117143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.090828 restraints weight = 7514.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 3.25
r_work: 0.3092 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4008  Z= 0.146
  Angle     :  0.662   8.915   5464  Z= 0.302
  Chirality :  0.040   0.133    662
  Planarity :  0.004   0.038    670
  Dihedral  :  4.898  58.598    555
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 35.82 %
    Favored  : 57.45 %
  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:  2.83 (0.38), residues: 508
  helix:  3.08 (0.26), residues: 350
  sheet: -1.48 (0.80), residues: 52
  loop : -0.63 (0.59), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 324 
 HIS   0.002   0.001   HIS B 170 
 PHE   0.008   0.001   PHE B 273 
 TYR   0.005   0.001   TYR A  95 
 ARG   0.011   0.001   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04110 (  295)
  hydrogen bonds       : angle       4.25722 (  876)
  covalent geometry    : bond        0.00327 ( 4008)
  covalent geometry    : angle       0.66249 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A  132 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8211 (mtp180)
REVERT: A  142 GLU cc_start: 0.8315 (mp0) cc_final: 0.7740 (mp0)
REVERT: A  245 GLN cc_start: 0.8327 (tm-30) cc_final: 0.8100 (tm-30)
REVERT: A  263 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7842 (ttpt)
REVERT: A  340 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8337 (m-30)
REVERT: A  351 GLU cc_start: 0.8815 (tp30) cc_final: 0.8324 (tp30)
REVERT: B  180 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8203 (mtm)
REVERT: B  250 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7862 (tm)
REVERT: B  254 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8723 (mp)
REVERT: B  340 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7978 (m-30)
REVERT: B  351 GLU cc_start: 0.8735 (tp30) cc_final: 0.8206 (tp30)
  outliers start: 28
  outliers final: 11
  residues processed: 127
  average time/residue: 0.7626
  time to fit residues: 102.3791
Evaluate side-chains
  126 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.116086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.090502 restraints weight = 7232.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 3.12
r_work: 0.3082 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4008  Z= 0.148
  Angle     :  0.673   8.081   5464  Z= 0.303
  Chirality :  0.040   0.128    662
  Planarity :  0.003   0.029    670
  Dihedral  :  4.910  59.825    555
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 36.30 %
    Favored  : 56.97 %
  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:  2.83 (0.38), residues: 508
  helix:  3.06 (0.26), residues: 348
  sheet: -1.54 (0.80), residues: 52
  loop : -0.41 (0.60), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 324 
 HIS   0.002   0.001   HIS B 170 
 PHE   0.025   0.001   PHE B 196 
 TYR   0.005   0.001   TYR A  95 
 ARG   0.007   0.001   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04161 (  295)
  hydrogen bonds       : angle       4.24930 (  876)
  covalent geometry    : bond        0.00331 ( 4008)
  covalent geometry    : angle       0.67271 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7319 (t)
REVERT: A   90 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7117 (mp0)
REVERT: A  132 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8229 (mtp180)
REVERT: A  142 GLU cc_start: 0.8352 (mp0) cc_final: 0.7724 (mp0)
REVERT: A  245 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8088 (tm-30)
REVERT: A  263 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7773 (ttpp)
REVERT: A  340 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8368 (m-30)
REVERT: A  351 GLU cc_start: 0.8819 (tp30) cc_final: 0.8303 (tp30)
REVERT: B  180 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8232 (mtm)
REVERT: B  250 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7829 (tm)
REVERT: B  254 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8663 (mp)
REVERT: B  340 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7974 (m-30)
REVERT: B  351 GLU cc_start: 0.8785 (tp30) cc_final: 0.8227 (tp30)
  outliers start: 28
  outliers final: 13
  residues processed: 131
  average time/residue: 0.8318
  time to fit residues: 114.4857
Evaluate side-chains
  133 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0870
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.118586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.094123 restraints weight = 7410.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.91
r_work: 0.3101 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4008  Z= 0.138
  Angle     :  0.715   9.854   5464  Z= 0.321
  Chirality :  0.040   0.129    662
  Planarity :  0.003   0.028    670
  Dihedral  :  4.931  59.899    555
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 37.98 %
    Favored  : 55.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.77 (0.38), residues: 508
  helix:  3.01 (0.26), residues: 348
  sheet: -1.55 (0.80), residues: 52
  loop : -0.42 (0.60), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 324 
 HIS   0.002   0.000   HIS B 170 
 PHE   0.030   0.001   PHE B 196 
 TYR   0.005   0.001   TYR B 357 
 ARG   0.006   0.000   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04147 (  295)
  hydrogen bonds       : angle       4.23689 (  876)
  covalent geometry    : bond        0.00307 ( 4008)
  covalent geometry    : angle       0.71521 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7248 (t)
REVERT: A  132 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8288 (mtp180)
REVERT: A  142 GLU cc_start: 0.8445 (mp0) cc_final: 0.7831 (mp0)
REVERT: A  245 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: A  263 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7845 (ttpp)
REVERT: A  340 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8359 (m-30)
REVERT: A  351 GLU cc_start: 0.8872 (tp30) cc_final: 0.8374 (tp30)
REVERT: B  132 ARG cc_start: 0.8524 (mtp-110) cc_final: 0.8148 (mtp180)
REVERT: B  180 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8290 (mtm)
REVERT: B  250 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8101 (tm)
REVERT: B  340 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8005 (m-30)
REVERT: B  351 GLU cc_start: 0.8849 (tp30) cc_final: 0.8316 (tp30)
  outliers start: 27
  outliers final: 16
  residues processed: 129
  average time/residue: 0.7513
  time to fit residues: 101.9953
Evaluate side-chains
  134 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0770
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
B 191 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 = 0.119503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.095117 restraints weight = 7443.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.91
r_work: 0.3111 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4008  Z= 0.138
  Angle     :  0.722   9.384   5464  Z= 0.322
  Chirality :  0.040   0.127    662
  Planarity :  0.003   0.028    670
  Dihedral  :  4.903  59.350    555
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 39.18 %
    Favored  : 54.81 %
  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:  2.75 (0.38), residues: 508
  helix:  2.99 (0.26), residues: 348
  sheet: -1.56 (0.80), residues: 52
  loop : -0.42 (0.60), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 324 
 HIS   0.003   0.001   HIS B 170 
 PHE   0.035   0.001   PHE B 196 
 TYR   0.012   0.001   TYR B 330 
 ARG   0.006   0.000   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04103 (  295)
  hydrogen bonds       : angle       4.22962 (  876)
  covalent geometry    : bond        0.00301 ( 4008)
  covalent geometry    : angle       0.72221 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.570 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7418 (t)
REVERT: A  142 GLU cc_start: 0.8421 (mp0) cc_final: 0.7791 (mp0)
REVERT: A  245 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8092 (tm-30)
REVERT: A  263 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7906 (ttpt)
REVERT: A  340 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8353 (m-30)
REVERT: A  351 GLU cc_start: 0.8874 (tp30) cc_final: 0.8387 (tp30)
REVERT: B  132 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.8155 (mtp180)
REVERT: B  180 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8315 (ttt)
REVERT: B  340 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8026 (m-30)
REVERT: B  351 GLU cc_start: 0.8851 (tp30) cc_final: 0.8542 (tp30)
  outliers start: 25
  outliers final: 18
  residues processed: 123
  average time/residue: 0.6849
  time to fit residues: 88.6039
Evaluate side-chains
  133 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  276 CYS
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    0.0980
   chunk 30 optimal weight:    0.4980
   chunk 38 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.118786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.092811 restraints weight = 7434.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.99
r_work: 0.3142 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4008  Z= 0.134
  Angle     :  0.724  10.635   5464  Z= 0.323
  Chirality :  0.040   0.126    662
  Planarity :  0.003   0.028    670
  Dihedral  :  4.872  57.920    555
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 38.94 %
    Favored  : 55.05 %
  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:  2.65 (0.38), residues: 508
  helix:  2.95 (0.26), residues: 350
  sheet: -1.57 (0.80), residues: 52
  loop : -0.67 (0.58), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 324 
 HIS   0.003   0.000   HIS B 170 
 PHE   0.036   0.001   PHE B 196 
 TYR   0.018   0.001   TYR B  95 
 ARG   0.005   0.000   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  295)
  hydrogen bonds       : angle       4.24758 (  876)
  covalent geometry    : bond        0.00288 ( 4008)
  covalent geometry    : angle       0.72359 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7615 (t)
REVERT: A  191 ASN cc_start: 0.8851 (t0) cc_final: 0.8533 (m-40)
REVERT: A  242 ASP cc_start: 0.8502 (m-30) cc_final: 0.7934 (t70)
REVERT: A  245 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8118 (tm-30)
REVERT: A  263 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7938 (ttpt)
REVERT: A  340 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8304 (m-30)
REVERT: A  351 GLU cc_start: 0.8885 (tp30) cc_final: 0.8476 (tp30)
REVERT: B  132 ARG cc_start: 0.8475 (mtp-110) cc_final: 0.8165 (mtp180)
REVERT: B  340 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7956 (m-30)
REVERT: B  351 GLU cc_start: 0.8880 (tp30) cc_final: 0.8628 (tp30)
  outliers start: 25
  outliers final: 20
  residues processed: 124
  average time/residue: 0.5968
  time to fit residues: 78.4128
Evaluate side-chains
  131 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  191 ASN
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  276 CYS
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0980
   chunk 35 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 37 optimal weight:    6.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.118689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.093683 restraints weight = 7422.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.87
r_work: 0.3150 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4008  Z= 0.133
  Angle     :  0.731  10.101   5464  Z= 0.327
  Chirality :  0.040   0.126    662
  Planarity :  0.003   0.028    670
  Dihedral  :  3.884  18.331    552
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 38.94 %
    Favored  : 55.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.66 (0.38), residues: 508
  helix:  2.95 (0.26), residues: 350
  sheet: -1.55 (0.80), residues: 52
  loop : -0.65 (0.59), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 324 
 HIS   0.002   0.000   HIS B 170 
 PHE   0.036   0.001   PHE B 196 
 TYR   0.010   0.001   TYR B 330 
 ARG   0.005   0.000   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04105 (  295)
  hydrogen bonds       : angle       4.26102 (  876)
  covalent geometry    : bond        0.00285 ( 4008)
  covalent geometry    : angle       0.73092 ( 5464)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7636 (t)
REVERT: A  191 ASN cc_start: 0.8838 (t0) cc_final: 0.8508 (m-40)
REVERT: A  242 ASP cc_start: 0.8551 (m-30) cc_final: 0.7981 (t70)
REVERT: A  245 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: A  263 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7942 (ttpt)
REVERT: A  340 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8313 (m-30)
REVERT: A  351 GLU cc_start: 0.8877 (tp30) cc_final: 0.8480 (tp30)
REVERT: B  132 ARG cc_start: 0.8467 (mtp-110) cc_final: 0.8168 (mtp180)
REVERT: B  340 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7984 (m-30)
REVERT: B  351 GLU cc_start: 0.8873 (tp30) cc_final: 0.8639 (tp30)
  outliers start: 22
  outliers final: 18
  residues processed: 124
  average time/residue: 0.6254
  time to fit residues: 82.1307
Evaluate side-chains
  130 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  191 ASN
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  276 CYS
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    0.1980
   chunk 47 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   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 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.118489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.092590 restraints weight = 7348.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.97
r_work: 0.3131 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4008  Z= 0.140
  Angle     :  0.730   9.752   5464  Z= 0.325
  Chirality :  0.041   0.129    662
  Planarity :  0.003   0.028    670
  Dihedral  :  3.888  15.688    552
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 39.66 %
    Favored  : 55.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.68 (0.38), residues: 508
  helix:  2.96 (0.26), residues: 350
  sheet: -1.57 (0.79), residues: 52
  loop : -0.61 (0.59), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 124 
 HIS   0.002   0.000   HIS B 170 
 PHE   0.006   0.001   PHE B 273 
 TYR   0.019   0.001   TYR B  95 
 ARG   0.005   0.000   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04123 (  295)
  hydrogen bonds       : angle       4.29541 (  876)
  covalent geometry    : bond        0.00305 ( 4008)
  covalent geometry    : angle       0.72966 ( 5464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3194.56 seconds
wall clock time: 56 minutes 31.80 seconds (3391.80 seconds total)