Starting phenix.real_space_refine
on Fri Aug 22 12:39:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggt_40020/08_2025/8ggt_40020.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggt_40020/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggt_40020/08_2025/8ggt_40020.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggt_40020/08_2025/8ggt_40020.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggt_40020/08_2025/8ggt_40020.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggt_40020/08_2025/8ggt_40020.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TRP:plan': 2, 'ASP:plan': 6, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 1}
          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: 0.92, per 1000 atoms: 0.44
  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: 0.20
  Conformation dependent library (CDL) restraints added in 93.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.08
  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: 0.31

  Time building geometry restraints manager: 0.27 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:             2.530
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.890
  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:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.030
-------------------------------------------------------------------------------
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   2160  Z= 0.252
  Angle     :  0.700  10.965   2963  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (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
 ARG   0.001   0.000   ARG R 151 
 TYR   0.009   0.001   TYR R 199 
 PHE   0.012   0.001   PHE R 139 
 TRP   0.010   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 2159)
  covalent geometry    : angle       0.70009 ( 2961)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.23885 (    2)
  hydrogen bonds       : bond        0.14554 (  160)
  hydrogen bonds       : angle       4.98303 (  480)

*********************** 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  : 0.077 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0627
  time to fit residues: 1.6180
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  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3610 r_free = 0.3610 target = 0.143789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.128848 restraints weight = 3096.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.131579 restraints weight = 1669.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.133537 restraints weight = 1090.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.134792 restraints weight = 799.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.135677 restraints weight = 638.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.0733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2160  Z= 0.153
  Angle     :  0.518   6.005   2963  Z= 0.294
  Chirality :  0.041   0.158    364
  Planarity :  0.004   0.033    358
  Dihedral  :  4.536  18.113    311
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  5.00 %
    Favored  : 93.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.50), residues: 277
  helix:  2.49 (0.35), residues: 209
  sheet:  None (None), residues: 0
  loop : -2.46 (0.63), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.009   0.001   TYR R 308 
 PHE   0.014   0.001   PHE R 139 
 TRP   0.007   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 2159)
  covalent geometry    : angle       0.51797 ( 2961)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.22166 (    2)
  hydrogen bonds       : bond        0.06624 (  160)
  hydrogen bonds       : angle       4.08884 (  480)

*********************** 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
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 21
  average time/residue: 0.0812
  time to fit residues: 1.9934
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  : 0.080 
-------------------------------------------------------------------------------
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 26 optimal weight:    0.0060
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0470
   chunk 0 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0980
   overall best weight:    0.2094

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.152780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.138029 restraints weight = 3034.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.140799 restraints weight = 1664.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.142662 restraints weight = 1091.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.143982 restraints weight = 806.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.144956 restraints weight = 643.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2160  Z= 0.107
  Angle     :  0.442   6.570   2963  Z= 0.245
  Chirality :  0.038   0.135    364
  Planarity :  0.003   0.025    358
  Dihedral  :  4.211  17.858    311
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  8.00 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.52), residues: 277
  helix:  2.92 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.38 (0.66), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.007   0.001   PHE R 108 
 TRP   0.007   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 2159)
  covalent geometry    : angle       0.44216 ( 2961)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       0.23391 (    2)
  hydrogen bonds       : bond        0.04638 (  160)
  hydrogen bonds       : angle       3.71827 (  480)

*********************** 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
  20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7337 (mtt) cc_final: 0.7035 (mtt)
REVERT: R  156 MET cc_start: 0.6861 (mmt) cc_final: 0.6366 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 20
  average time/residue: 0.0637
  time to fit residues: 1.5797
Evaluate side-chains
  16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 3 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 11 optimal weight:    0.1980
   chunk 23 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.149255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.135422 restraints weight = 3079.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.138831 restraints weight = 1743.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.140610 restraints weight = 981.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.141218 restraints weight = 750.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.142049 restraints weight = 641.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2160  Z= 0.139
  Angle     :  0.495   7.319   2963  Z= 0.272
  Chirality :  0.039   0.127    364
  Planarity :  0.004   0.025    358
  Dihedral  :  4.275  17.512    311
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.00 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.52), residues: 277
  helix:  2.84 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.33 (0.69), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.012   0.001   PHE R 139 
 TRP   0.005   0.001   TRP R 286 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 2159)
  covalent geometry    : angle       0.49526 ( 2961)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       0.32635 (    2)
  hydrogen bonds       : bond        0.05870 (  160)
  hydrogen bonds       : angle       3.78871 (  480)

*********************** 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
  23 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7426 (mtt) cc_final: 0.7128 (mtt)
REVERT: R   95 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8554 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 21
  average time/residue: 0.0556
  time to fit residues: 1.4577
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  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   95 LEU
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 14 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0370
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.149958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.135205 restraints weight = 3107.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.138589 restraints weight = 1850.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.141199 restraints weight = 1062.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.142369 restraints weight = 691.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.142652 restraints weight = 563.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2160  Z= 0.127
  Angle     :  0.485   8.196   2963  Z= 0.265
  Chirality :  0.039   0.127    364
  Planarity :  0.003   0.025    358
  Dihedral  :  4.238  17.530    311
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.50 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.52), residues: 277
  helix:  2.86 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.28 (0.69), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.009   0.001   TYR R 308 
 PHE   0.009   0.001   PHE R 139 
 TRP   0.005   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 2159)
  covalent geometry    : angle       0.48511 ( 2961)
  SS BOND              : bond        0.00031 (    1)
  SS BOND              : angle       0.26109 (    2)
  hydrogen bonds       : bond        0.05573 (  160)
  hydrogen bonds       : angle       3.72725 (  480)

*********************** 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
  20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7423 (mtt) cc_final: 0.7118 (mtt)
REVERT: R   95 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8473 (mp)
  outliers start: 3
  outliers final: 2
  residues processed: 19
  average time/residue: 0.0642
  time to fit residues: 1.5182
Evaluate side-chains
  20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
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  218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0370
   chunk 22 optimal weight:    0.4980
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.151281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.136509 restraints weight = 3015.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.139870 restraints weight = 1815.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.142382 restraints weight = 1046.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.143644 restraints weight = 680.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.143927 restraints weight = 559.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2160  Z= 0.123
  Angle     :  0.477   8.658   2963  Z= 0.260
  Chirality :  0.039   0.125    364
  Planarity :  0.003   0.025    358
  Dihedral  :  4.162  17.464    311
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.52), residues: 277
  helix:  2.89 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.31 (0.68), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.009   0.001   PHE R 139 
 TRP   0.005   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 2159)
  covalent geometry    : angle       0.47736 ( 2961)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.24608 (    2)
  hydrogen bonds       : bond        0.05405 (  160)
  hydrogen bonds       : angle       3.67191 (  480)

*********************** 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
  21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7435 (mtt) cc_final: 0.7128 (mtt)
REVERT: R   95 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8473 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 20
  average time/residue: 0.0347
  time to fit residues: 1.0008
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  : 0.083 
-------------------------------------------------------------------------------
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  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 27 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    0.4980
   chunk 22 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.149400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.135426 restraints weight = 3076.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.138778 restraints weight = 1749.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.141078 restraints weight = 986.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.141589 restraints weight = 719.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.141670 restraints weight = 602.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2160  Z= 0.128
  Angle     :  0.494   9.376   2963  Z= 0.267
  Chirality :  0.039   0.123    364
  Planarity :  0.003   0.025    358
  Dihedral  :  4.181  17.441    311
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.52), residues: 277
  helix:  2.87 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.27 (0.70), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.010   0.001   TYR R 185 
 PHE   0.008   0.001   PHE R 139 
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 2159)
  covalent geometry    : angle       0.49404 ( 2961)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.26694 (    2)
  hydrogen bonds       : bond        0.05551 (  160)
  hydrogen bonds       : angle       3.67394 (  480)

*********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7483 (mtt) cc_final: 0.7167 (mtt)
REVERT: R   95 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8493 (mp)
  outliers start: 5
  outliers final: 4
  residues processed: 23
  average time/residue: 0.0823
  time to fit residues: 2.2219
Evaluate side-chains
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0010
   chunk 12 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.4786

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.146882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.131910 restraints weight = 3054.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.134537 restraints weight = 1742.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.136267 restraints weight = 1171.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.137621 restraints weight = 881.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.138548 restraints weight = 706.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2160  Z= 0.124
  Angle     :  0.491  10.295   2963  Z= 0.263
  Chirality :  0.039   0.123    364
  Planarity :  0.003   0.025    358
  Dihedral  :  4.121  17.386    311
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.62 (0.52), residues: 277
  helix:  2.91 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.25 (0.72), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.008   0.001   PHE R 139 
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 2159)
  covalent geometry    : angle       0.49104 ( 2961)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.26353 (    2)
  hydrogen bonds       : bond        0.05438 (  160)
  hydrogen bonds       : angle       3.64156 (  480)

*********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7452 (mtt) cc_final: 0.7136 (mtt)
REVERT: R   95 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8435 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 22
  average time/residue: 0.0614
  time to fit residues: 1.6703
Evaluate side-chains
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 18 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0970
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.146606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.131648 restraints weight = 3072.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.134260 restraints weight = 1735.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.136164 restraints weight = 1164.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.137586 restraints weight = 862.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.138234 restraints weight = 686.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   2160  Z= 0.121
  Angle     :  0.497  10.871   2963  Z= 0.265
  Chirality :  0.038   0.120    364
  Planarity :  0.003   0.025    358
  Dihedral  :  4.096  17.370    311
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.52), residues: 277
  helix:  3.07 (0.35), residues: 202
  sheet:  None (None), residues: 0
  loop : -2.25 (0.67), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.007   0.001   PHE R 139 
 TRP   0.004   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 2159)
  covalent geometry    : angle       0.49758 ( 2961)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.25682 (    2)
  hydrogen bonds       : bond        0.05293 (  160)
  hydrogen bonds       : angle       3.60623 (  480)

*********************** 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
  22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7384 (mtt) cc_final: 0.7062 (mtt)
REVERT: R   95 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8410 (mp)
  outliers start: 5
  outliers final: 4
  residues processed: 20
  average time/residue: 0.0305
  time to fit residues: 0.8972
Evaluate side-chains
  22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.143761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.128656 restraints weight = 3254.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131375 restraints weight = 1808.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.133129 restraints weight = 1199.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.134414 restraints weight = 899.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.135351 restraints weight = 725.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2160  Z= 0.148
  Angle     :  0.531  11.139   2963  Z= 0.285
  Chirality :  0.039   0.122    364
  Planarity :  0.004   0.025    358
  Dihedral  :  4.239  17.362    311
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.52), residues: 277
  helix:  2.79 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.22 (0.74), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.009   0.001   TYR R 308 
 PHE   0.010   0.001   PHE R 139 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2159)
  covalent geometry    : angle       0.53090 ( 2961)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.32396 (    2)
  hydrogen bonds       : bond        0.06121 (  160)
  hydrogen bonds       : angle       3.74511 (  480)

********************** 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
  26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: R   40 MET cc_start: 0.7541 (mtt) cc_final: 0.7239 (mtt)
REVERT: R   95 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8485 (mp)
  outliers start: 5
  outliers final: 4
  residues processed: 23
  average time/residue: 0.0767
  time to fit residues: 2.0855
Evaluate side-chains
  25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0470
   chunk 3 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.3878

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.147518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132691 restraints weight = 3130.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.135259 restraints weight = 1751.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.137097 restraints weight = 1160.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.138514 restraints weight = 864.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.139305 restraints weight = 691.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   2160  Z= 0.119
  Angle     :  0.498  10.919   2963  Z= 0.265
  Chirality :  0.038   0.123    364
  Planarity :  0.003   0.025    358
  Dihedral  :  4.099  17.386    311
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.52), residues: 277
  helix:  2.96 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -2.21 (0.72), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 151 
 TYR   0.008   0.001   TYR R 308 
 PHE   0.007   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 2159)
  covalent geometry    : angle       0.49795 ( 2961)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.21450 (    2)
  hydrogen bonds       : bond        0.05247 (  160)
  hydrogen bonds       : angle       3.61110 (  480)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 655.18 seconds
wall clock time: 11 minutes 59.76 seconds (719.76 seconds total)