Starting phenix.real_space_refine
on Wed Jul 23 15:46:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ctj_26992/07_2025/8ctj_26992.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ctj_26992/07_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_26992/07_2025/8ctj_26992.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_2025/8ctj_26992.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_2025/8ctj_26992.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_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-5711/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: 2.78, per 1000 atoms: 0.84
  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: 0.83
  Conformation dependent library (CDL) restraints added in 400.8 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 3 sheets defined
      59.6% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 95
      removed outlier: 3.776A  pdb=" N   TYR A  94 " --> pdb=" O   TYR A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 100 through 110
      removed outlier: 4.056A  pdb=" N   GLU A 110 " --> pdb=" O   GLU A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 133
      removed outlier: 3.745A  pdb=" N   LEU A 131 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE A 132 " --> pdb=" O   CYS A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 251
      removed outlier: 3.647A  pdb=" N   MET A 227 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 228 " --> pdb=" O   TYR A 224 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   CYS A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   TYR A 251 " --> pdb=" O   TRP A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 285
      removed outlier: 3.586A  pdb=" N   PHE A 260 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 317
      removed outlier: 3.642A  pdb=" N   LEU A 294 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 353
      removed outlier: 4.554A  pdb=" N   MET A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 393
      removed outlier: 4.074A  pdb=" N   PHE A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ILE A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
      Proline residue:  A 366  - end of helix
    Processing helix  chain 'A' and resid 394 through 428
      removed outlier: 3.747A  pdb=" N   ARG A 427 " --> pdb=" O   THR A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 460
    Processing helix  chain 'A' and resid 465 through 471
      removed outlier: 4.007A  pdb=" N   PHE A 471 " --> pdb=" O   GLN A 467 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59
    Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59

    228 hydrogen bonds defined for protein.
    663 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.90

  Time building geometry restraints manager: 0.98 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:             0.510
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.240
  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:             0.010
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.970
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.316 
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: 0.1849
  time to fit residues: 23.7097
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  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.1182

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

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

Total number of N/Q/H flips: 4

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3400  Z= 0.187
  Angle     :  0.741  12.140   4607  Z= 0.382
  Chirality :  0.045   0.188    520
  Planarity :  0.006   0.054    551
  Dihedral  : 11.633 134.256    453
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.41), residues: 395
  helix:  0.91 (0.32), residues: 236
  sheet: -1.30 (0.74), residues: 47
  loop : -1.31 (0.56), residues: 112

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  210)
  hydrogen bonds       : angle       4.67457 (  663)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       1.60304 (    4)
  covalent geometry    : bond        0.00391 ( 3398)
  covalent geometry    : angle       0.74023 ( 4603)

*********************** 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  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.7050 (mmmt) cc_final: 0.6829 (mppt)
REVERT: A   80 ILE cc_start: 0.8246 (mt) cc_final: 0.7217 (mt)
REVERT: A   91 ASN cc_start: 0.7260 (m-40) cc_final: 0.6619 (p0)
REVERT: A  132 PHE cc_start: 0.6207 (t80) cc_final: 0.5949 (t80)
REVERT: A  206 PHE cc_start: 0.7196 (m-80) cc_final: 0.6761 (m-80)
REVERT: A  227 MET cc_start: 0.8379 (tmm) cc_final: 0.8038 (tmm)
REVERT: A  386 MET cc_start: 0.8417 (tpp) cc_final: 0.8042 (tpp)
REVERT: A  387 LYS cc_start: 0.8985 (tptt) cc_final: 0.8568 (ttmt)
REVERT: A  438 LEU cc_start: 0.7872 (mp) cc_final: 0.7193 (tp)
REVERT: A  453 LEU cc_start: 0.8319 (mt) cc_final: 0.7995 (mt)
REVERT: A  457 MET cc_start: 0.6446 (mtm) cc_final: 0.5703 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1705
  time to fit residues: 21.5418
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  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8382

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.203278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.177808 restraints weight = 5847.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.183771 restraints weight = 3804.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.188045 restraints weight = 2621.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5624
moved from start:          0.5564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3400  Z= 0.147
  Angle     :  0.642  11.501   4607  Z= 0.330
  Chirality :  0.042   0.138    520
  Planarity :  0.005   0.054    551
  Dihedral  : 11.125 124.569    453
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  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 (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:  0.51 (0.42), residues: 395
  helix:  1.46 (0.34), residues: 216
  sheet: -0.97 (0.73), residues: 49
  loop : -0.97 (0.54), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 177 
 HIS   0.011   0.002   HIS A 187 
 PHE   0.015   0.002   PHE A 404 
 TYR   0.021   0.002   TYR A  94 
 ARG   0.007   0.001   ARG A 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03994 (  210)
  hydrogen bonds       : angle       4.60601 (  663)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       2.42337 (    4)
  covalent geometry    : bond        0.00305 ( 3398)
  covalent geometry    : angle       0.63829 ( 4603)

*********************** 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
  108 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.384 
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: 0.8166 (mt) cc_final: 0.7347 (mt)
REVERT: A  119 GLN cc_start: 0.6865 (pt0) cc_final: 0.6272 (pt0)
REVERT: A  142 MET cc_start: 0.3362 (mpp) cc_final: 0.0824 (mtt)
REVERT: A  184 PHE cc_start: 0.8426 (t80) cc_final: 0.8202 (t80)
REVERT: A  227 MET cc_start: 0.8523 (tmm) cc_final: 0.8067 (tmm)
REVERT: A  270 MET cc_start: 0.5732 (mmp) cc_final: 0.5068 (mmp)
REVERT: A  298 GLU cc_start: 0.8039 (tp30) cc_final: 0.7577 (tp30)
REVERT: A  386 MET cc_start: 0.8163 (tpp) cc_final: 0.7780 (tpp)
REVERT: A  387 LYS cc_start: 0.8942 (tptt) cc_final: 0.8610 (tttp)
REVERT: A  435 TRP cc_start: 0.7839 (p-90) cc_final: 0.7325 (p-90)
REVERT: A  437 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7374 (mm-30)
REVERT: A  438 LEU cc_start: 0.8126 (mp) cc_final: 0.7859 (mp)
REVERT: A  457 MET cc_start: 0.6100 (mtm) cc_final: 0.4828 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1559
  time to fit residues: 20.2026
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  : 0.321 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0670
   chunk 21 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.4399 r_free = 0.4399 target = 0.204917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.178106 restraints weight = 5996.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.184164 restraints weight = 3877.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.188829 restraints weight = 2699.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5658
moved from start:          0.6320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3400  Z= 0.120
  Angle     :  0.597  10.032   4607  Z= 0.308
  Chirality :  0.041   0.174    520
  Planarity :  0.004   0.034    551
  Dihedral  : 10.489 119.255    453
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.37 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.43), residues: 395
  helix:  1.57 (0.34), residues: 222
  sheet: -0.87 (0.69), residues: 55
  loop : -0.93 (0.58), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  82 
 HIS   0.006   0.001   HIS A 187 
 PHE   0.009   0.002   PHE A 230 
 TYR   0.015   0.001   TYR A  94 
 ARG   0.003   0.000   ARG A 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03648 (  210)
  hydrogen bonds       : angle       4.26488 (  663)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       1.77932 (    4)
  covalent geometry    : bond        0.00258 ( 3398)
  covalent geometry    : angle       0.59541 ( 4603)

*********************** 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
  107 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.7805 (mp0) cc_final: 0.7592 (mp0)
REVERT: A   80 ILE cc_start: 0.8243 (mt) cc_final: 0.7610 (mt)
REVERT: A  132 PHE cc_start: 0.6236 (t80) cc_final: 0.5971 (t80)
REVERT: A  206 PHE cc_start: 0.8323 (m-80) cc_final: 0.7433 (m-80)
REVERT: A  227 MET cc_start: 0.8611 (tmm) cc_final: 0.8007 (tmm)
REVERT: A  259 GLN cc_start: 0.8123 (mp10) cc_final: 0.7589 (mp10)
REVERT: A  270 MET cc_start: 0.5932 (mmp) cc_final: 0.4706 (mmt)
REVERT: A  288 GLU cc_start: 0.5662 (tt0) cc_final: 0.5099 (tt0)
REVERT: A  298 GLU cc_start: 0.8062 (tp30) cc_final: 0.7815 (tp30)
REVERT: A  386 MET cc_start: 0.8270 (tpp) cc_final: 0.7874 (tpp)
REVERT: A  387 LYS cc_start: 0.8944 (tptt) cc_final: 0.8571 (tttp)
REVERT: A  435 TRP cc_start: 0.7910 (p-90) cc_final: 0.7421 (p-90)
REVERT: A  438 LEU cc_start: 0.8411 (mp) cc_final: 0.8193 (mp)
REVERT: A  457 MET cc_start: 0.6093 (mtm) cc_final: 0.4848 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1807
  time to fit residues: 22.7158
Evaluate side-chains
  88 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0070
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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 = 0.4355 r_free = 0.4355 target = 0.201969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.175946 restraints weight = 5916.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.182299 restraints weight = 3752.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.186795 restraints weight = 2528.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5674
moved from start:          0.6939

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= 0.127
  Angle     :  0.598   9.416   4607  Z= 0.317
  Chirality :  0.041   0.173    520
  Planarity :  0.004   0.031    551
  Dihedral  : 10.489 116.848    453
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.46
  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:  0.78 (0.43), residues: 395
  helix:  1.77 (0.35), residues: 218
  sheet: -0.75 (0.67), residues: 55
  loop : -1.15 (0.57), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.005   0.001   HIS A 187 
 PHE   0.026   0.002   PHE A 240 
 TYR   0.017   0.001   TYR A  94 
 ARG   0.003   0.000   ARG A 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03651 (  210)
  hydrogen bonds       : angle       4.25353 (  663)
  SS BOND              : bond        0.00661 (    2)
  SS BOND              : angle       2.00192 (    4)
  covalent geometry    : bond        0.00262 ( 3398)
  covalent geometry    : angle       0.59520 ( 4603)

*********************** 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
  98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8297 (mt) cc_final: 0.7751 (mt)
REVERT: A  132 PHE cc_start: 0.6421 (t80) cc_final: 0.6123 (t80)
REVERT: A  206 PHE cc_start: 0.8596 (m-80) cc_final: 0.7558 (m-80)
REVERT: A  221 LEU cc_start: 0.9343 (mt) cc_final: 0.9130 (mt)
REVERT: A  227 MET cc_start: 0.8601 (tmm) cc_final: 0.8215 (tmm)
REVERT: A  259 GLN cc_start: 0.8093 (mp10) cc_final: 0.7741 (mp10)
REVERT: A  270 MET cc_start: 0.5903 (mmp) cc_final: 0.5256 (mmp)
REVERT: A  298 GLU cc_start: 0.8056 (tp30) cc_final: 0.7810 (tp30)
REVERT: A  386 MET cc_start: 0.8445 (tpp) cc_final: 0.7984 (tpp)
REVERT: A  387 LYS cc_start: 0.8949 (tptt) cc_final: 0.8582 (tttp)
REVERT: A  457 MET cc_start: 0.6295 (mtm) cc_final: 0.5331 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1378
  time to fit residues: 16.7236
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  : 0.334 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.2184

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.195328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.170842 restraints weight = 6206.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.177055 restraints weight = 3791.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.181572 restraints weight = 2482.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5924
moved from start:          0.8973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3400  Z= 0.189
  Angle     :  0.758  11.804   4607  Z= 0.393
  Chirality :  0.045   0.148    520
  Planarity :  0.005   0.053    551
  Dihedral  : 10.936 114.866    453
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  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:  0.31 (0.43), residues: 395
  helix:  1.39 (0.35), residues: 218
  sheet: -1.17 (0.67), residues: 55
  loop : -1.24 (0.56), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 252 
 HIS   0.005   0.002   HIS A 331 
 PHE   0.044   0.003   PHE A 240 
 TYR   0.032   0.003   TYR A  94 
 ARG   0.006   0.001   ARG A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04494 (  210)
  hydrogen bonds       : angle       4.65142 (  663)
  SS BOND              : bond        0.00234 (    2)
  SS BOND              : angle       2.73957 (    4)
  covalent geometry    : bond        0.00400 ( 3398)
  covalent geometry    : angle       0.75413 ( 4603)

*********************** 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
  115 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8516 (mmmm) cc_final: 0.7469 (mmmt)
REVERT: A   80 ILE cc_start: 0.8332 (mt) cc_final: 0.7716 (mt)
REVERT: A  182 TYR cc_start: 0.6630 (m-80) cc_final: 0.6102 (m-80)
REVERT: A  184 PHE cc_start: 0.8748 (t80) cc_final: 0.8505 (t80)
REVERT: A  220 THR cc_start: 0.7817 (p) cc_final: 0.7348 (p)
REVERT: A  221 LEU cc_start: 0.9518 (mt) cc_final: 0.9273 (mt)
REVERT: A  222 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7974 (mp0)
REVERT: A  226 LEU cc_start: 0.8360 (tp) cc_final: 0.8126 (tp)
REVERT: A  227 MET cc_start: 0.8751 (tmm) cc_final: 0.8358 (tmm)
REVERT: A  259 GLN cc_start: 0.8344 (mp10) cc_final: 0.8067 (mp10)
REVERT: A  298 GLU cc_start: 0.8208 (tp30) cc_final: 0.7886 (tp30)
REVERT: A  386 MET cc_start: 0.8595 (tpp) cc_final: 0.8199 (tpp)
REVERT: A  387 LYS cc_start: 0.8977 (tptt) cc_final: 0.8546 (tttp)
REVERT: A  396 VAL cc_start: 0.7668 (m) cc_final: 0.7399 (t)
REVERT: A  401 TYR cc_start: 0.9137 (m-10) cc_final: 0.8819 (m-10)
REVERT: A  448 LEU cc_start: 0.9458 (pp) cc_final: 0.9193 (pp)
REVERT: A  451 MET cc_start: 0.7747 (mtt) cc_final: 0.7130 (mtt)
REVERT: A  457 MET cc_start: 0.7052 (mtm) cc_final: 0.6806 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1343
  time to fit residues: 19.0131
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  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0870
   chunk 29 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.3356

-------------------------------------------------------------------------------
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 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 = 0.4339 r_free = 0.4339 target = 0.200154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.174595 restraints weight = 5741.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.180865 restraints weight = 3537.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.184751 restraints weight = 2350.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5792
moved from start:          0.9268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3400  Z= 0.126
  Angle     :  0.631   7.403   4607  Z= 0.334
  Chirality :  0.042   0.145    520
  Planarity :  0.004   0.040    551
  Dihedral  : 10.305 107.988    453
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.43), residues: 395
  helix:  1.73 (0.35), residues: 218
  sheet: -1.00 (0.70), residues: 49
  loop : -1.28 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  82 
 HIS   0.005   0.001   HIS A 187 
 PHE   0.030   0.002   PHE A 240 
 TYR   0.017   0.002   TYR A 340 
 ARG   0.004   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  210)
  hydrogen bonds       : angle       4.39967 (  663)
  SS BOND              : bond        0.00541 (    2)
  SS BOND              : angle       2.70419 (    4)
  covalent geometry    : bond        0.00263 ( 3398)
  covalent geometry    : angle       0.62637 ( 4603)

*********************** 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
  108 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 HIS cc_start: 0.7353 (t70) cc_final: 0.7070 (m-70)
REVERT: A   61 ARG cc_start: 0.7906 (mmm160) cc_final: 0.7604 (mmm-85)
REVERT: A   80 ILE cc_start: 0.8296 (mt) cc_final: 0.7674 (mt)
REVERT: A   91 ASN cc_start: 0.7947 (m-40) cc_final: 0.7647 (m-40)
REVERT: A  132 PHE cc_start: 0.6551 (t80) cc_final: 0.6323 (t80)
REVERT: A  227 MET cc_start: 0.8613 (tmm) cc_final: 0.8304 (tmm)
REVERT: A  270 MET cc_start: 0.6007 (mmp) cc_final: 0.5525 (mmp)
REVERT: A  298 GLU cc_start: 0.8211 (tp30) cc_final: 0.7859 (tp30)
REVERT: A  371 ASP cc_start: 0.8150 (m-30) cc_final: 0.7873 (m-30)
REVERT: A  386 MET cc_start: 0.8279 (tpp) cc_final: 0.7801 (tpp)
REVERT: A  396 VAL cc_start: 0.7466 (m) cc_final: 0.7225 (t)
REVERT: A  401 TYR cc_start: 0.8905 (m-10) cc_final: 0.8649 (m-10)
REVERT: A  438 LEU cc_start: 0.8580 (mp) cc_final: 0.8130 (mp)
REVERT: A  448 LEU cc_start: 0.9478 (pp) cc_final: 0.9093 (pp)
REVERT: A  451 MET cc_start: 0.7835 (mtt) cc_final: 0.7187 (mtt)
REVERT: A  457 MET cc_start: 0.7238 (mtm) cc_final: 0.6781 (mtm)
REVERT: A  467 GLN cc_start: 0.7670 (tt0) cc_final: 0.7437 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1808
  time to fit residues: 23.7358
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  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.196652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.172498 restraints weight = 5991.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.178270 restraints weight = 3674.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.182495 restraints weight = 2450.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5971
moved from start:          1.0228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3400  Z= 0.178
  Angle     :  0.736  13.276   4607  Z= 0.381
  Chirality :  0.046   0.286    520
  Planarity :  0.005   0.040    551
  Dihedral  : 10.330 104.311    453
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.42), residues: 395
  helix:  1.48 (0.34), residues: 218
  sheet: -1.24 (0.66), residues: 55
  loop : -1.21 (0.56), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 460 
 HIS   0.009   0.002   HIS A 187 
 PHE   0.034   0.002   PHE A 240 
 TYR   0.021   0.002   TYR A  94 
 ARG   0.005   0.001   ARG A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04294 (  210)
  hydrogen bonds       : angle       4.64806 (  663)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       2.33815 (    4)
  covalent geometry    : bond        0.00386 ( 3398)
  covalent geometry    : angle       0.73308 ( 4603)

*********************** 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
  106 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.8280 (mt) cc_final: 0.7646 (mt)
REVERT: A  132 PHE cc_start: 0.6962 (t80) cc_final: 0.6745 (t80)
REVERT: A  182 TYR cc_start: 0.6932 (m-80) cc_final: 0.6142 (m-80)
REVERT: A  227 MET cc_start: 0.8479 (tmm) cc_final: 0.8070 (tmm)
REVERT: A  270 MET cc_start: 0.6125 (mmp) cc_final: 0.5240 (mmt)
REVERT: A  298 GLU cc_start: 0.8250 (tp30) cc_final: 0.7888 (tp30)
REVERT: A  371 ASP cc_start: 0.8209 (m-30) cc_final: 0.7944 (m-30)
REVERT: A  386 MET cc_start: 0.8470 (tpp) cc_final: 0.7994 (tpp)
REVERT: A  396 VAL cc_start: 0.7597 (m) cc_final: 0.7376 (t)
REVERT: A  401 TYR cc_start: 0.9135 (m-10) cc_final: 0.8796 (m-10)
REVERT: A  408 LEU cc_start: 0.8355 (mt) cc_final: 0.8126 (mt)
REVERT: A  436 ARG cc_start: 0.7845 (mmt180) cc_final: 0.7564 (mmm-85)
REVERT: A  448 LEU cc_start: 0.9514 (pp) cc_final: 0.9271 (pp)
REVERT: A  451 MET cc_start: 0.7875 (mtt) cc_final: 0.7249 (mtt)
REVERT: A  457 MET cc_start: 0.7493 (mtm) cc_final: 0.7216 (mtm)
REVERT: A  467 GLN cc_start: 0.7531 (tt0) cc_final: 0.7320 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1420
  time to fit residues: 18.6185
Evaluate side-chains
  88 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0980
   chunk 2 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   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 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 = 0.4330 r_free = 0.4330 target = 0.200232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.175629 restraints weight = 6061.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.181685 restraints weight = 3676.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.186127 restraints weight = 2422.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5897
moved from start:          1.0600

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= 0.133
  Angle     :  0.659   7.243   4607  Z= 0.343
  Chirality :  0.043   0.230    520
  Planarity :  0.004   0.037    551
  Dihedral  :  9.744  96.338    453
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 12.55
  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 (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 (0.43), residues: 395
  helix:  1.70 (0.35), residues: 218
  sheet: -0.79 (0.72), residues: 51
  loop : -1.12 (0.55), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  82 
 HIS   0.002   0.001   HIS A  43 
 PHE   0.030   0.002   PHE A 240 
 TYR   0.018   0.002   TYR A  52 
 ARG   0.005   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  210)
  hydrogen bonds       : angle       4.46515 (  663)
  SS BOND              : bond        0.00403 (    2)
  SS BOND              : angle       2.01508 (    4)
  covalent geometry    : bond        0.00283 ( 3398)
  covalent geometry    : angle       0.65629 ( 4603)

*********************** 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
  102 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.5759 (mmtm) cc_final: 0.5250 (pttt)
REVERT: A   80 ILE cc_start: 0.8347 (mt) cc_final: 0.7747 (mt)
REVERT: A   95 ASN cc_start: 0.9219 (m-40) cc_final: 0.8912 (m110)
REVERT: A  132 PHE cc_start: 0.6959 (t80) cc_final: 0.6749 (t80)
REVERT: A  182 TYR cc_start: 0.6778 (m-80) cc_final: 0.6114 (m-80)
REVERT: A  221 LEU cc_start: 0.9295 (mt) cc_final: 0.9044 (mt)
REVERT: A  227 MET cc_start: 0.8505 (tmm) cc_final: 0.8090 (tmm)
REVERT: A  270 MET cc_start: 0.5777 (mmp) cc_final: 0.5449 (mmp)
REVERT: A  288 GLU cc_start: 0.5583 (tt0) cc_final: 0.5231 (tt0)
REVERT: A  298 GLU cc_start: 0.8207 (tp30) cc_final: 0.7680 (tp30)
REVERT: A  365 ILE cc_start: 0.2336 (mt) cc_final: 0.2074 (mp)
REVERT: A  371 ASP cc_start: 0.8165 (m-30) cc_final: 0.7941 (m-30)
REVERT: A  386 MET cc_start: 0.8521 (tpp) cc_final: 0.8099 (tpp)
REVERT: A  396 VAL cc_start: 0.7472 (m) cc_final: 0.7224 (t)
REVERT: A  401 TYR cc_start: 0.9017 (m-10) cc_final: 0.8623 (m-10)
REVERT: A  408 LEU cc_start: 0.8292 (mt) cc_final: 0.8075 (mt)
REVERT: A  436 ARG cc_start: 0.7926 (mmt180) cc_final: 0.7680 (mmm-85)
REVERT: A  448 LEU cc_start: 0.9519 (pp) cc_final: 0.9291 (pp)
REVERT: A  451 MET cc_start: 0.7958 (mtt) cc_final: 0.7344 (mtt)
REVERT: A  457 MET cc_start: 0.7534 (mtm) cc_final: 0.7266 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1580
  time to fit residues: 19.5412
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  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 14 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.1980
   chunk 8 optimal weight:    6.9990
   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 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 = 0.4332 r_free = 0.4332 target = 0.200510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176064 restraints weight = 5942.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.182042 restraints weight = 3648.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.186534 restraints weight = 2415.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5914
moved from start:          1.0935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3400  Z= 0.133
  Angle     :  0.671   7.528   4607  Z= 0.350
  Chirality :  0.044   0.206    520
  Planarity :  0.004   0.040    551
  Dihedral  :  9.213  86.961    453
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  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:  0.70 (0.43), residues: 395
  helix:  1.70 (0.35), residues: 218
  sheet: -0.76 (0.72), residues: 51
  loop : -1.18 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  82 
 HIS   0.002   0.001   HIS A  43 
 PHE   0.031   0.002   PHE A 240 
 TYR   0.019   0.002   TYR A  83 
 ARG   0.008   0.001   ARG A 351 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03875 (  210)
  hydrogen bonds       : angle       4.44075 (  663)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       1.92327 (    4)
  covalent geometry    : bond        0.00283 ( 3398)
  covalent geometry    : angle       0.66857 ( 4603)

********************** 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
  105 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.5725 (mmtm) cc_final: 0.5096 (pttt)
REVERT: A   80 ILE cc_start: 0.8382 (mt) cc_final: 0.7794 (mt)
REVERT: A   91 ASN cc_start: 0.7800 (m-40) cc_final: 0.7558 (m-40)
REVERT: A   95 ASN cc_start: 0.9139 (m-40) cc_final: 0.8601 (m-40)
REVERT: A  182 TYR cc_start: 0.6787 (m-80) cc_final: 0.6129 (m-80)
REVERT: A  227 MET cc_start: 0.8435 (tmm) cc_final: 0.7997 (tmm)
REVERT: A  270 MET cc_start: 0.5782 (mmp) cc_final: 0.5491 (mmp)
REVERT: A  371 ASP cc_start: 0.8095 (m-30) cc_final: 0.7818 (m-30)
REVERT: A  386 MET cc_start: 0.8606 (tpp) cc_final: 0.8131 (tpp)
REVERT: A  396 VAL cc_start: 0.7712 (m) cc_final: 0.7492 (t)
REVERT: A  401 TYR cc_start: 0.9049 (m-10) cc_final: 0.8665 (m-10)
REVERT: A  436 ARG cc_start: 0.7968 (mmt180) cc_final: 0.7687 (mmm-85)
REVERT: A  451 MET cc_start: 0.8000 (mtt) cc_final: 0.7319 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1441
  time to fit residues: 18.4111
Evaluate side-chains
  95 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4274 r_free = 0.4274 target = 0.193741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.167336 restraints weight = 5998.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.173415 restraints weight = 3677.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.177992 restraints weight = 2480.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6061
moved from start:          1.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3400  Z= 0.179
  Angle     :  0.763   9.577   4607  Z= 0.396
  Chirality :  0.047   0.261    520
  Planarity :  0.005   0.063    551
  Dihedral  :  8.469  92.866    453
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.41), residues: 395
  helix:  1.16 (0.34), residues: 217
  sheet: -0.96 (0.74), residues: 51
  loop : -1.25 (0.53), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 460 
 HIS   0.004   0.001   HIS A 187 
 PHE   0.031   0.003   PHE A 240 
 TYR   0.023   0.003   TYR A  94 
 ARG   0.014   0.001   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 (  210)
  hydrogen bonds       : angle       4.73163 (  663)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       1.96979 (    4)
  covalent geometry    : bond        0.00387 ( 3398)
  covalent geometry    : angle       0.76121 ( 4603)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1384.91 seconds
wall clock time: 24 minutes 38.81 seconds (1478.81 seconds total)