Starting phenix.real_space_refine
on Tue Feb 11 03:28:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wd8_32434/02_2025/7wd8_32434.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wd8_32434/02_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_32434/02_2025/7wd8_32434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wd8_32434/02_2025/7wd8_32434.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wd8_32434/02_2025/7wd8_32434.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wd8_32434/02_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-5592/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: 2.93, per 1000 atoms: 0.73
  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 473.7 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: 0.56
  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: 1.10

  Time building geometry restraints manager: 1.07 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:             0.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.810
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.070
-------------------------------------------------------------------------------
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  : 0.470 
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: 0.2071
  time to fit residues: 51.6150
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  : 0.563 
-------------------------------------------------------------------------------
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 = 0.132482 restraints weight = 8394.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.136938 restraints weight = 5170.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.140206 restraints weight = 3550.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
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  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7321 (mt0) cc_final: 0.6190 (tm-30)
REVERT: E   65 LYS cc_start: 0.6434 (tttm) cc_final: 0.5780 (ttpp)
REVERT: E   82 GLN cc_start: 0.8199 (tt0) cc_final: 0.6715 (mp10)
REVERT: E  180 ASP cc_start: 0.7258 (m-30) cc_final: 0.6937 (m-30)
REVERT: F   79 ILE cc_start: 0.8212 (mm) cc_final: 0.7940 (mm)
REVERT: F   86 ASP cc_start: 0.7151 (m-30) cc_final: 0.6740 (m-30)
REVERT: F   92 CYS cc_start: 0.4157 (p) cc_final: 0.3667 (p)
REVERT: F   96 ARG cc_start: 0.8105 (tpt90) cc_final: 0.7869 (tpt90)
REVERT: F  106 THR cc_start: 0.7790 (t) cc_final: 0.7546 (t)
REVERT: F  199 GLU cc_start: 0.5043 (tm-30) cc_final: 0.4559 (mt-10)
REVERT: B  535 LYS cc_start: 0.8591 (ttmt) cc_final: 0.7958 (tttt)
REVERT: B  552 LEU cc_start: 0.9100 (mm) cc_final: 0.8865 (mm)
REVERT: B  559 PHE cc_start: 0.6478 (m-10) cc_final: 0.5779 (m-80)
REVERT: B  586 ASP cc_start: 0.7785 (t0) cc_final: 0.7579 (t0)
REVERT: B  587 ILE cc_start: 0.6989 (mm) cc_final: 0.6665 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1731
  time to fit residues: 31.7228
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  : 0.410 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   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:    0.5980
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.4097 r_free = 0.4097 target = 0.154575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.128853 restraints weight = 8555.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133434 restraints weight = 5321.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.136719 restraints weight = 3652.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.4946

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= 0.165
  Angle     :  0.585   7.742   5628  Z= 0.297
  Chirality :  0.044   0.159    635
  Planarity :  0.004   0.033    722
  Dihedral  :  4.548  27.602    559
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  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:  0.21 (0.35), residues: 516
  helix: -1.69 (1.14), residues: 18
  sheet:  1.07 (0.34), residues: 224
  loop : -0.52 (0.35), residues: 274

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   0.009   0.001   PHE E 153 
 TYR   0.009   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
  144 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.499 
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: 0.7516 (mt0) cc_final: 0.6313 (tm-30)
REVERT: E   63 LYS cc_start: 0.8088 (tttt) cc_final: 0.7577 (tppt)
REVERT: E   65 LYS cc_start: 0.6555 (tttm) cc_final: 0.5846 (ttpp)
REVERT: F   77 LEU cc_start: 0.8351 (tp) cc_final: 0.7875 (tp)
REVERT: F   79 ILE cc_start: 0.8156 (mm) cc_final: 0.7721 (mm)
REVERT: F   90 TYR cc_start: 0.7091 (m-10) cc_final: 0.6876 (m-10)
REVERT: F   96 ARG cc_start: 0.8315 (tpt90) cc_final: 0.7842 (tpt90)
REVERT: F  199 GLU cc_start: 0.4974 (tm-30) cc_final: 0.4419 (mt-10)
REVERT: B  535 LYS cc_start: 0.8472 (ttmt) cc_final: 0.7956 (tttt)
REVERT: B  552 LEU cc_start: 0.9054 (mm) cc_final: 0.8817 (mm)
REVERT: B  559 PHE cc_start: 0.6663 (m-10) cc_final: 0.6293 (m-80)
REVERT: B  583 GLU cc_start: 0.7478 (pm20) cc_final: 0.7137 (pm20)
REVERT: B  586 ASP cc_start: 0.7740 (t0) cc_final: 0.7532 (t0)
REVERT: B  588 THR cc_start: 0.8078 (m) cc_final: 0.7475 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1906
  time to fit residues: 32.7150
Evaluate side-chains
  112 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 18 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 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 = 0.4000 r_free = 0.4000 target = 0.147613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123373 restraints weight = 8562.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.127771 restraints weight = 5217.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.130862 restraints weight = 3547.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.5805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4130  Z= 0.231
  Angle     :  0.621   7.347   5628  Z= 0.316
  Chirality :  0.044   0.146    635
  Planarity :  0.005   0.052    722
  Dihedral  :  4.930  28.926    559
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  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:  0.39 (0.37), residues: 516
  helix: -1.79 (1.48), residues: 12
  sheet:  1.06 (0.35), residues: 211
  loop : -0.21 (0.36), residues: 293

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   0.013   0.002   PHE E 153 
 TYR   0.017   0.002   TYR F  53 
 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
  131 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.440 
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: 0.6416 (tm-30)
REVERT: E   63 LYS cc_start: 0.8338 (tttt) cc_final: 0.7880 (tppt)
REVERT: E   65 LYS cc_start: 0.6900 (tttm) cc_final: 0.6257 (ttpp)
REVERT: F    4 LEU cc_start: 0.8733 (mt) cc_final: 0.8384 (mt)
REVERT: F   79 ILE cc_start: 0.8372 (mm) cc_final: 0.7850 (mm)
REVERT: F   86 ASP cc_start: 0.6895 (m-30) cc_final: 0.6600 (m-30)
REVERT: F   92 CYS cc_start: 0.3375 (p) cc_final: 0.2923 (p)
REVERT: F   96 ARG cc_start: 0.8526 (tpt90) cc_final: 0.7954 (tpt90)
REVERT: F  170 GLN cc_start: 0.7180 (tt0) cc_final: 0.6803 (tt0)
REVERT: B  535 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8111 (tttt)
REVERT: B  559 PHE cc_start: 0.6564 (m-10) cc_final: 0.5907 (m-80)
REVERT: B  583 GLU cc_start: 0.7491 (pm20) cc_final: 0.6862 (pm20)
REVERT: B  586 ASP cc_start: 0.7512 (t0) cc_final: 0.7271 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1932
  time to fit residues: 30.3422
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  : 0.475 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 23 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.5982

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.149389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.124608 restraints weight = 8888.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.128967 restraints weight = 5397.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.132041 restraints weight = 3653.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.6074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4130  Z= 0.144
  Angle     :  0.570   7.266   5628  Z= 0.288
  Chirality :  0.044   0.161    635
  Planarity :  0.004   0.044    722
  Dihedral  :  4.509  27.646    559
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  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:  0.34 (0.36), residues: 516
  helix: -1.12 (1.23), residues: 18
  sheet:  1.31 (0.35), residues: 197
  loop : -0.43 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 195 
 HIS   0.002   0.001   HIS F  38 
 PHE   0.011   0.001   PHE E 153 
 TYR   0.010   0.001   TYR E 109 
 ARG   0.005   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
  136 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7699 (mt0) cc_final: 0.6364 (tm-30)
REVERT: E   58 THR cc_start: 0.8423 (p) cc_final: 0.8204 (t)
REVERT: E   63 LYS cc_start: 0.8293 (tttt) cc_final: 0.7776 (tppt)
REVERT: E   65 LYS cc_start: 0.6729 (tttm) cc_final: 0.6151 (ttpp)
REVERT: E  106 TRP cc_start: 0.7304 (p90) cc_final: 0.6892 (p90)
REVERT: F    4 LEU cc_start: 0.8687 (mt) cc_final: 0.8053 (tp)
REVERT: F   92 CYS cc_start: 0.3143 (p) cc_final: 0.1997 (p)
REVERT: F   96 ARG cc_start: 0.8339 (tpt90) cc_final: 0.7699 (tpt90)
REVERT: B  530 SER cc_start: 0.8359 (p) cc_final: 0.8042 (m)
REVERT: B  535 LYS cc_start: 0.8536 (ttmt) cc_final: 0.7681 (ttmt)
REVERT: B  536 ASN cc_start: 0.8933 (m-40) cc_final: 0.8685 (m-40)
REVERT: B  552 LEU cc_start: 0.8815 (mm) cc_final: 0.8587 (mm)
REVERT: B  559 PHE cc_start: 0.6350 (m-10) cc_final: 0.5766 (m-80)
REVERT: B  577 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7259 (mtm110)
REVERT: B  583 GLU cc_start: 0.7566 (pm20) cc_final: 0.7106 (pm20)
REVERT: B  586 ASP cc_start: 0.7609 (t0) cc_final: 0.7393 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1865
  time to fit residues: 30.6022
Evaluate side-chains
  108 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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  46 GLN
** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.140763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.117740 restraints weight = 8812.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.121617 restraints weight = 5492.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.124412 restraints weight = 3807.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.6927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4130  Z= 0.309
  Angle     :  0.714   8.569   5628  Z= 0.365
  Chirality :  0.046   0.137    635
  Planarity :  0.005   0.042    722
  Dihedral  :  5.529  25.560    559
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  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:  0.09 (0.36), residues: 516
  helix: -1.08 (3.05), residues: 6
  sheet:  0.83 (0.34), residues: 205
  loop : -0.45 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP E 110 
 HIS   0.007   0.002   HIS F  93 
 PHE   0.016   0.002   PHE E 173 
 TYR   0.021   0.002   TYR E 101 
 ARG   0.003   0.001   ARG F  65 

*********************** 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  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7555 (mt0) cc_final: 0.6315 (tm-30)
REVERT: E   55 ASP cc_start: 0.8497 (p0) cc_final: 0.8221 (p0)
REVERT: E   57 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6546 (mm-30)
REVERT: E   63 LYS cc_start: 0.8232 (tttt) cc_final: 0.7934 (tppt)
REVERT: E   99 LYS cc_start: 0.7979 (tttt) cc_final: 0.7630 (tttt)
REVERT: E  106 TRP cc_start: 0.7607 (p90) cc_final: 0.6797 (p-90)
REVERT: E  107 PHE cc_start: 0.8453 (m-10) cc_final: 0.7870 (m-80)
REVERT: F    4 LEU cc_start: 0.8677 (mt) cc_final: 0.8395 (mt)
REVERT: F   78 ASN cc_start: 0.8009 (m-40) cc_final: 0.7655 (m-40)
REVERT: F   79 ILE cc_start: 0.8300 (mm) cc_final: 0.7740 (mm)
REVERT: F   92 CYS cc_start: 0.3204 (p) cc_final: 0.2829 (p)
REVERT: F   96 ARG cc_start: 0.8539 (tpt90) cc_final: 0.8042 (tpt90)
REVERT: F  171 ASP cc_start: 0.7476 (m-30) cc_final: 0.7186 (m-30)
REVERT: B  535 LYS cc_start: 0.8673 (ttmt) cc_final: 0.7913 (ttmt)
REVERT: B  536 ASN cc_start: 0.9168 (m-40) cc_final: 0.8964 (m-40)
REVERT: B  552 LEU cc_start: 0.8776 (mm) cc_final: 0.8379 (mm)
REVERT: B  559 PHE cc_start: 0.6777 (m-10) cc_final: 0.6115 (m-80)
REVERT: B  565 PHE cc_start: 0.8182 (p90) cc_final: 0.7930 (p90)
REVERT: B  577 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7798 (mtm110)
REVERT: B  584 ILE cc_start: 0.7097 (mm) cc_final: 0.6400 (mm)
REVERT: B  586 ASP cc_start: 0.7353 (t0) cc_final: 0.7030 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1682
  time to fit residues: 27.2036
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  : 0.454 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0170
   chunk 26 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    9.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
F  46 GLN
** 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 = 0.3976 r_free = 0.3976 target = 0.146624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.122953 restraints weight = 8602.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.127179 restraints weight = 5210.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.130120 restraints weight = 3523.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.6978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4130  Z= 0.160
  Angle     :  0.600   7.509   5628  Z= 0.300
  Chirality :  0.044   0.147    635
  Planarity :  0.004   0.040    722
  Dihedral  :  4.794  27.972    559
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  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:  0.05 (0.35), residues: 516
  helix: -0.78 (1.71), residues: 12
  sheet:  0.89 (0.35), residues: 197
  loop : -0.49 (0.34), residues: 307

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   0.010   0.001   PHE E 153 
 TYR   0.010   0.001   TYR E 109 
 ARG   0.004   0.000   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
  137 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7688 (mt0) cc_final: 0.6355 (tm-30)
REVERT: E   63 LYS cc_start: 0.8154 (tttt) cc_final: 0.7682 (tppt)
REVERT: E   89 GLU cc_start: 0.7387 (pm20) cc_final: 0.7166 (tt0)
REVERT: E  107 PHE cc_start: 0.8314 (m-10) cc_final: 0.8080 (m-80)
REVERT: F    4 LEU cc_start: 0.8708 (mt) cc_final: 0.8010 (tp)
REVERT: F   77 LEU cc_start: 0.8139 (tp) cc_final: 0.7610 (tp)
REVERT: F   78 ASN cc_start: 0.7761 (m-40) cc_final: 0.7481 (m-40)
REVERT: F   79 ILE cc_start: 0.8200 (mm) cc_final: 0.7714 (mm)
REVERT: F   92 CYS cc_start: 0.3055 (p) cc_final: 0.1537 (p)
REVERT: F   96 ARG cc_start: 0.8468 (tpt90) cc_final: 0.7966 (tpt90)
REVERT: F  171 ASP cc_start: 0.7501 (m-30) cc_final: 0.7241 (m-30)
REVERT: B  530 SER cc_start: 0.8386 (p) cc_final: 0.8111 (m)
REVERT: B  535 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8218 (tttt)
REVERT: B  559 PHE cc_start: 0.6439 (m-10) cc_final: 0.5897 (m-80)
REVERT: B  586 ASP cc_start: 0.7448 (t0) cc_final: 0.7174 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1672
  time to fit residues: 27.9506
Evaluate side-chains
  108 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 18 optimal weight:    0.0770
   chunk 26 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0010
   chunk 44 optimal weight:    0.0000
   overall best weight:    0.3748

-------------------------------------------------------------------------------
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  46 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 = 0.4009 r_free = 0.4009 target = 0.148341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124890 restraints weight = 8397.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.128975 restraints weight = 5121.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.131749 restraints weight = 3485.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6672
moved from start:          0.7074

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= 0.165
  Angle     :  0.618  10.121   5628  Z= 0.306
  Chirality :  0.044   0.182    635
  Planarity :  0.004   0.042    722
  Dihedral  :  4.541  28.436    559
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.49 %
    Favored  : 96.32 %
  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:  0.22 (0.36), residues: 516
  helix: -0.44 (1.78), residues: 12
  sheet:  1.03 (0.37), residues: 190
  loop : -0.38 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E 161 
 HIS   0.002   0.001   HIS F  93 
 PHE   0.010   0.001   PHE E 153 
 TYR   0.016   0.001   TYR F  53 
 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
  128 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7780 (mt0) cc_final: 0.6352 (tm-30)
REVERT: E   63 LYS cc_start: 0.8045 (tttt) cc_final: 0.7588 (tppt)
REVERT: E   65 LYS cc_start: 0.6684 (tttm) cc_final: 0.6164 (ttpp)
REVERT: F    4 LEU cc_start: 0.8673 (mt) cc_final: 0.7927 (tp)
REVERT: F   77 LEU cc_start: 0.8172 (tp) cc_final: 0.7638 (tp)
REVERT: F   78 ASN cc_start: 0.7609 (m-40) cc_final: 0.7347 (m-40)
REVERT: F   79 ILE cc_start: 0.8164 (mm) cc_final: 0.7704 (mm)
REVERT: F   92 CYS cc_start: 0.3196 (p) cc_final: 0.1575 (p)
REVERT: F   96 ARG cc_start: 0.8310 (tpt90) cc_final: 0.7855 (tpt90)
REVERT: F  171 ASP cc_start: 0.7704 (m-30) cc_final: 0.7440 (m-30)
REVERT: B  535 LYS cc_start: 0.8693 (ttmt) cc_final: 0.7990 (ttmt)
REVERT: B  559 PHE cc_start: 0.6440 (m-10) cc_final: 0.5859 (m-80)
REVERT: B  584 ILE cc_start: 0.6653 (mm) cc_final: 0.5392 (mm)
REVERT: B  586 ASP cc_start: 0.7344 (t0) cc_final: 0.7115 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1519
  time to fit residues: 24.0789
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  : 0.355 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 43 optimal weight:    0.0570
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 44 optimal weight:    0.1980
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.0102

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

Flipped N/Q/H residues before XYZ refinement:
E   6 GLN
E 203 ASN
** F  46 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 = 0.3995 r_free = 0.3995 target = 0.147625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.124616 restraints weight = 8682.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.128639 restraints weight = 5237.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.131525 restraints weight = 3534.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.7231

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= 0.181
  Angle     :  0.590   7.580   5628  Z= 0.298
  Chirality :  0.044   0.150    635
  Planarity :  0.004   0.041    722
  Dihedral  :  4.603  26.297    559
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.46 %
    Favored  : 95.35 %
  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:  0.12 (0.36), residues: 516
  helix: -0.32 (1.78), residues: 12
  sheet:  0.87 (0.36), residues: 190
  loop : -0.39 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 161 
 HIS   0.004   0.001   HIS F  93 
 PHE   0.009   0.001   PHE E 153 
 TYR   0.017   0.002   TYR F 177 
 ARG   0.003   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
  129 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7744 (mt0) cc_final: 0.6437 (tm-30)
REVERT: E   55 ASP cc_start: 0.8146 (p0) cc_final: 0.7919 (p0)
REVERT: E   63 LYS cc_start: 0.8243 (tttt) cc_final: 0.7796 (tppt)
REVERT: E  141 SER cc_start: 0.8124 (m) cc_final: 0.7713 (p)
REVERT: F    4 LEU cc_start: 0.8684 (mt) cc_final: 0.7947 (tp)
REVERT: F   27 LYS cc_start: 0.8381 (tptt) cc_final: 0.7473 (mmmt)
REVERT: F   77 LEU cc_start: 0.8200 (tp) cc_final: 0.7675 (tp)
REVERT: F   78 ASN cc_start: 0.7587 (m-40) cc_final: 0.7325 (m-40)
REVERT: F   79 ILE cc_start: 0.8144 (mm) cc_final: 0.7673 (mm)
REVERT: F   92 CYS cc_start: 0.3100 (p) cc_final: 0.1611 (p)
REVERT: F   96 ARG cc_start: 0.8315 (tpt90) cc_final: 0.7866 (tpt90)
REVERT: F  171 ASP cc_start: 0.7710 (m-30) cc_final: 0.7463 (m-30)
REVERT: B  535 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8262 (tttt)
REVERT: B  559 PHE cc_start: 0.6387 (m-10) cc_final: 0.5843 (m-80)
REVERT: B  583 GLU cc_start: 0.7809 (pm20) cc_final: 0.7175 (pm20)
REVERT: B  584 ILE cc_start: 0.6622 (mm) cc_final: 0.5919 (mm)
REVERT: B  586 ASP cc_start: 0.7311 (t0) cc_final: 0.7105 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1688
  time to fit residues: 26.8629
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  : 0.573 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
E   6 GLN
** E  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 203 ASN
** F  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3960 r_free = 0.3960 target = 0.144379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.121395 restraints weight = 8620.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.125361 restraints weight = 5206.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.128202 restraints weight = 3525.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.7458

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= 0.224
  Angle     :  0.644   8.187   5628  Z= 0.326
  Chirality :  0.044   0.162    635
  Planarity :  0.005   0.048    722
  Dihedral  :  4.865  21.874    559
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.84 %
    Favored  : 94.96 %
  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 (0.36), residues: 516
  helix: -0.32 (1.80), residues: 12
  sheet:  0.59 (0.33), residues: 211
  loop : -0.42 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP E 161 
 HIS   0.005   0.001   HIS F  93 
 PHE   0.013   0.002   PHE E 173 
 TYR   0.034   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
  130 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    5 GLN cc_start: 0.7704 (mt0) cc_final: 0.6413 (tm-30)
REVERT: E   63 LYS cc_start: 0.8188 (tttt) cc_final: 0.7778 (tppt)
REVERT: E   85 SER cc_start: 0.8565 (m) cc_final: 0.8089 (t)
REVERT: E  112 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7421 (tp-100)
REVERT: E  141 SER cc_start: 0.8174 (m) cc_final: 0.7747 (p)
REVERT: F    4 LEU cc_start: 0.8692 (mt) cc_final: 0.8050 (tp)
REVERT: F   78 ASN cc_start: 0.7845 (m-40) cc_final: 0.7563 (m-40)
REVERT: F   79 ILE cc_start: 0.8076 (mm) cc_final: 0.7633 (mm)
REVERT: F   92 CYS cc_start: 0.3085 (p) cc_final: 0.1880 (p)
REVERT: F   96 ARG cc_start: 0.8500 (tpt90) cc_final: 0.8084 (tpt90)
REVERT: F  171 ASP cc_start: 0.7675 (m-30) cc_final: 0.7454 (m-30)
REVERT: F  179 MET cc_start: 0.6743 (tmm) cc_final: 0.6412 (tmm)
REVERT: B  529 LYS cc_start: 0.7354 (mmmt) cc_final: 0.7050 (mmmt)
REVERT: B  535 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8066 (ttmt)
REVERT: B  559 PHE cc_start: 0.6406 (m-10) cc_final: 0.5918 (m-80)
REVERT: B  583 GLU cc_start: 0.7676 (pm20) cc_final: 0.6988 (pm20)
REVERT: B  584 ILE cc_start: 0.6749 (mm) cc_final: 0.5586 (mm)
REVERT: B  586 ASP cc_start: 0.7347 (t0) cc_final: 0.7096 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1548
  time to fit residues: 25.0333
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  : 0.449 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0000
   chunk 42 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.0588

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

Flipped N/Q/H residues before XYZ refinement:
E   6 GLN
E  43 GLN
** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3986 r_free = 0.3986 target = 0.146795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.123666 restraints weight = 8694.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.127673 restraints weight = 5245.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.130383 restraints weight = 3550.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.7572

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= 0.178
  Angle     :  0.611   7.849   5628  Z= 0.308
  Chirality :  0.044   0.167    635
  Planarity :  0.005   0.042    722
  Dihedral  :  4.758  24.968    559
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.65 %
    Favored  : 95.16 %
  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: -0.11 (0.36), residues: 516
  helix: -0.65 (1.61), residues: 12
  sheet:  0.59 (0.33), residues: 211
  loop : -0.51 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 161 
 HIS   0.004   0.001   HIS F  93 
 PHE   0.012   0.001   PHE B 565 
 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: 1605.81 seconds
wall clock time: 29 minutes 40.77 seconds (1780.77 seconds total)