Starting phenix.real_space_refine
on Tue Feb 11 02:01:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ctj_26992/02_2025/8ctj_26992.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ctj_26992/02_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_26992/02_2025/8ctj_26992.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ctj_26992/02_2025/8ctj_26992.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ctj_26992/02_2025/8ctj_26992.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ctj_26992/02_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-5592/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: 2.37, per 1000 atoms: 0.72
  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: 0.81
  Conformation dependent library (CDL) restraints added in 405.7 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: 0.34
  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: 0.91

  Time building geometry restraints manager: 0.95 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:             0.250
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.560
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.900
-------------------------------------------------------------------------------
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  : 0.345 
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: 0.2068
  time to fit residues: 26.6327
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  : 0.518 
-------------------------------------------------------------------------------
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:    0.9980
   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:    1.1382

-------------------------------------------------------------------------------
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 = 0.4352 r_free = 0.4352 target = 0.201581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.175248 restraints weight = 5798.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.181266 restraints weight = 3733.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.185719 restraints weight = 2549.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5527
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3398  Z= 0.254
  Angle     :  0.753  12.307   4603  Z= 0.387
  Chirality :  0.045   0.189    520
  Planarity :  0.006   0.055    551
  Dihedral  : 11.655 134.008    453
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  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: -0.07 (0.41), residues: 395
  helix:  0.89 (0.32), residues: 236
  sheet: -1.32 (0.74), residues: 47
  loop : -1.33 (0.55), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 252 
 HIS   0.012   0.004   HIS A  43 
 PHE   0.027   0.003   PHE A 276 
 TYR   0.014   0.002   TYR A  52 
 ARG   0.013   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  : 0.334 
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: 0.7047 (mmmt) cc_final: 0.6800 (mppt)
REVERT: A   80 ILE cc_start: 0.8260 (mt) cc_final: 0.7233 (mt)
REVERT: A   91 ASN cc_start: 0.7270 (m-40) cc_final: 0.6624 (p0)
REVERT: A  132 PHE cc_start: 0.6233 (t80) cc_final: 0.5976 (t80)
REVERT: A  206 PHE cc_start: 0.7224 (m-80) cc_final: 0.6744 (m-80)
REVERT: A  227 MET cc_start: 0.8401 (tmm) cc_final: 0.8037 (tmm)
REVERT: A  386 MET cc_start: 0.8444 (tpp) cc_final: 0.8073 (tpp)
REVERT: A  387 LYS cc_start: 0.8980 (tptt) cc_final: 0.8557 (ttmt)
REVERT: A  438 LEU cc_start: 0.7899 (mp) cc_final: 0.7208 (tp)
REVERT: A  453 LEU cc_start: 0.8292 (mt) cc_final: 0.7976 (mt)
REVERT: A  457 MET cc_start: 0.6474 (mtm) cc_final: 0.5738 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1710
  time to fit residues: 21.6014
Evaluate side-chains
  91 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4378 r_free = 0.4378 target = 0.203705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.177805 restraints weight = 5928.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.183566 restraints weight = 3911.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.188011 restraints weight = 2708.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5619
moved from start:          0.5463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3398  Z= 0.197
  Angle     :  0.632  11.445   4603  Z= 0.326
  Chirality :  0.041   0.141    520
  Planarity :  0.004   0.033    551
  Dihedral  : 11.123 125.652    453
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  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 (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:  0.52 (0.42), residues: 395
  helix:  1.49 (0.34), residues: 218
  sheet: -0.98 (0.73), residues: 49
  loop : -1.04 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 177 
 HIS   0.008   0.002   HIS A 187 
 PHE   0.013   0.002   PHE A 280 
 TYR   0.021   0.002   TYR A  94 
 ARG   0.005   0.001   ARG A 393 

*********************** 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  : 0.367 
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: A   72 GLU cc_start: 0.8142 (mp0) cc_final: 0.7842 (mp0)
REVERT: A   80 ILE cc_start: 0.8157 (mt) cc_final: 0.7354 (mt)
REVERT: A   97 LYS cc_start: 0.8498 (tmtt) cc_final: 0.8269 (tptp)
REVERT: A  142 MET cc_start: 0.3536 (mpp) cc_final: 0.1832 (mtt)
REVERT: A  206 PHE cc_start: 0.7288 (m-80) cc_final: 0.6958 (m-80)
REVERT: A  227 MET cc_start: 0.8568 (tmm) cc_final: 0.8034 (tmm)
REVERT: A  270 MET cc_start: 0.5777 (mmp) cc_final: 0.4696 (mmp)
REVERT: A  298 GLU cc_start: 0.8084 (tp30) cc_final: 0.7659 (tp30)
REVERT: A  386 MET cc_start: 0.8218 (tpp) cc_final: 0.7805 (tpp)
REVERT: A  387 LYS cc_start: 0.8938 (tptt) cc_final: 0.8589 (tttp)
REVERT: A  435 TRP cc_start: 0.7781 (p-90) cc_final: 0.7361 (p-90)
REVERT: A  437 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: A  439 TRP cc_start: 0.8481 (p-90) cc_final: 0.8066 (p-90)
REVERT: A  457 MET cc_start: 0.6117 (mtm) cc_final: 0.4777 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1608
  time to fit residues: 20.9359
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  : 0.337 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   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 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 = 0.4354 r_free = 0.4354 target = 0.200223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.174336 restraints weight = 6163.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.180267 restraints weight = 4033.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.184794 restraints weight = 2802.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5821
moved from start:          0.7074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3398  Z= 0.238
  Angle     :  0.696  11.994   4603  Z= 0.363
  Chirality :  0.043   0.161    520
  Planarity :  0.005   0.047    551
  Dihedral  : 10.720 117.591    453
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.78 %
    Favored  : 94.94 %
  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:  0.38 (0.42), residues: 395
  helix:  1.48 (0.34), residues: 218
  sheet: -1.17 (0.66), residues: 55
  loop : -1.23 (0.55), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 252 
 HIS   0.006   0.002   HIS A 187 
 PHE   0.015   0.002   PHE A 260 
 TYR   0.026   0.002   TYR A  94 
 ARG   0.005   0.001   ARG A  39 

*********************** 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: 1
    poor density    : 108
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7646 (tpp80)
REVERT: A   80 ILE cc_start: 0.8334 (mt) cc_final: 0.7613 (mt)
REVERT: A  182 TYR cc_start: 0.6607 (m-80) cc_final: 0.6109 (m-80)
REVERT: A  184 PHE cc_start: 0.8628 (t80) cc_final: 0.8406 (t80)
REVERT: A  221 LEU cc_start: 0.9081 (mt) cc_final: 0.8684 (mt)
REVERT: A  227 MET cc_start: 0.8559 (tmm) cc_final: 0.7925 (tmm)
REVERT: A  259 GLN cc_start: 0.8242 (mp10) cc_final: 0.7808 (mp10)
REVERT: A  288 GLU cc_start: 0.5851 (tt0) cc_final: 0.5348 (tt0)
REVERT: A  298 GLU cc_start: 0.8080 (tp30) cc_final: 0.7721 (tp30)
REVERT: A  386 MET cc_start: 0.8387 (tpp) cc_final: 0.7898 (tpp)
REVERT: A  387 LYS cc_start: 0.8902 (tptt) cc_final: 0.8521 (tttp)
REVERT: A  435 TRP cc_start: 0.7840 (p-90) cc_final: 0.6952 (p-90)
REVERT: A  437 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7142 (mm-30)
REVERT: A  457 MET cc_start: 0.6620 (mtm) cc_final: 0.5765 (ttm)
REVERT: A  459 LEU cc_start: 0.7001 (mt) cc_final: 0.6673 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1855
  time to fit residues: 23.8077
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  : 0.350 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0870
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.4343 r_free = 0.4343 target = 0.199802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.174735 restraints weight = 5828.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.181014 restraints weight = 3662.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.185346 restraints weight = 2454.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5787
moved from start:          0.7409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3398  Z= 0.173
  Angle     :  0.640   9.046   4603  Z= 0.333
  Chirality :  0.045   0.375    520
  Planarity :  0.004   0.050    551
  Dihedral  : 10.471 116.835    453
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.81 %
    Favored  : 96.91 %
  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:  0.76 (0.43), residues: 395
  helix:  1.84 (0.35), residues: 216
  sheet: -0.98 (0.72), residues: 49
  loop : -1.17 (0.54), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  82 
 HIS   0.002   0.001   HIS A  43 
 PHE   0.010   0.001   PHE A 184 
 TYR   0.019   0.002   TYR A  94 
 ARG   0.003   0.000   ARG A 351 

*********************** 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
  106 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8247 (mmmm) cc_final: 0.8029 (mmmm)
REVERT: A   61 ARG cc_start: 0.7878 (mtp-110) cc_final: 0.7615 (tpp80)
REVERT: A   80 ILE cc_start: 0.8372 (mt) cc_final: 0.7765 (mt)
REVERT: A   97 LYS cc_start: 0.8742 (mttt) cc_final: 0.8529 (mmtt)
REVERT: A  132 PHE cc_start: 0.6396 (t80) cc_final: 0.6107 (t80)
REVERT: A  206 PHE cc_start: 0.8186 (m-80) cc_final: 0.7330 (m-80)
REVERT: A  221 LEU cc_start: 0.9224 (mt) cc_final: 0.8961 (mt)
REVERT: A  259 GLN cc_start: 0.8147 (mp10) cc_final: 0.7797 (mp10)
REVERT: A  270 MET cc_start: 0.6017 (mmp) cc_final: 0.5543 (mmp)
REVERT: A  386 MET cc_start: 0.8390 (tpp) cc_final: 0.7940 (tpp)
REVERT: A  387 LYS cc_start: 0.8897 (tptt) cc_final: 0.8443 (tttp)
REVERT: A  397 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8413 (pttt)
REVERT: A  437 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7061 (mm-30)
REVERT: A  457 MET cc_start: 0.6243 (mtm) cc_final: 0.5214 (ttm)
REVERT: A  459 LEU cc_start: 0.6723 (mt) cc_final: 0.6347 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1593
  time to fit residues: 20.2714
Evaluate side-chains
  91 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0770
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 = 0.4333 r_free = 0.4333 target = 0.199390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.172620 restraints weight = 5841.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.179004 restraints weight = 3638.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.183554 restraints weight = 2441.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5830
moved from start:          0.8046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3398  Z= 0.181
  Angle     :  0.631   8.521   4603  Z= 0.331
  Chirality :  0.044   0.360    520
  Planarity :  0.004   0.047    551
  Dihedral  : 10.328 113.990    453
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  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:  0.68 (0.43), residues: 395
  helix:  1.75 (0.35), residues: 218
  sheet: -0.99 (0.66), residues: 55
  loop : -1.19 (0.56), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  82 
 HIS   0.004   0.001   HIS A 187 
 PHE   0.021   0.002   PHE A 404 
 TYR   0.018   0.002   TYR A  94 
 ARG   0.002   0.000   ARG A  39 

*********************** 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
  107 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8283 (mmmm) cc_final: 0.7708 (mmmt)
REVERT: A   80 ILE cc_start: 0.8483 (mt) cc_final: 0.7847 (mt)
REVERT: A   90 TYR cc_start: 0.6679 (t80) cc_final: 0.6194 (t80)
REVERT: A   97 LYS cc_start: 0.8767 (mttt) cc_final: 0.8031 (mmmt)
REVERT: A  132 PHE cc_start: 0.6318 (t80) cc_final: 0.6040 (t80)
REVERT: A  143 HIS cc_start: 0.6495 (m-70) cc_final: 0.6061 (t-90)
REVERT: A  227 MET cc_start: 0.8486 (tmm) cc_final: 0.8026 (tmm)
REVERT: A  233 MET cc_start: 0.8220 (tpp) cc_final: 0.7992 (tpp)
REVERT: A  259 GLN cc_start: 0.8198 (mp10) cc_final: 0.7972 (mp10)
REVERT: A  270 MET cc_start: 0.5574 (mmp) cc_final: 0.5272 (mmt)
REVERT: A  371 ASP cc_start: 0.8211 (m-30) cc_final: 0.7937 (m-30)
REVERT: A  386 MET cc_start: 0.8318 (tpp) cc_final: 0.7909 (tpp)
REVERT: A  387 LYS cc_start: 0.8893 (tptt) cc_final: 0.8467 (tttp)
REVERT: A  436 ARG cc_start: 0.7568 (mmt180) cc_final: 0.7076 (mmm-85)
REVERT: A  453 LEU cc_start: 0.8514 (mt) cc_final: 0.8248 (mt)
REVERT: A  457 MET cc_start: 0.6363 (mtm) cc_final: 0.5732 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1909
  time to fit residues: 24.0873
Evaluate side-chains
  94 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  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:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0270
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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
A 394 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.200758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.174786 restraints weight = 5711.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.180834 restraints weight = 3544.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.185477 restraints weight = 2392.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5847
moved from start:          0.8745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3398  Z= 0.176
  Angle     :  0.611   6.103   4603  Z= 0.326
  Chirality :  0.043   0.331    520
  Planarity :  0.004   0.045    551
  Dihedral  : 10.195 110.955    453
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  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:  0.83 (0.43), residues: 395
  helix:  1.83 (0.35), residues: 218
  sheet: -0.85 (0.66), residues: 55
  loop : -1.10 (0.57), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 460 
 HIS   0.002   0.001   HIS A  43 
 PHE   0.042   0.002   PHE A 240 
 TYR   0.016   0.002   TYR A  94 
 ARG   0.006   0.001   ARG A 257 

*********************** 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
  110 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8307 (mmmm) cc_final: 0.7836 (mmmt)
REVERT: A   80 ILE cc_start: 0.8332 (mt) cc_final: 0.7857 (mt)
REVERT: A   90 TYR cc_start: 0.6581 (t80) cc_final: 0.6294 (t80)
REVERT: A  132 PHE cc_start: 0.6749 (t80) cc_final: 0.6466 (t80)
REVERT: A  143 HIS cc_start: 0.6592 (m-70) cc_final: 0.6121 (t-90)
REVERT: A  270 MET cc_start: 0.6087 (mmp) cc_final: 0.5545 (mmt)
REVERT: A  386 MET cc_start: 0.8379 (tpp) cc_final: 0.7975 (tpp)
REVERT: A  387 LYS cc_start: 0.8913 (tptt) cc_final: 0.8493 (tttp)
REVERT: A  438 LEU cc_start: 0.8753 (mp) cc_final: 0.8539 (mp)
REVERT: A  451 MET cc_start: 0.7757 (mtt) cc_final: 0.7153 (mtt)
REVERT: A  457 MET cc_start: 0.7017 (mtm) cc_final: 0.6639 (mtm)
REVERT: A  467 GLN cc_start: 0.7724 (tt0) cc_final: 0.7509 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1519
  time to fit residues: 20.3392
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  : 0.356 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 11 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 5 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
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 = 0.4356 r_free = 0.4356 target = 0.200468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.176340 restraints weight = 5682.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.182180 restraints weight = 3467.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.186519 restraints weight = 2318.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5864
moved from start:          0.9359

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= 0.169
  Angle     :  0.620   7.160   4603  Z= 0.327
  Chirality :  0.042   0.191    520
  Planarity :  0.004   0.042    551
  Dihedral  :  9.974 105.549    453
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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 (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:  0.85 (0.43), residues: 395
  helix:  1.83 (0.35), residues: 218
  sheet: -0.89 (0.70), residues: 49
  loop : -1.03 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 460 
 HIS   0.003   0.001   HIS A  43 
 PHE   0.035   0.002   PHE A 240 
 TYR   0.015   0.001   TYR A  94 
 ARG   0.003   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
  109 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8417 (mt) cc_final: 0.8009 (mt)
REVERT: A  143 HIS cc_start: 0.6674 (m-70) cc_final: 0.6181 (t-90)
REVERT: A  227 MET cc_start: 0.8147 (tmm) cc_final: 0.7680 (tmm)
REVERT: A  270 MET cc_start: 0.5871 (mmp) cc_final: 0.5345 (mmt)
REVERT: A  386 MET cc_start: 0.8393 (tpp) cc_final: 0.8034 (tpp)
REVERT: A  387 LYS cc_start: 0.8950 (tptt) cc_final: 0.8525 (tttp)
REVERT: A  396 VAL cc_start: 0.7700 (m) cc_final: 0.7481 (t)
REVERT: A  424 MET cc_start: 0.6303 (mmm) cc_final: 0.6097 (mmm)
REVERT: A  451 MET cc_start: 0.7905 (mtt) cc_final: 0.7296 (mtt)
REVERT: A  457 MET cc_start: 0.6916 (mtm) cc_final: 0.6372 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1596
  time to fit residues: 21.2273
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  : 0.375 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   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  43 HIS
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 = 0.4340 r_free = 0.4340 target = 0.198641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.174449 restraints weight = 5905.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.180437 restraints weight = 3647.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.184850 restraints weight = 2453.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5952
moved from start:          1.0272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3398  Z= 0.194
  Angle     :  0.657   7.458   4603  Z= 0.350
  Chirality :  0.044   0.222    520
  Planarity :  0.004   0.039    551
  Dihedral  :  9.953  99.504    453
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  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:  0.79 (0.43), residues: 395
  helix:  1.64 (0.34), residues: 218
  sheet: -0.74 (0.68), residues: 55
  loop : -0.83 (0.59), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  82 
 HIS   0.003   0.001   HIS A  43 
 PHE   0.037   0.002   PHE A 240 
 TYR   0.015   0.002   TYR A  90 
 ARG   0.003   0.000   ARG A 393 

*********************** 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  : 0.378 
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: A   43 HIS cc_start: 0.7072 (m90) cc_final: 0.6404 (m90)
REVERT: A   50 LYS cc_start: 0.5994 (mppt) cc_final: 0.5789 (pttt)
REVERT: A   57 LYS cc_start: 0.8397 (mmmm) cc_final: 0.8034 (mmmm)
REVERT: A   80 ILE cc_start: 0.8226 (mt) cc_final: 0.7316 (mt)
REVERT: A   95 ASN cc_start: 0.9211 (m110) cc_final: 0.8950 (m110)
REVERT: A  143 HIS cc_start: 0.6438 (m-70) cc_final: 0.6201 (t-90)
REVERT: A  182 TYR cc_start: 0.6616 (m-80) cc_final: 0.5931 (m-80)
REVERT: A  222 GLU cc_start: 0.8736 (mp0) cc_final: 0.8264 (mp0)
REVERT: A  227 MET cc_start: 0.7975 (tmm) cc_final: 0.7538 (tmm)
REVERT: A  270 MET cc_start: 0.5857 (mmp) cc_final: 0.5317 (mmt)
REVERT: A  386 MET cc_start: 0.8488 (tpp) cc_final: 0.8149 (tpp)
REVERT: A  387 LYS cc_start: 0.8847 (tptt) cc_final: 0.8449 (tttp)
REVERT: A  408 LEU cc_start: 0.7814 (mt) cc_final: 0.7613 (mt)
REVERT: A  451 MET cc_start: 0.7879 (mtt) cc_final: 0.7246 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1379
  time to fit residues: 19.1716
Evaluate side-chains
  99 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 1 optimal weight:    0.0770
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0070
   chunk 22 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4344 r_free = 0.4344 target = 0.198692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.174535 restraints weight = 5794.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.180667 restraints weight = 3577.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.185140 restraints weight = 2386.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5905
moved from start:          1.0635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3398  Z= 0.181
  Angle     :  0.662   7.774   4603  Z= 0.353
  Chirality :  0.044   0.200    520
  Planarity :  0.004   0.036    551
  Dihedral  :  9.620  92.255    453
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.16
  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:  0.91 (0.43), residues: 395
  helix:  1.79 (0.35), residues: 218
  sheet: -0.79 (0.71), residues: 49
  loop : -0.86 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  82 
 HIS   0.002   0.001   HIS A 187 
 PHE   0.034   0.002   PHE A 240 
 TYR   0.018   0.002   TYR A 340 
 ARG   0.005   0.000   ARG A  61 

********************** 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
  113 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8266 (mmmm) cc_final: 0.8038 (mmmm)
REVERT: A   80 ILE cc_start: 0.8372 (mt) cc_final: 0.7832 (mt)
REVERT: A   95 ASN cc_start: 0.8986 (m110) cc_final: 0.8746 (m110)
REVERT: A  143 HIS cc_start: 0.6762 (m-70) cc_final: 0.6363 (t-90)
REVERT: A  182 TYR cc_start: 0.6487 (m-80) cc_final: 0.5789 (m-80)
REVERT: A  222 GLU cc_start: 0.8773 (mp0) cc_final: 0.8360 (mp0)
REVERT: A  227 MET cc_start: 0.7895 (tmm) cc_final: 0.7491 (tmm)
REVERT: A  270 MET cc_start: 0.5568 (mmp) cc_final: 0.5129 (mmt)
REVERT: A  386 MET cc_start: 0.8489 (tpp) cc_final: 0.8183 (tpp)
REVERT: A  387 LYS cc_start: 0.8818 (tptt) cc_final: 0.8434 (tttp)
REVERT: A  448 LEU cc_start: 0.9497 (pp) cc_final: 0.9238 (pp)
REVERT: A  451 MET cc_start: 0.7956 (mtt) cc_final: 0.7366 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1310
  time to fit residues: 18.3670
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  : 0.349 
-------------------------------------------------------------------------------
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 31 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.4304 r_free = 0.4304 target = 0.195009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.171792 restraints weight = 5823.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.177963 restraints weight = 3439.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.182360 restraints weight = 2208.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6001
moved from start:          1.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3398  Z= 0.217
  Angle     :  0.695   8.202   4603  Z= 0.368
  Chirality :  0.045   0.213    520
  Planarity :  0.004   0.036    551
  Dihedral  :  9.257  87.981    453
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 13.90
  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:  0.71 (0.43), residues: 395
  helix:  1.58 (0.35), residues: 217
  sheet: -0.78 (0.68), residues: 55
  loop : -0.87 (0.58), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  82 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.031   0.002   PHE A 240 
 TYR   0.020   0.002   TYR A  94 
 ARG   0.005   0.001   ARG A  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1355.75 seconds
wall clock time: 24 minutes 53.43 seconds (1493.43 seconds total)