Starting phenix.real_space_refine
on Tue Mar  3 11:36:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wog_32651/03_2026/7wog_32651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wog_32651/03_2026/7wog_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wog_32651/03_2026/7wog_32651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wog_32651/03_2026/7wog_32651.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wog_32651/03_2026/7wog_32651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wog_32651/03_2026/7wog_32651.map"
  }
  resolution = 4.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.95, per 1000 atoms: 0.28
  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: 0.27
  Conformation dependent library (CDL) restraints added in 137.8 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: 0.11
  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: 0.42

  Time building geometry restraints manager: 0.37 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:             1.240
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.420
  Find NCS groups from input model:        0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.070
-------------------------------------------------------------------------------
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   3454  Z= 0.077
  Angle     :  0.415   3.236   4701  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG B  62 
 TYR   0.008   0.001   TYR A  59 
 PHE   0.004   0.000   PHE C 490 
 TRP   0.009   0.001   TRP A 103 
 HIS   0.001   0.000   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00139 ( 3448)
  covalent geometry    : angle       0.41487 ( 4689)
  SS BOND              : bond        0.00101 (    6)
  SS BOND              : angle       0.40952 (   12)
  hydrogen bonds       : bond        0.14833 (   71)
  hydrogen bonds       : angle       7.11920 (  189)

*********************** 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  : 0.118 
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: 0.5855 (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: 0.3635 (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: 0.1071
  time to fit residues: 11.9705
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  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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  98 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.199477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.174916 restraints weight = 7797.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.179717 restraints weight = 5159.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.183149 restraints weight = 3708.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.185650 restraints weight = 2833.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.187395 restraints weight = 2265.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.4446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5299
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3454  Z= 0.168
  Angle     :  0.614   5.487   4701  Z= 0.333
  Chirality :  0.045   0.142    502
  Planarity :  0.006   0.046    609
  Dihedral  :  4.386  20.532    481
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.11 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  3.78 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.25 (0.37), residues: 427
  helix: -5.26 (0.44), residues: 7
  sheet: -0.67 (0.43), residues: 129
  loop : -3.02 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 112 
 TYR   0.029   0.002   TYR A 106 
 PHE   0.015   0.002   PHE C 377 
 TRP   0.016   0.002   TRP A 103 
 HIS   0.002   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 3448)
  covalent geometry    : angle       0.61366 ( 4689)
  SS BOND              : bond        0.00340 (    6)
  SS BOND              : angle       0.75381 (   12)
  hydrogen bonds       : bond        0.03527 (   71)
  hydrogen bonds       : angle       6.16693 (  189)

*********************** 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
  82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.6902 (tpp80) cc_final: 0.6466 (tpp80)
REVERT: C  471 GLU cc_start: 0.7612 (pm20) cc_final: 0.7119 (pm20)
REVERT: A   34 MET cc_start: 0.6761 (mmm) cc_final: 0.5542 (mmp)
REVERT: A   51 ILE cc_start: 0.7744 (tt) cc_final: 0.7473 (tt)
REVERT: A   67 ARG cc_start: 0.7442 (mtm110) cc_final: 0.7232 (mtm110)
REVERT: A   72 ARG cc_start: 0.5551 (ttt90) cc_final: 0.5121 (mtp-110)
REVERT: A  103 TRP cc_start: 0.6097 (OUTLIER) cc_final: 0.5864 (p-90)
REVERT: A  112 TRP cc_start: 0.7484 (m-10) cc_final: 0.7272 (m100)
REVERT: B   73 SER cc_start: 0.8041 (p) cc_final: 0.7740 (t)
REVERT: B   97 SER cc_start: 0.7542 (m) cc_final: 0.7330 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0882
  time to fit residues: 8.4172
Evaluate side-chains
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0020
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN
A  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.196662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.170866 restraints weight = 7482.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.175951 restraints weight = 5004.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.179504 restraints weight = 3608.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.182181 restraints weight = 2752.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.184153 restraints weight = 2187.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.4398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5375
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3454  Z= 0.148
  Angle     :  0.581   4.908   4701  Z= 0.314
  Chirality :  0.045   0.140    502
  Planarity :  0.005   0.037    609
  Dihedral  :  4.297  17.711    481
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.38), residues: 427
  helix: -4.98 (0.73), residues: 7
  sheet: -0.62 (0.43), residues: 138
  loop : -2.97 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  40 
 TYR   0.027   0.002   TYR A 106 
 PHE   0.011   0.002   PHE C 342 
 TRP   0.034   0.003   TRP A 103 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3448)
  covalent geometry    : angle       0.58067 ( 4689)
  SS BOND              : bond        0.00230 (    6)
  SS BOND              : angle       0.83199 (   12)
  hydrogen bonds       : bond        0.03127 (   71)
  hydrogen bonds       : angle       6.14754 (  189)

*********************** 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
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  471 GLU cc_start: 0.7575 (pm20) cc_final: 0.6983 (pm20)
REVERT: A   34 MET cc_start: 0.6510 (mmm) cc_final: 0.5957 (mmm)
REVERT: A   51 ILE cc_start: 0.7774 (tt) cc_final: 0.7549 (tt)
REVERT: A   67 ARG cc_start: 0.7347 (mtm110) cc_final: 0.7026 (mtm110)
REVERT: A   72 ARG cc_start: 0.5809 (ttt90) cc_final: 0.5385 (mtp-110)
REVERT: A  112 TRP cc_start: 0.7461 (m-10) cc_final: 0.7170 (m100)
REVERT: B   37 TYR cc_start: 0.5316 (m-80) cc_final: 0.4791 (m-10)
REVERT: B   73 SER cc_start: 0.8042 (p) cc_final: 0.7735 (t)
REVERT: B  100 VAL cc_start: 0.8731 (t) cc_final: 0.8427 (t)
REVERT: B  106 THR cc_start: 0.7810 (m) cc_final: 0.7334 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 77
  average time/residue: 0.0830
  time to fit residues: 7.4889
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  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0770
   chunk 38 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN
A  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.194376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.168650 restraints weight = 7250.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.173631 restraints weight = 4765.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.177207 restraints weight = 3420.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.179864 restraints weight = 2595.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.181707 restraints weight = 2060.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5393
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3454  Z= 0.134
  Angle     :  0.557   5.673   4701  Z= 0.300
  Chirality :  0.044   0.142    502
  Planarity :  0.004   0.037    609
  Dihedral  :  4.410  19.565    481
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.39), residues: 427
  helix: -4.94 (0.77), residues: 7
  sheet: -0.57 (0.44), residues: 134
  loop : -2.85 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 346 
 TYR   0.021   0.002   TYR C 495 
 PHE   0.009   0.001   PHE C 342 
 TRP   0.021   0.002   TRP A 103 
 HIS   0.004   0.001   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3448)
  covalent geometry    : angle       0.55757 ( 4689)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       0.50880 (   12)
  hydrogen bonds       : bond        0.02981 (   71)
  hydrogen bonds       : angle       6.20457 (  189)

*********************** 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
  75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.6915 (tpp80) cc_final: 0.5647 (ttp80)
REVERT: C  471 GLU cc_start: 0.7678 (pm20) cc_final: 0.7053 (pm20)
REVERT: A   34 MET cc_start: 0.6474 (mmm) cc_final: 0.5845 (mmm)
REVERT: A   51 ILE cc_start: 0.7717 (tt) cc_final: 0.7450 (tt)
REVERT: A   67 ARG cc_start: 0.7258 (mtm110) cc_final: 0.7000 (mtm110)
REVERT: A  112 TRP cc_start: 0.7469 (m-10) cc_final: 0.7234 (m100)
REVERT: B   73 SER cc_start: 0.8013 (p) cc_final: 0.7726 (t)
REVERT: B   81 LEU cc_start: 0.7970 (tp) cc_final: 0.7630 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0926
  time to fit residues: 8.1276
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  : 0.122 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 18 optimal weight:    0.0570
   chunk 39 optimal weight:    0.0970
   chunk 30 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    0.2980
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.2696

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN
A  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.197968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.172712 restraints weight = 7527.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.177676 restraints weight = 5042.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.181071 restraints weight = 3645.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.183611 restraints weight = 2803.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.185590 restraints weight = 2240.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5317
moved from start:          0.4682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3454  Z= 0.108
  Angle     :  0.559   4.245   4701  Z= 0.299
  Chirality :  0.045   0.135    502
  Planarity :  0.004   0.037    609
  Dihedral  :  4.333  20.390    481
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.18 %
    Favored  : 87.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.93 (0.39), residues: 427
  helix: -4.63 (1.07), residues: 7
  sheet: -0.47 (0.45), residues: 133
  loop : -2.82 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  40 
 TYR   0.020   0.002   TYR B  37 
 PHE   0.012   0.001   PHE B 102 
 TRP   0.024   0.002   TRP A 103 
 HIS   0.002   0.000   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3448)
  covalent geometry    : angle       0.55906 ( 4689)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       0.35696 (   12)
  hydrogen bonds       : bond        0.02823 (   71)
  hydrogen bonds       : angle       5.96845 (  189)

*********************** 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
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.6904 (ptp90) cc_final: 0.6233 (ptp90)
REVERT: C  471 GLU cc_start: 0.7606 (pm20) cc_final: 0.6990 (pm20)
REVERT: A   34 MET cc_start: 0.6353 (mmm) cc_final: 0.5543 (mmp)
REVERT: B   73 SER cc_start: 0.7901 (p) cc_final: 0.7630 (t)
REVERT: B   81 LEU cc_start: 0.8041 (tp) cc_final: 0.7687 (tp)
REVERT: B  106 THR cc_start: 0.7716 (m) cc_final: 0.7205 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0923
  time to fit residues: 7.6635
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  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0770
   chunk 38 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.7742

-------------------------------------------------------------------------------
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 = 0.4508 r_free = 0.4508 target = 0.193520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.168660 restraints weight = 7588.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.173581 restraints weight = 5026.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.177106 restraints weight = 3609.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.179693 restraints weight = 2746.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.181579 restraints weight = 2181.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5428
moved from start:          0.5248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3454  Z= 0.157
  Angle     :  0.629   6.664   4701  Z= 0.330
  Chirality :  0.046   0.138    502
  Planarity :  0.005   0.036    609
  Dihedral  :  4.854  18.855    481
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 17.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.05 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.39), residues: 427
  helix: -4.04 (0.98), residues: 13
  sheet: -0.31 (0.46), residues: 122
  loop : -2.82 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  40 
 TYR   0.019   0.002   TYR A 106 
 PHE   0.010   0.001   PHE C 490 
 TRP   0.017   0.002   TRP A 103 
 HIS   0.002   0.001   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3448)
  covalent geometry    : angle       0.62893 ( 4689)
  SS BOND              : bond        0.00385 (    6)
  SS BOND              : angle       0.71567 (   12)
  hydrogen bonds       : bond        0.03218 (   71)
  hydrogen bonds       : angle       6.26218 (  189)

*********************** 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
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.6252 (mt) cc_final: 0.5749 (mm)
REVERT: C  457 ARG cc_start: 0.7303 (tpp-160) cc_final: 0.5955 (ttp80)
REVERT: C  471 GLU cc_start: 0.7623 (pm20) cc_final: 0.6994 (pm20)
REVERT: C  494 SER cc_start: 0.8002 (p) cc_final: 0.7797 (p)
REVERT: A   34 MET cc_start: 0.6388 (mmm) cc_final: 0.5704 (mmp)
REVERT: A   36 TRP cc_start: 0.6754 (m100) cc_final: 0.6360 (m100)
REVERT: B   81 LEU cc_start: 0.7981 (tp) cc_final: 0.7621 (tp)
REVERT: B  100 VAL cc_start: 0.8701 (t) cc_final: 0.8402 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0922
  time to fit residues: 7.6630
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  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 30 optimal weight:    0.1980
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4513 r_free = 0.4513 target = 0.193879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.169945 restraints weight = 7738.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.174794 restraints weight = 5048.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.178414 restraints weight = 3595.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.180944 restraints weight = 2688.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.182789 restraints weight = 2106.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.4393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5385
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3454  Z= 0.135
  Angle     :  0.606   6.930   4701  Z= 0.321
  Chirality :  0.046   0.137    502
  Planarity :  0.005   0.039    609
  Dihedral  :  4.774  20.606    481
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.58 %
    Favored  : 86.42 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.39), residues: 427
  helix: -3.74 (1.20), residues: 13
  sheet: -0.38 (0.47), residues: 126
  loop : -2.86 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  40 
 TYR   0.017   0.001   TYR B  37 
 PHE   0.013   0.001   PHE C 347 
 TRP   0.033   0.003   TRP A  47 
 HIS   0.001   0.000   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3448)
  covalent geometry    : angle       0.60587 ( 4689)
  SS BOND              : bond        0.00534 (    6)
  SS BOND              : angle       0.60004 (   12)
  hydrogen bonds       : bond        0.02980 (   71)
  hydrogen bonds       : angle       6.09990 (  189)

*********************** 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  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.7280 (tpp-160) cc_final: 0.5999 (ttp80)
REVERT: C  466 ARG cc_start: 0.3630 (mtp-110) cc_final: 0.3411 (mpt90)
REVERT: C  471 GLU cc_start: 0.7630 (pm20) cc_final: 0.7125 (pm20)
REVERT: C  494 SER cc_start: 0.8014 (p) cc_final: 0.7801 (p)
REVERT: A   36 TRP cc_start: 0.6695 (m100) cc_final: 0.6341 (m100)
REVERT: A   96 CYS cc_start: 0.3795 (p) cc_final: 0.3586 (p)
REVERT: B   40 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6872 (mmt-90)
REVERT: B   62 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7735 (mmm160)
REVERT: B   81 LEU cc_start: 0.7977 (tp) cc_final: 0.7665 (tp)
REVERT: B  106 THR cc_start: 0.7717 (m) cc_final: 0.7178 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1008
  time to fit residues: 8.5881
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  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0470
   chunk 18 optimal weight:    6.9990
   chunk 20 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.4678

-------------------------------------------------------------------------------
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 = 0.4526 r_free = 0.4526 target = 0.194683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.171260 restraints weight = 7799.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.176245 restraints weight = 5084.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.179795 restraints weight = 3598.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.182278 restraints weight = 2676.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.184093 restraints weight = 2083.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5367
moved from start:          0.5530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3454  Z= 0.113
  Angle     :  0.578   6.782   4701  Z= 0.305
  Chirality :  0.045   0.135    502
  Planarity :  0.005   0.041    609
  Dihedral  :  4.586  19.972    481
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.90 (0.39), residues: 427
  helix: -3.56 (1.33), residues: 13
  sheet: -0.35 (0.47), residues: 126
  loop : -2.80 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 346 
 TYR   0.021   0.001   TYR B  37 
 PHE   0.010   0.001   PHE C 347 
 TRP   0.026   0.003   TRP A  47 
 HIS   0.002   0.000   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 3448)
  covalent geometry    : angle       0.57803 ( 4689)
  SS BOND              : bond        0.00259 (    6)
  SS BOND              : angle       0.44497 (   12)
  hydrogen bonds       : bond        0.02850 (   71)
  hydrogen bonds       : angle       6.04357 (  189)

*********************** 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
  73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7103 (ptp90) cc_final: 0.6902 (ptp90)
REVERT: C  457 ARG cc_start: 0.7248 (tpp-160) cc_final: 0.6015 (ttp80)
REVERT: C  471 GLU cc_start: 0.7582 (pm20) cc_final: 0.7067 (pm20)
REVERT: A   36 TRP cc_start: 0.6727 (m100) cc_final: 0.6375 (m100)
REVERT: A   39 GLN cc_start: 0.7222 (tp40) cc_final: 0.6648 (tp-100)
REVERT: A   96 CYS cc_start: 0.3836 (p) cc_final: 0.3599 (p)
REVERT: B   40 ARG cc_start: 0.7206 (mmm-85) cc_final: 0.6878 (mmt-90)
REVERT: B   81 LEU cc_start: 0.7962 (tp) cc_final: 0.7619 (tp)
REVERT: B  106 THR cc_start: 0.7740 (m) cc_final: 0.7179 (p)
REVERT: B  107 LYS cc_start: 0.7371 (ttpp) cc_final: 0.6980 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1008
  time to fit residues: 8.5073
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0370
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0170
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.5296

-------------------------------------------------------------------------------
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 = 0.4526 r_free = 0.4526 target = 0.194828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.171123 restraints weight = 7617.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.175994 restraints weight = 5001.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.179440 restraints weight = 3580.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.181983 restraints weight = 2699.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.183949 restraints weight = 2117.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5384
moved from start:          0.5756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3454  Z= 0.119
  Angle     :  0.588   7.090   4701  Z= 0.308
  Chirality :  0.045   0.134    502
  Planarity :  0.005   0.041    609
  Dihedral  :  4.666  20.470    481
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.58 %
    Favored  : 86.42 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.40), residues: 427
  helix: -3.78 (1.15), residues: 15
  sheet: -0.36 (0.47), residues: 128
  loop : -2.79 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 346 
 TYR   0.029   0.001   TYR A 106 
 PHE   0.010   0.001   PHE C 347 
 TRP   0.023   0.002   TRP A  47 
 HIS   0.001   0.000   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3448)
  covalent geometry    : angle       0.58850 ( 4689)
  SS BOND              : bond        0.00331 (    6)
  SS BOND              : angle       0.43003 (   12)
  hydrogen bonds       : bond        0.02864 (   71)
  hydrogen bonds       : angle       6.10732 (  189)

*********************** 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
  73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7093 (ptp90) cc_final: 0.6869 (ptp90)
REVERT: C  457 ARG cc_start: 0.7329 (tpp-160) cc_final: 0.6041 (ttp80)
REVERT: C  466 ARG cc_start: 0.4184 (mpt90) cc_final: 0.3893 (mpt90)
REVERT: C  471 GLU cc_start: 0.7533 (pm20) cc_final: 0.7014 (pm20)
REVERT: C  494 SER cc_start: 0.7705 (p) cc_final: 0.7486 (p)
REVERT: A   36 TRP cc_start: 0.6666 (m100) cc_final: 0.6272 (m100)
REVERT: A   96 CYS cc_start: 0.3934 (p) cc_final: 0.3641 (p)
REVERT: B   81 LEU cc_start: 0.8010 (tp) cc_final: 0.7643 (tp)
REVERT: B  107 LYS cc_start: 0.7384 (ttpp) cc_final: 0.7067 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0944
  time to fit residues: 8.0370
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  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0980
   chunk 26 optimal weight:    0.0060
   chunk 11 optimal weight:    0.3980
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.4538 r_free = 0.4538 target = 0.195186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.171359 restraints weight = 7809.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.176278 restraints weight = 5206.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.179684 restraints weight = 3734.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.182154 restraints weight = 2812.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.184017 restraints weight = 2212.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5388
moved from start:          0.5912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3454  Z= 0.119
  Angle     :  0.608   6.357   4701  Z= 0.318
  Chirality :  0.045   0.131    502
  Planarity :  0.005   0.041    609
  Dihedral  :  4.755  19.737    481
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.40), residues: 427
  helix: -3.77 (1.16), residues: 15
  sheet: -0.32 (0.47), residues: 128
  loop : -2.73 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  19 
 TYR   0.027   0.001   TYR A 106 
 PHE   0.010   0.001   PHE C 347 
 TRP   0.022   0.002   TRP A  47 
 HIS   0.001   0.000   HIS B   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 3448)
  covalent geometry    : angle       0.60863 ( 4689)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       0.44702 (   12)
  hydrogen bonds       : bond        0.02947 (   71)
  hydrogen bonds       : angle       6.16532 (  189)

********************** 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
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7133 (ptp90) cc_final: 0.6928 (ptp90)
REVERT: C  457 ARG cc_start: 0.7249 (tpp-160) cc_final: 0.5917 (ttp80)
REVERT: C  471 GLU cc_start: 0.7451 (pm20) cc_final: 0.6955 (pm20)
REVERT: C  494 SER cc_start: 0.7798 (p) cc_final: 0.7597 (p)
REVERT: A   34 MET cc_start: 0.6392 (mmm) cc_final: 0.5929 (mmp)
REVERT: A   36 TRP cc_start: 0.6701 (m100) cc_final: 0.6235 (m100)
REVERT: A   96 CYS cc_start: 0.3897 (p) cc_final: 0.3614 (p)
REVERT: B   81 LEU cc_start: 0.7976 (tp) cc_final: 0.7612 (tp)
REVERT: B  100 VAL cc_start: 0.8663 (t) cc_final: 0.8429 (t)
REVERT: B  106 THR cc_start: 0.7730 (m) cc_final: 0.7173 (p)
REVERT: B  107 LYS cc_start: 0.7273 (ttpp) cc_final: 0.6872 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0941
  time to fit residues: 7.9099
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  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.0980
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4526 r_free = 0.4526 target = 0.194268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.171575 restraints weight = 7773.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.176423 restraints weight = 5099.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.179793 restraints weight = 3591.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.182210 restraints weight = 2670.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.183941 restraints weight = 2076.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5415
moved from start:          0.6141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3454  Z= 0.144
  Angle     :  0.632   6.529   4701  Z= 0.336
  Chirality :  0.047   0.192    502
  Planarity :  0.005   0.041    609
  Dihedral  :  4.983  20.213    481
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.89 (0.40), residues: 427
  helix: -3.92 (1.09), residues: 15
  sheet: -0.35 (0.47), residues: 128
  loop : -2.76 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  19 
 TYR   0.028   0.002   TYR A 106 
 PHE   0.010   0.001   PHE C 347 
 TRP   0.063   0.004   TRP A  47 
 HIS   0.001   0.000   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3448)
  covalent geometry    : angle       0.63200 ( 4689)
  SS BOND              : bond        0.00359 (    6)
  SS BOND              : angle       0.67534 (   12)
  hydrogen bonds       : bond        0.03148 (   71)
  hydrogen bonds       : angle       6.43011 (  189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 908.08 seconds
wall clock time: 16 minutes 11.78 seconds (971.78 seconds total)