Starting phenix.real_space_refine
on Tue Feb 11 00:32:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zcf_14629/02_2025/7zcf_14629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zcf_14629/02_2025/7zcf_14629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zcf_14629/02_2025/7zcf_14629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zcf_14629/02_2025/7zcf_14629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zcf_14629/02_2025/7zcf_14629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zcf_14629/02_2025/7zcf_14629.cif"
  }
  resolution = 4.0
  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=  -0.004 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2107      2.51       5
     N     556      2.21       5
     O     635      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 3
    Chain: "C"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1595
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "E"
      Number of atoms: 1703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1703
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 10, 'TRANS': 214}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.29, per 1000 atoms: 0.99
  Number of scatterers: 3312
  At special positions: 0
  Unit cell: (65.786, 91.567, 90.678, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     635      8.00
     N     556      7.00
     C    2107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 156 " - pdb=" SG  CYS E 222 " 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
  Links applied
    NAG-ASN
      " NAG C1301 " - " ASN C 343 "
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 377.3 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 6 sheets defined
      8.5% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.854A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE C 342 " --> pdb=" O   PHE C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 4.228A  pdb=" N   TYR C 369 " --> pdb=" O   TYR C 365 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 365 through 370'
    Processing helix  chain 'C' and resid 386 through 390
      removed outlier: 3.676A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 410
      removed outlier: 3.585A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN C 409 " --> pdb=" O   GLU C 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 443
      removed outlier: 3.877A  pdb=" N   SER C 443 " --> pdb=" O   ASN C 440 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 213 through 217
      removed outlier: 3.954A  pdb=" N   PHE E 217 " --> pdb=" O   PRO E 214 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.651A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
      removed outlier: 3.640A  pdb=" N   GLN C 493 " --> pdb=" O   TYR C 453 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 18 through 20
      removed outlier: 3.639A  pdb=" N   LEU E  80 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   THR E  68 " --> pdb=" O   GLN E  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59
      removed outlier: 5.179A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   TYR E  33 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139
    Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188
      removed outlier: 3.778A  pdb=" N   SER E 187 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   TRP E 169 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   TYR E 183 " --> pdb=" O   LEU E 167 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   LEU E 167 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR E 231 " --> pdb=" O   GLN E 224 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    132 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: 0.79

  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:
        1.23 -     1.35: 1057
        1.35 -     1.46: 899
        1.46 -     1.58: 1423
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3395
  Sorted by residual:
  bond pdb=" C   PRO E 174 "
       pdb=" O   PRO E 174 "
    ideal  model  delta    sigma   weight residual
    1.235  1.268 -0.033 1.30e-02 5.92e+03 6.36e+00
  bond pdb=" C   PRO E 174 "
       pdb=" N   GLY E 175 "
    ideal  model  delta    sigma   weight residual
    1.333  1.368 -0.036 1.57e-02 4.06e+03 5.19e+00
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C   SER E 228 "
       pdb=" N   PRO E 229 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.64e+00
  bond pdb=" C5  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.13e+00
  ... (remaining 3390 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 4379
        1.33 -     2.66: 180
        2.66 -     4.00: 46
        4.00 -     5.33: 7
        5.33 -     6.66: 2
  Bond angle restraints: 4614
  Sorted by residual:
  angle pdb=" N   SER E 140 "
        pdb=" CA  SER E 140 "
        pdb=" C   SER E 140 "
      ideal   model   delta    sigma   weight residual
     109.81  116.47   -6.66 2.21e+00 2.05e-01 9.08e+00
  angle pdb=" N   GLY C 526 "
        pdb=" CA  GLY C 526 "
        pdb=" C   GLY C 526 "
      ideal   model   delta    sigma   weight residual
     112.34  118.46   -6.12 2.04e+00 2.40e-01 8.99e+00
  angle pdb=" N   GLN E 110 "
        pdb=" CA  GLN E 110 "
        pdb=" C   GLN E 110 "
      ideal   model   delta    sigma   weight residual
     114.04  110.83    3.21 1.24e+00 6.50e-01 6.71e+00
  angle pdb=" O   PRO E 174 "
        pdb=" C   PRO E 174 "
        pdb=" N   GLY E 175 "
      ideal   model   delta    sigma   weight residual
     122.64  126.13   -3.49 1.35e+00 5.49e-01 6.68e+00
  angle pdb=" N   PRO C 337 "
        pdb=" CA  PRO C 337 "
        pdb=" C   PRO C 337 "
      ideal   model   delta    sigma   weight residual
     114.68  112.10    2.58 1.04e+00 9.25e-01 6.13e+00
  ... (remaining 4609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 1812
       17.95 -    35.91: 160
       35.91 -    53.86: 35
       53.86 -    71.82: 4
       71.82 -    89.77: 4
  Dihedral angle restraints: 2015
    sinusoidal: 790
      harmonic: 1225
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.90   45.10     1      1.00e+01 1.00e-02 2.82e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.62  -44.62     1      1.00e+01 1.00e-02 2.77e+01
  dihedral pdb=" CA  SER E 140 "
           pdb=" C   SER E 140 "
           pdb=" N   PRO E 141 "
           pdb=" CA  PRO E 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 2012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 398
       0.049 -    0.097: 80
       0.097 -    0.146: 19
       0.146 -    0.194: 2
       0.194 -    0.243: 1
  Chirality restraints: 500
  Sorted by residual:
  chirality pdb=" CB  ILE C 468 "
            pdb=" CA  ILE C 468 "
            pdb=" CG1 ILE C 468 "
            pdb=" CG2 ILE C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  ILE C 472 "
            pdb=" N   ILE C 472 "
            pdb=" C   ILE C 472 "
            pdb=" CB  ILE C 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.30e-01
  chirality pdb=" CB  VAL E 116 "
            pdb=" CA  VAL E 116 "
            pdb=" CG1 VAL E 116 "
            pdb=" CG2 VAL E 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.78e-01
  ... (remaining 497 not shown)

  Planarity restraints: 598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 336 "    0.035 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO C 337 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 337 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 337 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 506 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO C 507 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 507 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 507 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 411 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO C 412 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 412 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 412 "    0.018 5.00e-02 4.00e+02
  ... (remaining 595 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 42
        2.65 -     3.21: 2931
        3.21 -     3.78: 4503
        3.78 -     4.34: 6072
        4.34 -     4.90: 10024
  Nonbonded interactions: 23572
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 354 "
            pdb=" OG  SER C 399 "
     model   vdw
     2.089 3.040
  nonbonded pdb=" O   LEU C 455 "
            pdb=" OH  TYR E  33 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OD1 ASN C 331 "
            pdb=" N   ILE C 332 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OH  TYR C 421 "
            pdb=" O   PRO E  53 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" N   GLN E   3 "
            pdb=" OG  SER E  25 "
     model   vdw
     2.311 3.120
  ... (remaining 23567 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.630
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.330
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
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      :  0.003   0.036   3395  Z= 0.177
  Angle     :  0.658   6.658   4614  Z= 0.371
  Chirality :  0.045   0.243    500
  Planarity :  0.005   0.054    597
  Dihedral  : 14.299  89.770   1223
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.76 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  0.28 %
    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: -2.45 (0.40), residues: 420
  helix: -4.94 (0.47), residues: 8
  sheet: -0.46 (0.55), residues: 104
  loop : -2.12 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 353 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.015   0.001   PHE C 338 
 TYR   0.012   0.001   TYR C 473 
 ARG   0.002   0.000   ARG E  71 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1660
  time to fit residues: 14.4825
Evaluate side-chains
  58 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  139 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.159427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.140028 restraints weight = 5748.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.143048 restraints weight = 3540.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.145225 restraints weight = 2507.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3636
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3395  Z= 0.328
  Angle     :  0.759   7.701   4614  Z= 0.403
  Chirality :  0.050   0.184    500
  Planarity :  0.005   0.036    597
  Dihedral  :  6.927  49.956    496
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.33 %
    Favored  : 81.67 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.41 %
    Favored  : 84.08 %
  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: -2.76 (0.41), residues: 420
  helix: -4.78 (0.59), residues: 8
  sheet: -1.36 (0.49), residues: 123
  loop : -2.07 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 169 
 HIS   0.003   0.002   HIS C 519 
 PHE   0.019   0.003   PHE C 338 
 TYR   0.027   0.002   TYR C 473 
 ARG   0.006   0.001   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: C  331 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6896 (p0)
REVERT: E  139 GLN cc_start: 0.7484 (pt0) cc_final: 0.7245 (pt0)
  outliers start: 9
  outliers final: 7
  residues processed: 82
  average time/residue: 0.1491
  time to fit residues: 15.2728
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  331 ASN
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0030
   chunk 5 optimal weight:    0.0770
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0980
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.3348

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.167522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.149858 restraints weight = 5539.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.152595 restraints weight = 3502.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.154608 restraints weight = 2524.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3395  Z= 0.194
  Angle     :  0.668   6.450   4614  Z= 0.350
  Chirality :  0.046   0.173    500
  Planarity :  0.005   0.035    597
  Dihedral  :  6.482  51.755    493
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.19 %
    Favored  : 83.81 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.32 %
    Favored  : 79.61 %
  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: -2.75 (0.41), residues: 420
  helix: -4.79 (0.58), residues: 8
  sheet: -1.38 (0.49), residues: 120
  loop : -2.05 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.013   0.001   PHE C 456 
 TYR   0.023   0.001   TYR E 183 
 ARG   0.002   0.000   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: C  398 ASP cc_start: 0.8092 (m-30) cc_final: 0.7867 (m-30)
REVERT: C  401 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9192 (p)
REVERT: C  450 ASN cc_start: 0.8814 (p0) cc_final: 0.8232 (p0)
REVERT: E  215 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7683 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1398
  time to fit residues: 12.3561
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 1 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0870
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0370
   chunk 35 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    0.2980
   overall best weight:    0.2436

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.168616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150656 restraints weight = 5686.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.153523 restraints weight = 3653.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.155399 restraints weight = 2636.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3395  Z= 0.165
  Angle     :  0.642   6.609   4614  Z= 0.331
  Chirality :  0.045   0.170    500
  Planarity :  0.004   0.032    597
  Dihedral  :  6.135  51.718    493
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.90 %
    Favored  : 83.10 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 17.32 %
    Favored  : 78.21 %
  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: -2.70 (0.41), residues: 420
  helix: -4.84 (0.53), residues: 8
  sheet: -1.43 (0.50), residues: 118
  loop : -1.97 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.008   0.001   PHE C 342 
 TYR   0.023   0.001   TYR E 183 
 ARG   0.002   0.000   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: C  450 ASN cc_start: 0.8742 (p0) cc_final: 0.8219 (p0)
REVERT: E  139 GLN cc_start: 0.6855 (pt0) cc_final: 0.6128 (pt0)
REVERT: E  215 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7503 (tm-30)
REVERT: E  224 GLN cc_start: 0.8671 (pp30) cc_final: 0.8430 (pp30)
  outliers start: 16
  outliers final: 13
  residues processed: 73
  average time/residue: 0.1417
  time to fit residues: 12.9861
Evaluate side-chains
  76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 24 optimal weight:    0.0170
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 41 optimal weight:    0.3980
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 160 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.164400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.145670 restraints weight = 5802.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.148740 restraints weight = 3665.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.150889 restraints weight = 2613.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3395  Z= 0.204
  Angle     :  0.653   7.115   4614  Z= 0.340
  Chirality :  0.045   0.174    500
  Planarity :  0.004   0.032    597
  Dihedral  :  6.274  51.333    493
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.71 %
    Favored  : 84.29 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 18.99 %
    Favored  : 76.82 %
  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: -2.74 (0.41), residues: 420
  helix: -4.81 (0.56), residues: 8
  sheet: -1.49 (0.50), residues: 118
  loop : -1.98 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.001   0.000   HIS C 519 
 PHE   0.008   0.001   PHE E 232 
 TYR   0.022   0.001   TYR E 183 
 ARG   0.002   0.000   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: C  450 ASN cc_start: 0.8752 (p0) cc_final: 0.8292 (p0)
REVERT: C  498 GLN cc_start: 0.6713 (mm110) cc_final: 0.6509 (mm-40)
REVERT: E  139 GLN cc_start: 0.7216 (pt0) cc_final: 0.6676 (pt0)
REVERT: E  215 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7402 (tm-30)
REVERT: E  224 GLN cc_start: 0.8671 (pp30) cc_final: 0.8399 (pp30)
  outliers start: 15
  outliers final: 13
  residues processed: 74
  average time/residue: 0.1388
  time to fit residues: 12.9193
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0010
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.160038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.141354 restraints weight = 5986.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.144373 restraints weight = 3745.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.146458 restraints weight = 2671.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3395  Z= 0.239
  Angle     :  0.681   7.190   4614  Z= 0.356
  Chirality :  0.045   0.178    500
  Planarity :  0.004   0.033    597
  Dihedral  :  6.495  50.461    493
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.10 %
    Favored  : 81.90 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 20.67 %
    Favored  : 74.58 %
  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: -2.88 (0.41), residues: 420
  helix: -4.77 (0.60), residues: 8
  sheet: -1.56 (0.49), residues: 124
  loop : -2.11 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.009   0.001   PHE E 232 
 TYR   0.018   0.001   TYR E 183 
 ARG   0.003   0.000   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.387 
Fit side-chains
REVERT: C  353 TRP cc_start: 0.8814 (p-90) cc_final: 0.8290 (p-90)
REVERT: C  450 ASN cc_start: 0.8828 (p0) cc_final: 0.8405 (p0)
REVERT: E  139 GLN cc_start: 0.7255 (pt0) cc_final: 0.6617 (pt0)
REVERT: E  215 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7429 (tm-30)
REVERT: E  224 GLN cc_start: 0.8715 (pp30) cc_final: 0.8365 (pp30)
  outliers start: 17
  outliers final: 14
  residues processed: 70
  average time/residue: 0.1424
  time to fit residues: 12.5167
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.1980
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 20 optimal weight:    0.2980
   chunk 32 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0870
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.2556

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.163590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.145364 restraints weight = 5787.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.148433 restraints weight = 3626.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150528 restraints weight = 2580.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3395  Z= 0.168
  Angle     :  0.644   6.891   4614  Z= 0.333
  Chirality :  0.045   0.175    500
  Planarity :  0.004   0.033    597
  Dihedral  :  6.094  50.720    493
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.07 %
    Favored  : 74.30 %
  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: -2.80 (0.41), residues: 420
  helix: -4.80 (0.57), residues: 8
  sheet: -1.53 (0.49), residues: 124
  loop : -2.02 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.010   0.001   PHE E  27 
 TYR   0.015   0.001   TYR E 183 
 ARG   0.002   0.000   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8750 (p-90) cc_final: 0.8318 (p-90)
REVERT: C  450 ASN cc_start: 0.8695 (p0) cc_final: 0.8322 (p0)
REVERT: C  492 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8614 (mp)
REVERT: C  498 GLN cc_start: 0.6757 (mm110) cc_final: 0.6546 (mm-40)
REVERT: E  139 GLN cc_start: 0.7215 (pt0) cc_final: 0.6308 (pt0)
REVERT: E  215 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7391 (tm-30)
REVERT: E  224 GLN cc_start: 0.8650 (pp30) cc_final: 0.8380 (pp30)
  outliers start: 13
  outliers final: 10
  residues processed: 69
  average time/residue: 0.1408
  time to fit residues: 12.2447
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.0980
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0050
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.161680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.143241 restraints weight = 5816.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.146218 restraints weight = 3672.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.148320 restraints weight = 2621.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3395  Z= 0.197
  Angle     :  0.662   7.029   4614  Z= 0.342
  Chirality :  0.044   0.175    500
  Planarity :  0.004   0.033    597
  Dihedral  :  6.135  51.151    493
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.86 %
    Favored  : 82.14 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 21.51 %
    Favored  : 74.02 %
  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: -2.79 (0.42), residues: 420
  helix: -4.81 (0.57), residues: 8
  sheet: -1.54 (0.49), residues: 124
  loop : -2.01 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.008   0.001   PHE E 205 
 TYR   0.016   0.001   TYR E 183 
 ARG   0.002   0.000   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8837 (p-90) cc_final: 0.8283 (p-90)
REVERT: C  450 ASN cc_start: 0.8795 (p0) cc_final: 0.8432 (p0)
REVERT: C  462 LYS cc_start: 0.8939 (pptt) cc_final: 0.8618 (mmtt)
REVERT: C  498 GLN cc_start: 0.6773 (mm110) cc_final: 0.6544 (mm-40)
REVERT: E  139 GLN cc_start: 0.7311 (pt0) cc_final: 0.6690 (pt0)
REVERT: E  215 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: E  224 GLN cc_start: 0.8700 (pp30) cc_final: 0.8407 (pp30)
  outliers start: 16
  outliers final: 14
  residues processed: 73
  average time/residue: 0.1520
  time to fit residues: 13.6890
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 19 optimal weight:    0.0270
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0570
   chunk 30 optimal weight:    0.8980
   chunk 29 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:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.162521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.144085 restraints weight = 5820.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.147140 restraints weight = 3650.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.149254 restraints weight = 2586.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3395  Z= 0.193
  Angle     :  0.660   6.894   4614  Z= 0.341
  Chirality :  0.044   0.174    500
  Planarity :  0.004   0.033    597
  Dihedral  :  6.156  51.341    493
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.24 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 22.07 %
    Favored  : 73.46 %
  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: -2.82 (0.41), residues: 420
  helix: -4.81 (0.56), residues: 8
  sheet: -1.57 (0.48), residues: 124
  loop : -2.03 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.009   0.001   PHE E  27 
 TYR   0.014   0.001   TYR C 473 
 ARG   0.002   0.000   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8831 (p-90) cc_final: 0.8287 (p-90)
REVERT: C  450 ASN cc_start: 0.8823 (p0) cc_final: 0.8508 (p0)
REVERT: C  462 LYS cc_start: 0.8949 (pptt) cc_final: 0.8667 (mmtt)
REVERT: C  498 GLN cc_start: 0.6879 (mm110) cc_final: 0.6652 (mm-40)
REVERT: E  139 GLN cc_start: 0.7296 (pt0) cc_final: 0.6677 (pt0)
REVERT: E  215 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7491 (tm-30)
REVERT: E  224 GLN cc_start: 0.8678 (pp30) cc_final: 0.8386 (pp30)
  outliers start: 16
  outliers final: 16
  residues processed: 71
  average time/residue: 0.1472
  time to fit residues: 13.1365
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 41 optimal weight:    0.2980
   chunk 13 optimal weight:    0.0470
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.4678

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.159798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.141391 restraints weight = 5780.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.144313 restraints weight = 3676.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.146356 restraints weight = 2646.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.4466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3395  Z= 0.224
  Angle     :  0.680   6.959   4614  Z= 0.352
  Chirality :  0.045   0.175    500
  Planarity :  0.004   0.033    597
  Dihedral  :  6.301  51.698    493
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.86 %
    Favored  : 82.14 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 22.07 %
    Favored  : 73.46 %
  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: -2.89 (0.41), residues: 420
  helix: -4.77 (0.59), residues: 8
  sheet: -1.67 (0.48), residues: 124
  loop : -2.05 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 436 
 HIS   0.001   0.000   HIS C 519 
 PHE   0.009   0.001   PHE E 205 
 TYR   0.014   0.001   TYR E 183 
 ARG   0.003   0.000   ARG E  97 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8848 (p-90) cc_final: 0.8296 (p-90)
REVERT: C  450 ASN cc_start: 0.8787 (p0) cc_final: 0.8418 (p0)
REVERT: C  462 LYS cc_start: 0.8934 (pptt) cc_final: 0.8720 (mmtt)
REVERT: C  498 GLN cc_start: 0.6761 (mm110) cc_final: 0.6553 (mm-40)
REVERT: E  139 GLN cc_start: 0.7487 (pt0) cc_final: 0.6794 (pt0)
REVERT: E  215 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7473 (tm-30)
REVERT: E  224 GLN cc_start: 0.8668 (pp30) cc_final: 0.8351 (pp30)
  outliers start: 16
  outliers final: 16
  residues processed: 70
  average time/residue: 0.1429
  time to fit residues: 12.5683
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.0870
   chunk 41 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0000
   chunk 8 optimal weight:    0.0980
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0010
   overall best weight:    0.0568

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.168595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.150483 restraints weight = 5774.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.153568 restraints weight = 3582.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.155765 restraints weight = 2531.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3746 r_free = 0.3746    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3746 r_free = 0.3746    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3395  Z= 0.163
  Angle     :  0.645   7.773   4614  Z= 0.328
  Chirality :  0.044   0.166    500
  Planarity :  0.004   0.033    597
  Dihedral  :  5.827  51.106    493
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 24.02 %
    Favored  : 73.46 %
  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: -2.75 (0.41), residues: 420
  helix: -4.86 (0.51), residues: 8
  sheet: -1.34 (0.53), residues: 107
  loop : -2.06 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.000   HIS C 519 
 PHE   0.009   0.001   PHE E  27 
 TYR   0.016   0.001   TYR C 473 
 ARG   0.002   0.000   ARG C 408 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1730.55 seconds
wall clock time: 31 minutes 29.81 seconds (1889.81 seconds total)