Starting phenix.real_space_refine
on Mon Feb 10 19:58:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggo_40015/02_2025/8ggo_40015.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggo_40015/02_2025/8ggo_40015.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggo_40015/02_2025/8ggo_40015.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggo_40015/02_2025/8ggo_40015.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggo_40015/02_2025/8ggo_40015.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggo_40015/02_2025/8ggo_40015.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.028
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      13      5.16       5
     C    1403      2.51       5
     N     330      2.21       5
     O     349      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2095
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2080
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 189
          Unresolved non-hydrogen dihedrals: 131
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 92
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.64, per 1000 atoms: 1.26
  Number of scatterers: 2095
  At special positions: 0
  Unit cell: (56.4005, 82.4315, 64.2098, 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      13     16.00
     O     349      8.00
     N     330      7.00
     C    1403      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.04

  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: 0.50
  Conformation dependent library (CDL) restraints added in 303.6 milliseconds
  

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  534

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      89.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'R' and resid 37 through 61
      removed outlier: 3.566A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 66
      removed outlier: 3.587A  pdb=" N   GLN R  65 " --> pdb=" O   GLU R  62 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   THR R  66 " --> pdb=" O   ARG R  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 62 through 66'
    Processing helix  chain 'R' and resid 67 through 86
      removed outlier: 4.311A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
      removed outlier: 3.534A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.690A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.844A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.741A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.524A  pdb=" N   ILE R 291 " --> pdb=" O   LEU R 287 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.627A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 326
      removed outlier: 3.819A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
      removed outlier: 3.649A  pdb=" N   GLU R 338 " --> pdb=" O   ILE R 334 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU R 340 " --> pdb=" O   PHE R 336 " (cutoff:3.500A)

    161 hydrogen bonds defined for protein.
    483 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: 0.44

  Time building geometry restraints manager: 0.57 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: 359
        1.33 -     1.45: 594
        1.45 -     1.57: 1180
        1.57 -     1.69: 1
        1.69 -     1.81: 17
  Bond restraints: 2151
  Sorted by residual:
  bond pdb=" C   ARG R 328 "
       pdb=" N   SER R 329 "
    ideal  model  delta    sigma   weight residual
    1.331  1.250  0.081 2.07e-02 2.33e+03 1.51e+01
  bond pdb=" C   CYS R 327 "
       pdb=" N   ARG R 328 "
    ideal  model  delta    sigma   weight residual
    1.332  1.284  0.048 1.37e-02 5.33e+03 1.23e+01
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 6.96e+00
  bond pdb=" CA  VAL R  86 "
       pdb=" C   VAL R  86 "
    ideal  model  delta    sigma   weight residual
    1.523  1.487  0.036 1.37e-02 5.33e+03 6.77e+00
  bond pdb=" CA  VAL R  81 "
       pdb=" C   VAL R  81 "
    ideal  model  delta    sigma   weight residual
    1.523  1.493  0.031 1.27e-02 6.20e+03 5.77e+00
  ... (remaining 2146 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 2879
        1.85 -     3.71: 55
        3.71 -     5.56: 16
        5.56 -     7.42: 5
        7.42 -     9.27: 2
  Bond angle restraints: 2957
  Sorted by residual:
  angle pdb=" N   LEU R  84 "
        pdb=" CA  LEU R  84 "
        pdb=" C   LEU R  84 "
      ideal   model   delta    sigma   weight residual
     111.36  118.41   -7.05 1.09e+00 8.42e-01 4.18e+01
  angle pdb=" N   ALA R  85 "
        pdb=" CA  ALA R  85 "
        pdb=" C   ALA R  85 "
      ideal   model   delta    sigma   weight residual
     113.97  122.12   -8.15 1.28e+00 6.10e-01 4.05e+01
  angle pdb=" N   CYS R 327 "
        pdb=" CA  CYS R 327 "
        pdb=" C   CYS R 327 "
      ideal   model   delta    sigma   weight residual
     111.07  116.65   -5.58 1.07e+00 8.73e-01 2.72e+01
  angle pdb=" N   TYR R 326 "
        pdb=" CA  TYR R 326 "
        pdb=" C   TYR R 326 "
      ideal   model   delta    sigma   weight residual
     111.69  118.05   -6.36 1.23e+00 6.61e-01 2.67e+01
  angle pdb=" C   VAL R  87 "
        pdb=" N   PRO R  88 "
        pdb=" CA  PRO R  88 "
      ideal   model   delta    sigma   weight residual
     119.05  113.44    5.61 1.11e+00 8.12e-01 2.55e+01
  ... (remaining 2952 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.89: 1102
       14.89 -    29.77: 89
       29.77 -    44.65: 25
       44.65 -    59.53: 2
       59.53 -    74.41: 1
  Dihedral angle restraints: 1219
    sinusoidal: 397
      harmonic: 822
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -160.41   74.41     1      1.00e+01 1.00e-02 7.02e+01
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  SER R 207 "
           pdb=" C   SER R 207 "
           pdb=" N   PHE R 208 "
           pdb=" CA  PHE R 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.74  -16.26     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 1216 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 280
       0.048 -    0.096: 71
       0.096 -    0.144: 11
       0.144 -    0.191: 4
       0.191 -    0.239: 2
  Chirality restraints: 368
  Sorted by residual:
  chirality pdb=" CA  ALA R  85 "
            pdb=" N   ALA R  85 "
            pdb=" C   ALA R  85 "
            pdb=" CB  ALA R  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.25    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  PHE R  89 "
            pdb=" N   PHE R  89 "
            pdb=" C   PHE R  89 "
            pdb=" CB  PHE R  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  CYS R 327 "
            pdb=" N   CYS R 327 "
            pdb=" C   CYS R 327 "
            pdb=" CB  CYS R 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.95e-01
  ... (remaining 365 not shown)

  Planarity restraints: 354
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 327 "    0.016 2.00e-02 2.50e+03   3.05e-02 9.28e+00
        pdb=" C   CYS R 327 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   CYS R 327 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG R 328 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R  79 "    0.009 2.00e-02 2.50e+03   1.68e-02 2.83e+00
        pdb=" C   ASP R  79 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ASP R  79 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU R  80 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 328 "   -0.007 2.00e-02 2.50e+03   1.37e-02 1.89e+00
        pdb=" C   ARG R 328 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ARG R 328 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   SER R 329 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 351 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 610
        2.83 -     3.34: 2140
        3.34 -     3.86: 3322
        3.86 -     4.38: 3474
        4.38 -     4.90: 6381
  Nonbonded interactions: 15927
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAK G1I R 501 "
     model   vdw
     2.489 3.040
  nonbonded pdb=" O   ALA R 119 "
            pdb=" OG1 THR R 123 "
     model   vdw
     2.532 3.040
  ... (remaining 15922 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=0.00 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:             1.460
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.860
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
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      :  0.005   0.081   2151  Z= 0.360
  Angle     :  0.737   9.272   2957  Z= 0.481
  Chirality :  0.046   0.239    368
  Planarity :  0.004   0.030    354
  Dihedral  : 11.582  49.341    682
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  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:  2.30 (0.50), residues: 275
  helix:  2.14 (0.34), residues: 218
  sheet:  None (None), residues: 0
  loop : -0.93 (0.81), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.005   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R  89 
 TYR   0.010   0.001   TYR R 132 
 ARG   0.001   0.000   ARG R 151 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.229 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.1544
  time to fit residues: 2.7335
Evaluate side-chains
  11 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
R  93 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.135779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.120834 restraints weight = 2874.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.82
r_work: 0.3252 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2151  Z= 0.204
  Angle     :  0.493   5.213   2957  Z= 0.278
  Chirality :  0.040   0.116    368
  Planarity :  0.004   0.027    354
  Dihedral  :  4.628  19.872    308
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  2.96 %
    Favored  : 95.07 %
  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:  2.41 (0.51), residues: 275
  helix:  2.21 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.13 (0.78), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.005   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 108 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 328 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 12
  time to evaluate  : 0.230 
Fit side-chains
REVERT: R   82 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7290 (mtm)
  outliers start: 4
  outliers final: 1
  residues processed: 15
  average time/residue: 0.0688
  time to fit residues: 1.6760
Evaluate side-chains
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0370
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.3858

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.137422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122583 restraints weight = 2811.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.79
r_work: 0.3298 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2151  Z= 0.160
  Angle     :  0.455   5.223   2957  Z= 0.255
  Chirality :  0.038   0.116    368
  Planarity :  0.003   0.025    354
  Dihedral  :  4.306  19.820    308
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  4.93 %
    Favored  : 93.60 %
  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:  2.64 (0.51), residues: 275
  helix:  2.35 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.92 (0.80), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 108 
 TYR   0.008   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.231 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 13
  average time/residue: 0.0741
  time to fit residues: 1.5710
Evaluate side-chains
  11 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 10
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.132250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.117633 restraints weight = 2838.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.66
r_work: 0.3219 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2151  Z= 0.248
  Angle     :  0.502   5.279   2957  Z= 0.285
  Chirality :  0.040   0.116    368
  Planarity :  0.004   0.027    354
  Dihedral  :  4.492  20.344    308
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  6.40 %
    Favored  : 91.13 %
  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:  2.43 (0.52), residues: 275
  helix:  2.19 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.95 (0.84), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 101 
 TYR   0.012   0.002   TYR R 199 
 ARG   0.001   0.000   ARG R 175 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.223 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 15
  average time/residue: 0.0715
  time to fit residues: 1.6936
Evaluate side-chains
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.3442 r_free = 0.3442 target = 0.129772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.114778 restraints weight = 2907.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.80
r_work: 0.3197 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2151  Z= 0.240
  Angle     :  0.488   5.306   2957  Z= 0.277
  Chirality :  0.040   0.116    368
  Planarity :  0.004   0.028    354
  Dihedral  :  4.491  20.766    308
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.34 %
    Favored  : 87.68 %
  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:  2.34 (0.52), residues: 275
  helix:  2.15 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.09 (0.83), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.213 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 13
  average time/residue: 0.0691
  time to fit residues: 1.4817
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3445 r_free = 0.3445 target = 0.130148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.115212 restraints weight = 2860.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.79
r_work: 0.3194 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2151  Z= 0.226
  Angle     :  0.479   5.271   2957  Z= 0.272
  Chirality :  0.040   0.115    368
  Planarity :  0.004   0.029    354
  Dihedral  :  4.450  20.911    308
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 10.84 %
    Favored  : 86.70 %
  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:  2.34 (0.52), residues: 275
  helix:  2.24 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.43 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 10
  time to evaluate  : 0.211 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 14
  average time/residue: 0.0672
  time to fit residues: 1.5331
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7338

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.129469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.114537 restraints weight = 2868.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.79
r_work: 0.3193 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2151  Z= 0.235
  Angle     :  0.483   5.281   2957  Z= 0.274
  Chirality :  0.040   0.115    368
  Planarity :  0.004   0.029    354
  Dihedral  :  4.462  20.938    308
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.32 %
    Favored  : 85.71 %
  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:  2.30 (0.52), residues: 275
  helix:  2.21 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.44 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 175 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.243 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 13
  average time/residue: 0.0718
  time to fit residues: 1.5951
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6040

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.133168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.118433 restraints weight = 2911.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.71
r_work: 0.3217 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2151  Z= 0.204
  Angle     :  0.464   5.231   2957  Z= 0.263
  Chirality :  0.039   0.114    368
  Planarity :  0.004   0.029    354
  Dihedral  :  4.368  21.129    308
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.32 %
    Favored  : 85.71 %
  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:  2.36 (0.52), residues: 275
  helix:  2.26 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.48 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.228 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 13
  average time/residue: 0.0698
  time to fit residues: 1.4981
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
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 10 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.129397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.114385 restraints weight = 2930.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.81
r_work: 0.3187 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2151  Z= 0.245
  Angle     :  0.487   5.247   2957  Z= 0.276
  Chirality :  0.040   0.115    368
  Planarity :  0.004   0.029    354
  Dihedral  :  4.458  20.838    308
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.32 %
    Favored  : 85.71 %
  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:  2.24 (0.52), residues: 275
  helix:  2.18 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.51 (0.79), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 313 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 175 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.276 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 13
  average time/residue: 0.0736
  time to fit residues: 1.5761
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
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 10 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.134780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.120203 restraints weight = 2847.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.66
r_work: 0.3237 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2151  Z= 0.185
  Angle     :  0.455   5.227   2957  Z= 0.257
  Chirality :  0.039   0.114    368
  Planarity :  0.003   0.029    354
  Dihedral  :  4.320  21.297    308
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.30 %
    Favored  : 84.73 %
  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:  2.37 (0.52), residues: 275
  helix:  2.28 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.48 (0.79), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.223 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0717
  time to fit residues: 1.6116
Evaluate side-chains
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0770
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.131944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.116938 restraints weight = 2887.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.82
r_work: 0.3220 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2151  Z= 0.190
  Angle     :  0.454   5.210   2957  Z= 0.256
  Chirality :  0.039   0.112    368
  Planarity :  0.004   0.029    354
  Dihedral  :  4.268  21.152    308
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.79 %
    Favored  : 85.22 %
  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:  2.40 (0.52), residues: 275
  helix:  2.22 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.22 (0.81), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1448.63 seconds
wall clock time: 26 minutes 17.19 seconds (1577.19 seconds total)