Starting phenix.real_space_refine
on Sat May  2 08:31:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v8y_64855/05_2026/9v8y_64855.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v8y_64855/05_2026/9v8y_64855.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v8y_64855/05_2026/9v8y_64855.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v8y_64855/05_2026/9v8y_64855.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v8y_64855/05_2026/9v8y_64855.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v8y_64855/05_2026/9v8y_64855.map"
  }
  resolution = 3.28
  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=   0.071
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: 5
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     Cl      1      4.86       5
     C    2540      2.51       5
     N     568      2.21       5
     O     623      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3766
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3765
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 20, 'TRANS': 455}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.91, per 1000 atoms: 0.24
  Number of scatterers: 3766
  At special positions: 0
  Unit cell: (75.328, 71.048, 71.904, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      34     16.00
     O     623      8.00
     N     568      7.00
     C    2540      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: 0.29
  Conformation dependent library (CDL) restraints added in 133.6 milliseconds
  

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  862

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 1 sheets defined
      66.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 3.822A  pdb=" N   VAL A  70 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 85
      removed outlier: 5.322A  pdb=" N   TYR A  83 " --> pdb=" O   PRO A  79 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ASN A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 99
      removed outlier: 3.580A  pdb=" N   ILE A  97 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 116
      removed outlier: 3.649A  pdb=" N   MET A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 3.794A  pdb=" N   ALA A 136 " --> pdb=" O   GLY A 132 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 161
      removed outlier: 3.659A  pdb=" N   VAL A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 152 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 234 through 239
    Processing helix  chain 'A' and resid 239 through 248
      removed outlier: 3.861A  pdb=" N   VAL A 246 " --> pdb=" O   CYS A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 276
      removed outlier: 3.539A  pdb=" N   VAL A 271 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A 274 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LEU A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 294
      removed outlier: 3.684A  pdb=" N   ILE A 290 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 3.530A  pdb=" N   LYS A 299 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 300 " --> pdb=" O   TRP A 297 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLY A 301 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 296 through 301'
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 4.377A  pdb=" N   TRP A 306 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   PHE A 314 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 371
      removed outlier: 3.792A  pdb=" N   THR A 351 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE A 362 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY A 364 " --> pdb=" O   PHE A 360 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   PHE A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 396
      removed outlier: 3.744A  pdb=" N   THR A 394 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU A 395 " --> pdb=" O   ARG A 391 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   MET A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 430
      removed outlier: 3.835A  pdb=" N   TRP A 402 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 457
    Processing helix  chain 'A' and resid 458 through 461
    Processing helix  chain 'A' and resid 466 through 476
      removed outlier: 3.717A  pdb=" N   LEU A 472 " --> pdb=" O   TYR A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 491
      removed outlier: 3.879A  pdb=" N   LEU A 484 " --> pdb=" O   GLY A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
    Processing helix  chain 'A' and resid 519 through 524
      removed outlier: 4.349A  pdb=" N   SER A 524 " --> pdb=" O   LYS A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 541
      removed outlier: 3.631A  pdb=" N   PHE A 537 " --> pdb=" O   GLY A 533 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   VAL A 539 " --> pdb=" O   PHE A 535 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   TYR A 541 " --> pdb=" O   PHE A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 550
      No H-bonds generated for 'chain 'A' and resid 548 through 550'
    Processing helix  chain 'A' and resid 554 through 570
      removed outlier: 3.544A  pdb=" N   GLY A 561 " --> pdb=" O   GLY A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 581
      removed outlier: 3.689A  pdb=" N   HIS A 575 " --> pdb=" O   CYS A 571 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LEU A 576 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU A 577 " --> pdb=" O   PRO A 573 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLY A 578 " --> pdb=" O   LEU A 574 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU A 581 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547

    177 hydrogen bonds defined for protein.
    525 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: 0.52

  Time building geometry restraints manager: 0.39 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: 1079
        1.34 -     1.46: 1024
        1.46 -     1.58: 1733
        1.58 -     1.69: 1
        1.69 -     1.81: 50
  Bond restraints: 3887
  Sorted by residual:
  bond pdb=" CB  PRO A 303 "
       pdb=" CG  PRO A 303 "
    ideal  model  delta    sigma   weight residual
    1.492  1.609 -0.117 5.00e-02 4.00e+02 5.51e+00
  bond pdb=" C   VAL A 572 "
       pdb=" N   PRO A 573 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.020 1.20e-02 6.94e+03 2.89e+00
  bond pdb=" CB  THR A 311 "
       pdb=" CG2 THR A 311 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.55e+00
  bond pdb=" CG  LEU A 159 "
       pdb=" CD2 LEU A 159 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.52e+00
  bond pdb=" CB  ARG A  77 "
       pdb=" CG  ARG A  77 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.16e+00
  ... (remaining 3882 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 5142
        1.99 -     3.97: 130
        3.97 -     5.96: 22
        5.96 -     7.95: 5
        7.95 -     9.93: 4
  Bond angle restraints: 5303
  Sorted by residual:
  angle pdb=" CA  PRO A 303 "
        pdb=" N   PRO A 303 "
        pdb=" CD  PRO A 303 "
      ideal   model   delta    sigma   weight residual
     112.00  102.61    9.39 1.40e+00 5.10e-01 4.50e+01
  angle pdb=" N   VAL A 261 "
        pdb=" CA  VAL A 261 "
        pdb=" C   VAL A 261 "
      ideal   model   delta    sigma   weight residual
     112.04  107.78    4.26 1.40e+00 5.10e-01 9.24e+00
  angle pdb=" N   GLY A 310 "
        pdb=" CA  GLY A 310 "
        pdb=" C   GLY A 310 "
      ideal   model   delta    sigma   weight residual
     115.31  111.62    3.69 1.24e+00 6.50e-01 8.86e+00
  angle pdb=" CA  LEU A 167 "
        pdb=" CB  LEU A 167 "
        pdb=" CG  LEU A 167 "
      ideal   model   delta    sigma   weight residual
     116.30  125.58   -9.28 3.50e+00 8.16e-02 7.03e+00
  angle pdb=" N   PRO A 303 "
        pdb=" CD  PRO A 303 "
        pdb=" CG  PRO A 303 "
      ideal   model   delta    sigma   weight residual
     103.20   99.48    3.72 1.50e+00 4.44e-01 6.17e+00
  ... (remaining 5298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 2003
       17.62 -    35.25: 131
       35.25 -    52.87: 20
       52.87 -    70.49: 2
       70.49 -    88.11: 2
  Dihedral angle restraints: 2158
    sinusoidal: 797
      harmonic: 1361
  Sorted by residual:
  dihedral pdb=" CA  PRO A  79 "
           pdb=" C   PRO A  79 "
           pdb=" N   TYR A  80 "
           pdb=" CA  TYR A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.02   34.98     0      5.00e+00 4.00e-02 4.90e+01
  dihedral pdb=" CA  THR A 463 "
           pdb=" C   THR A 463 "
           pdb=" N   ASP A 464 "
           pdb=" CA  ASP A 464 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.43   22.57     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  LEU A 324 "
           pdb=" C   LEU A 324 "
           pdb=" N   THR A 325 "
           pdb=" CA  THR A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.76   21.24     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 2155 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 265
       0.026 -    0.051: 187
       0.051 -    0.077: 90
       0.077 -    0.103: 35
       0.103 -    0.128: 11
  Chirality restraints: 588
  Sorted by residual:
  chirality pdb=" CA  ARG A  77 "
            pdb=" N   ARG A  77 "
            pdb=" C   ARG A  77 "
            pdb=" CB  ARG A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CA  GLU A 109 "
            pdb=" N   GLU A 109 "
            pdb=" C   GLU A 109 "
            pdb=" CB  GLU A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.54e-01
  chirality pdb=" CA  PRO A 104 "
            pdb=" N   PRO A 104 "
            pdb=" C   PRO A 104 "
            pdb=" CB  PRO A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.53e-01
  ... (remaining 585 not shown)

  Planarity restraints: 640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 302 "   -0.088 5.00e-02 4.00e+02   1.26e-01 2.56e+01
        pdb=" N   PRO A 303 "    0.218 5.00e-02 4.00e+02
        pdb=" CA  PRO A 303 "   -0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO A 303 "   -0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  92 "    0.026 5.00e-02 4.00e+02   3.85e-02 2.37e+00
        pdb=" N   PRO A  93 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 389 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.79e+00
        pdb=" N   PRO A 390 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 390 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 390 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 637 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 49
        2.64 -     3.20: 3593
        3.20 -     3.77: 5936
        3.77 -     4.33: 8357
        4.33 -     4.90: 13537
  Nonbonded interactions: 31472
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  80 "
            pdb=" OD2 ASP A 474 "
     model   vdw
     2.070 3.040
  nonbonded pdb=" O   VAL A 100 "
            pdb=" OG1 THR A 527 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" OH  TYR A 317 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" O   PHE A 473 "
            pdb=" OG  SER A 477 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   PRO A 104 "
            pdb=" NE1 TRP A 523 "
     model   vdw
     2.220 3.120
  ... (remaining 31467 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:             0.930
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.150
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.000
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
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   0.117   3887  Z= 0.184
  Angle     :  0.809   9.934   5303  Z= 0.436
  Chirality :  0.043   0.128    588
  Planarity :  0.007   0.126    640
  Dihedral  : 12.349  88.114   1296
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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 (0.37), residues: 466
  helix: -1.84 (0.27), residues: 313
  sheet:  None (None), residues: 0
  loop : -1.95 (0.52), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 332 
 TYR   0.016   0.002   TYR A 292 
 PHE   0.020   0.002   PHE A 353 
 TRP   0.011   0.001   TRP A 251 
 HIS   0.001   0.001   HIS A 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 3887)
  covalent geometry    : angle       0.80942 ( 5303)
  hydrogen bonds       : bond        0.20247 (  177)
  hydrogen bonds       : angle       8.36146 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.125 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0634
  time to fit residues: 5.6388
Evaluate side-chains
  66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0470
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
A 312 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.197694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.169668 restraints weight = 4465.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.4010 rms_B_bonded: 2.14
r_work: 0.3854 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3887  Z= 0.151
  Angle     :  0.700   9.938   5303  Z= 0.345
  Chirality :  0.043   0.129    588
  Planarity :  0.005   0.073    640
  Dihedral  :  5.434  29.302    510
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.10 %
    Favored  : 88.38 %
  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: -2.37 (0.38), residues: 466
  helix: -1.37 (0.28), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.66 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.011   0.001   TYR A 292 
 PHE   0.013   0.002   PHE A  90 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3887)
  covalent geometry    : angle       0.69976 ( 5303)
  hydrogen bonds       : bond        0.04337 (  177)
  hydrogen bonds       : angle       5.04907 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  504 MET cc_start: 0.8869 (mmt) cc_final: 0.8651 (mmm)
  outliers start: 6
  outliers final: 2
  residues processed: 65
  average time/residue: 0.0506
  time to fit residues: 4.3477
Evaluate side-chains
  62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  453 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4295 r_free = 0.4295 target = 0.198912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.173013 restraints weight = 4360.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 2.02
r_work: 0.3874 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3887  Z= 0.134
  Angle     :  0.678   9.977   5303  Z= 0.326
  Chirality :  0.042   0.186    588
  Planarity :  0.004   0.058    640
  Dihedral  :  5.228  29.037    510
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.12 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.14 (0.39), residues: 466
  helix: -1.20 (0.28), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.56 (0.56), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.013   0.001   TYR A  80 
 PHE   0.018   0.001   PHE A 470 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.001   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3887)
  covalent geometry    : angle       0.67785 ( 5303)
  hydrogen bonds       : bond        0.03899 (  177)
  hydrogen bonds       : angle       4.74825 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  342 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7895 (mp)
REVERT: A  357 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7697 (t80)
REVERT: A  365 PHE cc_start: 0.7072 (t80) cc_final: 0.6809 (t80)
REVERT: A  504 MET cc_start: 0.8843 (mmt) cc_final: 0.8604 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 70
  average time/residue: 0.0536
  time to fit residues: 4.9365
Evaluate side-chains
  66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  453 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0980
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4260 r_free = 0.4260 target = 0.196300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.168440 restraints weight = 4420.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.13
r_work: 0.3842 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3887  Z= 0.135
  Angle     :  0.666  10.012   5303  Z= 0.320
  Chirality :  0.042   0.158    588
  Planarity :  0.004   0.052    640
  Dihedral  :  5.121  25.752    510
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 13.38 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.12 (0.39), residues: 466
  helix: -1.16 (0.28), residues: 323
  sheet:  None (None), residues: 0
  loop : -1.61 (0.57), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 332 
 TYR   0.012   0.001   TYR A  80 
 PHE   0.018   0.001   PHE A 406 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3887)
  covalent geometry    : angle       0.66599 ( 5303)
  hydrogen bonds       : bond        0.03728 (  177)
  hydrogen bonds       : angle       4.57714 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A   80 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7534 (p90)
REVERT: A  133 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8045 (tt)
REVERT: A  342 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7820 (mp)
REVERT: A  357 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7684 (t80)
REVERT: A  365 PHE cc_start: 0.7082 (t80) cc_final: 0.6869 (t80)
REVERT: A  504 MET cc_start: 0.8886 (mmt) cc_final: 0.8611 (mmm)
  outliers start: 13
  outliers final: 6
  residues processed: 75
  average time/residue: 0.0491
  time to fit residues: 4.9860
Evaluate side-chains
  73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TYR
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  453 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 6 optimal weight:    0.2980
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0000
   chunk 30 optimal weight:    0.2980
   chunk 41 optimal weight:    0.0570
   overall best weight:    0.2102

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.202887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.176240 restraints weight = 4402.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 2.13
r_work: 0.3922 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3887  Z= 0.112
  Angle     :  0.630   9.884   5303  Z= 0.300
  Chirality :  0.040   0.157    588
  Planarity :  0.004   0.048    640
  Dihedral  :  4.917  26.757    510
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 14.65 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.88 (0.39), residues: 466
  helix: -0.95 (0.28), residues: 326
  sheet:  None (None), residues: 0
  loop : -1.61 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 332 
 TYR   0.010   0.001   TYR A  80 
 PHE   0.017   0.001   PHE A 406 
 TRP   0.009   0.001   TRP A 251 
 HIS   0.001   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3887)
  covalent geometry    : angle       0.62965 ( 5303)
  hydrogen bonds       : bond        0.03403 (  177)
  hydrogen bonds       : angle       4.28050 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  231 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6362 (tp)
REVERT: A  262 TYR cc_start: 0.7342 (m-80) cc_final: 0.6582 (t80)
REVERT: A  342 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7719 (mp)
REVERT: A  357 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7591 (t80)
REVERT: A  504 MET cc_start: 0.8888 (mmt) cc_final: 0.8558 (mmm)
  outliers start: 15
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0457
  time to fit residues: 4.8269
Evaluate side-chains
  71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  453 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 14 optimal weight:    0.1980
   chunk 25 optimal weight:    0.5980
   chunk 7 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.200151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.172733 restraints weight = 4450.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 2.18
r_work: 0.3892 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3887  Z= 0.123
  Angle     :  0.672  11.260   5303  Z= 0.317
  Chirality :  0.042   0.182    588
  Planarity :  0.004   0.047    640
  Dihedral  :  4.839  25.574    510
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.67 %
    Favored  : 80.05 %
  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: -1.79 (0.39), residues: 466
  helix: -0.90 (0.28), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.52 (0.57), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.018   0.001   TYR A  80 
 PHE   0.018   0.001   PHE A 406 
 TRP   0.010   0.001   TRP A 485 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3887)
  covalent geometry    : angle       0.67150 ( 5303)
  hydrogen bonds       : bond        0.03460 (  177)
  hydrogen bonds       : angle       4.36319 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  342 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7746 (mp)
REVERT: A  357 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7586 (t80)
REVERT: A  504 MET cc_start: 0.8888 (mmt) cc_final: 0.8561 (mmm)
  outliers start: 13
  outliers final: 7
  residues processed: 70
  average time/residue: 0.0460
  time to fit residues: 4.3584
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  560 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   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  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.195493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.167417 restraints weight = 4520.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 2.20
r_work: 0.3820 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3887  Z= 0.151
  Angle     :  0.693  10.000   5303  Z= 0.329
  Chirality :  0.043   0.154    588
  Planarity :  0.004   0.045    640
  Dihedral  :  4.995  25.943    510
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 15.40 %
    Favored  : 80.81 %
  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: -1.78 (0.39), residues: 466
  helix: -0.91 (0.28), residues: 323
  sheet:  None (None), residues: 0
  loop : -1.45 (0.56), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.018   0.001   TYR A  80 
 PHE   0.020   0.002   PHE A 406 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.001   0.000   HIS A 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3887)
  covalent geometry    : angle       0.69291 ( 5303)
  hydrogen bonds       : bond        0.03572 (  177)
  hydrogen bonds       : angle       4.44075 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  342 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7756 (mp)
REVERT: A  357 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7626 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0502
  time to fit residues: 5.1054
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  560 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 44 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.195364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.168899 restraints weight = 4445.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 2.06
r_work: 0.3831 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   3887  Z= 0.148
  Angle     :  0.700  10.014   5303  Z= 0.334
  Chirality :  0.043   0.145    588
  Planarity :  0.004   0.043    640
  Dihedral  :  5.026  26.389    510
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 16.67 %
    Favored  : 79.55 %
  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: -1.73 (0.39), residues: 466
  helix: -0.88 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.42 (0.56), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.017   0.001   TYR A  80 
 PHE   0.012   0.001   PHE A 106 
 TRP   0.009   0.001   TRP A 251 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3887)
  covalent geometry    : angle       0.70034 ( 5303)
  hydrogen bonds       : bond        0.03580 (  177)
  hydrogen bonds       : angle       4.44667 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A  342 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7774 (mp)
REVERT: A  357 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7572 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 75
  average time/residue: 0.0448
  time to fit residues: 4.5492
Evaluate side-chains
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  560 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0870
   chunk 30 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0980
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.197113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.171254 restraints weight = 4393.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 2.06
r_work: 0.3868 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3887  Z= 0.130
  Angle     :  0.686  10.018   5303  Z= 0.324
  Chirality :  0.042   0.158    588
  Planarity :  0.004   0.043    640
  Dihedral  :  4.975  26.848    510
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 17.42 %
    Favored  : 78.28 %
  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: -1.67 (0.39), residues: 466
  helix: -0.84 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -1.39 (0.56), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 332 
 TYR   0.018   0.001   TYR A  80 
 PHE   0.038   0.002   PHE A 406 
 TRP   0.011   0.001   TRP A 485 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3887)
  covalent geometry    : angle       0.68613 ( 5303)
  hydrogen bonds       : bond        0.03461 (  177)
  hydrogen bonds       : angle       4.38454 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   99 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8493 (mm)
REVERT: A  148 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7208 (m-80)
REVERT: A  342 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7669 (mp)
REVERT: A  357 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7616 (t80)
  outliers start: 17
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0423
  time to fit residues: 4.1281
Evaluate side-chains
  73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  148 TYR
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  560 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0770
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.194679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.166937 restraints weight = 4501.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.18
r_work: 0.3841 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3887  Z= 0.146
  Angle     :  0.714  11.861   5303  Z= 0.338
  Chirality :  0.044   0.226    588
  Planarity :  0.004   0.042    640
  Dihedral  :  4.999  27.267    510
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.18 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.61 (0.39), residues: 466
  helix: -0.86 (0.28), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.18 (0.57), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 332 
 TYR   0.018   0.001   TYR A  80 
 PHE   0.033   0.002   PHE A 406 
 TRP   0.010   0.001   TRP A 485 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 3887)
  covalent geometry    : angle       0.71368 ( 5303)
  hydrogen bonds       : bond        0.03574 (  177)
  hydrogen bonds       : angle       4.43350 (  525)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   99 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8503 (mm)
REVERT: A  148 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7250 (m-80)
REVERT: A  342 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7685 (mp)
REVERT: A  357 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7568 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 71
  average time/residue: 0.0516
  time to fit residues: 4.8670
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  148 TYR
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  560 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0040
   chunk 30 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.194510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.166859 restraints weight = 4443.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 2.17
r_work: 0.3829 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3887  Z= 0.147
  Angle     :  0.715  11.357   5303  Z= 0.340
  Chirality :  0.044   0.212    588
  Planarity :  0.004   0.042    640
  Dihedral  :  5.011  26.909    510
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 17.42 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.70 (0.39), residues: 466
  helix: -0.92 (0.28), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.24 (0.57), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 332 
 TYR   0.019   0.001   TYR A 389 
 PHE   0.013   0.001   PHE A 407 
 TRP   0.011   0.001   TRP A 485 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3887)
  covalent geometry    : angle       0.71509 ( 5303)
  hydrogen bonds       : bond        0.03566 (  177)
  hydrogen bonds       : angle       4.43894 (  525)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 962.06 seconds
wall clock time: 17 minutes 11.38 seconds (1031.38 seconds total)