Starting phenix.real_space_refine
on Wed Mar  5 14:53:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggt_40020/03_2025/8ggt_40020.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggt_40020/03_2025/8ggt_40020.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggt_40020/03_2025/8ggt_40020.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggt_40020/03_2025/8ggt_40020.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggt_40020/03_2025/8ggt_40020.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggt_40020/03_2025/8ggt_40020.cif"
  }
  resolution = 3.5
  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=   0.023
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      15      5.16       5
     C    1405      2.51       5
     N     335      2.21       5
     O     350      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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2105
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2090
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 174
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 95
    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: 2.43, per 1000 atoms: 1.15
  Number of scatterers: 2105
  At special positions: 0
  Unit cell: (56.4005, 84.1669, 61.6067, 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      15     16.00
     O     350      8.00
     N     335      7.00
     C    1405      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=2.03

  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: 0.60
  Conformation dependent library (CDL) restraints added in 256.2 milliseconds
  

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  538

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 0 sheets defined
      86.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'R' and resid 37 through 61
      removed outlier: 3.787A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 96
      removed outlier: 3.580A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 5.254A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.739A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 3.722A  pdb=" N   LEU R 144 " --> pdb=" O   LYS R 140 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 140 through 145'
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.595A  pdb=" N   ALA R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 4.132A  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
      removed outlier: 3.835A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.842A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.674A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.554A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 327
      removed outlier: 3.715A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.544A  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

    160 hydrogen bonds defined for protein.
    480 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: 0.51

  Time building geometry restraints manager: 0.71 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: 385
        1.33 -     1.45: 561
        1.45 -     1.57: 1190
        1.57 -     1.69: 1
        1.69 -     1.81: 22
  Bond restraints: 2159
  Sorted by residual:
  bond pdb=" C   LEU R 287 "
       pdb=" O   LEU R 287 "
    ideal  model  delta    sigma   weight residual
    1.244  1.211  0.032 9.80e-03 1.04e+04 1.09e+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 7.10e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.576 -0.053 2.00e-02 2.50e+03 6.91e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 2.00e-02 2.50e+03 5.45e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.440 -0.046 2.00e-02 2.50e+03 5.28e+00
  ... (remaining 2154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 2914
        2.19 -     4.39: 34
        4.39 -     6.58: 8
        6.58 -     8.77: 4
        8.77 -    10.96: 1
  Bond angle restraints: 2961
  Sorted by residual:
  angle pdb=" N   PHE R 289 "
        pdb=" CA  PHE R 289 "
        pdb=" C   PHE R 289 "
      ideal   model   delta    sigma   weight residual
     111.07  118.45   -7.38 1.07e+00 8.73e-01 4.75e+01
  angle pdb=" N   TRP R 286 "
        pdb=" CA  TRP R 286 "
        pdb=" C   TRP R 286 "
      ideal   model   delta    sigma   weight residual
     113.97  121.51   -7.54 1.28e+00 6.10e-01 3.47e+01
  angle pdb=" CA  MET R  36 "
        pdb=" CB  MET R  36 "
        pdb=" CG  MET R  36 "
      ideal   model   delta    sigma   weight residual
     114.10  121.69   -7.59 2.00e+00 2.50e-01 1.44e+01
  angle pdb=" CB  MET R  36 "
        pdb=" CG  MET R  36 "
        pdb=" SD  MET R  36 "
      ideal   model   delta    sigma   weight residual
     112.70  123.66  -10.96 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" C   LEU R 287 "
        pdb=" N   PRO R 288 "
        pdb=" CA  PRO R 288 "
      ideal   model   delta    sigma   weight residual
     119.05  115.01    4.04 1.11e+00 8.12e-01 1.32e+01
  ... (remaining 2956 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 1124
       16.67 -    33.33: 81
       33.33 -    49.99: 25
       49.99 -    66.66: 2
       66.66 -    83.32: 3
  Dihedral angle restraints: 1235
    sinusoidal: 407
      harmonic: 828
  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 -169.32   83.32     1      1.00e+01 1.00e-02 8.48e+01
  dihedral pdb=" CA  LEU R 302 "
           pdb=" C   LEU R 302 "
           pdb=" N   ILE R 303 "
           pdb=" CA  ILE R 303 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.34  -18.66     0      5.00e+00 4.00e-02 1.39e+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 -161.81  -18.19     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 1232 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 254
       0.042 -    0.083: 90
       0.083 -    0.124: 18
       0.124 -    0.165: 0
       0.165 -    0.207: 2
  Chirality restraints: 364
  Sorted by residual:
  chirality pdb=" CA  TRP R 286 "
            pdb=" N   TRP R 286 "
            pdb=" C   TRP R 286 "
            pdb=" CB  TRP R 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.57   -0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CA  PHE R 289 "
            pdb=" N   PHE R 289 "
            pdb=" C   PHE R 289 "
            pdb=" CB  PHE R 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 361 not shown)

  Planarity restraints: 358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R  36 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" C   MET R  36 "    0.035 2.00e-02 2.50e+03
        pdb=" O   MET R  36 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY R  37 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 287 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO R 288 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO R 288 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 288 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 281 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.19e+00
        pdb=" C   THR R 281 "    0.026 2.00e-02 2.50e+03
        pdb=" O   THR R 281 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   PHE R 282 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 355 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 408
        2.77 -     3.30: 2079
        3.30 -     3.84: 3341
        3.84 -     4.37: 3350
        4.37 -     4.90: 6282
  Nonbonded interactions: 15460
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" NE1 TRP R  99 "
            pdb=" O   GLY R 102 "
     model   vdw
     2.504 3.120
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.527 3.040
  nonbonded pdb=" OG  SER R 165 "
            pdb=" N   PHE R 166 "
     model   vdw
     2.531 3.120
  ... (remaining 15455 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 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:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.270
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   2159  Z= 0.294
  Angle     :  0.700  10.965   2961  Z= 0.420
  Chirality :  0.041   0.207    364
  Planarity :  0.004   0.039    358
  Dihedral  : 13.407  78.387    694
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.88 (0.49), residues: 277
  helix:  2.41 (0.35), residues: 206
  sheet:  None (None), residues: 0
  loop : -2.50 (0.55), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 178 
 PHE   0.012   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 151 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1472
  time to fit residues: 3.8394
Evaluate side-chains
  16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0050
   chunk 7 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4172

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.146538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.131899 restraints weight = 3009.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.134607 restraints weight = 1622.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.136586 restraints weight = 1054.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.0730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2159  Z= 0.169
  Angle     :  0.490   6.438   2961  Z= 0.278
  Chirality :  0.039   0.156    364
  Planarity :  0.004   0.032    358
  Dihedral  :  4.430  17.988    311
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  5.50 %
    Favored  : 92.50 %
  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:  2.27 (0.50), residues: 277
  helix:  2.64 (0.35), residues: 209
  sheet:  None (None), residues: 0
  loop : -2.42 (0.62), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 286 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 139 
 TYR   0.008   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 328 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7385 (mtt) cc_final: 0.7103 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 19
  average time/residue: 0.1393
  time to fit residues: 3.3549
Evaluate side-chains
  20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  309 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0000
   chunk 13 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.147374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132574 restraints weight = 3028.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.135155 restraints weight = 1686.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.137165 restraints weight = 1122.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2159  Z= 0.185
  Angle     :  0.489   6.275   2961  Z= 0.273
  Chirality :  0.039   0.131    364
  Planarity :  0.004   0.025    358
  Dihedral  :  4.403  17.827    311
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  7.00 %
    Favored  : 91.00 %
  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:  2.35 (0.51), residues: 277
  helix:  2.72 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.38 (0.66), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 286 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.013   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 221 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7511 (mtt) cc_final: 0.7212 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 19
  average time/residue: 0.0885
  time to fit residues: 2.3767
Evaluate side-chains
  20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.146256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131897 restraints weight = 3013.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.135330 restraints weight = 1723.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.137812 restraints weight = 973.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2159  Z= 0.169
  Angle     :  0.476   6.968   2961  Z= 0.264
  Chirality :  0.039   0.130    364
  Planarity :  0.003   0.025    358
  Dihedral  :  4.292  17.721    311
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  9.00 %
    Favored  : 88.00 %
  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: 277
  helix:  2.78 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.34 (0.69), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 286 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7475 (mtt) cc_final: 0.7177 (mtt)
REVERT: R   95 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8553 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 22
  average time/residue: 0.1253
  time to fit residues: 3.4574
Evaluate side-chains
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 16
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.141428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.126686 restraints weight = 3177.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.129230 restraints weight = 1767.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.131063 restraints weight = 1180.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2159  Z= 0.258
  Angle     :  0.545   7.806   2961  Z= 0.301
  Chirality :  0.041   0.126    364
  Planarity :  0.004   0.028    358
  Dihedral  :  4.537  17.626    311
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.00 %
    Favored  : 84.00 %
  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:  2.09 (0.51), residues: 277
  helix:  2.50 (0.34), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.38 (0.70), residues: 69

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   0.016   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7610 (mtt) cc_final: 0.7328 (mtt)
  outliers start: 6
  outliers final: 4
  residues processed: 22
  average time/residue: 0.1738
  time to fit residues: 4.5712
Evaluate side-chains
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.144354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.129589 restraints weight = 3077.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.132317 restraints weight = 1724.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.134178 restraints weight = 1144.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2159  Z= 0.184
  Angle     :  0.506   8.992   2961  Z= 0.276
  Chirality :  0.039   0.129    364
  Planarity :  0.004   0.027    358
  Dihedral  :  4.379  17.679    311
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.00 %
    Favored  : 84.50 %
  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:  2.31 (0.52), residues: 277
  helix:  2.67 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.32 (0.71), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 185 
 ARG   0.001   0.000   ARG R 221 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7573 (mtt) cc_final: 0.7272 (mtt)
  outliers start: 5
  outliers final: 4
  residues processed: 22
  average time/residue: 0.1661
  time to fit residues: 4.6732
Evaluate side-chains
  22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0770
   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 = 0.3613 r_free = 0.3613 target = 0.144176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.129454 restraints weight = 3084.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.132012 restraints weight = 1712.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.133839 restraints weight = 1145.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2159  Z= 0.183
  Angle     :  0.500   9.294   2961  Z= 0.272
  Chirality :  0.039   0.124    364
  Planarity :  0.004   0.027    358
  Dihedral  :  4.310  17.562    311
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.00 %
    Favored  : 84.00 %
  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:  2.32 (0.51), residues: 277
  helix:  2.70 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.38 (0.70), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7567 (mtt) cc_final: 0.7269 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 23
  average time/residue: 0.1676
  time to fit residues: 4.6169
Evaluate side-chains
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0010
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5586

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.143687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.128697 restraints weight = 3184.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131292 restraints weight = 1749.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.133190 restraints weight = 1176.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2159  Z= 0.182
  Angle     :  0.511  10.264   2961  Z= 0.276
  Chirality :  0.039   0.124    364
  Planarity :  0.004   0.027    358
  Dihedral  :  4.284  17.487    311
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.50 %
    Favored  : 83.50 %
  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:  2.39 (0.52), residues: 277
  helix:  2.73 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.29 (0.72), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 221 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7561 (mtt) cc_final: 0.7261 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 21
  average time/residue: 0.0822
  time to fit residues: 2.4968
Evaluate side-chains
  22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.142601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.127959 restraints weight = 3161.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.131254 restraints weight = 1857.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.133638 restraints weight = 1081.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2159  Z= 0.214
  Angle     :  0.531  10.628   2961  Z= 0.286
  Chirality :  0.040   0.124    364
  Planarity :  0.004   0.027    358
  Dihedral  :  4.349  17.445    311
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.50 %
    Favored  : 83.00 %
  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: 277
  helix:  2.64 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.22 (0.74), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 139 
 TYR   0.008   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7619 (mtt) cc_final: 0.7331 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 21
  average time/residue: 0.0814
  time to fit residues: 2.4502
Evaluate side-chains
  24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    0.0770
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   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 = 0.3608 r_free = 0.3608 target = 0.143354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.128544 restraints weight = 3106.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.131124 restraints weight = 1736.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.133073 restraints weight = 1153.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2159  Z= 0.182
  Angle     :  0.520  11.041   2961  Z= 0.279
  Chirality :  0.039   0.123    364
  Planarity :  0.004   0.027    358
  Dihedral  :  4.266  17.472    311
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.50 %
    Favored  : 83.00 %
  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:  2.46 (0.52), residues: 277
  helix:  2.75 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.14 (0.75), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7590 (mtt) cc_final: 0.7293 (mtt)
  outliers start: 5
  outliers final: 4
  residues processed: 21
  average time/residue: 0.0846
  time to fit residues: 2.5344
Evaluate side-chains
  22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0040
   overall best weight:    0.6192

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.143324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.128465 restraints weight = 3133.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.131024 restraints weight = 1746.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.132946 restraints weight = 1167.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2159  Z= 0.197
  Angle     :  0.524  10.925   2961  Z= 0.282
  Chirality :  0.039   0.122    364
  Planarity :  0.004   0.027    358
  Dihedral  :  4.269  17.439    311
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.00 %
    Favored  : 83.00 %
  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:  2.42 (0.52), residues: 277
  helix:  2.72 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.14 (0.76), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.008   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 151 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1146.41 seconds
wall clock time: 20 minutes 44.41 seconds (1244.41 seconds total)