Starting phenix.real_space_refine
on Fri Aug 22 12:37:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iwm_35771/08_2025/8iwm_35771.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwm_35771/08_2025/8iwm_35771.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iwm_35771/08_2025/8iwm_35771.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwm_35771/08_2025/8iwm_35771.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwm_35771/08_2025/8iwm_35771.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwm_35771/08_2025/8iwm_35771.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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      14      5.16       5
     C    1323      2.51       5
     N     309      2.21       5
     O     334      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1980
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 1971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 1971
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 10, 'TRANS': 260}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 206
          Unresolved non-hydrogen angles: 269
          Unresolved non-hydrogen dihedrals: 186
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 7, 'TRP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 147
    Chain: "R"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'PEA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.79, per 1000 atoms: 0.40
  Number of scatterers: 1980
  At special positions: 0
  Unit cell: (60.256, 57.028, 79.624, 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      14     16.00
     O     334      8.00
     N     309      7.00
     C    1323      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 190 " 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: 0.18
  Conformation dependent library (CDL) restraints added in 136.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  516

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      88.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.04
  Creating SS restraints...
    Processing helix  chain 'R' and resid 37 through 59
      removed outlier: 4.501A  pdb=" N   ASN R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU R  52 " --> pdb=" O   PHE R  48 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   VAL R  53 " --> pdb=" O   GLY R  49 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE R  57 " --> pdb=" O   VAL R  53 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   LEU R  58 " --> pdb=" O   ILE R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 64
      removed outlier: 3.627A  pdb=" N   LEU R  63 " --> pdb=" O   PHE R  60 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   HIS R  64 " --> pdb=" O   LYS R  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 60 through 64'
    Processing helix  chain 'R' and resid 65 through 84
      removed outlier: 4.017A  pdb=" N   LEU R  70 " --> pdb=" O   PRO R  66 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL R  71 " --> pdb=" O   THR R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 84 through 96
      removed outlier: 4.214A  pdb=" N   PHE R  88 " --> pdb=" O   THR R  84 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL R  91 " --> pdb=" O   PRO R  87 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ARG R  92 " --> pdb=" O   PHE R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 116
      removed outlier: 4.517A  pdb=" N   CYS R 110 " --> pdb=" O   LYS R 106 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE R 111 " --> pdb=" O   PHE R 107 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP R 112 " --> pdb=" O   HIS R 108 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 117 through 136
      removed outlier: 3.826A  pdb=" N   PHE R 121 " --> pdb=" O   PHE R 117 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   HIS R 122 " --> pdb=" O   ALA R 118 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 144
    Processing helix  chain 'R' and resid 145 through 163
      removed outlier: 3.696A  pdb=" N   ILE R 153 " --> pdb=" O   SER R 149 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA R 154 " --> pdb=" O   GLY R 150 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   SER R 160 " --> pdb=" O   SER R 156 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL R 161 " --> pdb=" O   TRP R 157 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TYR R 163 " --> pdb=" O   PHE R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 164 through 169
      removed outlier: 3.810A  pdb=" N   TYR R 169 " --> pdb=" O   PHE R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 185
      removed outlier: 3.788A  pdb=" N   VAL R 182 " --> pdb=" O   GLU R 178 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA R 183 " --> pdb=" O   GLU R 179 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 195 through 232
      removed outlier: 3.805A  pdb=" N   LEU R 200 " --> pdb=" O   GLN R 196 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   LEU R 201 " --> pdb=" O   ASN R 197 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE R 206 " --> pdb=" O   CYS R 202 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU R 208 " --> pdb=" O   LEU R 204 " (cutoff:3.500A)
      Proline residue:  R 209  - end of helix
      removed outlier: 4.176A  pdb=" N   MET R 213 " --> pdb=" O   PRO R 209 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ILE R 220 " --> pdb=" O   LEU R 216 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA R 228 " --> pdb=" O   ALA R 224 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE R 231 " --> pdb=" O   GLN R 227 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLU R 232 " --> pdb=" O   ALA R 228 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 254 through 269
      removed outlier: 3.714A  pdb=" N   LYS R 258 " --> pdb=" O   ARG R 254 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   PHE R 267 " --> pdb=" O   ALA R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 280
      removed outlier: 4.008A  pdb=" N   TYR R 274 " --> pdb=" O   SER R 270 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE R 280 " --> pdb=" O   ILE R 276 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 283
      No H-bonds generated for 'chain 'R' and resid 281 through 283'
    Processing helix  chain 'R' and resid 289 through 292
    Processing helix  chain 'R' and resid 293 through 311
      removed outlier: 4.065A  pdb=" N   VAL R 300 " --> pdb=" O   LEU R 296 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR R 301 " --> pdb=" O   VAL R 297 " (cutoff:3.500A)
      Proline residue:  R 308  - end of helix
    Processing helix  chain 'R' and resid 315 through 323
      removed outlier: 3.686A  pdb=" N   ARG R 319 " --> pdb=" O   TYR R 315 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA R 321 " --> pdb=" O   TRP R 317 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 324 through 326
      No H-bonds generated for 'chain 'R' and resid 324 through 326'

    123 hydrogen bonds defined for protein.
    366 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.25

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 582
        1.34 -     1.46: 518
        1.46 -     1.58: 915
        1.58 -     1.70: 0
        1.70 -     1.81: 17
  Bond restraints: 2032
  Sorted by residual:
  bond pdb=" CA  ASN R 307 "
       pdb=" C   ASN R 307 "
    ideal  model  delta    sigma   weight residual
    1.524  1.545 -0.022 1.26e-02 6.30e+03 2.91e+00
  bond pdb=" N   PEA R 401 "
       pdb=" C1  PEA R 401 "
    ideal  model  delta    sigma   weight residual
    1.486  1.452  0.034 2.00e-02 2.50e+03 2.89e+00
  bond pdb=" CA  ASN R 195 "
       pdb=" C   ASN R 195 "
    ideal  model  delta    sigma   weight residual
    1.528  1.508  0.019 1.37e-02 5.33e+03 1.95e+00
  bond pdb=" CA  MET R 284 "
       pdb=" C   MET R 284 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.013 1.14e-02 7.69e+03 1.29e+00
  bond pdb=" C   TYR R 104 "
       pdb=" O   TYR R 104 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.15e-02 7.56e+03 1.24e+00
  ... (remaining 2027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 2687
        1.84 -     3.69: 82
        3.69 -     5.53: 10
        5.53 -     7.37: 4
        7.37 -     9.22: 1
  Bond angle restraints: 2784
  Sorted by residual:
  angle pdb=" N   ASP R 112 "
        pdb=" CA  ASP R 112 "
        pdb=" C   ASP R 112 "
      ideal   model   delta    sigma   weight residual
     111.03  105.07    5.96 1.11e+00 8.12e-01 2.88e+01
  angle pdb=" N   TYR R 301 "
        pdb=" CA  TYR R 301 "
        pdb=" C   TYR R 301 "
      ideal   model   delta    sigma   weight residual
     112.23  107.14    5.09 1.26e+00 6.30e-01 1.63e+01
  angle pdb=" N   ILE R  57 "
        pdb=" CA  ILE R  57 "
        pdb=" C   ILE R  57 "
      ideal   model   delta    sigma   weight residual
     111.62  108.60    3.02 7.90e-01 1.60e+00 1.46e+01
  angle pdb=" N   VAL R 182 "
        pdb=" CA  VAL R 182 "
        pdb=" C   VAL R 182 "
      ideal   model   delta    sigma   weight residual
     110.42  113.80   -3.38 9.60e-01 1.09e+00 1.24e+01
  angle pdb=" N   TYR R 302 "
        pdb=" CA  TYR R 302 "
        pdb=" C   TYR R 302 "
      ideal   model   delta    sigma   weight residual
     111.14  107.35    3.79 1.08e+00 8.57e-01 1.23e+01
  ... (remaining 2779 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.71: 957
       11.71 -    23.43: 112
       23.43 -    35.14: 62
       35.14 -    46.86: 21
       46.86 -    58.57: 6
  Dihedral angle restraints: 1158
    sinusoidal: 360
      harmonic: 798
  Sorted by residual:
  dihedral pdb=" CA  PHE R 115 "
           pdb=" C   PHE R 115 "
           pdb=" N   CYS R 116 "
           pdb=" CA  CYS R 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.73   22.27     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  LEU R 205 "
           pdb=" C   LEU R 205 "
           pdb=" N   PHE R 206 "
           pdb=" CA  PHE R 206 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.28   19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CB  CYS R 105 "
           pdb=" SG  CYS R 105 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  124.40  -31.40     1      1.00e+01 1.00e-02 1.41e+01
  ... (remaining 1155 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 164
       0.026 -    0.052: 105
       0.052 -    0.077: 49
       0.077 -    0.103: 18
       0.103 -    0.129: 7
  Chirality restraints: 343
  Sorted by residual:
  chirality pdb=" CA  PHE R 115 "
            pdb=" N   PHE R 115 "
            pdb=" C   PHE R 115 "
            pdb=" CB  PHE R 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  ASP R 112 "
            pdb=" N   ASP R 112 "
            pdb=" C   ASP R 112 "
            pdb=" CB  ASP R 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  VAL R 292 "
            pdb=" N   VAL R 292 "
            pdb=" C   VAL R 292 "
            pdb=" CB  VAL R 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 340 not shown)

  Planarity restraints: 338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 307 "    0.032 5.00e-02 4.00e+02   4.77e-02 3.65e+00
        pdb=" N   PRO R 308 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO R 308 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 308 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 192 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.07e+00
        pdb=" C   ALA R 192 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ALA R 192 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PRO R 193 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 140 "    0.008 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   TYR R 140 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   TYR R 140 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PRO R 141 "    0.010 2.00e-02 2.50e+03
  ... (remaining 335 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 835
        2.89 -     3.39: 1996
        3.39 -     3.90: 3109
        3.90 -     4.40: 3574
        4.40 -     4.90: 5679
  Nonbonded interactions: 15193
  Sorted by model distance:
  nonbonded pdb=" N   GLU R 232 "
            pdb=" OE1 GLU R 232 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" OG  SER R 114 "
            pdb=" N   PHE R 115 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" O   MET R  86 "
            pdb=" OG1 THR R  90 "
     model   vdw
     2.424 3.040
  nonbonded pdb=" O   SER R 166 "
            pdb=" OG  SER R 166 "
     model   vdw
     2.462 3.040
  nonbonded pdb=" O   VAL R 181 "
            pdb=" OG1 THR R 185 "
     model   vdw
     2.464 3.040
  ... (remaining 15188 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.350
  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:          0.020
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.790
  Find NCS groups from input model:        0.000
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2033  Z= 0.230
  Angle     :  0.760   9.218   2786  Z= 0.457
  Chirality :  0.043   0.129    343
  Planarity :  0.005   0.048    338
  Dihedral  : 14.982  58.570    639
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 28.42 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.66 (0.49), residues: 267
  helix: -1.82 (0.35), residues: 204
  sheet:  None (None), residues: 0
  loop : -0.73 (0.76), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG R 219 
 TYR   0.006   0.001   TYR R 140 
 PHE   0.026   0.002   PHE R 159 
 TRP   0.006   0.001   TRP R 157 
 HIS   0.002   0.001   HIS R 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 2032)
  covalent geometry    : angle       0.76008 ( 2784)
  SS BOND              : bond        0.00052 (    1)
  SS BOND              : angle       0.46411 (    2)
  hydrogen bonds       : bond        0.24934 (  123)
  hydrogen bonds       : angle       8.63676 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.044 
Fit side-chains
REVERT: R   92 ARG cc_start: 0.8321 (tmm-80) cc_final: 0.7891 (ttp-170)
REVERT: R  127 SER cc_start: 0.8784 (m) cc_final: 0.8536 (p)
REVERT: R  225 LYS cc_start: 0.8281 (tptp) cc_final: 0.7825 (ttpt)
REVERT: R  307 ASN cc_start: 0.7756 (t0) cc_final: 0.7547 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0334
  time to fit residues: 2.6237
Evaluate side-chains
  52 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   57 ILE
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  204 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0370
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
R 307 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.137954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.121858 restraints weight = 3277.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 2.05
r_work: 0.3580 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2033  Z= 0.125
  Angle     :  0.580   8.542   2786  Z= 0.294
  Chirality :  0.037   0.126    343
  Planarity :  0.004   0.034    338
  Dihedral  :  6.535  52.681    299
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 30.53 %
    Favored  : 62.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.50), residues: 267
  helix: -0.75 (0.37), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.56 (0.69), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG R 130 
 TYR   0.008   0.001   TYR R 163 
 PHE   0.016   0.001   PHE R 144 
 TRP   0.004   0.001   TRP R 298 
 HIS   0.002   0.001   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 2032)
  covalent geometry    : angle       0.58009 ( 2784)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       0.30273 (    2)
  hydrogen bonds       : bond        0.04258 (  123)
  hydrogen bonds       : angle       5.09346 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.080 
Fit side-chains
REVERT: R  106 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8108 (ttmt)
REVERT: R  225 LYS cc_start: 0.8156 (tptp) cc_final: 0.7794 (ttpt)
REVERT: R  322 ILE cc_start: 0.8017 (tt) cc_final: 0.7804 (tt)
  outliers start: 14
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0395
  time to fit residues: 2.8168
Evaluate side-chains
  54 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  106 LYS
Chi-restraints excluded: chain R residue  107 PHE
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  275 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 23 optimal weight:    0.1980
   chunk 6 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** R 307 ASN ** 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 = 0.3862 r_free = 0.3862 target = 0.137078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.121415 restraints weight = 3281.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.08
r_work: 0.3554 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2033  Z= 0.118
  Angle     :  0.560   8.300   2786  Z= 0.281
  Chirality :  0.038   0.127    343
  Planarity :  0.004   0.024    338
  Dihedral  :  5.213  49.724    290
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 32.63 %
    Favored  : 61.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.53), residues: 267
  helix: -0.06 (0.40), residues: 192
  sheet:  None (None), residues: 0
  loop : -1.66 (0.68), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG R 219 
 TYR   0.006   0.001   TYR R 163 
 PHE   0.020   0.001   PHE R 115 
 TRP   0.005   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 2032)
  covalent geometry    : angle       0.55976 ( 2784)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       0.20736 (    2)
  hydrogen bonds       : bond        0.04098 (  123)
  hydrogen bonds       : angle       4.74671 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.091 
Fit side-chains
REVERT: R  106 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8097 (ttmt)
REVERT: R  225 LYS cc_start: 0.8212 (tptp) cc_final: 0.7822 (ttpt)
REVERT: R  322 ILE cc_start: 0.8052 (tt) cc_final: 0.7812 (tt)
  outliers start: 12
  outliers final: 8
  residues processed: 54
  average time/residue: 0.0388
  time to fit residues: 2.6413
Evaluate side-chains
  55 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  106 LYS
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  124 CYS
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  306 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 25 optimal weight:    0.0060
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
** R 307 ASN ** 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 = 0.3863 r_free = 0.3863 target = 0.137233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.121749 restraints weight = 3222.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.06
r_work: 0.3548 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2033  Z= 0.113
  Angle     :  0.530   6.319   2786  Z= 0.267
  Chirality :  0.037   0.126    343
  Planarity :  0.003   0.022    338
  Dihedral  :  5.056  49.523    290
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 32.63 %
    Favored  : 62.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.53), residues: 267
  helix:  0.18 (0.40), residues: 193
  sheet:  None (None), residues: 0
  loop : -1.75 (0.69), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG R 219 
 TYR   0.006   0.001   TYR R 163 
 PHE   0.018   0.001   PHE R 115 
 TRP   0.006   0.001   TRP R 317 
 HIS   0.002   0.000   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2032)
  covalent geometry    : angle       0.53058 ( 2784)
  SS BOND              : bond        0.00236 (    1)
  SS BOND              : angle       0.23364 (    2)
  hydrogen bonds       : bond        0.03661 (  123)
  hydrogen bonds       : angle       4.51967 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.077 
Fit side-chains
REVERT: R  106 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8128 (ttmt)
REVERT: R  169 TYR cc_start: 0.8964 (m-80) cc_final: 0.8588 (m-80)
REVERT: R  225 LYS cc_start: 0.8190 (tptp) cc_final: 0.7703 (ttpt)
  outliers start: 10
  outliers final: 8
  residues processed: 53
  average time/residue: 0.0386
  time to fit residues: 2.5599
Evaluate side-chains
  55 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  106 LYS
Chi-restraints excluded: chain R residue  107 PHE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  306 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0040
   chunk 15 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** R 307 ASN ** 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 = 0.3866 r_free = 0.3866 target = 0.137424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.122112 restraints weight = 3231.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.06
r_work: 0.3576 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2033  Z= 0.111
  Angle     :  0.517   5.637   2786  Z= 0.264
  Chirality :  0.037   0.118    343
  Planarity :  0.003   0.024    338
  Dihedral  :  4.930  48.831    290
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 33.68 %
    Favored  : 60.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.53), residues: 267
  helix:  0.34 (0.40), residues: 193
  sheet:  None (None), residues: 0
  loop : -1.75 (0.69), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 219 
 TYR   0.007   0.001   TYR R 274 
 PHE   0.018   0.001   PHE R 115 
 TRP   0.006   0.001   TRP R 317 
 HIS   0.002   0.000   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 2032)
  covalent geometry    : angle       0.51751 ( 2784)
  SS BOND              : bond        0.00224 (    1)
  SS BOND              : angle       0.33107 (    2)
  hydrogen bonds       : bond        0.03614 (  123)
  hydrogen bonds       : angle       4.46391 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.083 
Fit side-chains
REVERT: R  106 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8145 (ttmt)
REVERT: R  225 LYS cc_start: 0.8209 (tptp) cc_final: 0.7730 (ttpt)
  outliers start: 11
  outliers final: 10
  residues processed: 53
  average time/residue: 0.0522
  time to fit residues: 3.3231
Evaluate side-chains
  54 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue   91 VAL
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  107 PHE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  124 CYS
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0770
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** R 307 ASN ** 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 = 0.3865 r_free = 0.3865 target = 0.137341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.122128 restraints weight = 3224.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.06
r_work: 0.3575 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2033  Z= 0.111
  Angle     :  0.521   5.148   2786  Z= 0.264
  Chirality :  0.037   0.118    343
  Planarity :  0.003   0.024    338
  Dihedral  :  4.878  48.497    290
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 33.16 %
    Favored  : 60.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.54), residues: 267
  helix:  0.56 (0.40), residues: 193
  sheet:  None (None), residues: 0
  loop : -1.73 (0.70), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 219 
 TYR   0.007   0.001   TYR R 274 
 PHE   0.019   0.001   PHE R 115 
 TRP   0.007   0.001   TRP R 317 
 HIS   0.002   0.000   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 2032)
  covalent geometry    : angle       0.52097 ( 2784)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       0.24986 (    2)
  hydrogen bonds       : bond        0.03615 (  123)
  hydrogen bonds       : angle       4.45171 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.078 
Fit side-chains
REVERT: R  106 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8071 (ttmt)
REVERT: R  169 TYR cc_start: 0.8892 (m-80) cc_final: 0.8527 (m-80)
REVERT: R  225 LYS cc_start: 0.8218 (tptp) cc_final: 0.7769 (ttpt)
  outliers start: 12
  outliers final: 10
  residues processed: 51
  average time/residue: 0.0389
  time to fit residues: 2.5137
Evaluate side-chains
  54 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  106 LYS
Chi-restraints excluded: chain R residue  107 PHE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  124 CYS
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  306 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 307 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.136809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.121880 restraints weight = 3240.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.06
r_work: 0.3574 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2033  Z= 0.112
  Angle     :  0.525   5.336   2786  Z= 0.267
  Chirality :  0.037   0.118    343
  Planarity :  0.003   0.027    338
  Dihedral  :  4.869  48.195    290
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 34.21 %
    Favored  : 59.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.53), residues: 267
  helix:  0.68 (0.40), residues: 192
  sheet:  None (None), residues: 0
  loop : -1.84 (0.69), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 219 
 TYR   0.007   0.001   TYR R 274 
 PHE   0.019   0.001   PHE R 115 
 TRP   0.008   0.001   TRP R 317 
 HIS   0.002   0.000   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 2032)
  covalent geometry    : angle       0.52427 ( 2784)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       1.09528 (    2)
  hydrogen bonds       : bond        0.03571 (  123)
  hydrogen bonds       : angle       4.42723 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.078 
Fit side-chains
REVERT: R  106 LYS cc_start: 0.8340 (mmmm) cc_final: 0.8111 (ttmt)
REVERT: R  169 TYR cc_start: 0.8962 (m-80) cc_final: 0.8582 (m-80)
REVERT: R  225 LYS cc_start: 0.8224 (tptp) cc_final: 0.7766 (ttpt)
  outliers start: 12
  outliers final: 10
  residues processed: 50
  average time/residue: 0.0433
  time to fit residues: 2.6935
Evaluate side-chains
  54 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  107 PHE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  124 CYS
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  306 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0000
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0980
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.138663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.124014 restraints weight = 3203.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 2.08
r_work: 0.3583 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2033  Z= 0.105
  Angle     :  0.520   5.507   2786  Z= 0.264
  Chirality :  0.037   0.114    343
  Planarity :  0.003   0.028    338
  Dihedral  :  4.762  47.830    290
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 35.26 %
    Favored  : 58.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.53), residues: 267
  helix:  0.82 (0.40), residues: 192
  sheet:  None (None), residues: 0
  loop : -1.83 (0.69), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R  92 
 TYR   0.006   0.001   TYR R 274 
 PHE   0.019   0.001   PHE R 115 
 TRP   0.008   0.001   TRP R 317 
 HIS   0.002   0.000   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 2032)
  covalent geometry    : angle       0.51969 ( 2784)
  SS BOND              : bond        0.00243 (    1)
  SS BOND              : angle       0.94050 (    2)
  hydrogen bonds       : bond        0.03376 (  123)
  hydrogen bonds       : angle       4.35032 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.077 
Fit side-chains
REVERT: R  106 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8084 (ttmt)
REVERT: R  129 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8620 (t0)
REVERT: R  169 TYR cc_start: 0.8888 (m-80) cc_final: 0.8560 (m-80)
REVERT: R  225 LYS cc_start: 0.8228 (tptp) cc_final: 0.7791 (ttpt)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0390
  time to fit residues: 2.4570
Evaluate side-chains
  53 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  107 PHE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  124 CYS
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 19 optimal weight:    0.4980
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0040
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** R 307 ASN ** 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 = 0.3882 r_free = 0.3882 target = 0.139141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.124301 restraints weight = 3146.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.07
r_work: 0.3591 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2033  Z= 0.106
  Angle     :  0.523   5.975   2786  Z= 0.266
  Chirality :  0.037   0.114    343
  Planarity :  0.003   0.028    338
  Dihedral  :  4.707  47.361    290
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 35.79 %
    Favored  : 58.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.54), residues: 267
  helix:  0.94 (0.39), residues: 192
  sheet:  None (None), residues: 0
  loop : -1.86 (0.70), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 219 
 TYR   0.006   0.001   TYR R 274 
 PHE   0.019   0.001   PHE R 115 
 TRP   0.009   0.001   TRP R 317 
 HIS   0.002   0.000   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 2032)
  covalent geometry    : angle       0.52248 ( 2784)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.70423 (    2)
  hydrogen bonds       : bond        0.03318 (  123)
  hydrogen bonds       : angle       4.31778 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.076 
Fit side-chains
REVERT: R  106 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8080 (ttmt)
REVERT: R  129 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8555 (t0)
REVERT: R  169 TYR cc_start: 0.8889 (m-80) cc_final: 0.8640 (m-80)
REVERT: R  225 LYS cc_start: 0.8215 (tptp) cc_final: 0.7782 (ttpt)
  outliers start: 10
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0345
  time to fit residues: 2.1637
Evaluate side-chains
  53 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  107 PHE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  124 CYS
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** R 307 ASN ** 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 = 0.3864 r_free = 0.3864 target = 0.137676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.122851 restraints weight = 3182.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.02
r_work: 0.3577 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2033  Z= 0.113
  Angle     :  0.563   8.938   2786  Z= 0.276
  Chirality :  0.037   0.117    343
  Planarity :  0.003   0.029    338
  Dihedral  :  4.771  47.401    290
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 35.26 %
    Favored  : 59.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.53), residues: 267
  helix:  0.93 (0.39), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.98 (0.70), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 219 
 TYR   0.006   0.001   TYR R 274 
 PHE   0.020   0.001   PHE R 115 
 TRP   0.009   0.001   TRP R 317 
 HIS   0.002   0.001   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2032)
  covalent geometry    : angle       0.56312 ( 2784)
  SS BOND              : bond        0.00199 (    1)
  SS BOND              : angle       0.73062 (    2)
  hydrogen bonds       : bond        0.03530 (  123)
  hydrogen bonds       : angle       4.36061 (  366)

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

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

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  534 Ramachandran restraints generated.
    267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.091 
Fit side-chains
REVERT: R  169 TYR cc_start: 0.8924 (m-80) cc_final: 0.8676 (m-80)
REVERT: R  225 LYS cc_start: 0.8231 (tptp) cc_final: 0.7789 (ttpt)
  outliers start: 10
  outliers final: 10
  residues processed: 51
  average time/residue: 0.0403
  time to fit residues: 2.6045
Evaluate side-chains
  55 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue  105 CYS
Chi-restraints excluded: chain R residue  107 PHE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  124 CYS
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0020
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9792

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

Flipped N/Q/H residues before XYZ refinement:
** R 307 ASN ** 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 = 0.3833 r_free = 0.3833 target = 0.135078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.120280 restraints weight = 3270.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.04
r_work: 0.3532 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3425 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2033  Z= 0.131
  Angle     :  0.575   6.928   2786  Z= 0.288
  Chirality :  0.038   0.124    343
  Planarity :  0.004   0.030    338
  Dihedral  :  4.985  48.402    290
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 34.21 %
    Favored  : 60.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.53), residues: 267
  helix:  0.77 (0.39), residues: 198
  sheet:  None (None), residues: 0
  loop : -2.18 (0.68), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R  92 
 TYR   0.008   0.001   TYR R 274 
 PHE   0.022   0.001   PHE R 115 
 TRP   0.008   0.001   TRP R 317 
 HIS   0.002   0.001   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 2032)
  covalent geometry    : angle       0.57476 ( 2784)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.91342 (    2)
  hydrogen bonds       : bond        0.03985 (  123)
  hydrogen bonds       : angle       4.54042 (  366)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 827.86 seconds
wall clock time: 15 minutes 4.01 seconds (904.01 seconds total)