Starting phenix.real_space_refine
on Fri May  9 15:09:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xwm_38738/05_2025/8xwm_38738.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xwm_38738/05_2025/8xwm_38738.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xwm_38738/05_2025/8xwm_38738.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xwm_38738/05_2025/8xwm_38738.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xwm_38738/05_2025/8xwm_38738.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xwm_38738/05_2025/8xwm_38738.cif"
  }
  resolution = 3.71
  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=   1.000
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      20      5.16       5
     C    1787      2.51       5
     N     461      2.21       5
     O     454      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2722
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 414
          Classifications: {'peptide': 65}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 97
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2308
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 9, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 30
  Time building chain proxies: 2.45, per 1000 atoms: 0.90
  Number of scatterers: 2722
  At special positions: 0
  Unit cell: (61.2125, 72.625, 93.375, 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      20     16.00
     O     454      8.00
     N     461      7.00
     C    1787      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  12 " - pdb=" SG  CYS D  38 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  14 " - pdb=" SG  CYS D  54 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  39 " - pdb=" SG  CYS R 286 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 119 " - pdb=" SG  CYS R 196 " 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: 0.76
  Conformation dependent library (CDL) restraints added in 353.2 milliseconds
  

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  694

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 2 sheets defined
      70.0% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'D' and resid 22 through 24
      No H-bonds generated for 'chain 'D' and resid 22 through 24'
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'R' and resid 44 through 76
      removed outlier: 3.585A  pdb=" N   LYS R  48 " --> pdb=" O   LEU R  44 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   SER R  76 " --> pdb=" O   VAL R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 111
      Proline residue:  R 102  - end of helix
    Processing helix  chain 'R' and resid 115 through 149
    Processing helix  chain 'R' and resid 153 through 160
      removed outlier: 3.898A  pdb=" N   THR R 156 " --> pdb=" O   ARG R 153 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   TYR R 160 " --> pdb=" O   GLN R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 183
      Proline residue:  R 179  - end of helix
    Processing helix  chain 'R' and resid 203 through 213
      removed outlier: 3.516A  pdb=" N   TRP R 207 " --> pdb=" O   ASN R 203 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   MET R 209 " --> pdb=" O   ALA R 205 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE R 213 " --> pdb=" O   MET R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 220 through 240
    Processing helix  chain 'R' and resid 245 through 279
      removed outlier: 3.915A  pdb=" N   ALA R 249 " --> pdb=" O   GLN R 245 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 285 through 304
      removed outlier: 3.578A  pdb=" N   ASP R 297 " --> pdb=" O   ASP R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 315
      Proline residue:  R 311  - end of helix
    Processing helix  chain 'R' and resid 318 through 329
      removed outlier: 3.617A  pdb=" N   ARG R 322 " --> pdb=" O   GLY R 318 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 26 through 32
      removed outlier: 4.200A  pdb=" N   VAL D  43 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187
      removed outlier: 3.794A  pdb=" N   ALA R 195 " --> pdb=" O   VAL R 187 " (cutoff:3.500A)

    194 hydrogen bonds defined for protein.
    570 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: 0.73

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 783
        1.33 -     1.46: 519
        1.46 -     1.58: 1451
        1.58 -     1.70: 0
        1.70 -     1.83: 27
  Bond restraints: 2780
  Sorted by residual:
  bond pdb=" CA  ILE D  66 "
       pdb=" CB  ILE D  66 "
    ideal  model  delta    sigma   weight residual
    1.540  1.522  0.019 1.25e-02 6.40e+03 2.21e+00
  bond pdb=" CA  ILE D  26 "
       pdb=" CB  ILE D  26 "
    ideal  model  delta    sigma   weight residual
    1.537  1.521  0.016 1.25e-02 6.40e+03 1.64e+00
  bond pdb=" CA  VAL D  43 "
       pdb=" CB  VAL D  43 "
    ideal  model  delta    sigma   weight residual
    1.537  1.521  0.016 1.26e-02 6.30e+03 1.62e+00
  bond pdb=" C   ALA D   5 "
       pdb=" O   ALA D   5 "
    ideal  model  delta    sigma   weight residual
    1.231  1.212  0.019 2.00e-02 2.50e+03 9.32e-01
  bond pdb=" N   ALA D   5 "
       pdb=" CA  ALA D   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.476 -0.018 1.90e-02 2.77e+03 9.26e-01
  ... (remaining 2775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 3553
        0.95 -     1.90: 200
        1.90 -     2.85: 26
        2.85 -     3.80: 13
        3.80 -     4.75: 9
  Bond angle restraints: 3801
  Sorted by residual:
  angle pdb=" C   ALA D   5 "
        pdb=" N   VAL D   6 "
        pdb=" CA  VAL D   6 "
      ideal   model   delta    sigma   weight residual
     122.75  118.66    4.09 1.45e+00 4.76e-01 7.98e+00
  angle pdb=" CA  VAL R 222 "
        pdb=" C   VAL R 222 "
        pdb=" N   PRO R 223 "
      ideal   model   delta    sigma   weight residual
     120.83  119.35    1.48 6.10e-01 2.69e+00 5.89e+00
  angle pdb=" CA  ALA D   5 "
        pdb=" C   ALA D   5 "
        pdb=" O   ALA D   5 "
      ideal   model   delta    sigma   weight residual
     120.80  117.01    3.79 1.70e+00 3.46e-01 4.98e+00
  angle pdb=" N   VAL R 222 "
        pdb=" CA  VAL R 222 "
        pdb=" C   VAL R 222 "
      ideal   model   delta    sigma   weight residual
     112.35  109.75    2.60 1.20e+00 6.94e-01 4.70e+00
  angle pdb=" C   VAL R 222 "
        pdb=" CA  VAL R 222 "
        pdb=" CB  VAL R 222 "
      ideal   model   delta    sigma   weight residual
     114.00  111.49    2.51 1.31e+00 5.83e-01 3.68e+00
  ... (remaining 3796 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 1489
       17.99 -    35.99: 136
       35.99 -    53.98: 20
       53.98 -    71.97: 5
       71.97 -    89.97: 2
  Dihedral angle restraints: 1652
    sinusoidal: 586
      harmonic: 1066
  Sorted by residual:
  dihedral pdb=" CB  CYS R 119 "
           pdb=" SG  CYS R 119 "
           pdb=" SG  CYS R 196 "
           pdb=" CB  CYS R 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   65.65   27.35     1      1.00e+01 1.00e-02 1.07e+01
  dihedral pdb=" CA  LEU R 182 "
           pdb=" C   LEU R 182 "
           pdb=" N   PHE R 183 "
           pdb=" CA  PHE R 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.42  -15.58     0      5.00e+00 4.00e-02 9.71e+00
  dihedral pdb=" CA  ARG R 153 "
           pdb=" CB  ARG R 153 "
           pdb=" CG  ARG R 153 "
           pdb=" CD  ARG R 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.73   56.73     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 1649 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 266
       0.025 -    0.051: 127
       0.051 -    0.076: 55
       0.076 -    0.101: 19
       0.101 -    0.127: 8
  Chirality restraints: 475
  Sorted by residual:
  chirality pdb=" CA  ILE R 282 "
            pdb=" N   ILE R 282 "
            pdb=" C   ILE R 282 "
            pdb=" CB  ILE R 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.01e-01
  chirality pdb=" CA  ALA D   5 "
            pdb=" N   ALA D   5 "
            pdb=" C   ALA D   5 "
            pdb=" CB  ALA D   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.61   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  VAL D  21 "
            pdb=" N   VAL D  21 "
            pdb=" C   VAL D  21 "
            pdb=" CB  VAL D  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  ... (remaining 472 not shown)

  Planarity restraints: 467
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D   5 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.14e+00
        pdb=" C   ALA D   5 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ALA D   5 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL D   6 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 178 "    0.016 5.00e-02 4.00e+02   2.35e-02 8.81e-01
        pdb=" N   PRO R 179 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO R 179 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 179 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 119 "    0.004 2.00e-02 2.50e+03   7.20e-03 5.19e-01
        pdb=" C   CYS R 119 "   -0.012 2.00e-02 2.50e+03
        pdb=" O   CYS R 119 "    0.005 2.00e-02 2.50e+03
        pdb=" N   LYS R 120 "    0.004 2.00e-02 2.50e+03
  ... (remaining 464 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 502
        2.77 -     3.30: 2718
        3.30 -     3.83: 4376
        3.83 -     4.37: 4544
        4.37 -     4.90: 8397
  Nonbonded interactions: 20537
  Sorted by model distance:
  nonbonded pdb=" O   ALA D   5 "
            pdb=" OG  SER R 193 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   ILE R 213 "
            pdb=" OG  SER R 217 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLY R 201 "
            pdb=" OG1 THR R 204 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OE1 GLU R 198 "
            pdb=" NE  ARG R 208 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" O   CYS D  12 "
            pdb=" NH2 ARG R 289 "
     model   vdw
     2.492 3.120
  ... (remaining 20532 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:             0.580
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     11.980
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
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      :  0.003   0.028   2784  Z= 0.171
  Angle     :  0.557   4.754   3809  Z= 0.324
  Chirality :  0.038   0.127    475
  Planarity :  0.003   0.024    467
  Dihedral  : 14.008  89.967    946
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.11 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.46), residues: 359
  helix:  2.12 (0.35), residues: 238
  sheet:  0.27 (1.03), residues: 31
  loop : -1.35 (0.61), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 112 
 HIS   0.001   0.000   HIS R 150 
 PHE   0.008   0.001   PHE R 233 
 TYR   0.004   0.001   TYR R 231 
 ARG   0.003   0.000   ARG R 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13011 (  194)
  hydrogen bonds       : angle       5.67069 (  570)
  SS BOND              : bond        0.00203 (    4)
  SS BOND              : angle       1.44623 (    8)
  covalent geometry    : bond        0.00312 ( 2780)
  covalent geometry    : angle       0.55324 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.298 
Fit side-chains
REVERT: D    9 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8163 (mm-30)
REVERT: D   53 VAL cc_start: 0.8605 (m) cc_final: 0.8202 (m)
REVERT: R  141 SER cc_start: 0.9067 (t) cc_final: 0.8603 (p)
REVERT: R  188 TYR cc_start: 0.8462 (m-80) cc_final: 0.8199 (m-10)
REVERT: R  245 GLN cc_start: 0.8201 (mp10) cc_final: 0.7898 (tt0)
REVERT: R  267 TYR cc_start: 0.8266 (t80) cc_final: 0.7526 (t80)
REVERT: R  277 MET cc_start: 0.8803 (ttp) cc_final: 0.8504 (ttm)
REVERT: R  319 GLN cc_start: 0.8430 (tt0) cc_final: 0.7692 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0969
  time to fit residues: 12.0085
Evaluate side-chains
  73 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
R  66 ASN
R  89 ASN
R 129 ASN
R 202 ASN
R 203 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.116840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.092969 restraints weight = 6360.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.094884 restraints weight = 3588.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.095915 restraints weight = 2581.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   2784  Z= 0.239
  Angle     :  0.657   7.598   3809  Z= 0.332
  Chirality :  0.044   0.123    475
  Planarity :  0.005   0.052    467
  Dihedral  :  3.970  14.879    391
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 14.44 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.45), residues: 359
  helix:  1.95 (0.34), residues: 239
  sheet:  0.22 (1.00), residues: 31
  loop : -1.63 (0.62), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 112 
 HIS   0.002   0.001   HIS R 323 
 PHE   0.014   0.002   PHE R 114 
 TYR   0.014   0.001   TYR R 197 
 ARG   0.003   0.001   ARG R 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05758 (  194)
  hydrogen bonds       : angle       4.70915 (  570)
  SS BOND              : bond        0.00651 (    4)
  SS BOND              : angle       1.65063 (    8)
  covalent geometry    : bond        0.00556 ( 2780)
  covalent geometry    : angle       0.65348 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.331 
Fit side-chains
REVERT: D    9 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8200 (mm-30)
REVERT: R  267 TYR cc_start: 0.8279 (t80) cc_final: 0.7914 (t80)
REVERT: R  319 GLN cc_start: 0.8296 (tt0) cc_final: 0.7864 (tm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 80
  average time/residue: 0.1081
  time to fit residues: 11.0305
Evaluate side-chains
  73 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   22 ASN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  286 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0770
   chunk 7 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.7142

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

Flipped N/Q/H residues before XYZ refinement:
R 245 GLN
R 310 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.118267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.093158 restraints weight = 6288.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.095369 restraints weight = 3428.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.096641 restraints weight = 2350.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   2784  Z= 0.134
  Angle     :  0.541   5.029   3809  Z= 0.284
  Chirality :  0.040   0.116    475
  Planarity :  0.004   0.035    467
  Dihedral  :  3.931  15.671    391
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 20.22 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.45), residues: 359
  helix:  2.21 (0.33), residues: 240
  sheet:  0.35 (1.03), residues: 31
  loop : -1.65 (0.62), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 112 
 HIS   0.002   0.000   HIS R 150 
 PHE   0.012   0.001   PHE D  32 
 TYR   0.013   0.001   TYR R 197 
 ARG   0.010   0.001   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04959 (  194)
  hydrogen bonds       : angle       4.37507 (  570)
  SS BOND              : bond        0.00154 (    4)
  SS BOND              : angle       1.43270 (    8)
  covalent geometry    : bond        0.00289 ( 2780)
  covalent geometry    : angle       0.53764 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: D    9 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7918 (mm-30)
REVERT: R  141 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8743 (p)
REVERT: R  267 TYR cc_start: 0.8304 (t80) cc_final: 0.8038 (t80)
REVERT: R  319 GLN cc_start: 0.8405 (tt0) cc_final: 0.7825 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0860
  time to fit residues: 8.8220
Evaluate side-chains
  75 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   22 ASN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  262 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN
R 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.118435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.095207 restraints weight = 6357.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.097001 restraints weight = 3549.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.098389 restraints weight = 2521.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2784  Z= 0.161
  Angle     :  0.561   5.150   3809  Z= 0.289
  Chirality :  0.041   0.125    475
  Planarity :  0.004   0.030    467
  Dihedral  :  3.842  15.492    391
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 20.58 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.45), residues: 359
  helix:  2.22 (0.33), residues: 240
  sheet:  0.36 (1.04), residues: 31
  loop : -1.56 (0.63), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 112 
 HIS   0.002   0.001   HIS R 150 
 PHE   0.012   0.001   PHE D  61 
 TYR   0.011   0.001   TYR R 197 
 ARG   0.005   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05042 (  194)
  hydrogen bonds       : angle       4.36453 (  570)
  SS BOND              : bond        0.00337 (    4)
  SS BOND              : angle       1.25319 (    8)
  covalent geometry    : bond        0.00364 ( 2780)
  covalent geometry    : angle       0.55833 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: D    9 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: D   16 ARG cc_start: 0.6508 (mtp-110) cc_final: 0.6246 (mtp180)
REVERT: R   68 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8791 (mm)
REVERT: R  141 SER cc_start: 0.9178 (OUTLIER) cc_final: 0.8717 (p)
REVERT: R  267 TYR cc_start: 0.8256 (t80) cc_final: 0.7937 (t80)
REVERT: R  277 MET cc_start: 0.8550 (ttm) cc_final: 0.8167 (ttm)
REVERT: R  319 GLN cc_start: 0.8345 (tt0) cc_final: 0.7852 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0897
  time to fit residues: 8.9614
Evaluate side-chains
  84 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   22 ASN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  286 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 216 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.117044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.093580 restraints weight = 6477.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.095564 restraints weight = 3687.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.096670 restraints weight = 2612.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2784  Z= 0.203
  Angle     :  0.643  13.467   3809  Z= 0.319
  Chirality :  0.042   0.128    475
  Planarity :  0.004   0.030    467
  Dihedral  :  3.903  14.320    391
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  8.30 %
    Allowed  : 20.94 %
    Favored  : 70.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.45), residues: 359
  helix:  1.98 (0.33), residues: 240
  sheet:  0.46 (1.04), residues: 31
  loop : -1.31 (0.66), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 112 
 HIS   0.002   0.001   HIS R 150 
 PHE   0.015   0.002   PHE R 130 
 TYR   0.010   0.001   TYR R 197 
 ARG   0.003   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05381 (  194)
  hydrogen bonds       : angle       4.45120 (  570)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       1.51898 (    8)
  covalent geometry    : bond        0.00467 ( 2780)
  covalent geometry    : angle       0.63949 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: D    9 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8162 (mm-30)
REVERT: D   16 ARG cc_start: 0.6612 (mtp-110) cc_final: 0.6242 (mtp180)
REVERT: R  267 TYR cc_start: 0.8370 (t80) cc_final: 0.7915 (t80)
REVERT: R  277 MET cc_start: 0.8541 (ttm) cc_final: 0.8182 (ttm)
REVERT: R  319 GLN cc_start: 0.8347 (tt0) cc_final: 0.7859 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 76
  average time/residue: 0.0882
  time to fit residues: 8.8241
Evaluate side-chains
  82 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   22 ASN
Chi-restraints excluded: chain D residue   39 SER
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  113 ILE
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  286 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN
R 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.118994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.095973 restraints weight = 6538.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.097908 restraints weight = 3697.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.099141 restraints weight = 2616.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2784  Z= 0.135
  Angle     :  0.578  11.429   3809  Z= 0.295
  Chirality :  0.040   0.126    475
  Planarity :  0.004   0.031    467
  Dihedral  :  3.753  13.596    391
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  7.22 %
    Allowed  : 21.30 %
    Favored  : 71.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.45), residues: 359
  helix:  2.15 (0.33), residues: 242
  sheet:  0.50 (1.06), residues: 31
  loop : -1.55 (0.64), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 112 
 HIS   0.002   0.000   HIS R 150 
 PHE   0.009   0.001   PHE R 130 
 TYR   0.011   0.001   TYR R 197 
 ARG   0.002   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04784 (  194)
  hydrogen bonds       : angle       4.19126 (  570)
  SS BOND              : bond        0.00163 (    4)
  SS BOND              : angle       1.21302 (    8)
  covalent geometry    : bond        0.00287 ( 2780)
  covalent geometry    : angle       0.57636 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: D    9 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8121 (mm-30)
REVERT: D   16 ARG cc_start: 0.6617 (mtp-110) cc_final: 0.6231 (mtp180)
REVERT: R  141 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8688 (p)
REVERT: R  267 TYR cc_start: 0.8335 (t80) cc_final: 0.7885 (t80)
REVERT: R  277 MET cc_start: 0.8542 (ttm) cc_final: 0.8193 (ttm)
REVERT: R  319 GLN cc_start: 0.8340 (tt0) cc_final: 0.7869 (tm-30)
  outliers start: 20
  outliers final: 15
  residues processed: 70
  average time/residue: 0.0908
  time to fit residues: 8.4089
Evaluate side-chains
  77 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   22 ASN
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  297 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 1 optimal weight:    8.9990
   chunk 0 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 17 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0870
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.119996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.096546 restraints weight = 6545.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.098724 restraints weight = 3621.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.100040 restraints weight = 2485.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2784  Z= 0.126
  Angle     :  0.600  10.454   3809  Z= 0.298
  Chirality :  0.041   0.155    475
  Planarity :  0.004   0.032    467
  Dihedral  :  3.659  13.680    391
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 24.19 %
    Favored  : 70.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.46), residues: 359
  helix:  2.22 (0.33), residues: 242
  sheet:  0.51 (1.06), residues: 31
  loop : -1.46 (0.65), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 112 
 HIS   0.002   0.001   HIS R 242 
 PHE   0.013   0.001   PHE D  32 
 TYR   0.009   0.001   TYR R 197 
 ARG   0.002   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  194)
  hydrogen bonds       : angle       4.09085 (  570)
  SS BOND              : bond        0.00136 (    4)
  SS BOND              : angle       1.08215 (    8)
  covalent geometry    : bond        0.00263 ( 2780)
  covalent geometry    : angle       0.59860 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: D   16 ARG cc_start: 0.6688 (mtp-110) cc_final: 0.6337 (mtp180)
REVERT: R   94 ASP cc_start: 0.7901 (t0) cc_final: 0.7387 (t0)
REVERT: R  123 SER cc_start: 0.8729 (m) cc_final: 0.8480 (t)
REVERT: R  267 TYR cc_start: 0.8351 (t80) cc_final: 0.7846 (t80)
REVERT: R  277 MET cc_start: 0.8555 (ttm) cc_final: 0.8114 (ttm)
REVERT: R  319 GLN cc_start: 0.8364 (tt0) cc_final: 0.7837 (tm-30)
  outliers start: 14
  outliers final: 14
  residues processed: 71
  average time/residue: 0.0906
  time to fit residues: 8.4868
Evaluate side-chains
  79 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  297 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.118788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.095033 restraints weight = 6338.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.097140 restraints weight = 3579.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.098463 restraints weight = 2504.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2784  Z= 0.148
  Angle     :  0.611   9.973   3809  Z= 0.303
  Chirality :  0.042   0.170    475
  Planarity :  0.004   0.031    467
  Dihedral  :  3.658  13.598    391
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 23.47 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.46), residues: 359
  helix:  2.14 (0.33), residues: 242
  sheet:  0.38 (1.03), residues: 31
  loop : -1.51 (0.65), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 112 
 HIS   0.002   0.000   HIS R 242 
 PHE   0.011   0.001   PHE R 130 
 TYR   0.008   0.001   TYR R 197 
 ARG   0.002   0.000   ARG R 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04784 (  194)
  hydrogen bonds       : angle       4.10749 (  570)
  SS BOND              : bond        0.00182 (    4)
  SS BOND              : angle       1.18132 (    8)
  covalent geometry    : bond        0.00328 ( 2780)
  covalent geometry    : angle       0.60969 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: D    9 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8116 (mm-30)
REVERT: R   94 ASP cc_start: 0.7896 (t0) cc_final: 0.7322 (t0)
REVERT: R  123 SER cc_start: 0.8733 (m) cc_final: 0.8496 (t)
REVERT: R  141 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8716 (p)
REVERT: R  277 MET cc_start: 0.8562 (ttm) cc_final: 0.8136 (ttm)
REVERT: R  319 GLN cc_start: 0.8372 (tt0) cc_final: 0.7901 (tm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 70
  average time/residue: 0.0877
  time to fit residues: 8.0914
Evaluate side-chains
  80 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   39 SER
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  297 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3748 r_free = 0.3748 target = 0.118184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.094190 restraints weight = 6346.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.096296 restraints weight = 3605.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.097456 restraints weight = 2523.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2784  Z= 0.160
  Angle     :  0.677  15.093   3809  Z= 0.321
  Chirality :  0.043   0.238    475
  Planarity :  0.004   0.030    467
  Dihedral  :  3.718  13.666    391
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 24.19 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.45), residues: 359
  helix:  2.10 (0.33), residues: 242
  sheet:  0.41 (1.03), residues: 31
  loop : -1.43 (0.65), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 112 
 HIS   0.001   0.000   HIS R 323 
 PHE   0.012   0.002   PHE D  32 
 TYR   0.008   0.001   TYR R 197 
 ARG   0.003   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04945 (  194)
  hydrogen bonds       : angle       4.12131 (  570)
  SS BOND              : bond        0.00204 (    4)
  SS BOND              : angle       1.23156 (    8)
  covalent geometry    : bond        0.00363 ( 2780)
  covalent geometry    : angle       0.67495 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: D    9 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8129 (mm-30)
REVERT: D   16 ARG cc_start: 0.7024 (mtp-110) cc_final: 0.6794 (mtp-110)
REVERT: R   94 ASP cc_start: 0.7937 (t0) cc_final: 0.7382 (t0)
REVERT: R  123 SER cc_start: 0.8781 (m) cc_final: 0.8540 (t)
REVERT: R  141 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8708 (p)
REVERT: R  267 TYR cc_start: 0.8323 (t80) cc_final: 0.7929 (t80)
REVERT: R  277 MET cc_start: 0.8582 (ttm) cc_final: 0.8159 (ttm)
REVERT: R  319 GLN cc_start: 0.8416 (tt0) cc_final: 0.7950 (tm-30)
  outliers start: 17
  outliers final: 15
  residues processed: 71
  average time/residue: 0.0937
  time to fit residues: 8.8831
Evaluate side-chains
  79 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   39 SER
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  286 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0870
   chunk 7 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7560

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.119563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.095662 restraints weight = 6388.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.097798 restraints weight = 3575.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.099140 restraints weight = 2483.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.4359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2784  Z= 0.128
  Angle     :  0.650  14.434   3809  Z= 0.304
  Chirality :  0.042   0.282    475
  Planarity :  0.003   0.031    467
  Dihedral  :  3.582  13.975    391
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 24.55 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.46), residues: 359
  helix:  2.18 (0.33), residues: 242
  sheet:  0.48 (1.04), residues: 31
  loop : -1.34 (0.65), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 112 
 HIS   0.001   0.000   HIS R 150 
 PHE   0.011   0.001   PHE R  59 
 TYR   0.008   0.001   TYR R 197 
 ARG   0.001   0.000   ARG R 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04579 (  194)
  hydrogen bonds       : angle       4.03333 (  570)
  SS BOND              : bond        0.00143 (    4)
  SS BOND              : angle       1.08294 (    8)
  covalent geometry    : bond        0.00273 ( 2780)
  covalent geometry    : angle       0.64921 ( 3801)

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

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

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  718 Ramachandran restraints generated.
    359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: D    9 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8095 (mm-30)
REVERT: D   16 ARG cc_start: 0.7035 (mtp-110) cc_final: 0.6826 (mtp-110)
REVERT: R   94 ASP cc_start: 0.7892 (t0) cc_final: 0.7393 (t0)
REVERT: R  123 SER cc_start: 0.8749 (m) cc_final: 0.8502 (t)
REVERT: R  267 TYR cc_start: 0.8322 (t80) cc_final: 0.7941 (t80)
REVERT: R  277 MET cc_start: 0.8574 (ttm) cc_final: 0.8132 (ttm)
REVERT: R  319 GLN cc_start: 0.8370 (tt0) cc_final: 0.7919 (tm-30)
  outliers start: 16
  outliers final: 15
  residues processed: 69
  average time/residue: 0.0923
  time to fit residues: 8.4251
Evaluate side-chains
  77 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   39 SER
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  286 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
R 306 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.118078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.094160 restraints weight = 6275.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096268 restraints weight = 3565.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.097531 restraints weight = 2497.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2784  Z= 0.174
  Angle     :  0.690  13.963   3809  Z= 0.326
  Chirality :  0.044   0.304    475
  Planarity :  0.004   0.030    467
  Dihedral  :  3.673  13.595    391
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 25.27 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.68 (0.45), residues: 359
  helix:  2.04 (0.33), residues: 242
  sheet:  0.38 (1.01), residues: 31
  loop : -1.34 (0.65), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 112 
 HIS   0.003   0.001   HIS R 306 
 PHE   0.016   0.002   PHE D  32 
 TYR   0.007   0.001   TYR R 197 
 ARG   0.002   0.000   ARG R 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04951 (  194)
  hydrogen bonds       : angle       4.11910 (  570)
  SS BOND              : bond        0.00232 (    4)
  SS BOND              : angle       1.27388 (    8)
  covalent geometry    : bond        0.00397 ( 2780)
  covalent geometry    : angle       0.68825 ( 3801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1222.03 seconds
wall clock time: 22 minutes 5.14 seconds (1325.14 seconds total)