Starting phenix.real_space_refine
on Wed Mar  5 21:07:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ctj_26992/03_2025/8ctj_26992.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ctj_26992/03_2025/8ctj_26992.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ctj_26992/03_2025/8ctj_26992.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ctj_26992/03_2025/8ctj_26992.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ctj_26992/03_2025/8ctj_26992.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ctj_26992/03_2025/8ctj_26992.cif"
  }
  resolution = 4.74
  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=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      18      5.16       5
     C    2202      2.51       5
     N     529      2.21       5
     O     562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3312
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3286
          Classifications: {'peptide': 401}
          Link IDs: {'PTRANS': 10, 'TRANS': 390}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'PEE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 27
  Time building chain proxies: 2.67, per 1000 atoms: 0.81
  Number of scatterers: 3312
  At special positions: 0
  Unit cell: (55.75, 57.98, 105.925, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P       1     15.00
     O     562      8.00
     N     529      7.00
     C    2202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  89 " - pdb=" SG  CYS A 431 " 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: 0.78
  Conformation dependent library (CDL) restraints added in 374.8 milliseconds
  

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  762

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 3 sheets defined
      59.6% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 95
      removed outlier: 3.776A  pdb=" N   TYR A  94 " --> pdb=" O   TYR A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 100 through 110
      removed outlier: 4.056A  pdb=" N   GLU A 110 " --> pdb=" O   GLU A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 133
      removed outlier: 3.745A  pdb=" N   LEU A 131 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE A 132 " --> pdb=" O   CYS A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 251
      removed outlier: 3.647A  pdb=" N   MET A 227 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 228 " --> pdb=" O   TYR A 224 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   CYS A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   TYR A 251 " --> pdb=" O   TRP A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 285
      removed outlier: 3.586A  pdb=" N   PHE A 260 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 317
      removed outlier: 3.642A  pdb=" N   LEU A 294 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 353
      removed outlier: 4.554A  pdb=" N   MET A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 393
      removed outlier: 4.074A  pdb=" N   PHE A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ILE A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
      Proline residue:  A 366  - end of helix
    Processing helix  chain 'A' and resid 394 through 428
      removed outlier: 3.747A  pdb=" N   ARG A 427 " --> pdb=" O   THR A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 460
    Processing helix  chain 'A' and resid 465 through 471
      removed outlier: 4.007A  pdb=" N   PHE A 471 " --> pdb=" O   GLN A 467 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59
    Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59

    228 hydrogen bonds defined for protein.
    663 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: 0.90

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 977
        1.34 -     1.47: 929
        1.47 -     1.60: 1461
        1.60 -     1.73: 1
        1.73 -     1.86: 30
  Bond restraints: 3398
  Sorted by residual:
  bond pdb=" O4P PEE A 601 "
       pdb=" P   PEE A 601 "
    ideal  model  delta    sigma   weight residual
    1.653  1.776 -0.123 2.00e-02 2.50e+03 3.81e+01
  bond pdb=" C1  PEE A 601 "
       pdb=" C2  PEE A 601 "
    ideal  model  delta    sigma   weight residual
    1.519  1.555 -0.036 2.00e-02 2.50e+03 3.19e+00
  bond pdb=" CA  ASP A  75 "
       pdb=" CB  ASP A  75 "
    ideal  model  delta    sigma   weight residual
    1.531  1.577 -0.047 3.12e-02 1.03e+03 2.25e+00
  bond pdb=" CB  CYS A  74 "
       pdb=" SG  CYS A  74 "
    ideal  model  delta    sigma   weight residual
    1.808  1.855 -0.047 3.30e-02 9.18e+02 2.05e+00
  bond pdb=" C2  PEE A 601 "
       pdb=" C3  PEE A 601 "
    ideal  model  delta    sigma   weight residual
    1.512  1.540 -0.028 2.00e-02 2.50e+03 2.03e+00
  ... (remaining 3393 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 4511
        2.78 -     5.57: 71
        5.57 -     8.35: 20
        8.35 -    11.14: 0
       11.14 -    13.92: 1
  Bond angle restraints: 4603
  Sorted by residual:
  angle pdb=" O1P PEE A 601 "
        pdb=" P   PEE A 601 "
        pdb=" O2P PEE A 601 "
      ideal   model   delta    sigma   weight residual
     119.43  133.35  -13.92 3.00e+00 1.11e-01 2.15e+01
  angle pdb=" CA  LYS A 213 "
        pdb=" CB  LYS A 213 "
        pdb=" CG  LYS A 213 "
      ideal   model   delta    sigma   weight residual
     114.10  121.83   -7.73 2.00e+00 2.50e-01 1.49e+01
  angle pdb=" N   GLN A 135 "
        pdb=" CA  GLN A 135 "
        pdb=" C   GLN A 135 "
      ideal   model   delta    sigma   weight residual
     110.44  106.16    4.28 1.20e+00 6.94e-01 1.27e+01
  angle pdb=" CA  TRP A 252 "
        pdb=" CB  TRP A 252 "
        pdb=" CG  TRP A 252 "
      ideal   model   delta    sigma   weight residual
     113.60  120.05   -6.45 1.90e+00 2.77e-01 1.15e+01
  angle pdb=" CA  MET A 231 "
        pdb=" CB  MET A 231 "
        pdb=" CG  MET A 231 "
      ideal   model   delta    sigma   weight residual
     114.10  120.85   -6.75 2.00e+00 2.50e-01 1.14e+01
  ... (remaining 4598 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.18: 1924
       29.18 -    58.35: 50
       58.35 -    87.53: 6
       87.53 -   116.71: 0
      116.71 -   145.89: 2
  Dihedral angle restraints: 1982
    sinusoidal: 805
      harmonic: 1177
  Sorted by residual:
  dihedral pdb=" CB  CYS A  89 "
           pdb=" SG  CYS A  89 "
           pdb=" SG  CYS A 431 "
           pdb=" CB  CYS A 431 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.73  -51.73     1      1.00e+01 1.00e-02 3.65e+01
  dihedral pdb=" O2  PEE A 601 "
           pdb=" C1  PEE A 601 "
           pdb=" C2  PEE A 601 "
           pdb=" O3P PEE A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.96   85.93 -145.89     1      3.00e+01 1.11e-03 1.95e+01
  dihedral pdb=" C3  PEE A 601 "
           pdb=" C1  PEE A 601 "
           pdb=" C2  PEE A 601 "
           pdb=" O3P PEE A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73 -156.57 -140.70     1      3.00e+01 1.11e-03 1.89e+01
  ... (remaining 1979 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 459
       0.077 -    0.155: 54
       0.155 -    0.232: 6
       0.232 -    0.309: 0
       0.309 -    0.387: 1
  Chirality restraints: 520
  Sorted by residual:
  chirality pdb=" C2  PEE A 601 "
            pdb=" C1  PEE A 601 "
            pdb=" C3  PEE A 601 "
            pdb=" O2  PEE A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.39 2.00e-01 2.50e+01 3.74e+00
  chirality pdb=" CB  ILE A  44 "
            pdb=" CA  ILE A  44 "
            pdb=" CG1 ILE A  44 "
            pdb=" CG2 ILE A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  THR A 405 "
            pdb=" CA  THR A 405 "
            pdb=" OG1 THR A 405 "
            pdb=" CG2 THR A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 517 not shown)

  Planarity restraints: 551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 371 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.62e+00
        pdb=" CG  ASP A 371 "   -0.041 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 371 "    0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 371 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 135 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.93e+00
        pdb=" C   GLN A 135 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   GLN A 135 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 136 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 404 "   -0.010 2.00e-02 2.50e+03   1.54e-02 4.17e+00
        pdb=" CG  PHE A 404 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 404 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 404 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 404 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 404 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 404 "    0.001 2.00e-02 2.50e+03
  ... (remaining 548 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 536
        2.77 -     3.30: 3273
        3.30 -     3.83: 5397
        3.83 -     4.37: 5945
        4.37 -     4.90: 10260
  Nonbonded interactions: 25411
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 340 "
            pdb=" OG  SER A 344 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER A  77 "
            pdb=" O   SER A 191 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ILE A 419 "
            pdb=" OG1 THR A 423 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ASN A 200 "
            pdb=" OG  SER A 203 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   SER A 399 "
            pdb=" ND1 HIS A 403 "
     model   vdw
     2.381 3.120
  ... (remaining 25406 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.830
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4996
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.123   3398  Z= 0.264
  Angle     :  0.917  13.923   4603  Z= 0.487
  Chirality :  0.051   0.387    520
  Planarity :  0.006   0.052    551
  Dihedral  : 14.667 145.887   1214
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  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: -0.72 (0.41), residues: 395
  helix:  0.26 (0.32), residues: 229
  sheet: -1.55 (0.73), residues: 47
  loop : -1.24 (0.56), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 244 
 HIS   0.001   0.000   HIS A  43 
 PHE   0.035   0.003   PHE A 379 
 TYR   0.018   0.003   TYR A 277 
 ARG   0.010   0.001   ARG A 112 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.1993 (mtt) cc_final: 0.1692 (mtt)
REVERT: A  227 MET cc_start: 0.8191 (tmm) cc_final: 0.7913 (tmm)
REVERT: A  270 MET cc_start: 0.4612 (mmt) cc_final: 0.3946 (mmt)
REVERT: A  386 MET cc_start: 0.8365 (tpp) cc_final: 0.7971 (tpp)
REVERT: A  438 LEU cc_start: 0.6769 (mp) cc_final: 0.6373 (tp)
REVERT: A  440 VAL cc_start: 0.9073 (t) cc_final: 0.8753 (p)
REVERT: A  453 LEU cc_start: 0.8336 (mt) cc_final: 0.8123 (mt)
REVERT: A  457 MET cc_start: 0.5495 (mtm) cc_final: 0.4779 (ptp)
REVERT: A  467 GLN cc_start: 0.8176 (tt0) cc_final: 0.7943 (tt0)
REVERT: A  468 ARG cc_start: 0.8817 (mtm180) cc_final: 0.7808 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1913
  time to fit residues: 24.5879
Evaluate side-chains
  87 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
A 135 GLN
A 143 HIS
A 356 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.201466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.175152 restraints weight = 5768.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.181140 restraints weight = 3711.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.185650 restraints weight = 2540.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5515
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3398  Z= 0.248
  Angle     :  0.740  12.140   4603  Z= 0.382
  Chirality :  0.045   0.188    520
  Planarity :  0.006   0.054    551
  Dihedral  : 11.633 134.256    453
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  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: -0.03 (0.41), residues: 395
  helix:  0.91 (0.32), residues: 236
  sheet: -1.30 (0.74), residues: 47
  loop : -1.31 (0.56), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 252 
 HIS   0.005   0.002   HIS A  43 
 PHE   0.025   0.003   PHE A 276 
 TYR   0.011   0.002   TYR A 118 
 ARG   0.009   0.001   ARG A 393 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.7050 (mmmt) cc_final: 0.6829 (mppt)
REVERT: A   80 ILE cc_start: 0.8246 (mt) cc_final: 0.7217 (mt)
REVERT: A   91 ASN cc_start: 0.7260 (m-40) cc_final: 0.6619 (p0)
REVERT: A  132 PHE cc_start: 0.6207 (t80) cc_final: 0.5949 (t80)
REVERT: A  206 PHE cc_start: 0.7196 (m-80) cc_final: 0.6761 (m-80)
REVERT: A  227 MET cc_start: 0.8379 (tmm) cc_final: 0.8038 (tmm)
REVERT: A  386 MET cc_start: 0.8417 (tpp) cc_final: 0.8042 (tpp)
REVERT: A  387 LYS cc_start: 0.8985 (tptt) cc_final: 0.8568 (ttmt)
REVERT: A  438 LEU cc_start: 0.7872 (mp) cc_final: 0.7193 (tp)
REVERT: A  453 LEU cc_start: 0.8319 (mt) cc_final: 0.7995 (mt)
REVERT: A  457 MET cc_start: 0.6446 (mtm) cc_final: 0.5703 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1734
  time to fit residues: 21.8626
Evaluate side-chains
  90 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 187 HIS
A 356 GLN
A 394 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.205317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.179199 restraints weight = 5982.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.184881 restraints weight = 3971.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.189188 restraints weight = 2780.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5614
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3398  Z= 0.202
  Angle     :  0.632  11.327   4603  Z= 0.326
  Chirality :  0.042   0.149    520
  Planarity :  0.005   0.033    551
  Dihedral  : 11.073 125.588    453
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  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:  0.53 (0.42), residues: 395
  helix:  1.54 (0.34), residues: 216
  sheet: -1.07 (0.75), residues: 47
  loop : -1.06 (0.53), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 177 
 HIS   0.008   0.002   HIS A 187 
 PHE   0.015   0.002   PHE A 404 
 TYR   0.021   0.002   TYR A  94 
 ARG   0.004   0.001   ARG A  39 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.8176 (mp0) cc_final: 0.7899 (mp0)
REVERT: A   80 ILE cc_start: 0.8184 (mt) cc_final: 0.7378 (mt)
REVERT: A   97 LYS cc_start: 0.8510 (tmtt) cc_final: 0.8267 (tptp)
REVERT: A  119 GLN cc_start: 0.6838 (pt0) cc_final: 0.6304 (pt0)
REVERT: A  142 MET cc_start: 0.3467 (mpp) cc_final: 0.1383 (mtt)
REVERT: A  184 PHE cc_start: 0.8366 (t80) cc_final: 0.8149 (t80)
REVERT: A  206 PHE cc_start: 0.7123 (m-80) cc_final: 0.6864 (m-80)
REVERT: A  227 MET cc_start: 0.8502 (tmm) cc_final: 0.8058 (tmm)
REVERT: A  270 MET cc_start: 0.5756 (mmp) cc_final: 0.4981 (mmp)
REVERT: A  298 GLU cc_start: 0.8094 (tp30) cc_final: 0.7642 (tp30)
REVERT: A  386 MET cc_start: 0.8173 (tpp) cc_final: 0.7776 (tpp)
REVERT: A  387 LYS cc_start: 0.8957 (tptt) cc_final: 0.8624 (tttp)
REVERT: A  435 TRP cc_start: 0.7835 (p-90) cc_final: 0.7397 (p-90)
REVERT: A  437 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7353 (mm-30)
REVERT: A  438 LEU cc_start: 0.8102 (mp) cc_final: 0.7871 (mp)
REVERT: A  439 TRP cc_start: 0.8380 (p-90) cc_final: 0.8127 (p-90)
REVERT: A  453 LEU cc_start: 0.8335 (mt) cc_final: 0.7950 (mt)
REVERT: A  457 MET cc_start: 0.6133 (mtm) cc_final: 0.5570 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1598
  time to fit residues: 20.8777
Evaluate side-chains
  92 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 32 optimal weight:    0.2980
   chunk 33 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
A 135 GLN
A 356 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.203507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.177275 restraints weight = 6036.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.183080 restraints weight = 3893.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.187594 restraints weight = 2719.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5695
moved from start:          0.6563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3398  Z= 0.178
  Angle     :  0.616  10.355   4603  Z= 0.320
  Chirality :  0.041   0.170    520
  Planarity :  0.004   0.034    551
  Dihedral  : 10.478 118.258    453
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  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:  0.70 (0.42), residues: 395
  helix:  1.71 (0.34), residues: 218
  sheet: -0.91 (0.65), residues: 57
  loop : -1.13 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 252 
 HIS   0.003   0.001   HIS A  43 
 PHE   0.011   0.002   PHE A 206 
 TYR   0.014   0.002   TYR A  94 
 ARG   0.005   0.001   ARG A 257 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.8204 (mp0) cc_final: 0.7796 (mp0)
REVERT: A   80 ILE cc_start: 0.8307 (mt) cc_final: 0.7664 (mt)
REVERT: A  132 PHE cc_start: 0.6383 (t80) cc_final: 0.6105 (t80)
REVERT: A  206 PHE cc_start: 0.7365 (m-80) cc_final: 0.6933 (m-80)
REVERT: A  227 MET cc_start: 0.8633 (tmm) cc_final: 0.8047 (tmm)
REVERT: A  259 GLN cc_start: 0.8158 (mp10) cc_final: 0.7675 (mp10)
REVERT: A  270 MET cc_start: 0.6014 (mmp) cc_final: 0.4801 (mmt)
REVERT: A  288 GLU cc_start: 0.5748 (tt0) cc_final: 0.5157 (tt0)
REVERT: A  298 GLU cc_start: 0.8061 (tp30) cc_final: 0.7766 (tp30)
REVERT: A  386 MET cc_start: 0.8399 (tpp) cc_final: 0.7918 (tpp)
REVERT: A  387 LYS cc_start: 0.8963 (tptt) cc_final: 0.8574 (tttp)
REVERT: A  424 MET cc_start: 0.7548 (mpp) cc_final: 0.7333 (mmm)
REVERT: A  435 TRP cc_start: 0.7906 (p-90) cc_final: 0.7167 (p-90)
REVERT: A  437 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7128 (mm-30)
REVERT: A  457 MET cc_start: 0.6322 (mtm) cc_final: 0.5178 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1666
  time to fit residues: 20.5317
Evaluate side-chains
  89 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
A 135 GLN
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.198323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.173328 restraints weight = 6298.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.179162 restraints weight = 4024.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.183452 restraints weight = 2762.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5892
moved from start:          0.8377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3398  Z= 0.238
  Angle     :  0.700  10.953   4603  Z= 0.366
  Chirality :  0.044   0.174    520
  Planarity :  0.005   0.037    551
  Dihedral  : 10.763 114.712    453
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.42), residues: 395
  helix:  1.14 (0.34), residues: 222
  sheet: -1.32 (0.65), residues: 55
  loop : -1.21 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 252 
 HIS   0.009   0.002   HIS A 187 
 PHE   0.018   0.002   PHE A 184 
 TYR   0.031   0.003   TYR A  94 
 ARG   0.006   0.001   ARG A  39 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8062 (mmmm)
REVERT: A   80 ILE cc_start: 0.8467 (mt) cc_final: 0.7869 (mt)
REVERT: A   97 LYS cc_start: 0.8838 (mttt) cc_final: 0.8141 (mmmt)
REVERT: A  143 HIS cc_start: 0.5783 (m-70) cc_final: 0.5372 (t-90)
REVERT: A  227 MET cc_start: 0.8590 (tmm) cc_final: 0.8031 (tmm)
REVERT: A  259 GLN cc_start: 0.8231 (mp10) cc_final: 0.7882 (mp10)
REVERT: A  298 GLU cc_start: 0.8286 (tp30) cc_final: 0.7977 (tp30)
REVERT: A  386 MET cc_start: 0.8495 (tpp) cc_final: 0.8015 (tpp)
REVERT: A  387 LYS cc_start: 0.8973 (tptt) cc_final: 0.8536 (tttp)
REVERT: A  396 VAL cc_start: 0.7603 (m) cc_final: 0.7350 (t)
REVERT: A  401 TYR cc_start: 0.8941 (m-10) cc_final: 0.8676 (m-10)
REVERT: A  424 MET cc_start: 0.7499 (mpp) cc_final: 0.7232 (mmm)
REVERT: A  448 LEU cc_start: 0.9376 (pp) cc_final: 0.9063 (pp)
REVERT: A  451 MET cc_start: 0.7358 (mtt) cc_final: 0.6680 (mtt)
REVERT: A  457 MET cc_start: 0.6873 (mtm) cc_final: 0.6309 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1470
  time to fit residues: 19.3718
Evaluate side-chains
  96 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0770
   chunk 23 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.197488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.172707 restraints weight = 6038.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.179065 restraints weight = 3749.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.183643 restraints weight = 2456.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5899
moved from start:          0.9116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3398  Z= 0.205
  Angle     :  0.680   9.587   4603  Z= 0.355
  Chirality :  0.045   0.341    520
  Planarity :  0.005   0.054    551
  Dihedral  : 10.495 109.698    453
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  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:  0.34 (0.42), residues: 395
  helix:  1.39 (0.34), residues: 224
  sheet: -1.29 (0.71), residues: 49
  loop : -1.26 (0.55), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  82 
 HIS   0.003   0.001   HIS A 331 
 PHE   0.023   0.002   PHE A 240 
 TYR   0.025   0.002   TYR A  94 
 ARG   0.005   0.001   ARG A 446 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8174 (mmmm)
REVERT: A   80 ILE cc_start: 0.8263 (mt) cc_final: 0.7675 (mt)
REVERT: A   81 THR cc_start: 0.8080 (p) cc_final: 0.7874 (p)
REVERT: A   97 LYS cc_start: 0.8753 (mttt) cc_final: 0.8061 (mmmt)
REVERT: A  132 PHE cc_start: 0.6526 (t80) cc_final: 0.6304 (t80)
REVERT: A  221 LEU cc_start: 0.9472 (mt) cc_final: 0.9271 (mt)
REVERT: A  273 LYS cc_start: 0.8369 (mttt) cc_final: 0.8035 (mmmm)
REVERT: A  298 GLU cc_start: 0.8192 (tp30) cc_final: 0.7905 (tp30)
REVERT: A  386 MET cc_start: 0.8461 (tpp) cc_final: 0.8038 (tpp)
REVERT: A  387 LYS cc_start: 0.8964 (tptt) cc_final: 0.8519 (tttp)
REVERT: A  396 VAL cc_start: 0.7492 (m) cc_final: 0.7206 (t)
REVERT: A  401 TYR cc_start: 0.9009 (m-10) cc_final: 0.8674 (m-10)
REVERT: A  448 LEU cc_start: 0.9429 (pp) cc_final: 0.9091 (pp)
REVERT: A  451 MET cc_start: 0.7527 (mtt) cc_final: 0.6805 (mtt)
REVERT: A  453 LEU cc_start: 0.8523 (mt) cc_final: 0.8318 (mt)
REVERT: A  457 MET cc_start: 0.6825 (mtm) cc_final: 0.6258 (mtm)
REVERT: A  467 GLN cc_start: 0.7757 (tt0) cc_final: 0.7509 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1495
  time to fit residues: 20.6293
Evaluate side-chains
  103 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.199785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.174893 restraints weight = 5929.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.181116 restraints weight = 3641.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.185598 restraints weight = 2405.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5906
moved from start:          0.9819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3398  Z= 0.183
  Angle     :  0.648   8.581   4603  Z= 0.337
  Chirality :  0.043   0.319    520
  Planarity :  0.004   0.041    551
  Dihedral  :  9.989 102.211    453
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  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:  0.55 (0.43), residues: 395
  helix:  1.62 (0.34), residues: 224
  sheet: -1.65 (0.66), residues: 55
  loop : -1.00 (0.57), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  82 
 HIS   0.003   0.001   HIS A 187 
 PHE   0.041   0.002   PHE A 240 
 TYR   0.019   0.002   TYR A  94 
 ARG   0.004   0.001   ARG A 446 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8476 (mmmm) cc_final: 0.8073 (mmmm)
REVERT: A   80 ILE cc_start: 0.8388 (mt) cc_final: 0.7877 (mt)
REVERT: A   95 ASN cc_start: 0.9212 (m110) cc_final: 0.8961 (m110)
REVERT: A  132 PHE cc_start: 0.6618 (t80) cc_final: 0.6343 (t80)
REVERT: A  288 GLU cc_start: 0.5787 (tt0) cc_final: 0.5482 (tt0)
REVERT: A  298 GLU cc_start: 0.8195 (tp30) cc_final: 0.7828 (tp30)
REVERT: A  386 MET cc_start: 0.8547 (tpp) cc_final: 0.8073 (tpp)
REVERT: A  387 LYS cc_start: 0.8975 (tptt) cc_final: 0.8512 (tttp)
REVERT: A  396 VAL cc_start: 0.7493 (m) cc_final: 0.7276 (t)
REVERT: A  401 TYR cc_start: 0.9025 (m-10) cc_final: 0.8708 (m-10)
REVERT: A  448 LEU cc_start: 0.9439 (pp) cc_final: 0.9192 (pp)
REVERT: A  451 MET cc_start: 0.7420 (mtt) cc_final: 0.6766 (mtt)
REVERT: A  457 MET cc_start: 0.7204 (mtm) cc_final: 0.6776 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1283
  time to fit residues: 17.1086
Evaluate side-chains
  97 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 7 optimal weight:    7.9990
   chunk 18 optimal weight:    0.2980
   chunk 5 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
A 135 GLN
A 356 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.200642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.175510 restraints weight = 5789.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.181744 restraints weight = 3530.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.186372 restraints weight = 2323.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5875
moved from start:          1.0240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3398  Z= 0.176
  Angle     :  0.674   8.009   4603  Z= 0.347
  Chirality :  0.044   0.272    520
  Planarity :  0.004   0.038    551
  Dihedral  :  9.560  95.181    453
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  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:  0.63 (0.42), residues: 395
  helix:  1.63 (0.35), residues: 219
  sheet: -1.26 (0.68), residues: 49
  loop : -0.99 (0.55), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  82 
 HIS   0.002   0.001   HIS A  43 
 PHE   0.037   0.002   PHE A 240 
 TYR   0.019   0.002   TYR A 118 
 ARG   0.004   0.000   ARG A  61 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.5918 (mmtm) cc_final: 0.5414 (pttt)
REVERT: A   80 ILE cc_start: 0.8280 (mt) cc_final: 0.7661 (mt)
REVERT: A   95 ASN cc_start: 0.9226 (m110) cc_final: 0.8965 (m110)
REVERT: A  132 PHE cc_start: 0.6729 (t80) cc_final: 0.6470 (t80)
REVERT: A  227 MET cc_start: 0.8213 (tmm) cc_final: 0.8004 (tmm)
REVERT: A  288 GLU cc_start: 0.5753 (tt0) cc_final: 0.5384 (tt0)
REVERT: A  298 GLU cc_start: 0.8123 (tp30) cc_final: 0.7748 (tp30)
REVERT: A  386 MET cc_start: 0.8622 (tpp) cc_final: 0.8173 (tpp)
REVERT: A  387 LYS cc_start: 0.8975 (tptt) cc_final: 0.8514 (tttp)
REVERT: A  396 VAL cc_start: 0.7559 (m) cc_final: 0.7319 (t)
REVERT: A  401 TYR cc_start: 0.9019 (m-10) cc_final: 0.8703 (m-10)
REVERT: A  437 GLU cc_start: 0.7202 (tp30) cc_final: 0.6336 (tp30)
REVERT: A  438 LEU cc_start: 0.8714 (mp) cc_final: 0.8459 (mp)
REVERT: A  448 LEU cc_start: 0.9446 (pp) cc_final: 0.9234 (pp)
REVERT: A  451 MET cc_start: 0.7378 (mtt) cc_final: 0.6724 (mtt)
REVERT: A  457 MET cc_start: 0.7388 (mtm) cc_final: 0.6802 (mtm)
REVERT: A  467 GLN cc_start: 0.7446 (tt0) cc_final: 0.7240 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1304
  time to fit residues: 16.3946
Evaluate side-chains
  96 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0040
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0470
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5892

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.201445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.176778 restraints weight = 5898.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.182649 restraints weight = 3645.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.187205 restraints weight = 2435.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5915
moved from start:          1.0826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3398  Z= 0.174
  Angle     :  0.642   7.664   4603  Z= 0.333
  Chirality :  0.043   0.267    520
  Planarity :  0.004   0.035    551
  Dihedral  :  8.763  82.758    453
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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:  0.72 (0.42), residues: 395
  helix:  1.71 (0.35), residues: 219
  sheet: -1.17 (0.69), residues: 53
  loop : -0.96 (0.54), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  82 
 HIS   0.003   0.001   HIS A  43 
 PHE   0.034   0.002   PHE A 240 
 TYR   0.014   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A  61 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.5835 (mmtm) cc_final: 0.5343 (pttt)
REVERT: A   80 ILE cc_start: 0.8450 (mt) cc_final: 0.7873 (mt)
REVERT: A   95 ASN cc_start: 0.9302 (m110) cc_final: 0.9021 (m110)
REVERT: A  132 PHE cc_start: 0.6915 (t80) cc_final: 0.6638 (t80)
REVERT: A  227 MET cc_start: 0.8027 (tmm) cc_final: 0.7802 (tmm)
REVERT: A  270 MET cc_start: 0.5494 (mmp) cc_final: 0.5241 (mmt)
REVERT: A  298 GLU cc_start: 0.8225 (tp30) cc_final: 0.7758 (tp30)
REVERT: A  386 MET cc_start: 0.8643 (tpp) cc_final: 0.8174 (tpp)
REVERT: A  387 LYS cc_start: 0.8904 (tptt) cc_final: 0.8508 (tttp)
REVERT: A  396 VAL cc_start: 0.7638 (m) cc_final: 0.7393 (t)
REVERT: A  401 TYR cc_start: 0.8980 (m-10) cc_final: 0.8672 (m-10)
REVERT: A  437 GLU cc_start: 0.7333 (tp30) cc_final: 0.6500 (tp30)
REVERT: A  438 LEU cc_start: 0.8630 (mp) cc_final: 0.8428 (mp)
REVERT: A  451 MET cc_start: 0.7500 (mtt) cc_final: 0.6781 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1362
  time to fit residues: 17.4221
Evaluate side-chains
  93 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0470
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.203248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.177768 restraints weight = 5847.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.184125 restraints weight = 3566.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.188546 restraints weight = 2353.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5926
moved from start:          1.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3398  Z= 0.190
  Angle     :  0.676   8.346   4603  Z= 0.351
  Chirality :  0.044   0.264    520
  Planarity :  0.004   0.035    551
  Dihedral  :  8.171  84.040    453
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  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:  0.81 (0.43), residues: 395
  helix:  1.74 (0.35), residues: 219
  sheet: -0.87 (0.74), residues: 49
  loop : -0.95 (0.55), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  82 
 HIS   0.003   0.001   HIS A  43 
 PHE   0.035   0.002   PHE A 240 
 TYR   0.020   0.002   TYR A  94 
 ARG   0.004   0.000   ARG A 446 

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.5786 (mmtm) cc_final: 0.5164 (pttt)
REVERT: A   80 ILE cc_start: 0.8499 (mt) cc_final: 0.7845 (mt)
REVERT: A  132 PHE cc_start: 0.7094 (t80) cc_final: 0.6788 (t80)
REVERT: A  206 PHE cc_start: 0.8613 (m-80) cc_final: 0.7551 (m-80)
REVERT: A  221 LEU cc_start: 0.9292 (mt) cc_final: 0.9008 (mt)
REVERT: A  227 MET cc_start: 0.8024 (tmm) cc_final: 0.7642 (tmm)
REVERT: A  234 CYS cc_start: 0.7444 (m) cc_final: 0.7205 (m)
REVERT: A  298 GLU cc_start: 0.8158 (tp30) cc_final: 0.7823 (tp30)
REVERT: A  386 MET cc_start: 0.8683 (tpp) cc_final: 0.8027 (tpp)
REVERT: A  387 LYS cc_start: 0.8791 (tptt) cc_final: 0.8430 (tttp)
REVERT: A  396 VAL cc_start: 0.7851 (m) cc_final: 0.7631 (t)
REVERT: A  401 TYR cc_start: 0.8994 (m-10) cc_final: 0.8680 (m-10)
REVERT: A  436 ARG cc_start: 0.8343 (mmt180) cc_final: 0.7998 (mmm-85)
REVERT: A  437 GLU cc_start: 0.7305 (tp30) cc_final: 0.6427 (tp30)
REVERT: A  447 LEU cc_start: 0.8246 (tp) cc_final: 0.8007 (tp)
REVERT: A  448 LEU cc_start: 0.9481 (pp) cc_final: 0.9280 (pp)
REVERT: A  451 MET cc_start: 0.7517 (mtt) cc_final: 0.6845 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1480
  time to fit residues: 19.5000
Evaluate side-chains
  98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0670
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.0922

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.197130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.172993 restraints weight = 6005.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.179177 restraints weight = 3658.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.183539 restraints weight = 2399.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6056
moved from start:          1.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3398  Z= 0.232
  Angle     :  0.757   9.510   4603  Z= 0.391
  Chirality :  0.047   0.294    520
  Planarity :  0.005   0.038    551
  Dihedral  :  8.102  87.065    453
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  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:  0.54 (0.42), residues: 395
  helix:  1.48 (0.34), residues: 218
  sheet: -1.08 (0.72), residues: 49
  loop : -0.93 (0.55), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  82 
 HIS   0.004   0.002   HIS A 143 
 PHE   0.034   0.002   PHE A 240 
 TYR   0.022   0.003   TYR A  94 
 ARG   0.016   0.001   ARG A 392 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1326.37 seconds
wall clock time: 23 minutes 39.78 seconds (1419.78 seconds total)