Starting phenix.real_space_refine
on Fri Aug 22 13:02:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t69_41066/08_2025/8t69_41066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t69_41066/08_2025/8t69_41066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t69_41066/08_2025/8t69_41066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t69_41066/08_2025/8t69_41066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t69_41066/08_2025/8t69_41066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t69_41066/08_2025/8t69_41066.cif"
  }
  resolution = 2.89
  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=   0.032
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      28      5.16       5
     C    1950      2.51       5
     N     450      2.21       5
     O     495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2923
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 2900
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 23, 'TRANS': 362}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'YHL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.08, per 1000 atoms: 0.37
  Number of scatterers: 2923
  At special positions: 0
  Unit cell: (70.741, 62.304, 64.251, 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      28     16.00
     O     495      8.00
     N     450      7.00
     C    1950      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.28
  Conformation dependent library (CDL) restraints added in 120.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  696

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      90.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 39
    Processing helix  chain 'A' and resid 43 through 49
      removed outlier: 3.740A  pdb=" N   TYR A  47 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 157
      removed outlier: 4.391A  pdb=" N   LYS A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA A 139 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A 144 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      Proline residue:  A 147  - end of helix
      removed outlier: 3.961A  pdb=" N   ASN A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ARG A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 178
      removed outlier: 3.734A  pdb=" N   PHE A 178 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 211
      removed outlier: 4.156A  pdb=" N   GLY A 203 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   MET A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 246
      Proline residue:  A 236  - end of helix
    Processing helix  chain 'A' and resid 249 through 271
    Processing helix  chain 'A' and resid 284 through 290
    Processing helix  chain 'A' and resid 291 through 312
      removed outlier: 3.802A  pdb=" N   ASN A 305 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET A 306 " --> pdb=" O   CYS A 302 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   GLY A 307 " --> pdb=" O   PHE A 303 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      Proline residue:  A 316  - end of helix
      No H-bonds generated for 'chain 'A' and resid 313 through 318'
    Processing helix  chain 'A' and resid 319 through 325
      removed outlier: 3.755A  pdb=" N   MET A 323 " --> pdb=" O   MET A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 333
      removed outlier: 4.082A  pdb=" N   GLY A 331 " --> pdb=" O   LYS A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 356
      removed outlier: 4.191A  pdb=" N   ILE A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   HIS A 353 " --> pdb=" O   GLY A 349 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LYS A 354 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 374
    Processing helix  chain 'A' and resid 375 through 378
    Processing helix  chain 'A' and resid 380 through 383
    Processing helix  chain 'A' and resid 384 through 414
      Proline residue:  A 404  - end of helix
      removed outlier: 3.939A  pdb=" N   GLY A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 410 " --> pdb=" O   MET A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 447
      removed outlier: 4.137A  pdb=" N   GLY A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   TYR A 433 " --> pdb=" O   PHE A 429 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
      removed outlier: 4.193A  pdb=" N   GLY A 441 " --> pdb=" O   PRO A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 465 through 471

    236 hydrogen bonds defined for protein.
    690 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: 0.50

  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:
        1.21 -     1.33: 511
        1.33 -     1.45: 707
        1.45 -     1.57: 1728
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 2994
  Sorted by residual:
  bond pdb=" C16 YHL A 901 "
       pdb=" N7  YHL A 901 "
    ideal  model  delta    sigma   weight residual
    1.445  1.510 -0.065 2.00e-02 2.50e+03 1.04e+01
  bond pdb=" C6  YHL A 901 "
       pdb=" N7  YHL A 901 "
    ideal  model  delta    sigma   weight residual
    1.443  1.503 -0.060 2.00e-02 2.50e+03 9.06e+00
  bond pdb=" C8  YHL A 901 "
       pdb=" N7  YHL A 901 "
    ideal  model  delta    sigma   weight residual
    1.451  1.503 -0.052 2.00e-02 2.50e+03 6.68e+00
  bond pdb=" C   ILE A 375 "
       pdb=" N   PRO A 376 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.026 1.19e-02 7.06e+03 4.73e+00
  bond pdb=" C5  YHL A 901 "
       pdb=" C6  YHL A 901 "
    ideal  model  delta    sigma   weight residual
    1.550  1.523  0.027 2.00e-02 2.50e+03 1.78e+00
  ... (remaining 2989 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 3941
        1.51 -     3.02: 99
        3.02 -     4.54: 22
        4.54 -     6.05: 9
        6.05 -     7.56: 3
  Bond angle restraints: 4074
  Sorted by residual:
  angle pdb=" N   TYR A 158 "
        pdb=" CA  TYR A 158 "
        pdb=" C   TYR A 158 "
      ideal   model   delta    sigma   weight residual
     109.81  117.37   -7.56 2.21e+00 2.05e-01 1.17e+01
  angle pdb=" C   CYS A 374 "
        pdb=" N   ILE A 375 "
        pdb=" CA  ILE A 375 "
      ideal   model   delta    sigma   weight residual
     120.33  122.97   -2.64 8.00e-01 1.56e+00 1.09e+01
  angle pdb=" C   ILE A 435 "
        pdb=" N   GLY A 436 "
        pdb=" CA  GLY A 436 "
      ideal   model   delta    sigma   weight residual
     121.13  123.23   -2.10 7.30e-01 1.88e+00 8.28e+00
  angle pdb=" C   PHE A 245 "
        pdb=" N   VAL A 246 "
        pdb=" CA  VAL A 246 "
      ideal   model   delta    sigma   weight residual
     123.16  120.46    2.70 1.06e+00 8.90e-01 6.46e+00
  angle pdb=" N   PRO A 236 "
        pdb=" CA  PRO A 236 "
        pdb=" C   PRO A 236 "
      ideal   model   delta    sigma   weight residual
     110.70  113.71   -3.01 1.22e+00 6.72e-01 6.09e+00
  ... (remaining 4069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.55: 1600
       12.55 -    25.10: 135
       25.10 -    37.65: 34
       37.65 -    50.20: 8
       50.20 -    62.76: 1
  Dihedral angle restraints: 1778
    sinusoidal: 685
      harmonic: 1093
  Sorted by residual:
  dihedral pdb=" CA  VAL A 417 "
           pdb=" C   VAL A 417 "
           pdb=" N   TYR A 418 "
           pdb=" CA  TYR A 418 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.60  -20.40     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  VAL A 332 "
           pdb=" C   VAL A 332 "
           pdb=" N   ALA A 333 "
           pdb=" CA  ALA A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.38  -18.62     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  SER A 401 "
           pdb=" C   SER A 401 "
           pdb=" N   MET A 402 "
           pdb=" CA  MET A 402 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.78  -16.22     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 1775 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 348
       0.042 -    0.084: 101
       0.084 -    0.127: 33
       0.127 -    0.169: 2
       0.169 -    0.211: 1
  Chirality restraints: 485
  Sorted by residual:
  chirality pdb=" C16 YHL A 901 "
            pdb=" C15 YHL A 901 "
            pdb=" C17 YHL A 901 "
            pdb=" N7  YHL A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.61    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" C5  YHL A 901 "
            pdb=" C18 YHL A 901 "
            pdb=" C4  YHL A 901 "
            pdb=" C6  YHL A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.70   -0.16 2.00e-01 2.50e+01 6.08e-01
  chirality pdb=" CA  TYR A 158 "
            pdb=" N   TYR A 158 "
            pdb=" C   TYR A 158 "
            pdb=" CB  TYR A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 482 not shown)

  Planarity restraints: 498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 436 "    0.031 5.00e-02 4.00e+02   4.74e-02 3.60e+00
        pdb=" N   PRO A 437 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 437 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 437 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 235 "   -0.030 5.00e-02 4.00e+02   4.52e-02 3.28e+00
        pdb=" N   PRO A 236 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 236 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 236 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 202 "    0.007 2.00e-02 2.50e+03   1.41e-02 1.99e+00
        pdb=" C   ALA A 202 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ALA A 202 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY A 203 "    0.008 2.00e-02 2.50e+03
  ... (remaining 495 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 1061
        2.88 -     3.39: 3156
        3.39 -     3.89: 4993
        3.89 -     4.40: 5728
        4.40 -     4.90: 9896
  Nonbonded interactions: 24834
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 411 "
            pdb=" OG  SER A 416 "
     model   vdw
     2.381 3.040
  nonbonded pdb=" OH  TYR A  47 "
            pdb=" O   SER A 179 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" O   MET A 397 "
            pdb=" OG  SER A 401 "
     model   vdw
     2.424 3.040
  nonbonded pdb=" O   TYR A 341 "
            pdb=" OG1 THR A 345 "
     model   vdw
     2.428 3.040
  nonbonded pdb=" OH  TYR A 341 "
            pdb=" OD2 ASP A 399 "
     model   vdw
     2.449 3.040
  ... (remaining 24829 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.410
  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:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.290
  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:6.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
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      :  0.004   0.065   2994  Z= 0.196
  Angle     :  0.670   7.561   4074  Z= 0.359
  Chirality :  0.044   0.211    485
  Planarity :  0.006   0.047    498
  Dihedral  : 10.446  62.755   1082
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  3.22 %
    Favored  : 96.14 %
  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 aren not related in a simple way.
  whole:  1.12 (0.45), residues: 382
  helix:  1.02 (0.31), residues: 296
  sheet:  None (None), residues: 0
  loop :  0.11 (0.75), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 217 
 TYR   0.017   0.001   TYR A 422 
 PHE   0.016   0.002   PHE A 238 
 TRP   0.005   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 2994)
  covalent geometry    : angle       0.67001 ( 4074)
  hydrogen bonds       : bond        0.13408 (  236)
  hydrogen bonds       : angle       6.51743 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.7044 (t0) cc_final: 0.6738 (t0)
REVERT: A  319 MET cc_start: 0.6211 (mtm) cc_final: 0.5653 (mmp)
REVERT: A  403 MET cc_start: 0.8573 (mmm) cc_final: 0.8127 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 59
  average time/residue: 0.4144
  time to fit residues: 25.3658
Evaluate side-chains
  43 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0870
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.5958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.153656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.136767 restraints weight = 3177.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.25
r_work: 0.3398 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2994  Z= 0.160
  Angle     :  0.642   6.642   4074  Z= 0.325
  Chirality :  0.043   0.147    485
  Planarity :  0.006   0.046    498
  Dihedral  :  4.950  22.345    439
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  :  8.04 %
    Favored  : 89.07 %
  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 aren not related in a simple way.
  whole:  1.62 (0.45), residues: 382
  helix:  1.34 (0.31), residues: 306
  sheet:  None (None), residues: 0
  loop :  0.31 (0.78), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 217 
 TYR   0.016   0.001   TYR A 422 
 PHE   0.015   0.002   PHE A 176 
 TRP   0.005   0.001   TRP A 451 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 2994)
  covalent geometry    : angle       0.64238 ( 4074)
  hydrogen bonds       : bond        0.05059 (  236)
  hydrogen bonds       : angle       5.27942 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A   19 ARG cc_start: 0.7375 (mtm180) cc_final: 0.7162 (mtm180)
REVERT: A   33 ASP cc_start: 0.6834 (t0) cc_final: 0.6583 (t0)
REVERT: A  169 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7590 (tpp)
REVERT: A  319 MET cc_start: 0.6388 (mtm) cc_final: 0.5745 (mmp)
  outliers start: 9
  outliers final: 5
  residues processed: 49
  average time/residue: 0.4796
  time to fit residues: 24.3484
Evaluate side-chains
  48 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  372 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.155011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.140454 restraints weight = 3200.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.04
r_work: 0.3390 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2994  Z= 0.169
  Angle     :  0.636   6.772   4074  Z= 0.322
  Chirality :  0.043   0.149    485
  Planarity :  0.006   0.049    498
  Dihedral  :  4.792  20.285    439
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  8.04 %
    Favored  : 88.42 %
  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 aren not related in a simple way.
  whole:  1.55 (0.45), residues: 382
  helix:  1.37 (0.31), residues: 310
  sheet:  None (None), residues: 0
  loop : -0.22 (0.77), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 217 
 TYR   0.018   0.002   TYR A 422 
 PHE   0.012   0.002   PHE A 238 
 TRP   0.006   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 2994)
  covalent geometry    : angle       0.63589 ( 4074)
  hydrogen bonds       : bond        0.05140 (  236)
  hydrogen bonds       : angle       5.12393 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.6894 (t0) cc_final: 0.6603 (t0)
REVERT: A  169 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7475 (tpp)
REVERT: A  319 MET cc_start: 0.6621 (mtm) cc_final: 0.5955 (mmp)
  outliers start: 11
  outliers final: 5
  residues processed: 51
  average time/residue: 0.4869
  time to fit residues: 25.6608
Evaluate side-chains
  49 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  372 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    0.2980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.154628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.136902 restraints weight = 3122.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.37
r_work: 0.3484 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2994  Z= 0.154
  Angle     :  0.601   6.785   4074  Z= 0.304
  Chirality :  0.042   0.139    485
  Planarity :  0.006   0.047    498
  Dihedral  :  4.584  18.777    439
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  8.36 %
    Favored  : 88.10 %
  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 aren not related in a simple way.
  whole:  1.72 (0.45), residues: 382
  helix:  1.52 (0.31), residues: 311
  sheet:  None (None), residues: 0
  loop : -0.37 (0.76), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 217 
 TYR   0.016   0.001   TYR A 422 
 PHE   0.011   0.001   PHE A 348 
 TRP   0.006   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2994)
  covalent geometry    : angle       0.60112 ( 4074)
  hydrogen bonds       : bond        0.04747 (  236)
  hydrogen bonds       : angle       5.01601 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A   19 ARG cc_start: 0.7502 (mtm180) cc_final: 0.7294 (mtm180)
REVERT: A   33 ASP cc_start: 0.6814 (t0) cc_final: 0.6486 (t0)
REVERT: A  169 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7468 (tpp)
REVERT: A  276 GLN cc_start: 0.6380 (OUTLIER) cc_final: 0.5848 (mt0)
REVERT: A  319 MET cc_start: 0.6613 (mtm) cc_final: 0.5952 (mmp)
REVERT: A  350 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7310 (pt)
  outliers start: 11
  outliers final: 6
  residues processed: 50
  average time/residue: 0.4874
  time to fit residues: 25.1374
Evaluate side-chains
  51 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  350 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0050
   chunk 10 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.155165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.137617 restraints weight = 3125.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.34
r_work: 0.3473 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2994  Z= 0.150
  Angle     :  0.590   6.762   4074  Z= 0.298
  Chirality :  0.042   0.141    485
  Planarity :  0.006   0.047    498
  Dihedral  :  4.478  17.684    439
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  :  9.00 %
    Favored  : 88.10 %
  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 aren not related in a simple way.
  whole:  1.74 (0.45), residues: 382
  helix:  1.56 (0.31), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.61 (0.79), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 217 
 TYR   0.017   0.001   TYR A 422 
 PHE   0.012   0.001   PHE A 238 
 TRP   0.006   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 2994)
  covalent geometry    : angle       0.58962 ( 4074)
  hydrogen bonds       : bond        0.04681 (  236)
  hydrogen bonds       : angle       4.91501 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.6783 (t0) cc_final: 0.6448 (t0)
REVERT: A  169 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7465 (tpp)
REVERT: A  276 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5857 (mt0)
REVERT: A  319 MET cc_start: 0.6701 (mtm) cc_final: 0.6049 (mmp)
REVERT: A  350 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7299 (pt)
  outliers start: 9
  outliers final: 5
  residues processed: 46
  average time/residue: 0.5214
  time to fit residues: 24.7388
Evaluate side-chains
  48 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  350 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.155664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.136124 restraints weight = 3051.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.57
r_work: 0.3443 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2994  Z= 0.170
  Angle     :  0.616   6.797   4074  Z= 0.310
  Chirality :  0.043   0.146    485
  Planarity :  0.006   0.047    498
  Dihedral  :  4.531  18.337    439
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  8.68 %
    Favored  : 87.78 %
  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 aren not related in a simple way.
  whole:  1.54 (0.45), residues: 382
  helix:  1.47 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.93 (0.79), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.019   0.002   TYR A 422 
 PHE   0.013   0.002   PHE A 238 
 TRP   0.006   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 2994)
  covalent geometry    : angle       0.61555 ( 4074)
  hydrogen bonds       : bond        0.04975 (  236)
  hydrogen bonds       : angle       5.00005 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.6617 (t0) cc_final: 0.6266 (t0)
REVERT: A  169 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6602 (tpt)
REVERT: A  276 GLN cc_start: 0.6051 (OUTLIER) cc_final: 0.5589 (mt0)
REVERT: A  319 MET cc_start: 0.6739 (mtm) cc_final: 0.5978 (mmp)
REVERT: A  350 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6838 (pt)
  outliers start: 11
  outliers final: 6
  residues processed: 47
  average time/residue: 0.5317
  time to fit residues: 25.7544
Evaluate side-chains
  50 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  350 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 12 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.167233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.147272 restraints weight = 3102.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 1.58
r_work: 0.3587 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3474 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2994  Z= 0.142
  Angle     :  0.575   6.727   4074  Z= 0.292
  Chirality :  0.041   0.138    485
  Planarity :  0.006   0.047    498
  Dihedral  :  4.387  17.933    439
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  9.65 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.45), residues: 382
  helix:  1.61 (0.31), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.90 (0.78), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 413 
 TYR   0.018   0.001   TYR A 422 
 PHE   0.012   0.001   PHE A 238 
 TRP   0.005   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 2994)
  covalent geometry    : angle       0.57486 ( 4074)
  hydrogen bonds       : bond        0.04526 (  236)
  hydrogen bonds       : angle       4.86663 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.7096 (t0) cc_final: 0.6756 (t0)
REVERT: A  169 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7091 (tpt)
REVERT: A  230 MET cc_start: 0.8065 (mmm) cc_final: 0.7853 (tpt)
REVERT: A  276 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.5901 (mt0)
REVERT: A  319 MET cc_start: 0.6964 (mtm) cc_final: 0.6259 (mmp)
REVERT: A  350 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7388 (pt)
  outliers start: 11
  outliers final: 5
  residues processed: 47
  average time/residue: 0.5118
  time to fit residues: 24.8344
Evaluate side-chains
  48 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  350 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.146297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.127113 restraints weight = 3236.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.45
r_work: 0.3361 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2994  Z= 0.163
  Angle     :  0.603   6.831   4074  Z= 0.304
  Chirality :  0.043   0.145    485
  Planarity :  0.006   0.047    498
  Dihedral  :  4.461  18.819    439
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  :  9.65 %
    Favored  : 86.50 %
  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 aren not related in a simple way.
  whole:  1.61 (0.45), residues: 382
  helix:  1.53 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.02 (0.78), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 471 
 TYR   0.019   0.001   TYR A 422 
 PHE   0.013   0.002   PHE A 238 
 TRP   0.009   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 2994)
  covalent geometry    : angle       0.60311 ( 4074)
  hydrogen bonds       : bond        0.04873 (  236)
  hydrogen bonds       : angle       4.94059 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.6976 (t0) cc_final: 0.6635 (t0)
REVERT: A  169 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7012 (tpt)
REVERT: A  276 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.5889 (mt0)
REVERT: A  319 MET cc_start: 0.7010 (mtm) cc_final: 0.6376 (mmp)
REVERT: A  350 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7432 (pt)
  outliers start: 12
  outliers final: 6
  residues processed: 47
  average time/residue: 0.4856
  time to fit residues: 23.5308
Evaluate side-chains
  49 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  350 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 28 optimal weight:    0.0040
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.2992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.150607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.131405 restraints weight = 3205.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.46
r_work: 0.3431 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2994  Z= 0.122
  Angle     :  0.545   6.670   4074  Z= 0.277
  Chirality :  0.040   0.127    485
  Planarity :  0.006   0.047    498
  Dihedral  :  4.198  16.824    439
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 11.90 %
    Favored  : 85.53 %
  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 aren not related in a simple way.
  whole:  2.02 (0.46), residues: 382
  helix:  1.81 (0.31), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.82 (0.78), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.015   0.001   TYR A 422 
 PHE   0.010   0.001   PHE A 238 
 TRP   0.006   0.001   TRP A 358 
 HIS   0.000   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 2994)
  covalent geometry    : angle       0.54470 ( 4074)
  hydrogen bonds       : bond        0.04003 (  236)
  hydrogen bonds       : angle       4.67606 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.6845 (t0) cc_final: 0.6518 (t0)
REVERT: A  169 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6939 (tpt)
REVERT: A  230 MET cc_start: 0.8004 (mmm) cc_final: 0.7803 (tpt)
REVERT: A  276 GLN cc_start: 0.6305 (OUTLIER) cc_final: 0.5824 (mt0)
REVERT: A  319 MET cc_start: 0.6945 (mtm) cc_final: 0.6338 (mmp)
  outliers start: 8
  outliers final: 4
  residues processed: 49
  average time/residue: 0.4710
  time to fit residues: 23.7992
Evaluate side-chains
  48 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  405 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.147208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.127966 restraints weight = 3156.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.45
r_work: 0.3382 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2994  Z= 0.155
  Angle     :  0.597   6.793   4074  Z= 0.301
  Chirality :  0.042   0.145    485
  Planarity :  0.006   0.045    498
  Dihedral  :  4.332  16.014    439
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 11.90 %
    Favored  : 84.89 %
  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 aren not related in a simple way.
  whole:  1.81 (0.45), residues: 382
  helix:  1.69 (0.31), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.03 (0.77), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 471 
 TYR   0.018   0.001   TYR A 422 
 PHE   0.017   0.001   PHE A 238 
 TRP   0.008   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 2994)
  covalent geometry    : angle       0.59657 ( 4074)
  hydrogen bonds       : bond        0.04591 (  236)
  hydrogen bonds       : angle       4.81218 (  690)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.6915 (t0) cc_final: 0.6575 (t0)
REVERT: A  169 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7021 (tpt)
REVERT: A  230 MET cc_start: 0.8017 (mmm) cc_final: 0.7812 (tpt)
REVERT: A  276 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.5896 (mt0)
REVERT: A  319 MET cc_start: 0.7020 (mtm) cc_final: 0.6415 (mmp)
REVERT: A  350 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7333 (pt)
  outliers start: 10
  outliers final: 4
  residues processed: 48
  average time/residue: 0.5020
  time to fit residues: 24.8708
Evaluate side-chains
  48 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  405 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 23 optimal weight:    0.2980
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.4498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.148598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.129451 restraints weight = 3172.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.47
r_work: 0.3386 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2994  Z= 0.134
  Angle     :  0.568   6.703   4074  Z= 0.289
  Chirality :  0.041   0.134    485
  Planarity :  0.006   0.045    498
  Dihedral  :  4.258  15.221    439
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.54 %
    Favored  : 84.89 %
  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 aren not related in a simple way.
  whole:  1.95 (0.46), residues: 382
  helix:  1.76 (0.31), residues: 315
  sheet:  None (None), residues: 0
  loop : -0.89 (0.79), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 471 
 TYR   0.016   0.001   TYR A 422 
 PHE   0.015   0.001   PHE A 238 
 TRP   0.007   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2994)
  covalent geometry    : angle       0.56821 ( 4074)
  hydrogen bonds       : bond        0.04244 (  236)
  hydrogen bonds       : angle       4.73015 (  690)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1219.30 seconds
wall clock time: 21 minutes 33.64 seconds (1293.64 seconds total)