Starting phenix.real_space_refine
on Wed Mar  5 19:35:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zcf_14629/03_2025/7zcf_14629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zcf_14629/03_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_14629/03_2025/7zcf_14629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zcf_14629/03_2025/7zcf_14629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zcf_14629/03_2025/7zcf_14629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zcf_14629/03_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-5624/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: 3.85, per 1000 atoms: 1.16
  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: 0.82
  Conformation dependent library (CDL) restraints added in 389.2 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: 0.74

  Time building geometry restraints manager: 0.99 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:             5.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.250
  Find NCS groups from input model:        0.040
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.060
-------------------------------------------------------------------------------
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  : 0.387 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1708
  time to fit residues: 14.7963
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  : 0.407 
-------------------------------------------------------------------------------
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 = 38)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.140025 restraints weight = 5748.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.143082 restraints weight = 3543.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.145001 restraints weight = 2508.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
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  49.955    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  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: C  331 ASN cc_start: 0.7186 (OUTLIER) cc_final: 0.6900 (p0)
REVERT: E  139 GLN cc_start: 0.7493 (pt0) cc_final: 0.7251 (pt0)
  outliers start: 9
  outliers final: 7
  residues processed: 82
  average time/residue: 0.1405
  time to fit residues: 14.3781
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  : 0.382 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0020
   chunk 5 optimal weight:    0.0870
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.3104

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.167981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.150366 restraints weight = 5520.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.153150 restraints weight = 3537.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155076 restraints weight = 2554.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.3267

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= 0.193
  Angle     :  0.664   6.439   4614  Z= 0.347
  Chirality :  0.046   0.171    500
  Planarity :  0.005   0.034    597
  Dihedral  :  6.439  51.755    493
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.19 %
    Favored  : 83.81 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 17.32 %
    Favored  : 79.33 %
  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: -4.79 (0.57), residues: 8
  sheet: -1.37 (0.49), residues: 120
  loop : -2.04 (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   0.024   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
  77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: C  398 ASP cc_start: 0.8063 (m-30) cc_final: 0.7821 (m-30)
REVERT: C  401 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9192 (p)
REVERT: C  450 ASN cc_start: 0.8808 (p0) cc_final: 0.8222 (p0)
REVERT: E  215 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7698 (tm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 70
  average time/residue: 0.1581
  time to fit residues: 13.9004
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
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 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  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:    0.0060
   chunk 1 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0050
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    0.1980
   overall best weight:    0.2410

-------------------------------------------------------------------------------
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
E 160 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.168963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.151044 restraints weight = 5665.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.153882 restraints weight = 3617.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.155884 restraints weight = 2609.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3749 r_free = 0.3749    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3749 r_free = 0.3749    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3395  Z= 0.165
  Angle     :  0.641   6.804   4614  Z= 0.330
  Chirality :  0.045   0.170    500
  Planarity :  0.004   0.032    597
  Dihedral  :  6.110  51.748    493
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.43 %
    Favored  : 83.57 %
  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: -2.69 (0.41), residues: 420
  helix: -4.85 (0.53), residues: 8
  sheet: -1.42 (0.50), residues: 118
  loop : -1.96 (0.37), 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   0.009   0.001   PHE C 456 
 TYR   0.024   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
  86 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: C  450 ASN cc_start: 0.8723 (p0) cc_final: 0.8209 (p0)
REVERT: E  139 GLN cc_start: 0.6873 (pt0) cc_final: 0.6513 (pt0)
REVERT: E  215 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7489 (tm-30)
REVERT: E  224 GLN cc_start: 0.8673 (pp30) cc_final: 0.8427 (pp30)
  outliers start: 16
  outliers final: 12
  residues processed: 76
  average time/residue: 0.1418
  time to fit residues: 13.5152
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0870
   chunk 8 optimal weight:    0.1980
   chunk 24 optimal weight:    0.0670
   chunk 6 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0050
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.2110

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.168423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.149852 restraints weight = 5760.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.152982 restraints weight = 3592.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.155144 restraints weight = 2547.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3395  Z= 0.165
  Angle     :  0.633   6.832   4614  Z= 0.327
  Chirality :  0.044   0.168    500
  Planarity :  0.004   0.033    597
  Dihedral  :  5.989  51.783    493
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 19.27 %
    Favored  : 76.54 %
  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: -2.72 (0.41), residues: 420
  helix: -4.88 (0.50), residues: 8
  sheet: -1.32 (0.51), residues: 114
  loop : -2.04 (0.36), residues: 298

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   0.010   0.001   PHE E 232 
 TYR   0.023   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
  79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: E  139 GLN cc_start: 0.7122 (pt0) cc_final: 0.6685 (pt0)
REVERT: E  215 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: E  224 GLN cc_start: 0.8642 (pp30) cc_final: 0.8380 (pp30)
  outliers start: 15
  outliers final: 13
  residues processed: 68
  average time/residue: 0.1453
  time to fit residues: 12.3230
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0370
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.160996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.142049 restraints weight = 6033.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.145065 restraints weight = 3818.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.147190 restraints weight = 2739.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3918

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= 0.232
  Angle     :  0.671   7.165   4614  Z= 0.351
  Chirality :  0.045   0.174    500
  Planarity :  0.004   0.033    597
  Dihedral  :  6.406  50.937    493
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.62 %
    Favored  : 82.38 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 19.27 %
    Favored  : 75.98 %
  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: -2.77 (0.41), residues: 420
  helix: -4.85 (0.53), residues: 8
  sheet: -1.45 (0.48), residues: 128
  loop : -2.04 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.009   0.001   PHE E 205 
 TYR   0.022   0.002   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
  77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: C  450 ASN cc_start: 0.8834 (p0) cc_final: 0.8376 (p0)
REVERT: E  139 GLN cc_start: 0.7222 (pt0) cc_final: 0.6674 (pt0)
REVERT: E  215 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: E  224 GLN cc_start: 0.8658 (pp30) cc_final: 0.8371 (pp30)
  outliers start: 17
  outliers final: 15
  residues processed: 68
  average time/residue: 0.1439
  time to fit residues: 12.2660
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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   35 SER
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  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:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.1980
   chunk 39 optimal weight:    0.0020
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.2388

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.165125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.147058 restraints weight = 5750.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.150099 restraints weight = 3604.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.152207 restraints weight = 2562.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3716 r_free = 0.3716    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3716 r_free = 0.3716    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.3816

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= 0.167
  Angle     :  0.642   6.884   4614  Z= 0.332
  Chirality :  0.044   0.174    500
  Planarity :  0.004   0.034    597
  Dihedral  :  6.087  50.961    493
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.76 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.79 %
    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: -2.74 (0.41), residues: 420
  helix: -4.83 (0.54), residues: 8
  sheet: -1.39 (0.50), residues: 118
  loop : -2.03 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.009   0.001   PHE E  27 
 TYR   0.017   0.001   TYR E 183 
 ARG   0.002   0.000   ARG E  71 

*********************** 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  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: C  450 ASN cc_start: 0.8700 (p0) cc_final: 0.8240 (p0)
REVERT: E  139 GLN cc_start: 0.7146 (pt0) cc_final: 0.6680 (pt0)
REVERT: E  215 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7390 (tm-30)
REVERT: E  224 GLN cc_start: 0.8631 (pp30) cc_final: 0.8362 (pp30)
  outliers start: 13
  outliers final: 12
  residues processed: 70
  average time/residue: 0.1772
  time to fit residues: 15.6978
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
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  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
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:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0570
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.159820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.141228 restraints weight = 5835.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.144172 restraints weight = 3698.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.146228 restraints weight = 2654.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3395  Z= 0.261
  Angle     :  0.699   7.210   4614  Z= 0.369
  Chirality :  0.045   0.179    500
  Planarity :  0.004   0.034    597
  Dihedral  :  6.489  51.155    493
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.10 %
    Favored  : 81.90 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 20.95 %
    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: -2.88 (0.41), residues: 420
  helix: -4.81 (0.56), residues: 8
  sheet: -1.53 (0.49), residues: 126
  loop : -2.12 (0.37), residues: 286

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   0.011   0.002   PHE E 205 
 TYR   0.018   0.002   TYR E 183 
 ARG   0.003   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
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.408 
Fit side-chains
REVERT: C  353 TRP cc_start: 0.8860 (p-90) cc_final: 0.8368 (p-90)
REVERT: C  450 ASN cc_start: 0.8858 (p0) cc_final: 0.8363 (p0)
REVERT: C  462 LYS cc_start: 0.8946 (pptt) cc_final: 0.8689 (mmtt)
REVERT: E   71 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7886 (ptm-80)
REVERT: E   82 MET cc_start: 0.7831 (mmm) cc_final: 0.7592 (mmm)
REVERT: E  139 GLN cc_start: 0.7369 (pt0) cc_final: 0.6667 (pt0)
REVERT: E  215 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7409 (tm-30)
REVERT: E  224 GLN cc_start: 0.8737 (pp30) cc_final: 0.8389 (pp30)
  outliers start: 17
  outliers final: 15
  residues processed: 69
  average time/residue: 0.1801
  time to fit residues: 15.4686
Evaluate side-chains
  76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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  429 PHE
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   71 ARG
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  240 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 19 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0270
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 30 optimal weight:    0.3980
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.2436

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.163622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.145301 restraints weight = 5801.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.148377 restraints weight = 3615.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.150512 restraints weight = 2557.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3685 r_free = 0.3685    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3685 r_free = 0.3685    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.4222

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= 0.179
  Angle     :  0.669   6.899   4614  Z= 0.348
  Chirality :  0.045   0.175    500
  Planarity :  0.004   0.035    597
  Dihedral  :  6.123  50.739    493
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.05 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.63 %
    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: -2.82 (0.41), residues: 420
  helix: -4.82 (0.55), residues: 8
  sheet: -1.49 (0.49), residues: 124
  loop : -2.07 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.009   0.001   PHE E  27 
 TYR   0.017   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
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.354 
Fit side-chains
REVERT: C  353 TRP cc_start: 0.8755 (p-90) cc_final: 0.8325 (p-90)
REVERT: C  450 ASN cc_start: 0.8769 (p0) cc_final: 0.8353 (p0)
REVERT: C  462 LYS cc_start: 0.8937 (pptt) cc_final: 0.8717 (mmtt)
REVERT: C  492 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8597 (mp)
REVERT: E  139 GLN cc_start: 0.7275 (pt0) cc_final: 0.6466 (pt0)
REVERT: E  215 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7417 (tm-30)
REVERT: E  224 GLN cc_start: 0.8650 (pp30) cc_final: 0.8369 (pp30)
  outliers start: 12
  outliers final: 10
  residues processed: 67
  average time/residue: 0.1364
  time to fit residues: 11.5579
Evaluate side-chains
  72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  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  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
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:    0.9990
   chunk 5 optimal weight:    0.0000
   chunk 17 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 14 optimal weight:    0.2980
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.4184

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.160736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.142100 restraints weight = 5808.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.145061 restraints weight = 3713.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.147142 restraints weight = 2676.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3395  Z= 0.214
  Angle     :  0.683   7.171   4614  Z= 0.354
  Chirality :  0.045   0.175    500
  Planarity :  0.004   0.034    597
  Dihedral  :  6.201  51.501    493
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.38 %
    Favored  : 82.62 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 22.63 %
    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: -2.84 (0.41), residues: 420
  helix: -4.82 (0.55), residues: 8
  sheet: -1.57 (0.49), 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   0.000   0.000   HIS C 519 
 PHE   0.009   0.001   PHE E 205 
 TYR   0.017   0.001   TYR C 473 
 ARG   0.002   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
  77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.390 
Fit side-chains
REVERT: C  353 TRP cc_start: 0.8834 (p-90) cc_final: 0.8302 (p-90)
REVERT: C  450 ASN cc_start: 0.8882 (p0) cc_final: 0.8403 (p0)
REVERT: C  462 LYS cc_start: 0.8944 (pptt) cc_final: 0.8720 (mmtt)
REVERT: E  139 GLN cc_start: 0.7351 (pt0) cc_final: 0.6753 (pt0)
REVERT: E  215 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7496 (tm-30)
REVERT: E  224 GLN cc_start: 0.8679 (pp30) cc_final: 0.8350 (pp30)
  outliers start: 14
  outliers final: 13
  residues processed: 70
  average time/residue: 0.1695
  time to fit residues: 14.6419
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
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  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  240 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.0170
   chunk 41 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0770
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0050
   overall best weight:    0.2990

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.163039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.144755 restraints weight = 5807.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.147785 restraints weight = 3610.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.149849 restraints weight = 2555.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.4348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3395  Z= 0.194
  Angle     :  0.675   7.168   4614  Z= 0.347
  Chirality :  0.045   0.174    500
  Planarity :  0.004   0.044    597
  Dihedral  :  6.097  51.337    493
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.76 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 22.63 %
    Favored  : 73.18 %
  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: -4.85 (0.53), residues: 8
  sheet: -1.51 (0.49), residues: 124
  loop : -2.06 (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   0.009   0.001   PHE E  27 
 TYR   0.017   0.001   TYR C 473 
 ARG   0.008   0.000   ARG E  71 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1781.82 seconds
wall clock time: 31 minutes 36.47 seconds (1896.47 seconds total)