Starting phenix.real_space_refine
on Tue Mar  3 11:51:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ctj_26992/03_2026/8ctj_26992.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ctj_26992/03_2026/8ctj_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_2026/8ctj_26992.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ctj_26992/03_2026/8ctj_26992.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ctj_26992/03_2026/8ctj_26992.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ctj_26992/03_2026/8ctj_26992.cif"
  }
  resolution = 4.74
  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=   0.005
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.84, per 1000 atoms: 0.25
  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: 0.26
  Conformation dependent library (CDL) restraints added in 89.0 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: 0.10
  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: 0.54

  Time building geometry restraints manager: 0.34 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:             0.210
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.150
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.710
-------------------------------------------------------------------------------
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   3400  Z= 0.229
  Angle     :  0.922  13.923   4607  Z= 0.489
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.010   0.001   ARG A 112 
 TYR   0.018   0.003   TYR A 277 
 PHE   0.035   0.003   PHE A 379 
 TRP   0.018   0.002   TRP A 244 
 HIS   0.001   0.000   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 3398)
  covalent geometry    : angle       0.91738 ( 4603)
  SS BOND              : bond        0.00366 (    2)
  SS BOND              : angle       3.23547 (    4)
  hydrogen bonds       : bond        0.08706 (  210)
  hydrogen bonds       : angle       5.67420 (  663)

*********************** 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  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.1994 (mtt) cc_final: 0.1692 (mtt)
REVERT: A  227 MET cc_start: 0.8191 (tmm) cc_final: 0.7912 (tmm)
REVERT: A  270 MET cc_start: 0.4612 (mmt) cc_final: 0.3934 (mmt)
REVERT: A  386 MET cc_start: 0.8365 (tpp) cc_final: 0.7974 (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: 0.8751 (p)
REVERT: A  453 LEU cc_start: 0.8336 (mt) cc_final: 0.8133 (mt)
REVERT: A  457 MET cc_start: 0.5495 (mtm) cc_final: 0.4813 (ptp)
REVERT: A  467 GLN cc_start: 0.8176 (tt0) cc_final: 0.7944 (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: 0.0812
  time to fit residues: 10.4534
Evaluate side-chains
  86 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0020
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.204729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.177755 restraints weight = 5929.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.183625 restraints weight = 3869.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.188084 restraints weight = 2696.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.191346 restraints weight = 1959.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.193973 restraints weight = 1483.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5330
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3400  Z= 0.141
  Angle     :  0.650   9.634   4607  Z= 0.338
  Chirality :  0.043   0.182    520
  Planarity :  0.005   0.047    551
  Dihedral  : 11.364 132.691    453
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.42), residues: 395
  helix:  1.12 (0.32), residues: 236
  sheet: -1.02 (0.68), residues: 52
  loop : -1.25 (0.60), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 393 
 TYR   0.010   0.002   TYR A 340 
 PHE   0.022   0.002   PHE A 276 
 TRP   0.010   0.001   TRP A 252 
 HIS   0.005   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3398)
  covalent geometry    : angle       0.64913 ( 4603)
  SS BOND              : bond        0.00159 (    2)
  SS BOND              : angle       1.55177 (    4)
  hydrogen bonds       : bond        0.03789 (  210)
  hydrogen bonds       : angle       4.60418 (  663)

*********************** 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
  103 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.081 
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: symmetry clash
REVERT: A   80 ILE cc_start: 0.8153 (mt) cc_final: 0.7795 (mp)
REVERT: A   91 ASN cc_start: 0.6889 (m-40) cc_final: 0.6227 (p0)
REVERT: A  206 PHE cc_start: 0.7004 (m-80) cc_final: 0.6610 (m-80)
REVERT: A  227 MET cc_start: 0.8290 (tmm) cc_final: 0.7913 (tmm)
REVERT: A  386 MET cc_start: 0.8186 (tpp) cc_final: 0.7811 (tpp)
REVERT: A  387 LYS cc_start: 0.8981 (tptt) cc_final: 0.8568 (ttmt)
REVERT: A  438 LEU cc_start: 0.7350 (mp) cc_final: 0.6810 (tp)
REVERT: A  451 MET cc_start: 0.6692 (mtt) cc_final: 0.6482 (mtp)
REVERT: A  453 LEU cc_start: 0.8390 (mt) cc_final: 0.8048 (mt)
REVERT: A  457 MET cc_start: 0.6181 (mtm) cc_final: 0.5526 (ptp)
REVERT: A  467 GLN cc_start: 0.8092 (tt0) cc_final: 0.7889 (tt0)
REVERT: A  468 ARG cc_start: 0.8803 (mtm180) cc_final: 0.7535 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0775
  time to fit residues: 9.4115
Evaluate side-chains
  83 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
A 356 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.206764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.180400 restraints weight = 6043.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.186269 restraints weight = 4011.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.190711 restraints weight = 2785.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.194079 restraints weight = 2010.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.196477 restraints weight = 1490.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5428
moved from start:          0.4486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3400  Z= 0.132
  Angle     :  0.596  10.005   4607  Z= 0.306
  Chirality :  0.040   0.137    520
  Planarity :  0.004   0.028    551
  Dihedral  : 11.085 127.638    453
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.42), residues: 395
  helix:  1.44 (0.34), residues: 224
  sheet: -0.88 (0.69), residues: 54
  loop : -0.83 (0.60), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  61 
 TYR   0.016   0.002   TYR A 118 
 PHE   0.021   0.002   PHE A 404 
 TRP   0.017   0.001   TRP A 177 
 HIS   0.006   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3398)
  covalent geometry    : angle       0.59247 ( 4603)
  SS BOND              : bond        0.00543 (    2)
  SS BOND              : angle       2.20847 (    4)
  hydrogen bonds       : bond        0.03660 (  210)
  hydrogen bonds       : angle       4.45977 (  663)

*********************** 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
  98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8095 (mt) cc_final: 0.7705 (mt)
REVERT: A   91 ASN cc_start: 0.7555 (m-40) cc_final: 0.6880 (p0)
REVERT: A   97 LYS cc_start: 0.8532 (tmtt) cc_final: 0.8292 (tptp)
REVERT: A  142 MET cc_start: 0.3488 (mpp) cc_final: 0.1668 (mtt)
REVERT: A  206 PHE cc_start: 0.6954 (m-80) cc_final: 0.6750 (m-80)
REVERT: A  227 MET cc_start: 0.8454 (tmm) cc_final: 0.7945 (tmm)
REVERT: A  270 MET cc_start: 0.5572 (mmp) cc_final: 0.5209 (mmt)
REVERT: A  298 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6907 (tp30)
REVERT: A  386 MET cc_start: 0.8182 (tpp) cc_final: 0.7848 (tpp)
REVERT: A  387 LYS cc_start: 0.8909 (tptt) cc_final: 0.8567 (tttp)
REVERT: A  438 LEU cc_start: 0.7869 (mp) cc_final: 0.7249 (tp)
REVERT: A  453 LEU cc_start: 0.8295 (mt) cc_final: 0.7931 (mt)
REVERT: A  457 MET cc_start: 0.6042 (mtm) cc_final: 0.5516 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0665
  time to fit residues: 7.9602
Evaluate side-chains
  79 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    0.2980
   chunk 16 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 143 HIS
** 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 = 0.4361 r_free = 0.4361 target = 0.201006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.178034 restraints weight = 6122.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.183565 restraints weight = 3947.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.187520 restraints weight = 2704.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.190348 restraints weight = 1916.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.192508 restraints weight = 1418.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5846
moved from start:          0.7223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3400  Z= 0.213
  Angle     :  0.805  13.058   4607  Z= 0.413
  Chirality :  0.046   0.249    520
  Planarity :  0.006   0.076    551
  Dihedral  : 11.260 120.192    453
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.41), residues: 395
  helix:  1.20 (0.33), residues: 218
  sheet: -1.37 (0.62), residues: 58
  loop : -1.27 (0.56), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  39 
 TYR   0.025   0.003   TYR A 277 
 PHE   0.028   0.003   PHE A 276 
 TRP   0.021   0.002   TRP A 252 
 HIS   0.004   0.002   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 3398)
  covalent geometry    : angle       0.80316 ( 4603)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       1.92530 (    4)
  hydrogen bonds       : bond        0.04798 (  210)
  hydrogen bonds       : angle       4.85611 (  663)

*********************** 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
  109 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8301 (mt) cc_final: 0.7571 (mt)
REVERT: A  143 HIS cc_start: 0.6721 (m170) cc_final: 0.6420 (m-70)
REVERT: A  206 PHE cc_start: 0.7330 (m-80) cc_final: 0.7062 (m-80)
REVERT: A  227 MET cc_start: 0.8687 (tmm) cc_final: 0.8274 (tmm)
REVERT: A  259 GLN cc_start: 0.8124 (mp10) cc_final: 0.7723 (mp10)
REVERT: A  270 MET cc_start: 0.5743 (mmp) cc_final: 0.5158 (mmt)
REVERT: A  298 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7221 (tp30)
REVERT: A  386 MET cc_start: 0.8295 (tpp) cc_final: 0.7874 (tpp)
REVERT: A  387 LYS cc_start: 0.8848 (tptt) cc_final: 0.8491 (tttp)
REVERT: A  435 TRP cc_start: 0.8005 (p-90) cc_final: 0.7104 (p-90)
REVERT: A  437 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6904 (tp30)
REVERT: A  438 LEU cc_start: 0.8562 (mp) cc_final: 0.8354 (mp)
REVERT: A  451 MET cc_start: 0.7515 (mtt) cc_final: 0.7274 (mtp)
REVERT: A  457 MET cc_start: 0.6558 (mtm) cc_final: 0.5628 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0697
  time to fit residues: 9.0699
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4313 r_free = 0.4313 target = 0.197545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.171529 restraints weight = 5776.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.177753 restraints weight = 3619.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.182420 restraints weight = 2427.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.185368 restraints weight = 1699.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.188007 restraints weight = 1263.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5799
moved from start:          0.7915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3400  Z= 0.148
  Angle     :  0.663  11.306   4607  Z= 0.346
  Chirality :  0.043   0.191    520
  Planarity :  0.004   0.053    551
  Dihedral  : 10.773 117.418    453
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.42), residues: 395
  helix:  1.53 (0.34), residues: 218
  sheet: -1.38 (0.69), residues: 51
  loop : -1.07 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  39 
 TYR   0.024   0.002   TYR A  94 
 PHE   0.019   0.002   PHE A 184 
 TRP   0.011   0.001   TRP A  82 
 HIS   0.003   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3398)
  covalent geometry    : angle       0.66194 ( 4603)
  SS BOND              : bond        0.00624 (    2)
  SS BOND              : angle       1.52574 (    4)
  hydrogen bonds       : bond        0.03994 (  210)
  hydrogen bonds       : angle       4.59448 (  663)

*********************** 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
  105 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8327 (mt) cc_final: 0.7716 (mt)
REVERT: A  227 MET cc_start: 0.8673 (tmm) cc_final: 0.8235 (tmm)
REVERT: A  259 GLN cc_start: 0.8190 (mp10) cc_final: 0.7802 (mp10)
REVERT: A  270 MET cc_start: 0.5652 (mmp) cc_final: 0.5003 (mmt)
REVERT: A  272 GLU cc_start: 0.9040 (pp20) cc_final: 0.8811 (pp20)
REVERT: A  273 LYS cc_start: 0.7791 (mttp) cc_final: 0.6997 (ttmt)
REVERT: A  298 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7488 (tp30)
REVERT: A  386 MET cc_start: 0.8565 (tpp) cc_final: 0.8096 (tpp)
REVERT: A  387 LYS cc_start: 0.8906 (tptt) cc_final: 0.8467 (tttp)
REVERT: A  404 PHE cc_start: 0.7845 (t80) cc_final: 0.7556 (t80)
REVERT: A  424 MET cc_start: 0.7208 (mmp) cc_final: 0.7004 (mmm)
REVERT: A  437 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6661 (tp30)
REVERT: A  439 TRP cc_start: 0.8365 (p-90) cc_final: 0.7575 (p-90)
REVERT: A  451 MET cc_start: 0.7726 (mtt) cc_final: 0.7099 (mtt)
REVERT: A  457 MET cc_start: 0.6779 (mtm) cc_final: 0.6219 (mtm)
REVERT: A  459 LEU cc_start: 0.6716 (mt) cc_final: 0.6356 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0823
  time to fit residues: 10.2422
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  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.186310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.163291 restraints weight = 5977.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.168958 restraints weight = 3708.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.173080 restraints weight = 2469.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.175601 restraints weight = 1717.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.177961 restraints weight = 1277.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6133
moved from start:          1.0567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   3400  Z= 0.265
  Angle     :  0.912  13.621   4607  Z= 0.472
  Chirality :  0.050   0.154    520
  Planarity :  0.007   0.055    551
  Dihedral  : 11.490 118.527    453
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 21.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  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 are not related in a simple way.
  whole: -0.79 (0.40), residues: 395
  helix:  0.29 (0.33), residues: 218
  sheet: -1.76 (0.64), residues: 53
  loop : -1.20 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 309 
 TYR   0.035   0.003   TYR A  94 
 PHE   0.037   0.003   PHE A 240 
 TRP   0.021   0.003   TRP A 252 
 HIS   0.008   0.002   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 3398)
  covalent geometry    : angle       0.91039 ( 4603)
  SS BOND              : bond        0.00301 (    2)
  SS BOND              : angle       2.16270 (    4)
  hydrogen bonds       : bond        0.05413 (  210)
  hydrogen bonds       : angle       5.54715 (  663)

*********************** 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
  117 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7707 (mmm160)
REVERT: A   80 ILE cc_start: 0.8324 (mt) cc_final: 0.7544 (mt)
REVERT: A   84 LEU cc_start: 0.8767 (tp) cc_final: 0.8355 (tp)
REVERT: A  177 TRP cc_start: 0.8212 (p90) cc_final: 0.7314 (p90)
REVERT: A  182 TYR cc_start: 0.6350 (m-80) cc_final: 0.5961 (m-80)
REVERT: A  184 PHE cc_start: 0.9156 (t80) cc_final: 0.8779 (t80)
REVERT: A  227 MET cc_start: 0.8602 (tmm) cc_final: 0.8233 (tmm)
REVERT: A  386 MET cc_start: 0.8602 (tpp) cc_final: 0.8240 (tpp)
REVERT: A  387 LYS cc_start: 0.8904 (tptt) cc_final: 0.8456 (tttp)
REVERT: A  408 LEU cc_start: 0.8421 (mt) cc_final: 0.8192 (mt)
REVERT: A  436 ARG cc_start: 0.7499 (mpp-170) cc_final: 0.7153 (tpp80)
REVERT: A  437 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6619 (mm-30)
REVERT: A  448 LEU cc_start: 0.9515 (pp) cc_final: 0.9230 (pp)
REVERT: A  451 MET cc_start: 0.7995 (mtt) cc_final: 0.7295 (mtt)
REVERT: A  453 LEU cc_start: 0.8376 (mt) cc_final: 0.8053 (mt)
REVERT: A  457 MET cc_start: 0.7244 (mtm) cc_final: 0.6800 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0679
  time to fit residues: 9.6336
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  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.4268 r_free = 0.4268 target = 0.191648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.168434 restraints weight = 6087.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.174431 restraints weight = 3669.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.178717 restraints weight = 2396.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.181648 restraints weight = 1637.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.183923 restraints weight = 1181.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6043
moved from start:          1.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3400  Z= 0.159
  Angle     :  0.721  10.592   4607  Z= 0.372
  Chirality :  0.045   0.160    520
  Planarity :  0.005   0.047    551
  Dihedral  : 10.956 117.834    453
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.41), residues: 395
  helix:  0.99 (0.33), residues: 218
  sheet: -1.14 (0.74), residues: 44
  loop : -1.13 (0.54), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 392 
 TYR   0.024   0.002   TYR A  94 
 PHE   0.039   0.002   PHE A 240 
 TRP   0.016   0.002   TRP A  82 
 HIS   0.005   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3398)
  covalent geometry    : angle       0.71551 ( 4603)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       2.99646 (    4)
  hydrogen bonds       : bond        0.04232 (  210)
  hydrogen bonds       : angle       4.87188 (  663)

*********************** 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
  113 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8374 (mt) cc_final: 0.7579 (mt)
REVERT: A  143 HIS cc_start: 0.5713 (m-70) cc_final: 0.5102 (t-90)
REVERT: A  177 TRP cc_start: 0.8322 (p90) cc_final: 0.7289 (p90)
REVERT: A  227 MET cc_start: 0.8454 (tmm) cc_final: 0.8149 (tmm)
REVERT: A  265 VAL cc_start: 0.7905 (t) cc_final: 0.7683 (t)
REVERT: A  270 MET cc_start: 0.5874 (mmp) cc_final: 0.5531 (mmp)
REVERT: A  386 MET cc_start: 0.8463 (tpp) cc_final: 0.8035 (tpp)
REVERT: A  451 MET cc_start: 0.7887 (mtt) cc_final: 0.7222 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0541
  time to fit residues: 7.6748
Evaluate side-chains
  86 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0980
   chunk 28 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.195000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.170470 restraints weight = 5984.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.176504 restraints weight = 3644.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.180945 restraints weight = 2414.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.184076 restraints weight = 1677.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.186564 restraints weight = 1214.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5978
moved from start:          1.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3400  Z= 0.132
  Angle     :  0.672   9.544   4607  Z= 0.350
  Chirality :  0.043   0.151    520
  Planarity :  0.005   0.045    551
  Dihedral  : 10.547 114.958    453
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.43), residues: 395
  helix:  1.44 (0.34), residues: 218
  sheet: -1.21 (0.71), residues: 53
  loop : -0.96 (0.61), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 392 
 TYR   0.019   0.002   TYR A 182 
 PHE   0.031   0.002   PHE A 240 
 TRP   0.018   0.001   TRP A  82 
 HIS   0.003   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3398)
  covalent geometry    : angle       0.66824 ( 4603)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       2.52244 (    4)
  hydrogen bonds       : bond        0.04069 (  210)
  hydrogen bonds       : angle       4.62234 (  663)

*********************** 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
  109 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8437 (mt) cc_final: 0.7944 (mt)
REVERT: A   84 LEU cc_start: 0.8085 (tp) cc_final: 0.7852 (tp)
REVERT: A  227 MET cc_start: 0.8318 (tmm) cc_final: 0.7870 (tmm)
REVERT: A  386 MET cc_start: 0.8457 (tpp) cc_final: 0.8072 (tpp)
REVERT: A  436 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7530 (mmm-85)
REVERT: A  447 LEU cc_start: 0.8334 (tp) cc_final: 0.8126 (tp)
REVERT: A  451 MET cc_start: 0.7717 (mtt) cc_final: 0.7070 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0640
  time to fit residues: 8.5718
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  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0870
   overall best weight:    1.1964

-------------------------------------------------------------------------------
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 ** 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 = 0.4253 r_free = 0.4253 target = 0.191079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.167385 restraints weight = 6205.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.173335 restraints weight = 3817.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.177559 restraints weight = 2526.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.180670 restraints weight = 1779.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.182839 restraints weight = 1286.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6110
moved from start:          1.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3400  Z= 0.175
  Angle     :  0.734   9.428   4607  Z= 0.380
  Chirality :  0.045   0.188    520
  Planarity :  0.005   0.045    551
  Dihedral  : 10.723 113.565    453
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.42), residues: 395
  helix:  1.17 (0.33), residues: 218
  sheet: -0.92 (0.69), residues: 51
  loop : -1.17 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 392 
 TYR   0.025   0.003   TYR A  90 
 PHE   0.034   0.002   PHE A 240 
 TRP   0.015   0.002   TRP A  82 
 HIS   0.018   0.003   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3398)
  covalent geometry    : angle       0.73110 ( 4603)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       2.39554 (    4)
  hydrogen bonds       : bond        0.04293 (  210)
  hydrogen bonds       : angle       4.86198 (  663)

*********************** 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
  113 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 PHE cc_start: 0.7327 (t80) cc_final: 0.6973 (t80)
REVERT: A   80 ILE cc_start: 0.8454 (mt) cc_final: 0.7680 (mt)
REVERT: A   84 LEU cc_start: 0.8307 (tp) cc_final: 0.8096 (tp)
REVERT: A  178 GLN cc_start: 0.7086 (pp30) cc_final: 0.6816 (pp30)
REVERT: A  227 MET cc_start: 0.8148 (tmm) cc_final: 0.7815 (tmm)
REVERT: A  305 ARG cc_start: 0.7072 (ptt-90) cc_final: 0.5794 (ttm110)
REVERT: A  386 MET cc_start: 0.8627 (tpp) cc_final: 0.8232 (tpp)
REVERT: A  424 MET cc_start: 0.6779 (mmp) cc_final: 0.6421 (mmm)
REVERT: A  436 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7435 (mmm-85)
REVERT: A  447 LEU cc_start: 0.8385 (tp) cc_final: 0.8041 (tp)
REVERT: A  451 MET cc_start: 0.7835 (mtt) cc_final: 0.7206 (mtt)
REVERT: A  469 PHE cc_start: 0.8065 (m-10) cc_final: 0.7710 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0712
  time to fit residues: 9.7736
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  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.192160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.167225 restraints weight = 5981.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.173544 restraints weight = 3656.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.178014 restraints weight = 2425.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.181170 restraints weight = 1684.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.183414 restraints weight = 1211.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6022
moved from start:          1.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3400  Z= 0.142
  Angle     :  0.694   8.797   4607  Z= 0.356
  Chirality :  0.043   0.146    520
  Planarity :  0.005   0.045    551
  Dihedral  : 10.497 110.331    453
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.43), residues: 395
  helix:  1.34 (0.34), residues: 218
  sheet: -1.27 (0.67), residues: 55
  loop : -0.88 (0.63), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 436 
 TYR   0.017   0.002   TYR A 340 
 PHE   0.030   0.002   PHE A 240 
 TRP   0.017   0.002   TRP A  82 
 HIS   0.003   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3398)
  covalent geometry    : angle       0.69064 ( 4603)
  SS BOND              : bond        0.00029 (    2)
  SS BOND              : angle       2.29893 (    4)
  hydrogen bonds       : bond        0.04133 (  210)
  hydrogen bonds       : angle       4.57466 (  663)

********************** 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
  116 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8539 (mt) cc_final: 0.7791 (mt)
REVERT: A   84 LEU cc_start: 0.8113 (tp) cc_final: 0.7733 (tp)
REVERT: A   95 ASN cc_start: 0.8749 (m-40) cc_final: 0.8178 (m110)
REVERT: A   97 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7816 (mmmm)
REVERT: A  143 HIS cc_start: 0.5986 (m-70) cc_final: 0.5607 (t-90)
REVERT: A  227 MET cc_start: 0.8158 (tmm) cc_final: 0.7845 (tmm)
REVERT: A  305 ARG cc_start: 0.6982 (ptt-90) cc_final: 0.5730 (ttm110)
REVERT: A  386 MET cc_start: 0.8729 (tpp) cc_final: 0.8380 (tpp)
REVERT: A  387 LYS cc_start: 0.8862 (tptt) cc_final: 0.8338 (ptmt)
REVERT: A  424 MET cc_start: 0.6952 (mmp) cc_final: 0.6652 (mmm)
REVERT: A  436 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7746 (tpp80)
REVERT: A  447 LEU cc_start: 0.8269 (tp) cc_final: 0.7981 (tp)
REVERT: A  451 MET cc_start: 0.7631 (mtt) cc_final: 0.7019 (mtt)
REVERT: A  453 LEU cc_start: 0.8535 (mt) cc_final: 0.8269 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0635
  time to fit residues: 9.0403
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  : 0.088 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4283 r_free = 0.4283 target = 0.193348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.167203 restraints weight = 6154.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.173577 restraints weight = 3703.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.178033 restraints weight = 2436.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.181334 restraints weight = 1705.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.183617 restraints weight = 1245.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6015
moved from start:          1.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3400  Z= 0.137
  Angle     :  0.687   8.649   4607  Z= 0.353
  Chirality :  0.042   0.149    520
  Planarity :  0.005   0.045    551
  Dihedral  : 10.342 105.945    453
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.44), residues: 395
  helix:  1.40 (0.34), residues: 219
  sheet: -1.47 (0.64), residues: 59
  loop : -0.73 (0.64), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 392 
 TYR   0.035   0.002   TYR A 237 
 PHE   0.028   0.002   PHE A 240 
 TRP   0.017   0.002   TRP A  82 
 HIS   0.003   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3398)
  covalent geometry    : angle       0.68440 ( 4603)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       2.24842 (    4)
  hydrogen bonds       : bond        0.04045 (  210)
  hydrogen bonds       : angle       4.50284 (  663)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 718.81 seconds
wall clock time: 13 minutes 0.06 seconds (780.06 seconds total)