Starting phenix.real_space_refine
on Wed Jun  4 19:11:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wd8_32434/06_2025/7wd8_32434.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wd8_32434/06_2025/7wd8_32434.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wd8_32434/06_2025/7wd8_32434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wd8_32434/06_2025/7wd8_32434.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wd8_32434/06_2025/7wd8_32434.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wd8_32434/06_2025/7wd8_32434.cif"
  }
  resolution = 4.3
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2540      2.51       5
     N     678      2.21       5
     O     793      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4029
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 163
          Classifications: {'peptide': 20}
          Link IDs: {'PTRANS': 3, 'TRANS': 16}
    Chain: "E"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1662
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201}
    Chain: "F"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1656
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201}
    Chain: "B"
      Number of atoms: 548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 548
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 4, 'TRANS': 67}
  Time building chain proxies: 3.04, per 1000 atoms: 0.75
  Number of scatterers: 4029
  At special positions: 0
  Unit cell: (95.091, 96.184, 64.487, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     793      8.00
     N     678      7.00
     C    2540      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 138 " - pdb=" SG  CYS F 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " 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: 0.90
  Conformation dependent library (CDL) restraints added in 500.8 milliseconds
  

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  984

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 12 sheets defined
      5.5% alpha, 47.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'F' and resid 83 through 87
      removed outlier: 4.004A  pdb=" N   ALA F  87 " --> pdb=" O   GLU F  84 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 125 through 131
      removed outlier: 3.997A  pdb=" N   SER F 131 " --> pdb=" O   GLU F 127 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 187 through 192
      removed outlier: 3.509A  pdb=" N   GLU F 191 " --> pdb=" O   LYS F 187 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ARG F 192 " --> pdb=" O   ASP F 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 187 through 192'
    Processing helix  chain 'B' and resid 525 through 530
      removed outlier: 4.061A  pdb=" N   LYS B 529 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   SER B 530 " --> pdb=" O   PRO B 527 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328
      removed outlier: 6.749A  pdb=" N   ILE A 326 " --> pdb=" O   ASN B 542 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR B 553 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA B 575 " --> pdb=" O   GLY B 566 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY B 566 " --> pdb=" O   ALA B 575 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 5
      removed outlier: 3.611A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER E  25 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN E   5 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 9 through 12
      removed outlier: 3.687A  pdb=" N   THR E 117 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL E  12 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   THR E 114 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   MET E  34 " --> pdb=" O   MET E  50 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   MET E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   TRP E  36 " --> pdb=" O   ILE E  48 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU E  57 " --> pdb=" O   HIS E  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 9 through 12
      removed outlier: 3.687A  pdb=" N   THR E 117 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL E  12 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   THR E 114 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TRP E 106 " --> pdb=" O   ASP E 100 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 127 through 131
      removed outlier: 6.585A  pdb=" N   TYR E 182 " --> pdb=" O   GLY E 151 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 127 through 131
      removed outlier: 6.585A  pdb=" N   TYR E 182 " --> pdb=" O   GLY E 151 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 158 through 161
      removed outlier: 3.532A  pdb=" N   LYS E 215 " --> pdb=" O   CYS E 202 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR E 211 " --> pdb=" O   HIS E 206 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 7
      removed outlier: 3.759A  pdb=" N   SER F  22 " --> pdb=" O   SER F   7 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ASP F  74 " --> pdb=" O   SER F  71 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   SER F  71 " --> pdb=" O   ASP F  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 10 through 14
      removed outlier: 6.866A  pdb=" N   TRP F  39 " --> pdb=" O   LEU F  51 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER F  57 " --> pdb=" O   TYR F  53 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 14
      removed outlier: 4.016A  pdb=" N   HIS F  94 " --> pdb=" O   ALA F 101 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ALA F 101 " --> pdb=" O   HIS F  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 118 through 122
      removed outlier: 3.752A  pdb=" N   VAL F 137 " --> pdb=" O   PHE F 122 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   TYR F 177 " --> pdb=" O   ASN F 142 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER F 180 " --> pdb=" O   SER F 166 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER F 166 " --> pdb=" O   SER F 180 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 149 through 154
      removed outlier: 3.665A  pdb=" N   TYR F 196 " --> pdb=" O   PHE F 213 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE F 213 " --> pdb=" O   TYR F 196 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA F 200 " --> pdb=" O   ILE F 209 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE F 209 " --> pdb=" O   ALA F 200 " (cutoff:3.500A)

    149 hydrogen bonds defined for protein.
    381 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: 1.15

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1291
        1.35 -     1.46: 1003
        1.46 -     1.58: 1812
        1.58 -     1.70: 0
        1.70 -     1.82: 24
  Bond restraints: 4130
  Sorted by residual:
  bond pdb=" N   GLN B 580 "
       pdb=" CA  GLN B 580 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.85e-01
  bond pdb=" CA  VAL E 190 "
       pdb=" CB  VAL E 190 "
    ideal  model  delta    sigma   weight residual
    1.546  1.538  0.009 8.80e-03 1.29e+04 9.41e-01
  bond pdb=" C   PHE E 153 "
       pdb=" O   PHE E 153 "
    ideal  model  delta    sigma   weight residual
    1.240  1.230  0.010 1.29e-02 6.01e+03 6.53e-01
  bond pdb=" C   SER F   7 "
       pdb=" O   SER F   7 "
    ideal  model  delta    sigma   weight residual
    1.240  1.230  0.010 1.29e-02 6.01e+03 6.25e-01
  bond pdb=" CB  PRO F 145 "
       pdb=" CG  PRO F 145 "
    ideal  model  delta    sigma   weight residual
    1.506  1.477  0.029 3.90e-02 6.57e+02 5.71e-01
  ... (remaining 4125 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 5514
        1.50 -     3.00: 100
        3.00 -     4.50: 11
        4.50 -     6.00: 2
        6.00 -     7.50: 1
  Bond angle restraints: 5628
  Sorted by residual:
  angle pdb=" C   LYS E  65 "
        pdb=" N   ASP E  66 "
        pdb=" CA  ASP E  66 "
      ideal   model   delta    sigma   weight residual
     121.54  126.28   -4.74 1.91e+00 2.74e-01 6.15e+00
  angle pdb=" N   GLY B 526 "
        pdb=" CA  GLY B 526 "
        pdb=" C   GLY B 526 "
      ideal   model   delta    sigma   weight residual
     112.34  116.05   -3.71 2.04e+00 2.40e-01 3.30e+00
  angle pdb=" C   TYR F 144 "
        pdb=" N   PRO F 145 "
        pdb=" CA  PRO F 145 "
      ideal   model   delta    sigma   weight residual
     127.00  131.31   -4.31 2.40e+00 1.74e-01 3.22e+00
  angle pdb=" NE  ARG F  65 "
        pdb=" CZ  ARG F  65 "
        pdb=" NH1 ARG F  65 "
      ideal   model   delta    sigma   weight residual
     121.50  119.88    1.62 1.00e+00 1.00e+00 2.64e+00
  angle pdb=" CA  LEU E 184 "
        pdb=" CB  LEU E 184 "
        pdb=" CG  LEU E 184 "
      ideal   model   delta    sigma   weight residual
     116.30  121.81   -5.51 3.50e+00 8.16e-02 2.48e+00
  ... (remaining 5623 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.72: 2394
       11.72 -    23.45: 69
       23.45 -    35.17: 19
       35.17 -    46.89: 3
       46.89 -    58.61: 1
  Dihedral angle restraints: 2486
    sinusoidal: 962
      harmonic: 1524
  Sorted by residual:
  dihedral pdb=" CA  TYR E 101 "
           pdb=" C   TYR E 101 "
           pdb=" N   ASP E 102 "
           pdb=" CA  ASP E 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.46   22.54     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  PRO B 527 "
           pdb=" C   PRO B 527 "
           pdb=" N   LYS B 528 "
           pdb=" CA  LYS B 528 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.83  -15.17     0      5.00e+00 4.00e-02 9.20e+00
  dihedral pdb=" CA  CYS B 525 "
           pdb=" C   CYS B 525 "
           pdb=" N   GLY B 526 "
           pdb=" CA  GLY B 526 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.45   13.55     0      5.00e+00 4.00e-02 7.34e+00
  ... (remaining 2483 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 407
       0.029 -    0.058: 145
       0.058 -    0.087: 26
       0.087 -    0.116: 52
       0.116 -    0.145: 5
  Chirality restraints: 635
  Sorted by residual:
  chirality pdb=" CA  ILE F 148 "
            pdb=" N   ILE F 148 "
            pdb=" C   ILE F 148 "
            pdb=" CB  ILE F 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CA  ILE B 584 "
            pdb=" N   ILE B 584 "
            pdb=" C   ILE B 584 "
            pdb=" CB  ILE B 584 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CA  HIS F  80 "
            pdb=" N   HIS F  80 "
            pdb=" C   HIS F  80 "
            pdb=" CB  HIS F  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.63   -0.12 2.00e-01 2.50e+01 3.52e-01
  ... (remaining 632 not shown)

  Planarity restraints: 722
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 578 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO B 579 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 579 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 579 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 173 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO E 174 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO E 174 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E 174 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP E 195 "   -0.023 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO E 196 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO E 196 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E 196 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 719 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 641
        2.78 -     3.31: 3473
        3.31 -     3.84: 6321
        3.84 -     4.37: 6980
        4.37 -     4.90: 12506
  Nonbonded interactions: 29921
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 327 "
            pdb=" OG1 THR B 531 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD1 ASN E 140 "
            pdb=" N   SER E 141 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OD1 ASN A 334 "
            pdb=" N   LEU A 335 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" OD2 ASP F 174 "
            pdb=" OG1 THR F 176 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OD2 ASP E  55 "
            pdb=" NZ  LYS B 537 "
     model   vdw
     2.334 3.120
  ... (remaining 29916 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:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.760
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6160
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      :  0.002   0.029   4135  Z= 0.100
  Angle     :  0.507   7.502   5638  Z= 0.280
  Chirality :  0.041   0.145    635
  Planarity :  0.005   0.042    722
  Dihedral  :  6.426  58.615   1487
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.07 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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: -0.96 (0.31), residues: 516
  helix: -3.53 (0.66), residues: 18
  sheet: -0.06 (0.30), residues: 219
  loop : -0.86 (0.31), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 110 
 HIS   0.007   0.001   HIS F  80 
 PHE   0.006   0.001   PHE F 102 
 TYR   0.011   0.001   TYR E 103 
 ARG   0.003   0.000   ARG F  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27312 (  126)
  hydrogen bonds       : angle      10.80264 (  381)
  SS BOND              : bond        0.00219 (    5)
  SS BOND              : angle       0.56789 (   10)
  covalent geometry    : bond        0.00188 ( 4130)
  covalent geometry    : angle       0.50666 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 VAL cc_start: 0.4988 (t) cc_final: 0.4697 (t)
REVERT: E    5 GLN cc_start: 0.6832 (mt0) cc_final: 0.6417 (tm-30)
REVERT: E    6 GLN cc_start: 0.7567 (mt0) cc_final: 0.7314 (mt0)
REVERT: E   65 LYS cc_start: 0.5878 (tttm) cc_final: 0.5573 (ttpp)
REVERT: E   82 GLN cc_start: 0.7258 (tt0) cc_final: 0.6232 (mp10)
REVERT: E  148 LEU cc_start: 0.7730 (tp) cc_final: 0.7499 (tp)
REVERT: E  178 GLN cc_start: 0.7258 (tt0) cc_final: 0.6581 (pm20)
REVERT: E  180 ASP cc_start: 0.6898 (m-30) cc_final: 0.6681 (m-30)
REVERT: E  189 THR cc_start: 0.6413 (m) cc_final: 0.6169 (p)
REVERT: F   86 ASP cc_start: 0.7319 (m-30) cc_final: 0.6747 (m-30)
REVERT: B  535 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7924 (ttmt)
REVERT: B  559 PHE cc_start: 0.6026 (m-10) cc_final: 0.5416 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2008
  time to fit residues: 50.0973
Evaluate side-chains
  125 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  43 GLN
E 203 ASN
F 194 ASN
** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.157533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.132479 restraints weight = 8394.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.136970 restraints weight = 5170.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.140195 restraints weight = 3553.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6522
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4135  Z= 0.134
  Angle     :  0.604   6.140   5638  Z= 0.313
  Chirality :  0.044   0.157    635
  Planarity :  0.005   0.032    722
  Dihedral  :  4.449  29.257    559
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.71 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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: -0.16 (0.34), residues: 516
  helix: -3.99 (0.83), residues: 6
  sheet:  0.64 (0.33), residues: 216
  loop : -0.58 (0.33), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 110 
 HIS   0.003   0.001   HIS F  38 
 PHE   0.015   0.001   PHE F  75 
 TYR   0.010   0.001   TYR E 103 
 ARG   0.006   0.001   ARG F  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04014 (  126)
  hydrogen bonds       : angle       6.99725 (  381)
  SS BOND              : bond        0.01185 (    5)
  SS BOND              : angle       1.49884 (   10)
  covalent geometry    : bond        0.00292 ( 4130)
  covalent geometry    : angle       0.60161 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7350 (mt0) cc_final: 0.6186 (tm-30)
REVERT: E   65 LYS cc_start: 0.6482 (tttm) cc_final: 0.5816 (ttpp)
REVERT: E   82 GLN cc_start: 0.8219 (tt0) cc_final: 0.6712 (mp10)
REVERT: E  180 ASP cc_start: 0.7270 (m-30) cc_final: 0.6950 (m-30)
REVERT: F   79 ILE cc_start: 0.8248 (mm) cc_final: 0.7973 (mm)
REVERT: F   86 ASP cc_start: 0.7139 (m-30) cc_final: 0.6720 (m-30)
REVERT: F   92 CYS cc_start: 0.4151 (p) cc_final: 0.3648 (p)
REVERT: F   96 ARG cc_start: 0.8123 (tpt90) cc_final: 0.7854 (tpt90)
REVERT: F  106 THR cc_start: 0.7774 (t) cc_final: 0.7514 (t)
REVERT: F  199 GLU cc_start: 0.5052 (tm-30) cc_final: 0.4556 (mt-10)
REVERT: B  535 LYS cc_start: 0.8599 (ttmt) cc_final: 0.7939 (tttt)
REVERT: B  552 LEU cc_start: 0.9091 (mm) cc_final: 0.8851 (mm)
REVERT: B  559 PHE cc_start: 0.6474 (m-10) cc_final: 0.5767 (m-80)
REVERT: B  586 ASP cc_start: 0.7813 (t0) cc_final: 0.7603 (t0)
REVERT: B  587 ILE cc_start: 0.6980 (mm) cc_final: 0.6654 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1899
  time to fit residues: 34.5521
Evaluate side-chains
  123 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
E   6 GLN
E  35 ASN
E 203 ASN
F 142 ASN
** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 542 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.155690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.129998 restraints weight = 8556.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.134529 restraints weight = 5350.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.137676 restraints weight = 3700.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.4840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4135  Z= 0.112
  Angle     :  0.581   7.690   5638  Z= 0.294
  Chirality :  0.044   0.161    635
  Planarity :  0.004   0.035    722
  Dihedral  :  4.493  28.022    559
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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:  0.14 (0.35), residues: 516
  helix: -2.10 (1.16), residues: 12
  sheet:  1.05 (0.33), residues: 224
  loop : -0.61 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 195 
 HIS   0.004   0.001   HIS F  38 
 PHE   0.008   0.001   PHE E 153 
 TYR   0.008   0.001   TYR E 109 
 ARG   0.003   0.000   ARG F  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03276 (  126)
  hydrogen bonds       : angle       6.14926 (  381)
  SS BOND              : bond        0.00618 (    5)
  SS BOND              : angle       1.43516 (   10)
  covalent geometry    : bond        0.00246 ( 4130)
  covalent geometry    : angle       0.57883 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7478 (mt0) cc_final: 0.6319 (tm-30)
REVERT: E   63 LYS cc_start: 0.8077 (tttt) cc_final: 0.7546 (tppt)
REVERT: E   65 LYS cc_start: 0.6478 (tttm) cc_final: 0.5883 (ttpp)
REVERT: E   81 MET cc_start: 0.8678 (ttp) cc_final: 0.8421 (ttm)
REVERT: E   82 GLN cc_start: 0.8228 (tt0) cc_final: 0.6794 (mp10)
REVERT: F   77 LEU cc_start: 0.8321 (tp) cc_final: 0.7883 (tp)
REVERT: F   79 ILE cc_start: 0.8100 (mm) cc_final: 0.7712 (mm)
REVERT: F   86 ASP cc_start: 0.7122 (m-30) cc_final: 0.6820 (m-30)
REVERT: F   96 ARG cc_start: 0.8252 (tpt90) cc_final: 0.7816 (tpt90)
REVERT: F  199 GLU cc_start: 0.4941 (tm-30) cc_final: 0.4396 (mt-10)
REVERT: B  535 LYS cc_start: 0.8463 (ttmt) cc_final: 0.7949 (tttt)
REVERT: B  552 LEU cc_start: 0.9072 (mm) cc_final: 0.8829 (mm)
REVERT: B  559 PHE cc_start: 0.6607 (m-10) cc_final: 0.6103 (m-80)
REVERT: B  586 ASP cc_start: 0.7723 (t0) cc_final: 0.7503 (t0)
REVERT: B  588 THR cc_start: 0.8130 (m) cc_final: 0.7571 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2138
  time to fit residues: 37.5265
Evaluate side-chains
  113 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0470
   chunk 6 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 16 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 4 optimal weight:   10.0000
   overall best weight:    2.2082

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

Flipped N/Q/H residues before XYZ refinement:
E   6 GLN
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 203 ASN
F  93 HIS
** F  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 160 GLN
** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.146172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.121703 restraints weight = 8593.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.126039 restraints weight = 5303.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.129054 restraints weight = 3613.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.5782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4135  Z= 0.186
  Angle     :  0.658   7.767   5638  Z= 0.336
  Chirality :  0.044   0.143    635
  Planarity :  0.005   0.054    722
  Dihedral  :  5.090  27.942    559
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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:  0.32 (0.36), residues: 516
  helix: -1.93 (1.51), residues: 12
  sheet:  1.01 (0.35), residues: 209
  loop : -0.26 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 110 
 HIS   0.005   0.001   HIS F  94 
 PHE   0.009   0.002   PHE E 153 
 TYR   0.017   0.002   TYR F  53 
 ARG   0.004   0.001   ARG F  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  126)
  hydrogen bonds       : angle       6.38174 (  381)
  SS BOND              : bond        0.00781 (    5)
  SS BOND              : angle       1.85229 (   10)
  covalent geometry    : bond        0.00422 ( 4130)
  covalent geometry    : angle       0.65364 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7603 (mt0) cc_final: 0.6494 (tm-30)
REVERT: F    4 LEU cc_start: 0.8684 (mt) cc_final: 0.8378 (mt)
REVERT: F   86 ASP cc_start: 0.7060 (m-30) cc_final: 0.6710 (m-30)
REVERT: F   92 CYS cc_start: 0.3166 (p) cc_final: 0.2749 (p)
REVERT: F   96 ARG cc_start: 0.8492 (tpt90) cc_final: 0.7992 (tpt90)
REVERT: B  535 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8154 (tttt)
REVERT: B  559 PHE cc_start: 0.6555 (m-10) cc_final: 0.5940 (m-80)
REVERT: B  583 GLU cc_start: 0.7677 (pm20) cc_final: 0.7205 (pm20)
REVERT: B  586 ASP cc_start: 0.7439 (t0) cc_final: 0.7193 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.2041
  time to fit residues: 32.3167
Evaluate side-chains
  101 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 44 optimal weight:    0.4980
   chunk 46 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
E 203 ASN
** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.147231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.122720 restraints weight = 8956.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.126919 restraints weight = 5470.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.129987 restraints weight = 3742.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.6214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4135  Z= 0.125
  Angle     :  0.608   7.404   5638  Z= 0.311
  Chirality :  0.045   0.165    635
  Planarity :  0.005   0.046    722
  Dihedral  :  4.820  22.956    559
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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:  0.24 (0.36), residues: 516
  helix: -1.34 (1.24), residues: 18
  sheet:  1.14 (0.37), residues: 189
  loop : -0.36 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 161 
 HIS   0.003   0.001   HIS F  93 
 PHE   0.009   0.001   PHE E  29 
 TYR   0.011   0.001   TYR E 109 
 ARG   0.005   0.001   ARG F  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 (  126)
  hydrogen bonds       : angle       5.99242 (  381)
  SS BOND              : bond        0.00680 (    5)
  SS BOND              : angle       1.47881 (   10)
  covalent geometry    : bond        0.00284 ( 4130)
  covalent geometry    : angle       0.60578 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7725 (mt0) cc_final: 0.6359 (tm-30)
REVERT: F    4 LEU cc_start: 0.8731 (mt) cc_final: 0.8366 (mt)
REVERT: F   78 ASN cc_start: 0.7741 (m-40) cc_final: 0.7488 (m-40)
REVERT: F   79 ILE cc_start: 0.8101 (mm) cc_final: 0.7744 (mm)
REVERT: F   92 CYS cc_start: 0.3171 (p) cc_final: 0.2699 (p)
REVERT: F   96 ARG cc_start: 0.8521 (tpt90) cc_final: 0.7947 (tpt90)
REVERT: B  535 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8001 (tttt)
REVERT: B  536 ASN cc_start: 0.8968 (m-40) cc_final: 0.8754 (m110)
REVERT: B  559 PHE cc_start: 0.6479 (m-10) cc_final: 0.5894 (m-80)
REVERT: B  577 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7260 (mtm110)
REVERT: B  583 GLU cc_start: 0.7525 (pm20) cc_final: 0.7115 (pm20)
REVERT: B  586 ASP cc_start: 0.7456 (t0) cc_final: 0.7159 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1724
  time to fit residues: 28.2994
Evaluate side-chains
  109 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 6 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 8 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 112 GLN
** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 170 GLN
** F 202 HIS ** 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 = 0.4014 r_free = 0.4014 target = 0.149175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.125492 restraints weight = 8579.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.129661 restraints weight = 5261.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.132610 restraints weight = 3589.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
moved from start:          0.6373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4135  Z= 0.106
  Angle     :  0.583   7.131   5638  Z= 0.297
  Chirality :  0.044   0.161    635
  Planarity :  0.004   0.047    722
  Dihedral  :  4.611  25.625    559
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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:  0.29 (0.36), residues: 516
  helix: -1.09 (1.46), residues: 12
  sheet:  1.15 (0.36), residues: 189
  loop : -0.35 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 161 
 HIS   0.002   0.001   HIS F  93 
 PHE   0.007   0.001   PHE E  29 
 TYR   0.009   0.001   TYR E 109 
 ARG   0.005   0.000   ARG F  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03130 (  126)
  hydrogen bonds       : angle       5.59601 (  381)
  SS BOND              : bond        0.00645 (    5)
  SS BOND              : angle       1.42679 (   10)
  covalent geometry    : bond        0.00239 ( 4130)
  covalent geometry    : angle       0.58009 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7671 (mt0) cc_final: 0.6290 (tm-30)
REVERT: E   58 THR cc_start: 0.8383 (p) cc_final: 0.8162 (t)
REVERT: F    4 LEU cc_start: 0.8728 (mt) cc_final: 0.8148 (tp)
REVERT: F   37 MET cc_start: 0.7829 (tpp) cc_final: 0.7528 (tpp)
REVERT: F   79 ILE cc_start: 0.8175 (mm) cc_final: 0.7637 (mm)
REVERT: F   92 CYS cc_start: 0.3145 (p) cc_final: 0.1998 (p)
REVERT: F   96 ARG cc_start: 0.8359 (tpt90) cc_final: 0.7771 (tpt90)
REVERT: B  530 SER cc_start: 0.8249 (p) cc_final: 0.7943 (m)
REVERT: B  535 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8079 (tttt)
REVERT: B  559 PHE cc_start: 0.6573 (m-10) cc_final: 0.6004 (m-80)
REVERT: B  577 ARG cc_start: 0.7892 (ttm110) cc_final: 0.7200 (mtm110)
REVERT: B  586 ASP cc_start: 0.7554 (t0) cc_final: 0.7334 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1770
  time to fit residues: 27.7218
Evaluate side-chains
  104 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 15 optimal weight:    0.0070
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    1.0804

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

Flipped N/Q/H residues before XYZ refinement:
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 112 GLN
E 203 ASN
** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 202 HIS ** 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 = 0.4014 r_free = 0.4014 target = 0.148922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.124470 restraints weight = 8674.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.128626 restraints weight = 5328.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.131593 restraints weight = 3657.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.6625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4135  Z= 0.119
  Angle     :  0.607   6.524   5638  Z= 0.311
  Chirality :  0.044   0.144    635
  Planarity :  0.005   0.049    722
  Dihedral  :  4.692  27.255    559
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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:  0.34 (0.36), residues: 516
  helix: -0.26 (1.86), residues: 12
  sheet:  1.08 (0.36), residues: 191
  loop : -0.29 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 161 
 HIS   0.004   0.001   HIS F  93 
 PHE   0.008   0.001   PHE E 173 
 TYR   0.010   0.001   TYR E 109 
 ARG   0.004   0.000   ARG F  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03237 (  126)
  hydrogen bonds       : angle       5.62282 (  381)
  SS BOND              : bond        0.00655 (    5)
  SS BOND              : angle       2.19781 (   10)
  covalent geometry    : bond        0.00274 ( 4130)
  covalent geometry    : angle       0.60049 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7557 (mt0) cc_final: 0.6662 (tm-30)
REVERT: E   35 ASN cc_start: 0.8033 (m-40) cc_final: 0.7824 (m-40)
REVERT: E   58 THR cc_start: 0.8426 (p) cc_final: 0.8174 (t)
REVERT: E  112 GLN cc_start: 0.7856 (tp40) cc_final: 0.7542 (tp-100)
REVERT: F    4 LEU cc_start: 0.8722 (mt) cc_final: 0.8097 (tp)
REVERT: F   77 LEU cc_start: 0.8201 (tp) cc_final: 0.7670 (tp)
REVERT: F   78 ASN cc_start: 0.7663 (m-40) cc_final: 0.7396 (m-40)
REVERT: F   79 ILE cc_start: 0.7991 (mm) cc_final: 0.7491 (mm)
REVERT: F   92 CYS cc_start: 0.3196 (p) cc_final: 0.2129 (p)
REVERT: F   96 ARG cc_start: 0.8346 (tpt90) cc_final: 0.7822 (tpt90)
REVERT: F  109 GLU cc_start: 0.7452 (pp20) cc_final: 0.7250 (pp20)
REVERT: B  530 SER cc_start: 0.8275 (p) cc_final: 0.7989 (m)
REVERT: B  535 LYS cc_start: 0.8618 (ttmt) cc_final: 0.7959 (ttmt)
REVERT: B  559 PHE cc_start: 0.6415 (m-10) cc_final: 0.5861 (m-80)
REVERT: B  586 ASP cc_start: 0.7494 (t0) cc_final: 0.7262 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2200
  time to fit residues: 35.1383
Evaluate side-chains
  101 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 18 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** F 202 HIS ** 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 = 0.4013 r_free = 0.4013 target = 0.148627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.124342 restraints weight = 8460.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.128385 restraints weight = 5205.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.131269 restraints weight = 3595.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.6832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4135  Z= 0.122
  Angle     :  0.610   6.082   5638  Z= 0.313
  Chirality :  0.044   0.173    635
  Planarity :  0.005   0.048    722
  Dihedral  :  4.747  25.441    559
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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:  0.29 (0.36), residues: 516
  helix: -0.60 (1.67), residues: 12
  sheet:  1.09 (0.36), residues: 185
  loop : -0.30 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 195 
 HIS   0.003   0.001   HIS F  93 
 PHE   0.008   0.001   PHE E  29 
 TYR   0.010   0.001   TYR E 109 
 ARG   0.004   0.001   ARG F  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03099 (  126)
  hydrogen bonds       : angle       5.60257 (  381)
  SS BOND              : bond        0.00595 (    5)
  SS BOND              : angle       1.86817 (   10)
  covalent geometry    : bond        0.00283 ( 4130)
  covalent geometry    : angle       0.60549 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7588 (mt0) cc_final: 0.6673 (tm-30)
REVERT: E   35 ASN cc_start: 0.8187 (m-40) cc_final: 0.7925 (m-40)
REVERT: E  112 GLN cc_start: 0.7740 (tp40) cc_final: 0.7399 (tp-100)
REVERT: F    4 LEU cc_start: 0.8704 (mt) cc_final: 0.8084 (tp)
REVERT: F   77 LEU cc_start: 0.8149 (tp) cc_final: 0.7639 (tp)
REVERT: F   78 ASN cc_start: 0.7889 (m-40) cc_final: 0.7619 (m-40)
REVERT: F   79 ILE cc_start: 0.8172 (mm) cc_final: 0.7657 (mm)
REVERT: F   92 CYS cc_start: 0.3192 (p) cc_final: 0.2070 (p)
REVERT: F   96 ARG cc_start: 0.8397 (tpt90) cc_final: 0.7804 (tpt90)
REVERT: F  179 MET cc_start: 0.7159 (tmm) cc_final: 0.6625 (tmm)
REVERT: B  535 LYS cc_start: 0.8669 (ttmt) cc_final: 0.7818 (ttmt)
REVERT: B  559 PHE cc_start: 0.6469 (m-10) cc_final: 0.5838 (m-80)
REVERT: B  583 GLU cc_start: 0.7666 (pm20) cc_final: 0.6861 (pm20)
REVERT: B  586 ASP cc_start: 0.7452 (t0) cc_final: 0.7244 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2406
  time to fit residues: 38.7349
Evaluate side-chains
  98 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 18 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 170 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 = 0.3935 r_free = 0.3935 target = 0.142926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.119641 restraints weight = 8737.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.123584 restraints weight = 5356.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.126365 restraints weight = 3673.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6795
moved from start:          0.7453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4135  Z= 0.206
  Angle     :  0.727   8.687   5638  Z= 0.370
  Chirality :  0.046   0.141    635
  Planarity :  0.006   0.081    722
  Dihedral  :  5.548  23.678    559
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.84 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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: -0.15 (0.36), residues: 516
  helix: -1.17 (2.85), residues: 6
  sheet:  0.63 (0.35), residues: 200
  loop : -0.55 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP E 110 
 HIS   0.009   0.002   HIS F  93 
 PHE   0.015   0.002   PHE E 173 
 TYR   0.017   0.002   TYR E 101 
 ARG   0.008   0.001   ARG B 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  126)
  hydrogen bonds       : angle       6.02801 (  381)
  SS BOND              : bond        0.00837 (    5)
  SS BOND              : angle       2.30011 (   10)
  covalent geometry    : bond        0.00467 ( 4130)
  covalent geometry    : angle       0.72098 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7488 (mt0) cc_final: 0.6728 (tm-30)
REVERT: E   55 ASP cc_start: 0.8171 (p0) cc_final: 0.7766 (p0)
REVERT: E   57 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6505 (mm-30)
REVERT: E   85 SER cc_start: 0.8570 (m) cc_final: 0.8062 (t)
REVERT: E  106 TRP cc_start: 0.7546 (p90) cc_final: 0.6885 (p-90)
REVERT: E  112 GLN cc_start: 0.7622 (tp40) cc_final: 0.7247 (tp-100)
REVERT: F    4 LEU cc_start: 0.8671 (mt) cc_final: 0.8407 (mt)
REVERT: F   59 GLU cc_start: 0.7921 (tp30) cc_final: 0.7696 (tp30)
REVERT: F   79 ILE cc_start: 0.8106 (mm) cc_final: 0.7620 (mm)
REVERT: F   92 CYS cc_start: 0.3194 (p) cc_final: 0.2858 (p)
REVERT: F   96 ARG cc_start: 0.8545 (tpt90) cc_final: 0.8057 (tpt90)
REVERT: F  171 ASP cc_start: 0.7586 (m-30) cc_final: 0.7352 (m-30)
REVERT: F  179 MET cc_start: 0.7505 (tmm) cc_final: 0.7095 (tmm)
REVERT: B  535 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8169 (ttmt)
REVERT: B  559 PHE cc_start: 0.6472 (m-10) cc_final: 0.6007 (m-80)
REVERT: B  583 GLU cc_start: 0.7598 (pm20) cc_final: 0.6943 (pm20)
REVERT: B  586 ASP cc_start: 0.7556 (t0) cc_final: 0.7308 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2426
  time to fit residues: 38.4667
Evaluate side-chains
  106 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0270
   chunk 50 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   chunk 19 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 203 ASN
F 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.147709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.123937 restraints weight = 8403.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.127981 restraints weight = 5149.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.130881 restraints weight = 3522.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.7407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4135  Z= 0.110
  Angle     :  0.639   9.203   5638  Z= 0.323
  Chirality :  0.045   0.163    635
  Planarity :  0.005   0.051    722
  Dihedral  :  4.970  26.724    559
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.29 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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: -0.02 (0.36), residues: 516
  helix: -0.74 (1.66), residues: 12
  sheet:  0.75 (0.35), residues: 208
  loop : -0.54 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 195 
 HIS   0.002   0.001   HIS F  94 
 PHE   0.009   0.001   PHE E  29 
 TYR   0.012   0.001   TYR E 103 
 ARG   0.007   0.001   ARG B 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03239 (  126)
  hydrogen bonds       : angle       5.71030 (  381)
  SS BOND              : bond        0.00539 (    5)
  SS BOND              : angle       1.55025 (   10)
  covalent geometry    : bond        0.00249 ( 4130)
  covalent geometry    : angle       0.63594 ( 5628)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7650 (mt0) cc_final: 0.6739 (tm-30)
REVERT: E   34 MET cc_start: 0.7048 (mmm) cc_final: 0.6674 (mmm)
REVERT: E   85 SER cc_start: 0.8511 (m) cc_final: 0.8003 (t)
REVERT: F    4 LEU cc_start: 0.8710 (mt) cc_final: 0.8117 (tp)
REVERT: F   37 MET cc_start: 0.7167 (tpp) cc_final: 0.6891 (tpp)
REVERT: F   59 GLU cc_start: 0.7858 (tp30) cc_final: 0.7656 (tp30)
REVERT: F   79 ILE cc_start: 0.8071 (mm) cc_final: 0.7617 (mm)
REVERT: F   92 CYS cc_start: 0.3114 (p) cc_final: 0.1696 (p)
REVERT: F   96 ARG cc_start: 0.8463 (tpt90) cc_final: 0.7912 (tpt90)
REVERT: F  171 ASP cc_start: 0.7771 (m-30) cc_final: 0.7528 (m-30)
REVERT: F  179 MET cc_start: 0.7325 (tmm) cc_final: 0.6919 (tmm)
REVERT: B  535 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8194 (tttt)
REVERT: B  559 PHE cc_start: 0.6277 (m-10) cc_final: 0.5883 (m-80)
REVERT: B  583 GLU cc_start: 0.7824 (pm20) cc_final: 0.7157 (pm20)
REVERT: B  586 ASP cc_start: 0.7615 (t0) cc_final: 0.7393 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1641
  time to fit residues: 27.2166
Evaluate side-chains
  110 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0010
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  43 GLN
E 203 ASN
** F 170 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 = 0.4016 r_free = 0.4016 target = 0.149057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.125360 restraints weight = 8587.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.129360 restraints weight = 5284.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.132274 restraints weight = 3650.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.7500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4135  Z= 0.112
  Angle     :  0.630   8.677   5638  Z= 0.318
  Chirality :  0.045   0.156    635
  Planarity :  0.005   0.050    722
  Dihedral  :  4.829  26.136    559
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.07 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.14 %
    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:  0.02 (0.37), residues: 516
  helix: -0.51 (1.69), residues: 12
  sheet:  0.69 (0.35), residues: 205
  loop : -0.41 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 195 
 HIS   0.003   0.001   HIS F  93 
 PHE   0.010   0.001   PHE E  29 
 TYR   0.016   0.001   TYR F  53 
 ARG   0.006   0.001   ARG B 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03084 (  126)
  hydrogen bonds       : angle       5.60446 (  381)
  SS BOND              : bond        0.00571 (    5)
  SS BOND              : angle       1.59055 (   10)
  covalent geometry    : bond        0.00255 ( 4130)
  covalent geometry    : angle       0.62741 ( 5628)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2062.39 seconds
wall clock time: 38 minutes 28.13 seconds (2308.13 seconds total)