Starting phenix.real_space_refine
on Wed Mar  5 22:41:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wd8_32434/03_2025/7wd8_32434.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wd8_32434/03_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_32434/03_2025/7wd8_32434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wd8_32434/03_2025/7wd8_32434.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wd8_32434/03_2025/7wd8_32434.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wd8_32434/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.01, 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: 0.84
  Conformation dependent library (CDL) restraints added in 457.6 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: 0.61
  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: 1.18

  Time building geometry restraints manager: 1.04 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:             0.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.000
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.420
-------------------------------------------------------------------------------
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   4130  Z= 0.119
  Angle     :  0.507   7.502   5628  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 

*********************** 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  : 0.510 
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: 0.1983
  time to fit residues: 49.5698
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  : 0.464 
-------------------------------------------------------------------------------
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   4130  Z= 0.188
  Angle     :  0.602   6.140   5628  Z= 0.312
  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 

*********************** 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  : 0.448 
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: 0.1759
  time to fit residues: 32.1370
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  : 0.456 
-------------------------------------------------------------------------------
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   4130  Z= 0.157
  Angle     :  0.579   7.690   5628  Z= 0.293
  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 

*********************** 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  : 0.414 
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: 0.1866
  time to fit residues: 32.9331
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  : 0.452 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 16 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 4 optimal weight:   10.0000
   overall best weight:    2.1440

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.147420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123178 restraints weight = 8527.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.127515 restraints weight = 5211.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.130657 restraints weight = 3562.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.5632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4130  Z= 0.255
  Angle     :  0.633   7.579   5628  Z= 0.323
  Chirality :  0.044   0.146    635
  Planarity :  0.005   0.051    722
  Dihedral  :  4.936  28.557    559
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  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:  0.36 (0.37), residues: 516
  helix: -1.89 (1.53), residues: 12
  sheet:  0.97 (0.35), residues: 217
  loop : -0.20 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 110 
 HIS   0.005   0.001   HIS F  94 
 PHE   0.008   0.002   PHE E 153 
 TYR   0.016   0.002   TYR E 109 
 ARG   0.004   0.001   ARG F  24 

*********************** 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  : 0.467 
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: 0.7596 (mt0) cc_final: 0.6374 (tm-30)
REVERT: E   63 LYS cc_start: 0.8214 (tttt) cc_final: 0.7773 (tppt)
REVERT: E   65 LYS cc_start: 0.6474 (tttm) cc_final: 0.6109 (ttpp)
REVERT: F    4 LEU cc_start: 0.8738 (mt) cc_final: 0.8398 (mt)
REVERT: F   79 ILE cc_start: 0.8309 (mm) cc_final: 0.7800 (mm)
REVERT: F   86 ASP cc_start: 0.7120 (m-30) cc_final: 0.6770 (m-30)
REVERT: F   92 CYS cc_start: 0.3324 (p) cc_final: 0.2819 (p)
REVERT: F   96 ARG cc_start: 0.8523 (tpt90) cc_final: 0.7951 (tpt90)
REVERT: B  535 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8116 (tttt)
REVERT: B  559 PHE cc_start: 0.6543 (m-10) cc_final: 0.5945 (m-80)
REVERT: B  583 GLU cc_start: 0.7501 (pm20) cc_final: 0.7119 (pm20)
REVERT: B  586 ASP cc_start: 0.7490 (t0) cc_final: 0.7167 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1988
  time to fit residues: 31.2958
Evaluate side-chains
  100 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 23 optimal weight:    0.0270
   chunk 33 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0570
   chunk 44 optimal weight:    0.2980
   chunk 46 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 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 = 0.4040 r_free = 0.4040 target = 0.150677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.125576 restraints weight = 8893.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.129942 restraints weight = 5499.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.133117 restraints weight = 3783.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.5965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4130  Z= 0.162
  Angle     :  0.591   6.917   5628  Z= 0.301
  Chirality :  0.045   0.161    635
  Planarity :  0.005   0.046    722
  Dihedral  :  4.595  23.596    559
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  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: -1.31 (1.23), residues: 18
  sheet:  1.24 (0.35), residues: 206
  loop : -0.42 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E  36 
 HIS   0.002   0.001   HIS F  38 
 PHE   0.009   0.001   PHE E  29 
 TYR   0.011   0.001   TYR E 109 
 ARG   0.006   0.001   ARG F  24 

*********************** 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
  139 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7624 (mt0) cc_final: 0.6423 (tm-30)
REVERT: E  100 ASP cc_start: 0.4609 (t0) cc_final: 0.4398 (t0)
REVERT: E  106 TRP cc_start: 0.7400 (p90) cc_final: 0.6982 (p90)
REVERT: F    4 LEU cc_start: 0.8705 (mt) cc_final: 0.8384 (mt)
REVERT: F   92 CYS cc_start: 0.3233 (p) cc_final: 0.2732 (p)
REVERT: F   96 ARG cc_start: 0.8345 (tpt90) cc_final: 0.7852 (tpt90)
REVERT: B  530 SER cc_start: 0.8355 (p) cc_final: 0.8027 (m)
REVERT: B  535 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7706 (ttmt)
REVERT: B  536 ASN cc_start: 0.8991 (m-40) cc_final: 0.8700 (m-40)
REVERT: B  552 LEU cc_start: 0.8849 (mm) cc_final: 0.8595 (mm)
REVERT: B  559 PHE cc_start: 0.6520 (m-10) cc_final: 0.5930 (m-80)
REVERT: B  573 THR cc_start: 0.9023 (p) cc_final: 0.7488 (p)
REVERT: B  583 GLU cc_start: 0.7475 (pm20) cc_final: 0.6932 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1824
  time to fit residues: 30.7172
Evaluate side-chains
  111 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
E 112 GLN
** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  41 GLN
** 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 = 0.3938 r_free = 0.3938 target = 0.143436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.119873 restraints weight = 8687.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.123939 restraints weight = 5345.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.126899 restraints weight = 3672.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.6722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4130  Z= 0.300
  Angle     :  0.696   8.566   5628  Z= 0.354
  Chirality :  0.046   0.143    635
  Planarity :  0.005   0.044    722
  Dihedral  :  5.295  23.760    559
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  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:  0.30 (0.36), residues: 516
  helix: -1.16 (3.03), residues: 6
  sheet:  0.96 (0.36), residues: 200
  loop : -0.26 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP E 110 
 HIS   0.008   0.002   HIS F  93 
 PHE   0.014   0.002   PHE E 153 
 TYR   0.016   0.002   TYR E 101 
 ARG   0.006   0.001   ARG B 567 

*********************** 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
  132 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7508 (mt0) cc_final: 0.6293 (tm-30)
REVERT: E   55 ASP cc_start: 0.8714 (p0) cc_final: 0.8420 (p0)
REVERT: E   57 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6521 (mm-30)
REVERT: E  106 TRP cc_start: 0.7613 (p90) cc_final: 0.6781 (p-90)
REVERT: F    4 LEU cc_start: 0.8698 (mt) cc_final: 0.8396 (mt)
REVERT: F   78 ASN cc_start: 0.7911 (m-40) cc_final: 0.7550 (m-40)
REVERT: F   79 ILE cc_start: 0.8307 (mm) cc_final: 0.7789 (mm)
REVERT: F   86 ASP cc_start: 0.7207 (m-30) cc_final: 0.6990 (m-30)
REVERT: F   92 CYS cc_start: 0.3133 (p) cc_final: 0.2755 (p)
REVERT: F   96 ARG cc_start: 0.8497 (tpt90) cc_final: 0.7997 (tpt90)
REVERT: B  535 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8102 (tttt)
REVERT: B  536 ASN cc_start: 0.9161 (m-40) cc_final: 0.8861 (m-40)
REVERT: B  559 PHE cc_start: 0.6628 (m-10) cc_final: 0.6035 (m-80)
REVERT: B  583 GLU cc_start: 0.7645 (pm20) cc_final: 0.6936 (pm20)
REVERT: B  584 ILE cc_start: 0.6952 (mm) cc_final: 0.5947 (mm)
REVERT: B  586 ASP cc_start: 0.7080 (t0) cc_final: 0.6875 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1636
  time to fit residues: 26.6731
Evaluate side-chains
  103 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 20 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
E 112 GLN
** F  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.146201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.122085 restraints weight = 8848.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.126211 restraints weight = 5454.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.129230 restraints weight = 3754.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start:          0.6885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4130  Z= 0.199
  Angle     :  0.628   7.778   5628  Z= 0.319
  Chirality :  0.045   0.140    635
  Planarity :  0.004   0.044    722
  Dihedral  :  4.947  25.800    559
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  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:  0.10 (0.36), residues: 516
  helix: -0.78 (1.74), residues: 12
  sheet:  0.86 (0.34), residues: 206
  loop : -0.46 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 195 
 HIS   0.004   0.001   HIS F  93 
 PHE   0.013   0.002   PHE E 153 
 TYR   0.011   0.001   TYR F 144 
 ARG   0.004   0.001   ARG F  24 

*********************** 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
  132 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7588 (mt0) cc_final: 0.6380 (tm-30)
REVERT: E   50 MET cc_start: 0.6743 (ttp) cc_final: 0.6499 (ttp)
REVERT: F    4 LEU cc_start: 0.8722 (mt) cc_final: 0.8358 (mt)
REVERT: F   78 ASN cc_start: 0.7826 (m-40) cc_final: 0.7536 (m-40)
REVERT: F   79 ILE cc_start: 0.8243 (mm) cc_final: 0.7741 (mm)
REVERT: F   86 ASP cc_start: 0.7240 (m-30) cc_final: 0.7037 (m-30)
REVERT: F   92 CYS cc_start: 0.3136 (p) cc_final: 0.2703 (p)
REVERT: F   96 ARG cc_start: 0.8535 (tpt90) cc_final: 0.7983 (tpt90)
REVERT: F  171 ASP cc_start: 0.7533 (m-30) cc_final: 0.7262 (m-30)
REVERT: B  535 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8195 (tttt)
REVERT: B  559 PHE cc_start: 0.6371 (m-10) cc_final: 0.5846 (m-80)
REVERT: B  584 ILE cc_start: 0.6733 (mm) cc_final: 0.5630 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1669
  time to fit residues: 27.0670
Evaluate side-chains
  105 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0010
   chunk 44 optimal weight:    0.0470
   overall best weight:    0.4884

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.149902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.125855 restraints weight = 8505.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.129991 restraints weight = 5200.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.132950 restraints weight = 3554.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6652
moved from start:          0.6955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   4130  Z= 0.166
  Angle     :  0.617   8.338   5628  Z= 0.310
  Chirality :  0.044   0.156    635
  Planarity :  0.004   0.046    722
  Dihedral  :  4.667  27.546    559
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.26 %
    Favored  : 95.54 %
  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:  0.26 (0.36), residues: 516
  helix: -0.53 (1.78), residues: 12
  sheet:  1.05 (0.36), residues: 191
  loop : -0.35 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP E 161 
 HIS   0.002   0.001   HIS F  93 
 PHE   0.012   0.002   PHE E 153 
 TYR   0.010   0.001   TYR E 109 
 ARG   0.004   0.000   ARG F  24 

*********************** 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
  129 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7842 (mt0) cc_final: 0.6444 (tm-30)
REVERT: F    4 LEU cc_start: 0.8674 (mt) cc_final: 0.7972 (tp)
REVERT: F   78 ASN cc_start: 0.7797 (m-40) cc_final: 0.7543 (m-40)
REVERT: F   79 ILE cc_start: 0.8238 (mm) cc_final: 0.7794 (mm)
REVERT: F   86 ASP cc_start: 0.7230 (m-30) cc_final: 0.7013 (m-30)
REVERT: F   92 CYS cc_start: 0.2992 (p) cc_final: 0.1445 (p)
REVERT: F   96 ARG cc_start: 0.8435 (tpt90) cc_final: 0.7868 (tpt90)
REVERT: F  171 ASP cc_start: 0.7686 (m-30) cc_final: 0.7403 (m-30)
REVERT: B  529 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7505 (mmtm)
REVERT: B  530 SER cc_start: 0.8354 (p) cc_final: 0.8075 (m)
REVERT: B  535 LYS cc_start: 0.8756 (ttmt) cc_final: 0.7815 (ttmt)
REVERT: B  552 LEU cc_start: 0.8732 (mm) cc_final: 0.8502 (mm)
REVERT: B  559 PHE cc_start: 0.6234 (m-10) cc_final: 0.5741 (m-80)
REVERT: B  584 ILE cc_start: 0.6638 (mm) cc_final: 0.5437 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1636
  time to fit residues: 25.9999
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  : 0.406 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 15 optimal weight:    0.2980
   chunk 44 optimal weight:    0.1980
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 170 GLN ** 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 = 0.3963 r_free = 0.3963 target = 0.145078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.120784 restraints weight = 8772.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.124925 restraints weight = 5355.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.127883 restraints weight = 3664.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.7252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4130  Z= 0.255
  Angle     :  0.678   8.622   5628  Z= 0.345
  Chirality :  0.045   0.182    635
  Planarity :  0.005   0.046    722
  Dihedral  :  4.951  21.418    559
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.23 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  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:  0.03 (0.36), residues: 516
  helix: -1.09 (2.89), residues: 6
  sheet:  0.69 (0.35), residues: 200
  loop : -0.39 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E 161 
 HIS   0.006   0.001   HIS F  93 
 PHE   0.013   0.002   PHE E 173 
 TYR   0.020   0.002   TYR F 177 
 ARG   0.002   0.000   ARG F  24 

*********************** 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
  128 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7835 (mt0) cc_final: 0.6501 (tm-30)
REVERT: E   35 ASN cc_start: 0.8223 (m-40) cc_final: 0.7993 (m-40)
REVERT: E   55 ASP cc_start: 0.8304 (p0) cc_final: 0.7950 (p0)
REVERT: E   57 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6594 (mm-30)
REVERT: E   70 LEU cc_start: 0.8268 (mm) cc_final: 0.8041 (mt)
REVERT: E   85 SER cc_start: 0.8533 (m) cc_final: 0.8023 (t)
REVERT: E  106 TRP cc_start: 0.7410 (p90) cc_final: 0.6451 (p-90)
REVERT: E  112 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7621 (tp-100)
REVERT: E  142 MET cc_start: 0.7344 (tpt) cc_final: 0.6915 (tpp)
REVERT: F    4 LEU cc_start: 0.8697 (mt) cc_final: 0.8332 (mt)
REVERT: F   78 ASN cc_start: 0.7908 (m-40) cc_final: 0.7639 (m-40)
REVERT: F   79 ILE cc_start: 0.8309 (mm) cc_final: 0.7817 (mm)
REVERT: F   86 ASP cc_start: 0.7259 (m-30) cc_final: 0.7057 (m-30)
REVERT: F   92 CYS cc_start: 0.3125 (p) cc_final: 0.2698 (p)
REVERT: F   96 ARG cc_start: 0.8575 (tpt90) cc_final: 0.8006 (tpt90)
REVERT: F  109 GLU cc_start: 0.7414 (pp20) cc_final: 0.7059 (pp20)
REVERT: F  171 ASP cc_start: 0.7685 (m-30) cc_final: 0.7418 (m-30)
REVERT: B  535 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8031 (ttmt)
REVERT: B  559 PHE cc_start: 0.6491 (m-10) cc_final: 0.5914 (m-80)
REVERT: B  583 GLU cc_start: 0.7643 (pm20) cc_final: 0.6948 (pm20)
REVERT: B  584 ILE cc_start: 0.6827 (mm) cc_final: 0.5711 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1539
  time to fit residues: 24.5294
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  : 0.475 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0070
   chunk 39 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.2004

-------------------------------------------------------------------------------
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 ** 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 = 0.3982 r_free = 0.3982 target = 0.146610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.122903 restraints weight = 8590.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.126935 restraints weight = 5271.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.129782 restraints weight = 3625.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.7431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4130  Z= 0.202
  Angle     :  0.659   8.686   5628  Z= 0.334
  Chirality :  0.045   0.175    635
  Planarity :  0.005   0.047    722
  Dihedral  :  4.869  25.800    559
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.46 %
    Favored  : 95.35 %
  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: -0.12 (0.36), residues: 516
  helix: -0.75 (1.67), residues: 12
  sheet:  0.65 (0.35), residues: 200
  loop : -0.54 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E 161 
 HIS   0.004   0.001   HIS F  93 
 PHE   0.012   0.002   PHE E 173 
 TYR   0.021   0.002   TYR F 177 
 ARG   0.003   0.000   ARG F  24 

********************** 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
  127 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7785 (mt0) cc_final: 0.6499 (tm-30)
REVERT: E   70 LEU cc_start: 0.8190 (mm) cc_final: 0.7914 (mt)
REVERT: E  106 TRP cc_start: 0.7496 (p90) cc_final: 0.6622 (p-90)
REVERT: E  112 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7541 (tp-100)
REVERT: F    4 LEU cc_start: 0.8698 (mt) cc_final: 0.8048 (tp)
REVERT: F   78 ASN cc_start: 0.7936 (m-40) cc_final: 0.7681 (m-40)
REVERT: F   79 ILE cc_start: 0.8071 (mm) cc_final: 0.7608 (mm)
REVERT: F   92 CYS cc_start: 0.3105 (p) cc_final: 0.1904 (p)
REVERT: F   96 ARG cc_start: 0.8579 (tpt90) cc_final: 0.8052 (tpt90)
REVERT: F  109 GLU cc_start: 0.7456 (pp20) cc_final: 0.7082 (pp20)
REVERT: F  171 ASP cc_start: 0.7677 (m-30) cc_final: 0.7454 (m-30)
REVERT: F  179 MET cc_start: 0.6586 (tmm) cc_final: 0.6235 (tmm)
REVERT: B  535 LYS cc_start: 0.8860 (ttmt) cc_final: 0.7886 (ttmt)
REVERT: B  559 PHE cc_start: 0.6331 (m-10) cc_final: 0.5857 (m-80)
REVERT: B  583 GLU cc_start: 0.7634 (pm20) cc_final: 0.6960 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1558
  time to fit residues: 24.4243
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  : 0.402 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** E  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 203 ASN
** F 170 GLN ** 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 = 0.3981 r_free = 0.3981 target = 0.146247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.122345 restraints weight = 8632.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126372 restraints weight = 5275.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.129290 restraints weight = 3614.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.7594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4130  Z= 0.201
  Angle     :  0.643   7.724   5628  Z= 0.329
  Chirality :  0.044   0.158    635
  Planarity :  0.005   0.045    722
  Dihedral  :  4.894  25.601    559
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.04 %
    Favored  : 94.77 %
  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: -0.17 (0.36), residues: 516
  helix: -0.56 (1.74), residues: 12
  sheet:  0.55 (0.34), residues: 208
  loop : -0.55 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 161 
 HIS   0.004   0.001   HIS F  93 
 PHE   0.011   0.001   PHE E 173 
 TYR   0.015   0.002   TYR F 177 
 ARG   0.003   0.001   ARG F  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1627.88 seconds
wall clock time: 29 minutes 3.23 seconds (1743.23 seconds total)