Starting phenix.real_space_refine
on Wed Mar  5 19:28:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wog_32651/03_2025/7wog_32651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wog_32651/03_2025/7wog_32651.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wog_32651/03_2025/7wog_32651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wog_32651/03_2025/7wog_32651.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wog_32651/03_2025/7wog_32651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wog_32651/03_2025/7wog_32651.cif"
  }
  resolution = 4.06
  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=   0.001 sd=   0.021
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      16      5.16       5
     C    2122      2.51       5
     N     569      2.21       5
     O     655      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 3362
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1580
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 184}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 937
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 845
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 7, 'TRANS': 104}
  Time building chain proxies: 2.92, per 1000 atoms: 0.87
  Number of scatterers: 3362
  At special positions: 0
  Unit cell: (69.16, 91.504, 87.248, 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      16     16.00
     O     655      8.00
     N     569      7.00
     C    2122      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=2.03
    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 A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  91 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 424.4 milliseconds
  

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  794

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 7 sheets defined
      6.5% alpha, 25.4% 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 342
      removed outlier: 3.591A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.831A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 390
      removed outlier: 3.841A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.962A  pdb=" N   THR A  91 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 86
      removed outlier: 3.909A  pdb=" N   GLU B  86 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358
    Processing sheet with id=AA2, first strand: chain 'C' and resid 356 through 358
      removed outlier: 4.174A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 21
    Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.756A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   THR A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   MET A  34 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.520A  pdb=" N   TYR B  90 " --> pdb=" O   TYR B  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23

    82 hydrogen bonds defined for protein.
    189 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: 0.77

  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 -     1.34: 1085
        1.34 -     1.46: 897
        1.46 -     1.58: 1446
        1.58 -     1.70: 0
        1.70 -     1.81: 20
  Bond restraints: 3448
  Sorted by residual:
  bond pdb=" N   GLY C 504 "
       pdb=" CA  GLY C 504 "
    ideal  model  delta    sigma   weight residual
    1.454  1.444  0.010 1.79e-02 3.12e+03 3.09e-01
  bond pdb=" C   LYS C 462 "
       pdb=" N   PRO C 463 "
    ideal  model  delta    sigma   weight residual
    1.334  1.346 -0.012 2.34e-02 1.83e+03 2.72e-01
  bond pdb=" C   LYS A  76 "
       pdb=" N   ASN A  77 "
    ideal  model  delta    sigma   weight residual
    1.331  1.337 -0.006 1.29e-02 6.01e+03 2.23e-01
  bond pdb=" N   ASN A  77 "
       pdb=" CA  ASN A  77 "
    ideal  model  delta    sigma   weight residual
    1.457  1.462 -0.005 1.31e-02 5.83e+03 1.73e-01
  bond pdb=" CZ  ARG B 112 "
       pdb=" NH2 ARG B 112 "
    ideal  model  delta    sigma   weight residual
    1.330  1.325  0.005 1.30e-02 5.92e+03 1.69e-01
  ... (remaining 3443 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.65: 4288
        0.65 -     1.29: 302
        1.29 -     1.94: 64
        1.94 -     2.59: 21
        2.59 -     3.24: 14
  Bond angle restraints: 4689
  Sorted by residual:
  angle pdb=" C   LYS A  76 "
        pdb=" N   ASN A  77 "
        pdb=" CA  ASN A  77 "
      ideal   model   delta    sigma   weight residual
     121.56  124.80   -3.24 1.56e+00 4.11e-01 4.30e+00
  angle pdb=" N   ASN A  77 "
        pdb=" CA  ASN A  77 "
        pdb=" C   ASN A  77 "
      ideal   model   delta    sigma   weight residual
     110.42  112.79   -2.37 1.46e+00 4.69e-01 2.64e+00
  angle pdb=" NE  ARG C 357 "
        pdb=" CZ  ARG C 357 "
        pdb=" NH1 ARG C 357 "
      ideal   model   delta    sigma   weight residual
     121.50  120.03    1.47 1.00e+00 1.00e+00 2.16e+00
  angle pdb=" NE  ARG B  40 "
        pdb=" CZ  ARG B  40 "
        pdb=" NH1 ARG B  40 "
      ideal   model   delta    sigma   weight residual
     121.50  120.05    1.45 1.00e+00 1.00e+00 2.09e+00
  angle pdb=" NE  ARG C 457 "
        pdb=" CZ  ARG C 457 "
        pdb=" NH1 ARG C 457 "
      ideal   model   delta    sigma   weight residual
     121.50  120.06    1.44 1.00e+00 1.00e+00 2.08e+00
  ... (remaining 4684 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.09: 1876
       11.09 -    22.19: 114
       22.19 -    33.28: 30
       33.28 -    44.37: 10
       44.37 -    55.46: 3
  Dihedral angle restraints: 2033
    sinusoidal: 779
      harmonic: 1254
  Sorted by residual:
  dihedral pdb=" CA  LYS A  76 "
           pdb=" C   LYS A  76 "
           pdb=" N   ASN A  77 "
           pdb=" CA  ASN A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.87  -18.13     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" N   ARG C 457 "
           pdb=" CA  ARG C 457 "
           pdb=" CB  ARG C 457 "
           pdb=" CG  ARG C 457 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.54  -55.46     3      1.50e+01 4.44e-03 9.35e+00
  dihedral pdb=" CA  CYS A  22 "
           pdb=" CB  CYS A  22 "
           pdb=" SG  CYS A  22 "
           pdb=" SG  CYS A  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00 -124.56   51.56     1      2.00e+01 2.50e-03 9.08e+00
  ... (remaining 2030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 293
       0.026 -    0.052: 130
       0.052 -    0.079: 35
       0.079 -    0.105: 28
       0.105 -    0.131: 16
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" CA  ILE B  67 "
            pdb=" N   ILE B  67 "
            pdb=" C   ILE B  67 "
            pdb=" CB  ILE B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  ILE B  49 "
            pdb=" N   ILE B  49 "
            pdb=" C   ILE B  49 "
            pdb=" CB  ILE B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CB  VAL C 433 "
            pdb=" CA  VAL C 433 "
            pdb=" CG1 VAL C 433 "
            pdb=" CG2 VAL C 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.53e-01
  ... (remaining 499 not shown)

  Planarity restraints: 609
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 372 "    0.021 5.00e-02 4.00e+02   3.20e-02 1.64e+00
        pdb=" N   PRO C 373 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C 373 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 373 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B   6 "   -0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO B   7 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B   7 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B   7 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 336 "    0.016 5.00e-02 4.00e+02   2.35e-02 8.82e-01
        pdb=" N   PRO C 337 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO C 337 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C 337 "    0.013 5.00e-02 4.00e+02
  ... (remaining 606 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1012
        2.81 -     3.34: 2783
        3.34 -     3.86: 5344
        3.86 -     4.38: 5893
        4.38 -     4.90: 10189
  Nonbonded interactions: 25221
  Sorted by model distance:
  nonbonded pdb=" O   THR C 393 "
            pdb=" OG1 THR C 523 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   TRP C 353 "
            pdb=" OH  TYR A 106 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   SER A  31 "
            pdb=" OG  SER A 102 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OG  SER C 349 "
            pdb=" O   LEU C 452 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" NH1 ARG A  67 "
            pdb=" O   SER A  85 "
     model   vdw
     2.360 3.120
  ... (remaining 25216 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.700
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5154
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      :  0.001   0.013   3448  Z= 0.091
  Angle     :  0.415   3.236   4689  Z= 0.239
  Chirality :  0.041   0.131    502
  Planarity :  0.003   0.032    609
  Dihedral  :  8.085  55.464   1221
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  :  6.76 %
    Favored  : 89.46 %
  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: -3.98 (0.34), residues: 427
  helix:  None (None), residues: 0
  sheet: -1.23 (0.39), residues: 126
  loop : -3.58 (0.30), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 103 
 HIS   0.001   0.000   HIS B  99 
 PHE   0.004   0.000   PHE C 490 
 TYR   0.008   0.001   TYR A  59 
 ARG   0.001   0.000   ARG B  62 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 PHE cc_start: 0.6498 (m-10) cc_final: 0.5856 (m-10)
REVERT: C  358 ILE cc_start: 0.6075 (mm) cc_final: 0.5858 (mm)
REVERT: C  380 TYR cc_start: 0.7645 (m-80) cc_final: 0.7217 (m-80)
REVERT: C  408 ARG cc_start: 0.6717 (ptm-80) cc_final: 0.5396 (mmm-85)
REVERT: C  452 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7789 (pt)
REVERT: A    4 LEU cc_start: 0.0399 (OUTLIER) cc_final: 0.0053 (tm)
REVERT: A   11 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6667 (pp)
REVERT: A   34 MET cc_start: 0.6625 (mmm) cc_final: 0.6264 (mmm)
REVERT: A   83 MET cc_start: 0.5214 (mtp) cc_final: 0.3636 (mtp)
REVERT: B  102 PHE cc_start: 0.6892 (m-80) cc_final: 0.6553 (m-10)
REVERT: B  106 THR cc_start: 0.7464 (m) cc_final: 0.7132 (p)
  outliers start: 14
  outliers final: 3
  residues processed: 98
  average time/residue: 0.2397
  time to fit residues: 26.8465
Evaluate side-chains
  86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0270
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
C 334 ASN
C 354 ASN
C 409 GLN
C 437 ASN
C 448 ASN
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 GLN
B  98 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.199813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.175412 restraints weight = 7793.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.180182 restraints weight = 5139.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.183626 restraints weight = 3703.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5353
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3448  Z= 0.241
  Angle     :  0.602   5.659   4689  Z= 0.327
  Chirality :  0.045   0.171    502
  Planarity :  0.005   0.041    609
  Dihedral  :  4.300  20.666    481
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.41 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.05 %
    Favored  : 95.68 %
  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: -3.25 (0.37), residues: 427
  helix: -5.23 (0.46), residues: 7
  sheet: -0.65 (0.43), residues: 129
  loop : -3.03 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 103 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.014   0.002   PHE C 377 
 TYR   0.027   0.002   TYR A 106 
 ARG   0.005   0.001   ARG B 112 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.6887 (tpp80) cc_final: 0.6426 (tpp80)
REVERT: C  471 GLU cc_start: 0.7590 (pm20) cc_final: 0.7070 (pm20)
REVERT: A   34 MET cc_start: 0.6757 (mmm) cc_final: 0.5527 (mmp)
REVERT: A   51 ILE cc_start: 0.7714 (tt) cc_final: 0.7441 (tt)
REVERT: A   67 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7159 (mtp180)
REVERT: A   74 ASN cc_start: 0.7002 (m-40) cc_final: 0.6755 (m-40)
REVERT: A   77 ASN cc_start: 0.6189 (p0) cc_final: 0.5986 (p0)
REVERT: A  103 TRP cc_start: 0.6123 (OUTLIER) cc_final: 0.5879 (p-90)
REVERT: A  112 TRP cc_start: 0.7505 (m-10) cc_final: 0.7296 (m100)
REVERT: B   73 SER cc_start: 0.8026 (p) cc_final: 0.7726 (t)
REVERT: B  102 PHE cc_start: 0.7049 (m-80) cc_final: 0.6722 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2097
  time to fit residues: 19.7708
Evaluate side-chains
  78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0030
   chunk 21 optimal weight:    0.0670
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 35 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.2326

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.201258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.176685 restraints weight = 7600.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.181545 restraints weight = 5041.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.184947 restraints weight = 3619.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5293
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3448  Z= 0.142
  Angle     :  0.519   4.831   4689  Z= 0.278
  Chirality :  0.044   0.157    502
  Planarity :  0.004   0.037    609
  Dihedral  :  3.827  18.222    481
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  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: -2.99 (0.38), residues: 427
  helix: -4.73 (0.96), residues: 7
  sheet: -0.18 (0.45), residues: 127
  loop : -3.00 (0.33), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 103 
 HIS   0.003   0.001   HIS C 505 
 PHE   0.011   0.001   PHE C 342 
 TYR   0.020   0.001   TYR A 106 
 ARG   0.003   0.001   ARG C 346 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  471 GLU cc_start: 0.7503 (pm20) cc_final: 0.6915 (pm20)
REVERT: A   34 MET cc_start: 0.6437 (mmm) cc_final: 0.5567 (mmp)
REVERT: B   37 TYR cc_start: 0.5276 (m-80) cc_final: 0.4940 (m-10)
REVERT: B   73 SER cc_start: 0.8020 (p) cc_final: 0.7660 (t)
REVERT: B   85 ASP cc_start: 0.7383 (m-30) cc_final: 0.7104 (m-30)
REVERT: B  102 PHE cc_start: 0.6891 (m-80) cc_final: 0.6497 (m-10)
REVERT: B  106 THR cc_start: 0.7718 (m) cc_final: 0.7332 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2037
  time to fit residues: 18.8849
Evaluate side-chains
  73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  77 ASN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.194383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.170105 restraints weight = 7519.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.174805 restraints weight = 5016.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.178130 restraints weight = 3627.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5457
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3448  Z= 0.233
  Angle     :  0.603   5.575   4689  Z= 0.320
  Chirality :  0.045   0.129    502
  Planarity :  0.005   0.035    609
  Dihedral  :  4.522  16.968    481
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.97 %
    Favored  : 96.76 %
  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: -2.94 (0.38), residues: 427
  helix: -4.55 (1.14), residues: 7
  sheet: -0.38 (0.45), residues: 127
  loop : -2.84 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 103 
 HIS   0.004   0.001   HIS C 505 
 PHE   0.010   0.002   PHE B 102 
 TYR   0.022   0.002   TYR A 106 
 ARG   0.005   0.001   ARG A  67 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.7375 (tpp80) cc_final: 0.6846 (tpp80)
REVERT: C  471 GLU cc_start: 0.7638 (pm20) cc_final: 0.7024 (pm20)
REVERT: A   34 MET cc_start: 0.6516 (mmm) cc_final: 0.5979 (mmm)
REVERT: A   39 GLN cc_start: 0.7402 (tp40) cc_final: 0.6961 (tp40)
REVERT: A   45 LEU cc_start: 0.8163 (mt) cc_final: 0.7744 (mt)
REVERT: B   73 SER cc_start: 0.7993 (p) cc_final: 0.7700 (t)
REVERT: B  102 PHE cc_start: 0.6896 (m-80) cc_final: 0.6505 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 78
  average time/residue: 0.1888
  time to fit residues: 17.2681
Evaluate side-chains
  74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.0270
   chunk 26 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.196578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.172414 restraints weight = 7647.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.176986 restraints weight = 5182.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.180276 restraints weight = 3793.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5410
moved from start:          0.4610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3448  Z= 0.159
  Angle     :  0.563   5.293   4689  Z= 0.299
  Chirality :  0.044   0.132    502
  Planarity :  0.004   0.037    609
  Dihedral  :  4.413  19.896    481
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.70 %
    Favored  : 97.03 %
  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 (0.39), residues: 427
  helix: -4.23 (1.46), residues: 7
  sheet: -0.51 (0.44), residues: 134
  loop : -2.75 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A  36 
 HIS   0.002   0.001   HIS B  99 
 PHE   0.009   0.001   PHE B 102 
 TYR   0.024   0.002   TYR B  37 
 ARG   0.003   0.001   ARG A  72 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.7379 (tpp80) cc_final: 0.6509 (tpp-160)
REVERT: C  471 GLU cc_start: 0.7554 (pm20) cc_final: 0.6954 (pm20)
REVERT: C  494 SER cc_start: 0.7836 (p) cc_final: 0.7459 (t)
REVERT: A   34 MET cc_start: 0.6353 (mmm) cc_final: 0.5521 (mmp)
REVERT: A   39 GLN cc_start: 0.7245 (tp40) cc_final: 0.6964 (tp40)
REVERT: A   45 LEU cc_start: 0.8192 (mt) cc_final: 0.7910 (mt)
REVERT: B   73 SER cc_start: 0.7967 (p) cc_final: 0.7694 (t)
REVERT: B   81 LEU cc_start: 0.8002 (tp) cc_final: 0.7693 (tp)
REVERT: B  102 PHE cc_start: 0.6705 (m-80) cc_final: 0.6419 (m-10)
REVERT: B  106 THR cc_start: 0.7781 (m) cc_final: 0.7268 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2246
  time to fit residues: 18.9586
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0770
   chunk 23 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** C 448 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 = 0.4517 r_free = 0.4517 target = 0.194347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.169560 restraints weight = 7747.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.174370 restraints weight = 5177.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.177930 restraints weight = 3744.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5459
moved from start:          0.4925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3448  Z= 0.199
  Angle     :  0.593   5.799   4689  Z= 0.314
  Chirality :  0.045   0.135    502
  Planarity :  0.005   0.035    609
  Dihedral  :  4.529  18.482    481
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.11 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  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: -2.97 (0.38), residues: 427
  helix: -3.66 (1.24), residues: 13
  sheet: -0.41 (0.45), residues: 131
  loop : -2.88 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 112 
 HIS   0.002   0.001   HIS B  99 
 PHE   0.008   0.001   PHE B 102 
 TYR   0.017   0.001   TYR A 106 
 ARG   0.006   0.001   ARG B  40 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7054 (ptp90) cc_final: 0.6344 (ptp90)
REVERT: C  358 ILE cc_start: 0.6266 (mt) cc_final: 0.5811 (mm)
REVERT: C  457 ARG cc_start: 0.7417 (tpp80) cc_final: 0.5722 (ttp80)
REVERT: C  471 GLU cc_start: 0.7541 (pm20) cc_final: 0.6927 (pm20)
REVERT: A   39 GLN cc_start: 0.7214 (tp40) cc_final: 0.6964 (tp40)
REVERT: A   45 LEU cc_start: 0.8257 (mt) cc_final: 0.7898 (mt)
REVERT: B   73 SER cc_start: 0.7983 (p) cc_final: 0.7699 (t)
REVERT: B   81 LEU cc_start: 0.7901 (tp) cc_final: 0.7541 (tp)
REVERT: B  102 PHE cc_start: 0.6772 (m-80) cc_final: 0.6506 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2133
  time to fit residues: 18.0381
Evaluate side-chains
  68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.193076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.167581 restraints weight = 7641.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.172429 restraints weight = 5114.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.175887 restraints weight = 3710.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5472
moved from start:          0.5299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3448  Z= 0.206
  Angle     :  0.621   7.208   4689  Z= 0.327
  Chirality :  0.045   0.132    502
  Planarity :  0.005   0.036    609
  Dihedral  :  4.760  20.736    481
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -2.97 (0.39), residues: 427
  helix: -3.61 (1.29), residues: 13
  sheet: -0.35 (0.46), residues: 129
  loop : -2.90 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A  36 
 HIS   0.001   0.001   HIS B  99 
 PHE   0.013   0.002   PHE C 347 
 TYR   0.019   0.002   TYR B  37 
 ARG   0.007   0.001   ARG C 493 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7002 (ptp90) cc_final: 0.6714 (ptp90)
REVERT: C  358 ILE cc_start: 0.6139 (mt) cc_final: 0.5938 (mt)
REVERT: C  457 ARG cc_start: 0.7358 (tpp80) cc_final: 0.5853 (ttp80)
REVERT: C  466 ARG cc_start: 0.4027 (mtp180) cc_final: 0.3568 (mpt90)
REVERT: C  471 GLU cc_start: 0.7548 (pm20) cc_final: 0.6869 (pm20)
REVERT: A   36 TRP cc_start: 0.6509 (m100) cc_final: 0.6216 (m100)
REVERT: A   39 GLN cc_start: 0.7286 (tp40) cc_final: 0.7022 (tp40)
REVERT: B   36 TRP cc_start: 0.6717 (m100) cc_final: 0.6369 (m-10)
REVERT: B   62 ARG cc_start: 0.7948 (mmm160) cc_final: 0.7646 (mmm160)
REVERT: B   73 SER cc_start: 0.7993 (p) cc_final: 0.7747 (t)
REVERT: B   85 ASP cc_start: 0.7548 (m-30) cc_final: 0.7277 (m-30)
REVERT: B  100 VAL cc_start: 0.8793 (t) cc_final: 0.8503 (t)
REVERT: B  102 PHE cc_start: 0.6724 (m-80) cc_final: 0.6440 (m-10)
REVERT: B  106 THR cc_start: 0.7676 (m) cc_final: 0.7118 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.2117
  time to fit residues: 18.2880
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 31 optimal weight:    0.4980
   chunk 26 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.192756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.168815 restraints weight = 7720.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.173581 restraints weight = 5062.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.177002 restraints weight = 3631.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5479
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3448  Z= 0.214
  Angle     :  0.616   7.351   4689  Z= 0.327
  Chirality :  0.046   0.132    502
  Planarity :  0.005   0.040    609
  Dihedral  :  4.842  21.018    481
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.05 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  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: -3.00 (0.39), residues: 427
  helix: -3.81 (1.15), residues: 15
  sheet: -0.41 (0.46), residues: 129
  loop : -2.86 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP A  47 
 HIS   0.003   0.001   HIS B  99 
 PHE   0.011   0.001   PHE C 347 
 TYR   0.017   0.002   TYR C 453 
 ARG   0.007   0.001   ARG C 493 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.6997 (ptp90) cc_final: 0.6753 (ptp90)
REVERT: C  466 ARG cc_start: 0.3958 (mtp180) cc_final: 0.3350 (mpt90)
REVERT: C  471 GLU cc_start: 0.7543 (pm20) cc_final: 0.6845 (pm20)
REVERT: C  494 SER cc_start: 0.7853 (p) cc_final: 0.7646 (p)
REVERT: A   36 TRP cc_start: 0.6564 (m100) cc_final: 0.6293 (m100)
REVERT: A   39 GLN cc_start: 0.7283 (tp40) cc_final: 0.6969 (tp40)
REVERT: A   45 LEU cc_start: 0.8346 (mt) cc_final: 0.8088 (mt)
REVERT: B   36 TRP cc_start: 0.6714 (m100) cc_final: 0.6434 (m-10)
REVERT: B   73 SER cc_start: 0.8035 (p) cc_final: 0.7815 (t)
REVERT: B  102 PHE cc_start: 0.6828 (m-80) cc_final: 0.6485 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.2096
  time to fit residues: 18.3728
Evaluate side-chains
  68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0970
   chunk 38 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.194065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.171033 restraints weight = 7696.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.175478 restraints weight = 5189.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.178749 restraints weight = 3771.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5457
moved from start:          0.5767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3448  Z= 0.187
  Angle     :  0.619   6.833   4689  Z= 0.327
  Chirality :  0.045   0.134    502
  Planarity :  0.005   0.042    609
  Dihedral  :  4.890  21.052    481
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.11 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.39), residues: 427
  helix: -3.95 (1.05), residues: 15
  sheet: -0.30 (0.47), residues: 128
  loop : -2.81 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A  47 
 HIS   0.002   0.001   HIS B  99 
 PHE   0.011   0.001   PHE C 347 
 TYR   0.031   0.002   TYR A 106 
 ARG   0.006   0.001   ARG A  67 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7038 (ptp90) cc_final: 0.6801 (ptp90)
REVERT: C  466 ARG cc_start: 0.3948 (mtp180) cc_final: 0.3116 (mpt90)
REVERT: C  471 GLU cc_start: 0.7484 (pm20) cc_final: 0.6857 (pm20)
REVERT: A   36 TRP cc_start: 0.6370 (m100) cc_final: 0.6035 (m100)
REVERT: A   39 GLN cc_start: 0.7240 (tp40) cc_final: 0.6853 (tp40)
REVERT: A   45 LEU cc_start: 0.8314 (mt) cc_final: 0.8091 (mt)
REVERT: B   36 TRP cc_start: 0.6710 (m100) cc_final: 0.6351 (m-10)
REVERT: B   62 ARG cc_start: 0.7770 (mmm160) cc_final: 0.7567 (mmm160)
REVERT: B  102 PHE cc_start: 0.6861 (m-80) cc_final: 0.6501 (m-10)
REVERT: B  106 THR cc_start: 0.7707 (m) cc_final: 0.7113 (p)
REVERT: B  107 LYS cc_start: 0.7202 (ttpp) cc_final: 0.6727 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2292
  time to fit residues: 18.7897
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.0070
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0010
   chunk 31 optimal weight:    0.0010
   chunk 39 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.2410

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.196719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.174001 restraints weight = 7577.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.178531 restraints weight = 5068.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.181854 restraints weight = 3641.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5370
moved from start:          0.5704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3448  Z= 0.137
  Angle     :  0.571   6.662   4689  Z= 0.298
  Chirality :  0.044   0.138    502
  Planarity :  0.004   0.045    609
  Dihedral  :  4.507  20.221    481
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.18 %
    Favored  : 87.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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: -2.68 (0.40), residues: 427
  helix: -3.61 (1.27), residues: 13
  sheet: -0.05 (0.48), residues: 119
  loop : -2.65 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A  36 
 HIS   0.001   0.000   HIS B  99 
 PHE   0.010   0.001   PHE C 347 
 TYR   0.020   0.001   TYR A 106 
 ARG   0.005   0.001   ARG C 493 

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  466 ARG cc_start: 0.3964 (mtp180) cc_final: 0.3398 (mpt180)
REVERT: C  471 GLU cc_start: 0.7380 (pm20) cc_final: 0.6784 (pm20)
REVERT: A   19 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6730 (tpp80)
REVERT: A   36 TRP cc_start: 0.6380 (m100) cc_final: 0.6179 (m100)
REVERT: A   38 ARG cc_start: 0.6639 (ptt180) cc_final: 0.5260 (ptt180)
REVERT: A   39 GLN cc_start: 0.7232 (tp40) cc_final: 0.6956 (tp40)
REVERT: B   73 SER cc_start: 0.7968 (p) cc_final: 0.7756 (t)
REVERT: B  102 PHE cc_start: 0.6594 (m-80) cc_final: 0.6341 (m-10)
REVERT: B  106 THR cc_start: 0.7710 (m) cc_final: 0.7165 (p)
REVERT: B  107 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6743 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2380
  time to fit residues: 19.3885
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0270
   chunk 2 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.194282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.170559 restraints weight = 7776.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.175323 restraints weight = 5111.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.178779 restraints weight = 3651.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5448
moved from start:          0.5913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3448  Z= 0.179
  Angle     :  0.612   6.514   4689  Z= 0.321
  Chirality :  0.045   0.133    502
  Planarity :  0.005   0.045    609
  Dihedral  :  4.769  20.950    481
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.82 %
    Favored  : 86.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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: -2.71 (0.40), residues: 427
  helix: -3.96 (1.03), residues: 15
  sheet: -0.22 (0.47), residues: 125
  loop : -2.61 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 103 
 HIS   0.001   0.000   HIS B   8 
 PHE   0.009   0.001   PHE B 102 
 TYR   0.028   0.002   TYR A 106 
 ARG   0.006   0.001   ARG C 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1718.18 seconds
wall clock time: 30 minutes 26.74 seconds (1826.74 seconds total)