Starting phenix.real_space_refine
on Fri Aug 22 13:41:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sc1_40334/08_2025/8sc1_40334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sc1_40334/08_2025/8sc1_40334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sc1_40334/08_2025/8sc1_40334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sc1_40334/08_2025/8sc1_40334.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sc1_40334/08_2025/8sc1_40334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sc1_40334/08_2025/8sc1_40334.map"
  }
  resolution = 2.92
  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=   0.000 sd=   0.034
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      30      5.16       5
     C    2270      2.51       5
     N     559      2.21       5
     O     588      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 3447
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 446, 3447
          Classifications: {'peptide': 446}
          Link IDs: {'PTRANS': 22, 'TRANS': 423}
          Chain breaks: 1
  Time building chain proxies: 1.19, per 1000 atoms: 0.35
  Number of scatterers: 3447
  At special positions: 0
  Unit cell: (92.02, 84.28, 65.36, 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      30     16.00
     O     588      8.00
     N     559      7.00
     C    2270      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 142 " distance=2.04

  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 151.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  816

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 2 sheets defined
      83.4% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 31
      removed outlier: 3.559A  pdb=" N   ILE A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 54 through 63
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.873A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 104 through 109
      removed outlier: 3.997A  pdb=" N   SER A 108 " --> pdb=" O   PRO A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 141 through 145
    Processing helix  chain 'A' and resid 146 through 173
      removed outlier: 3.961A  pdb=" N   LEU A 150 " --> pdb=" O   TRP A 146 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLN A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   GLY A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   TYR A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 194
      removed outlier: 3.953A  pdb=" N   ALA A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 228
      removed outlier: 3.838A  pdb=" N   VAL A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LYS A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 258
      removed outlier: 3.705A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR A 245 " --> pdb=" O   GLN A 241 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 279
      Proline residue:  A 271  - end of helix
      removed outlier: 3.881A  pdb=" N   LEU A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A 275 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU A 276 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 339
      removed outlier: 3.522A  pdb=" N   LEU A 337 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 372
      removed outlier: 3.551A  pdb=" N   ILE A 365 " --> pdb=" O   TYR A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 385
      removed outlier: 3.558A  pdb=" N   VAL A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 400
      removed outlier: 3.682A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 420
      removed outlier: 3.537A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 456
      removed outlier: 4.048A  pdb=" N   ILE A 433 " --> pdb=" O   TRP A 429 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA A 454 " --> pdb=" O   CYS A 450 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 471
      removed outlier: 4.522A  pdb=" N   ASN A 463 " --> pdb=" O   THR A 459 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   LEU A 464 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   MET A 467 " --> pdb=" O   ASN A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 487
      removed outlier: 3.626A  pdb=" N   ILE A 475 " --> pdb=" O   SER A 471 " (cutoff:3.500A)
      Proline residue:  A 481  - end of helix
    Processing helix  chain 'A' and resid 488 through 490
      No H-bonds generated for 'chain 'A' and resid 488 through 490'
    Processing helix  chain 'A' and resid 493 through 511
      removed outlier: 3.742A  pdb=" N   GLY A 508 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LEU A 511 " --> pdb=" O   ALA A 507 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50
      removed outlier: 3.540A  pdb=" N   HIS A  49 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91

    238 hydrogen bonds defined for protein.
    684 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: 0.46

  Time building geometry restraints manager: 0.38 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.35: 1064
        1.35 -     1.47: 908
        1.47 -     1.59: 1520
        1.59 -     1.71: 0
        1.71 -     1.84: 45
  Bond restraints: 3537
  Sorted by residual:
  bond pdb=" CA  THR A 480 "
       pdb=" C   THR A 480 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 1.29e-02 6.01e+03 7.91e-01
  bond pdb=" CB  CYS A  88 "
       pdb=" SG  CYS A  88 "
    ideal  model  delta    sigma   weight residual
    1.808  1.836 -0.028 3.30e-02 9.18e+02 6.96e-01
  bond pdb=" CA  LEU A 494 "
       pdb=" C   LEU A 494 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.26e-02 6.30e+03 6.91e-01
  bond pdb=" C   ILE A 387 "
       pdb=" O   ILE A 387 "
    ideal  model  delta    sigma   weight residual
    1.240  1.250 -0.010 1.26e-02 6.30e+03 6.41e-01
  bond pdb=" C   GLY A 253 "
       pdb=" O   GLY A 253 "
    ideal  model  delta    sigma   weight residual
    1.235  1.245 -0.010 1.35e-02 5.49e+03 5.59e-01
  ... (remaining 3532 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 4509
        1.21 -     2.42: 252
        2.42 -     3.64: 40
        3.64 -     4.85: 12
        4.85 -     6.06: 8
  Bond angle restraints: 4821
  Sorted by residual:
  angle pdb=" N   VAL A 212 "
        pdb=" CA  VAL A 212 "
        pdb=" C   VAL A 212 "
      ideal   model   delta    sigma   weight residual
     109.34  115.13   -5.79 2.08e+00 2.31e-01 7.74e+00
  angle pdb=" CA  CYS A 121 "
        pdb=" CB  CYS A 121 "
        pdb=" SG  CYS A 121 "
      ideal   model   delta    sigma   weight residual
     114.40  120.46   -6.06 2.30e+00 1.89e-01 6.94e+00
  angle pdb=" CA  CYS A  50 "
        pdb=" CB  CYS A  50 "
        pdb=" SG  CYS A  50 "
      ideal   model   delta    sigma   weight residual
     114.40  120.45   -6.05 2.30e+00 1.89e-01 6.93e+00
  angle pdb=" N   TYR A 404 "
        pdb=" CA  TYR A 404 "
        pdb=" C   TYR A 404 "
      ideal   model   delta    sigma   weight residual
     109.81  115.25   -5.44 2.21e+00 2.05e-01 6.05e+00
  angle pdb=" CA  TRP A 261 "
        pdb=" CB  TRP A 261 "
        pdb=" CG  TRP A 261 "
      ideal   model   delta    sigma   weight residual
     113.60  118.11   -4.51 1.90e+00 2.77e-01 5.64e+00
  ... (remaining 4816 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.66: 1924
       14.66 -    29.32: 99
       29.32 -    43.97: 24
       43.97 -    58.63: 9
       58.63 -    73.29: 2
  Dihedral angle restraints: 2058
    sinusoidal: 782
      harmonic: 1276
  Sorted by residual:
  dihedral pdb=" CA  TYR A  72 "
           pdb=" C   TYR A  72 "
           pdb=" N   THR A  73 "
           pdb=" CA  THR A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.79  -22.21     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  CYS A  50 "
           pdb=" C   CYS A  50 "
           pdb=" N   GLN A  51 "
           pdb=" CA  GLN A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.88   17.12     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ARG A 399 "
           pdb=" C   ARG A 399 "
           pdb=" N   VAL A 400 "
           pdb=" CA  VAL A 400 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.03  -16.97     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 2055 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 321
       0.027 -    0.055: 158
       0.055 -    0.082: 54
       0.082 -    0.110: 14
       0.110 -    0.137: 14
  Chirality restraints: 561
  Sorted by residual:
  chirality pdb=" CA  PRO A 341 "
            pdb=" N   PRO A 341 "
            pdb=" C   PRO A 341 "
            pdb=" CB  PRO A 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.71e-01
  chirality pdb=" CA  TYR A  72 "
            pdb=" N   TYR A  72 "
            pdb=" C   TYR A  72 "
            pdb=" CB  TYR A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.82e-01
  chirality pdb=" CA  VAL A  74 "
            pdb=" N   VAL A  74 "
            pdb=" C   VAL A  74 "
            pdb=" CB  VAL A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 558 not shown)

  Planarity restraints: 597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 182 "    0.014 2.00e-02 2.50e+03   2.83e-02 7.98e+00
        pdb=" C   THR A 182 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   THR A 182 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 183 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  72 "    0.011 2.00e-02 2.50e+03   1.70e-02 5.78e+00
        pdb=" CG  TYR A  72 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  72 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  72 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  72 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  72 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  72 "    0.021 2.00e-02 2.50e+03
        pdb=" OH  TYR A  72 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 206 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   ARG A 206 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ARG A 206 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 207 "    0.013 2.00e-02 2.50e+03
  ... (remaining 594 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 781
        2.79 -     3.32: 3376
        3.32 -     3.85: 5235
        3.85 -     4.37: 6164
        4.37 -     4.90: 10862
  Nonbonded interactions: 26418
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 147 "
            pdb=" OH  TYR A 199 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" NH2 ARG A 402 "
            pdb=" OE2 GLU A 455 "
     model   vdw
     2.384 3.120
  nonbonded pdb=" O   GLY A 476 "
            pdb=" OG1 THR A 480 "
     model   vdw
     2.476 3.040
  nonbonded pdb=" N   ASP A 426 "
            pdb=" OD1 ASP A 426 "
     model   vdw
     2.508 3.120
  nonbonded pdb=" N   ASP A 149 "
            pdb=" OD1 ASP A 149 "
     model   vdw
     2.564 3.120
  ... (remaining 26413 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:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.240
  Find NCS groups from input model:        0.020
  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:7.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3540  Z= 0.152
  Angle     :  0.685   6.060   4827  Z= 0.399
  Chirality :  0.040   0.137    561
  Planarity :  0.008   0.058    597
  Dihedral  : 10.470  73.290   1233
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.39), residues: 442
  helix: -1.04 (0.27), residues: 298
  sheet:  None (None), residues: 0
  loop :  1.20 (0.58), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG A 262 
 TYR   0.023   0.003   TYR A  72 
 PHE   0.014   0.002   PHE A  22 
 TRP   0.022   0.002   TRP A 261 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3537)
  covalent geometry    : angle       0.67940 ( 4821)
  SS BOND              : bond        0.00605 (    3)
  SS BOND              : angle       2.57538 (    6)
  hydrogen bonds       : bond        0.14640 (  238)
  hydrogen bonds       : angle       6.22326 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8286 (tt0) cc_final: 0.7836 (mm-40)
REVERT: A  218 MET cc_start: 0.7361 (mmm) cc_final: 0.6832 (mtm)
REVERT: A  351 MET cc_start: 0.8254 (mtt) cc_final: 0.7981 (mtm)
REVERT: A  396 THR cc_start: 0.7819 (m) cc_final: 0.7451 (p)
REVERT: A  408 MET cc_start: 0.8154 (mmm) cc_final: 0.7936 (mmm)
REVERT: A  480 THR cc_start: 0.7728 (m) cc_final: 0.7442 (m)
REVERT: A  492 GLN cc_start: 0.6991 (mt0) cc_final: 0.6666 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.4503
  time to fit residues: 24.7330
Evaluate side-chains
  36 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   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 = 0.4177 r_free = 0.4177 target = 0.199269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.154798 restraints weight = 3652.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 1.99
r_work: 0.3485 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3540  Z= 0.136
  Angle     :  0.591   6.515   4827  Z= 0.305
  Chirality :  0.038   0.115    561
  Planarity :  0.005   0.034    597
  Dihedral  :  4.074  15.666    480
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  4.32 %
    Favored  : 93.24 %
  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:  1.21 (0.40), residues: 442
  helix:  0.87 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop :  1.01 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 402 
 TYR   0.010   0.001   TYR A 240 
 PHE   0.014   0.001   PHE A  32 
 TRP   0.018   0.002   TRP A 261 
 HIS   0.002   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3537)
  covalent geometry    : angle       0.58218 ( 4821)
  SS BOND              : bond        0.00290 (    3)
  SS BOND              : angle       2.86756 (    6)
  hydrogen bonds       : bond        0.05192 (  238)
  hydrogen bonds       : angle       4.29467 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8609 (tt0) cc_final: 0.8022 (tm-30)
REVERT: A   92 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6502 (mp0)
REVERT: A  239 MET cc_start: 0.6620 (ptp) cc_final: 0.5248 (tpt)
REVERT: A  396 THR cc_start: 0.7701 (m) cc_final: 0.7287 (p)
REVERT: A  408 MET cc_start: 0.8068 (mmm) cc_final: 0.7857 (mmm)
REVERT: A  492 GLN cc_start: 0.7054 (mt0) cc_final: 0.6251 (tp-100)
  outliers start: 9
  outliers final: 1
  residues processed: 41
  average time/residue: 0.4551
  time to fit residues: 19.3441
Evaluate side-chains
  33 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  402 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.197902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.153775 restraints weight = 3633.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 1.95
r_work: 0.3473 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3540  Z= 0.135
  Angle     :  0.560   6.024   4827  Z= 0.289
  Chirality :  0.037   0.116    561
  Planarity :  0.004   0.034    597
  Dihedral  :  3.828  14.936    480
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  6.49 %
    Favored  : 91.62 %
  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 (0.40), residues: 442
  helix:  1.27 (0.29), residues: 314
  sheet:  None (None), residues: 0
  loop :  1.15 (0.60), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 402 
 TYR   0.007   0.001   TYR A 240 
 PHE   0.012   0.001   PHE A  22 
 TRP   0.015   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3537)
  covalent geometry    : angle       0.55326 ( 4821)
  SS BOND              : bond        0.00414 (    3)
  SS BOND              : angle       2.58830 (    6)
  hydrogen bonds       : bond        0.05262 (  238)
  hydrogen bonds       : angle       4.10555 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8574 (tt0) cc_final: 0.8009 (tm-30)
REVERT: A   92 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6539 (mp0)
REVERT: A  396 THR cc_start: 0.7589 (m) cc_final: 0.7076 (p)
REVERT: A  408 MET cc_start: 0.8040 (mmm) cc_final: 0.7818 (mmm)
REVERT: A  440 MET cc_start: 0.8527 (ttm) cc_final: 0.8261 (ttt)
REVERT: A  451 LEU cc_start: 0.6602 (mp) cc_final: 0.6142 (tt)
REVERT: A  492 GLN cc_start: 0.7282 (mt0) cc_final: 0.6697 (tm-30)
  outliers start: 7
  outliers final: 3
  residues processed: 38
  average time/residue: 0.4576
  time to fit residues: 18.0765
Evaluate side-chains
  38 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  467 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   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 = 0.4158 r_free = 0.4158 target = 0.197117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.152084 restraints weight = 3573.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 1.92
r_work: 0.3462 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3540  Z= 0.140
  Angle     :  0.566   5.933   4827  Z= 0.292
  Chirality :  0.037   0.116    561
  Planarity :  0.005   0.035    597
  Dihedral  :  3.762  14.790    480
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  6.22 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.71 (0.40), residues: 442
  helix:  1.34 (0.29), residues: 316
  sheet:  None (None), residues: 0
  loop :  0.87 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 402 
 TYR   0.007   0.001   TYR A 457 
 PHE   0.012   0.001   PHE A  22 
 TRP   0.015   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3537)
  covalent geometry    : angle       0.55858 ( 4821)
  SS BOND              : bond        0.00292 (    3)
  SS BOND              : angle       2.62644 (    6)
  hydrogen bonds       : bond        0.05398 (  238)
  hydrogen bonds       : angle       4.06770 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8619 (tt0) cc_final: 0.8027 (tm-30)
REVERT: A   92 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6620 (mp0)
REVERT: A  241 GLN cc_start: 0.6882 (mm-40) cc_final: 0.6387 (tm-30)
REVERT: A  396 THR cc_start: 0.7550 (m) cc_final: 0.7014 (p)
REVERT: A  408 MET cc_start: 0.8068 (mmm) cc_final: 0.7812 (mmm)
REVERT: A  451 LEU cc_start: 0.6739 (mp) cc_final: 0.6205 (tt)
REVERT: A  492 GLN cc_start: 0.7553 (mt0) cc_final: 0.7313 (mp10)
  outliers start: 10
  outliers final: 4
  residues processed: 49
  average time/residue: 0.3619
  time to fit residues: 18.4625
Evaluate side-chains
  43 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain A residue  505 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0870
   chunk 23 optimal weight:    0.0570
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0020
   overall best weight:    0.4286

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.199915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.155240 restraints weight = 3595.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 1.90
r_work: 0.3496 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3540  Z= 0.111
  Angle     :  0.507   5.806   4827  Z= 0.259
  Chirality :  0.036   0.115    561
  Planarity :  0.004   0.032    597
  Dihedral  :  3.545  13.420    480
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  7.84 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.41), residues: 442
  helix:  1.87 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop :  1.43 (0.58), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 402 
 TYR   0.007   0.001   TYR A 352 
 PHE   0.012   0.001   PHE A  22 
 TRP   0.013   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 3537)
  covalent geometry    : angle       0.50102 ( 4821)
  SS BOND              : bond        0.00202 (    3)
  SS BOND              : angle       2.23974 (    6)
  hydrogen bonds       : bond        0.04320 (  238)
  hydrogen bonds       : angle       3.88622 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8522 (tt0) cc_final: 0.7921 (tm-30)
REVERT: A   92 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6626 (mp0)
REVERT: A  239 MET cc_start: 0.6505 (ptp) cc_final: 0.5039 (tpt)
REVERT: A  396 THR cc_start: 0.7593 (m) cc_final: 0.7060 (p)
REVERT: A  408 MET cc_start: 0.8046 (mmm) cc_final: 0.7824 (mmm)
REVERT: A  451 LEU cc_start: 0.6707 (mp) cc_final: 0.6184 (tt)
REVERT: A  492 GLN cc_start: 0.7428 (mt0) cc_final: 0.7217 (mp10)
  outliers start: 9
  outliers final: 1
  residues processed: 43
  average time/residue: 0.4025
  time to fit residues: 18.0909
Evaluate side-chains
  40 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4164 r_free = 0.4164 target = 0.197511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.152232 restraints weight = 3588.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 1.93
r_work: 0.3460 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3540  Z= 0.134
  Angle     :  0.550   5.642   4827  Z= 0.283
  Chirality :  0.037   0.117    561
  Planarity :  0.005   0.038    597
  Dihedral  :  3.638  16.904    480
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  8.65 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.40), residues: 442
  helix:  1.57 (0.29), residues: 316
  sheet:  None (None), residues: 0
  loop :  0.99 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 402 
 TYR   0.008   0.001   TYR A 352 
 PHE   0.012   0.001   PHE A  22 
 TRP   0.014   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3537)
  covalent geometry    : angle       0.54288 ( 4821)
  SS BOND              : bond        0.00264 (    3)
  SS BOND              : angle       2.54378 (    6)
  hydrogen bonds       : bond        0.05151 (  238)
  hydrogen bonds       : angle       3.98370 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8574 (tt0) cc_final: 0.7963 (tm-30)
REVERT: A   92 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6633 (mp0)
REVERT: A  241 GLN cc_start: 0.6912 (mm-40) cc_final: 0.6423 (tm-30)
REVERT: A  396 THR cc_start: 0.7606 (m) cc_final: 0.7068 (p)
REVERT: A  408 MET cc_start: 0.8116 (mmm) cc_final: 0.7866 (mmm)
REVERT: A  451 LEU cc_start: 0.6885 (mp) cc_final: 0.6333 (tt)
REVERT: A  492 GLN cc_start: 0.7656 (mt0) cc_final: 0.7413 (mp10)
  outliers start: 8
  outliers final: 4
  residues processed: 43
  average time/residue: 0.3979
  time to fit residues: 17.8631
Evaluate side-chains
  42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0970
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0980
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
A  97 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.200306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.153078 restraints weight = 3665.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.54
r_work: 0.3483 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3540  Z= 0.108
  Angle     :  0.499   5.443   4827  Z= 0.257
  Chirality :  0.035   0.115    561
  Planarity :  0.004   0.033    597
  Dihedral  :  3.506  17.104    480
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  8.92 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.41), residues: 442
  helix:  2.01 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop :  1.46 (0.57), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 402 
 TYR   0.008   0.001   TYR A 352 
 PHE   0.012   0.001   PHE A  22 
 TRP   0.012   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 3537)
  covalent geometry    : angle       0.49393 ( 4821)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       2.16661 (    6)
  hydrogen bonds       : bond        0.04146 (  238)
  hydrogen bonds       : angle       3.85350 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8430 (tt0) cc_final: 0.7938 (tm-30)
REVERT: A   92 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6687 (mp0)
REVERT: A  239 MET cc_start: 0.6427 (ptp) cc_final: 0.4974 (tpt)
REVERT: A  241 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6643 (tm-30)
REVERT: A  396 THR cc_start: 0.7797 (m) cc_final: 0.7336 (p)
REVERT: A  408 MET cc_start: 0.8134 (mmm) cc_final: 0.7921 (mmm)
REVERT: A  451 LEU cc_start: 0.7179 (mp) cc_final: 0.6649 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 41
  average time/residue: 0.4416
  time to fit residues: 18.8325
Evaluate side-chains
  44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  467 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.197354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.152186 restraints weight = 3607.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 1.95
r_work: 0.3456 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3540  Z= 0.142
  Angle     :  0.561   5.635   4827  Z= 0.289
  Chirality :  0.037   0.118    561
  Planarity :  0.005   0.038    597
  Dihedral  :  3.635  16.779    480
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 1.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  9.19 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.40), residues: 442
  helix:  1.57 (0.29), residues: 316
  sheet:  None (None), residues: 0
  loop :  0.99 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 402 
 TYR   0.009   0.001   TYR A 352 
 PHE   0.012   0.001   PHE A  22 
 TRP   0.014   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3537)
  covalent geometry    : angle       0.55363 ( 4821)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       2.60086 (    6)
  hydrogen bonds       : bond        0.05370 (  238)
  hydrogen bonds       : angle       3.99409 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8580 (tt0) cc_final: 0.8028 (tm-30)
REVERT: A   92 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6829 (mp0)
REVERT: A  239 MET cc_start: 0.6742 (ptp) cc_final: 0.5502 (tpt)
REVERT: A  241 GLN cc_start: 0.7159 (mm-40) cc_final: 0.6758 (tm-30)
REVERT: A  271 PRO cc_start: 0.6683 (Cg_exo) cc_final: 0.6469 (Cg_endo)
REVERT: A  396 THR cc_start: 0.7766 (m) cc_final: 0.7261 (p)
REVERT: A  408 MET cc_start: 0.8301 (mmm) cc_final: 0.8083 (mmm)
REVERT: A  451 LEU cc_start: 0.7161 (mp) cc_final: 0.6592 (tt)
  outliers start: 10
  outliers final: 4
  residues processed: 45
  average time/residue: 0.4413
  time to fit residues: 20.6661
Evaluate side-chains
  42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  467 MET
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4161 r_free = 0.4161 target = 0.196608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.150899 restraints weight = 3586.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.99
r_work: 0.3445 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3540  Z= 0.146
  Angle     :  0.570   5.706   4827  Z= 0.294
  Chirality :  0.037   0.118    561
  Planarity :  0.005   0.036    597
  Dihedral  :  3.703  16.963    480
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  9.73 %
    Favored  : 87.84 %
  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:  1.71 (0.40), residues: 442
  helix:  1.39 (0.29), residues: 322
  sheet: -1.24 (1.21), residues: 10
  loop :  0.93 (0.62), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 402 
 TYR   0.009   0.001   TYR A 352 
 PHE   0.012   0.001   PHE A  22 
 TRP   0.013   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3537)
  covalent geometry    : angle       0.56268 ( 4821)
  SS BOND              : bond        0.00281 (    3)
  SS BOND              : angle       2.68438 (    6)
  hydrogen bonds       : bond        0.05544 (  238)
  hydrogen bonds       : angle       4.03370 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8433 (tt0) cc_final: 0.7927 (tm-30)
REVERT: A   92 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6788 (mp0)
REVERT: A  241 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6777 (tm-30)
REVERT: A  396 THR cc_start: 0.7818 (m) cc_final: 0.7356 (p)
REVERT: A  408 MET cc_start: 0.8102 (mmm) cc_final: 0.7893 (mmm)
REVERT: A  451 LEU cc_start: 0.7334 (mp) cc_final: 0.6815 (tt)
  outliers start: 9
  outliers final: 3
  residues processed: 43
  average time/residue: 0.4207
  time to fit residues: 18.8004
Evaluate side-chains
  41 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  467 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0170
   chunk 26 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.5222

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.197706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.151483 restraints weight = 3602.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.08
r_work: 0.3490 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3540  Z= 0.118
  Angle     :  0.527   6.110   4827  Z= 0.272
  Chirality :  0.036   0.130    561
  Planarity :  0.004   0.033    597
  Dihedral  :  3.567  16.946    480
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.08 %
    Favored  : 87.84 %
  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:  2.22 (0.41), residues: 442
  helix:  1.73 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop :  1.06 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 402 
 TYR   0.009   0.001   TYR A 352 
 PHE   0.013   0.001   PHE A  22 
 TRP   0.013   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3537)
  covalent geometry    : angle       0.52094 ( 4821)
  SS BOND              : bond        0.00202 (    3)
  SS BOND              : angle       2.32370 (    6)
  hydrogen bonds       : bond        0.04568 (  238)
  hydrogen bonds       : angle       3.92553 (  684)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
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Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
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Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   51 GLN cc_start: 0.8500 (tt0) cc_final: 0.7931 (tm-30)
REVERT: A   92 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6839 (mp0)
REVERT: A  239 MET cc_start: 0.6630 (ptp) cc_final: 0.5014 (tpt)
REVERT: A  241 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6683 (tm-30)
REVERT: A  396 THR cc_start: 0.7734 (m) cc_final: 0.7233 (p)
REVERT: A  408 MET cc_start: 0.8208 (mmm) cc_final: 0.7987 (mmm)
REVERT: A  451 LEU cc_start: 0.7092 (mp) cc_final: 0.6522 (tt)
  outliers start: 4
  outliers final: 3
  residues processed: 40
  average time/residue: 0.4381
  time to fit residues: 18.2098
Evaluate side-chains
  39 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.088 
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Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  467 MET
Rotamers are restrained with sigma=1.00
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XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0370
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.4858

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

No N/Q/H corrections needed this macrocycle
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ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.198195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.152220 restraints weight = 3642.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.09
r_work: 0.3491 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3540  Z= 0.115
  Angle     :  0.519   5.774   4827  Z= 0.267
  Chirality :  0.035   0.125    561
  Planarity :  0.004   0.035    597
  Dihedral  :  3.498  16.693    480
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.81 %
    Favored  : 87.84 %
  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:  2.26 (0.40), residues: 442
  helix:  1.77 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop :  1.04 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 402 
 TYR   0.009   0.001   TYR A 352 
 PHE   0.012   0.001   PHE A  22 
 TRP   0.014   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3537)
  covalent geometry    : angle       0.51322 ( 4821)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       2.30675 (    6)
  hydrogen bonds       : bond        0.04415 (  238)
  hydrogen bonds       : angle       3.89214 (  684)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1338.11 seconds
wall clock time: 23 minutes 25.42 seconds (1405.42 seconds total)