Starting phenix.real_space_refine
on Tue Feb  3 14:01:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9utd_64489/02_2026/9utd_64489.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9utd_64489/02_2026/9utd_64489.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9utd_64489/02_2026/9utd_64489.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9utd_64489/02_2026/9utd_64489.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9utd_64489/02_2026/9utd_64489.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9utd_64489/02_2026/9utd_64489.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.027
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: 6
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     Cl      2      4.86       5
     Na      1      4.78       5
     C    2265      2.51       5
     N     534      2.21       5
     O     560      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3380
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3366
          Classifications: {'peptide': 428}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 15, 'TRANS': 412}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 14
          Unusual residues: {' NA': 1, 'CFA': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.06, per 1000 atoms: 0.31
  Number of scatterers: 3380
  At special positions: 0
  Unit cell: (81.6, 62.9, 70.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      18     16.00
     Na      1     11.00
     O     560      8.00
     N     534      7.00
     C    2265      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 464 " - pdb=" SG  CYS A 467 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 156.3 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  796

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      78.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 57
      removed outlier: 3.578A  pdb=" N   CYS A  55 " --> pdb=" O   ALA A  51 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER A  57 " --> pdb=" O   PHE A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'A' and resid 66 through 75
      removed outlier: 3.530A  pdb=" N   SER A  70 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 111
      removed outlier: 3.730A  pdb=" N   ILE A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN A  83 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLU A 111 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 131 through 161
      removed outlier: 3.503A  pdb=" N   LEU A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ASN A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   SER A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL A 151 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ILE A 152 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 164
      No H-bonds generated for 'chain 'A' and resid 162 through 164'
    Processing helix  chain 'A' and resid 169 through 182
    Processing helix  chain 'A' and resid 193 through 219
      removed outlier: 3.542A  pdb=" N   SER A 197 " --> pdb=" O   TYR A 193 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLY A 202 " --> pdb=" O   PHE A 198 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   THR A 207 " --> pdb=" O   MET A 203 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TRP A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA A 212 " --> pdb=" O   ALA A 208 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 246
      removed outlier: 3.687A  pdb=" N   THR A 240 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASN A 241 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE A 246 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 253
      removed outlier: 3.831A  pdb=" N   THR A 252 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 253 " --> pdb=" O   HIS A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 248 through 253'
    Processing helix  chain 'A' and resid 266 through 275
      removed outlier: 3.632A  pdb=" N   LEU A 270 " --> pdb=" O   TYR A 267 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   LEU A 274 " --> pdb=" O   MET A 271 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   TYR A 275 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 292
      Proline residue:  A 282  - end of helix
      removed outlier: 3.501A  pdb=" N   TYR A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 295
      No H-bonds generated for 'chain 'A' and resid 293 through 295'
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 308 through 323
    Processing helix  chain 'A' and resid 323 through 342
      removed outlier: 4.126A  pdb=" N   GLY A 327 " --> pdb=" O   PHE A 323 " (cutoff:3.500A)
      Proline residue:  A 332  - end of helix
    Processing helix  chain 'A' and resid 348 through 356
      removed outlier: 3.774A  pdb=" N   ARG A 352 " --> pdb=" O   SER A 348 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 354 " --> pdb=" O   CYS A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 370
      removed outlier: 3.621A  pdb=" N   ALA A 367 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 384
      removed outlier: 4.279A  pdb=" N   SER A 378 " --> pdb=" O   GLY A 374 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ALA A 379 " --> pdb=" O   PRO A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 389
    Processing helix  chain 'A' and resid 390 through 401
      removed outlier: 3.655A  pdb=" N   SER A 394 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   MET A 398 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR A 401 " --> pdb=" O   HIS A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 409
      removed outlier: 3.534A  pdb=" N   ASN A 409 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 438
      removed outlier: 4.022A  pdb=" N   MET A 424 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 459

    194 hydrogen bonds defined for protein.
    558 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: 0.56

  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:
        1.22 -     1.34: 987
        1.34 -     1.46: 956
        1.46 -     1.58: 1523
        1.58 -     1.70: 0
        1.70 -     1.82: 29
  Bond restraints: 3495
  Sorted by residual:
  bond pdb=" C1' CFA A 601 "
       pdb=" O1' CFA A 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.396 -0.064 2.00e-02 2.50e+03 1.01e+01
  bond pdb=" C2' CFA A 601 "
       pdb="CL3  CFA A 601 "
    ideal  model  delta    sigma   weight residual
    1.727  1.783 -0.056 2.00e-02 2.50e+03 7.86e+00
  bond pdb=" N   LYS A 307 "
       pdb=" CA  LYS A 307 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.22e-02 6.72e+03 7.26e+00
  bond pdb=" N   ASN A 308 "
       pdb=" CA  ASN A 308 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.16e-02 7.43e+03 7.20e+00
  bond pdb=" C4' CFA A 601 "
       pdb="CL4  CFA A 601 "
    ideal  model  delta    sigma   weight residual
    1.733  1.782 -0.049 2.00e-02 2.50e+03 6.11e+00
  ... (remaining 3490 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 4596
        1.58 -     3.15: 156
        3.15 -     4.73: 16
        4.73 -     6.31: 7
        6.31 -     7.88: 4
  Bond angle restraints: 4779
  Sorted by residual:
  angle pdb=" N   ASN A 241 "
        pdb=" CA  ASN A 241 "
        pdb=" C   ASN A 241 "
      ideal   model   delta    sigma   weight residual
     111.82  107.77    4.05 1.16e+00 7.43e-01 1.22e+01
  angle pdb=" CA  ASN A 308 "
        pdb=" C   ASN A 308 "
        pdb=" O   ASN A 308 "
      ideal   model   delta    sigma   weight residual
     121.38  118.01    3.37 1.06e+00 8.90e-01 1.01e+01
  angle pdb=" O1  CFA A 601 "
        pdb=" C1  CFA A 601 "
        pdb=" O2  CFA A 601 "
      ideal   model   delta    sigma   weight residual
     128.33  120.45    7.88 3.00e+00 1.11e-01 6.91e+00
  angle pdb=" N   VAL A 253 "
        pdb=" CA  VAL A 253 "
        pdb=" C   VAL A 253 "
      ideal   model   delta    sigma   weight residual
     113.00  109.64    3.36 1.30e+00 5.92e-01 6.69e+00
  angle pdb=" CA  TYR A  69 "
        pdb=" CB  TYR A  69 "
        pdb=" CG  TYR A  69 "
      ideal   model   delta    sigma   weight residual
     113.90  118.42   -4.52 1.80e+00 3.09e-01 6.32e+00
  ... (remaining 4774 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 1736
       17.96 -    35.91: 164
       35.91 -    53.86: 29
       53.86 -    71.82: 4
       71.82 -    89.77: 3
  Dihedral angle restraints: 1936
    sinusoidal: 691
      harmonic: 1245
  Sorted by residual:
  dihedral pdb=" CA  LEU A 357 "
           pdb=" C   LEU A 357 "
           pdb=" N   PRO A 358 "
           pdb=" CA  PRO A 358 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.51   30.49     0      5.00e+00 4.00e-02 3.72e+01
  dihedral pdb=" CB  GLU A 222 "
           pdb=" CG  GLU A 222 "
           pdb=" CD  GLU A 222 "
           pdb=" OE1 GLU A 222 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.77   89.77     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  ASN A 241 "
           pdb=" CB  ASN A 241 "
           pdb=" CG  ASN A 241 "
           pdb=" OD1 ASN A 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -173.20  -66.80     2      2.00e+01 2.50e-03 1.01e+01
  ... (remaining 1933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 256
       0.027 -    0.054: 170
       0.054 -    0.081: 72
       0.081 -    0.107: 25
       0.107 -    0.134: 8
  Chirality restraints: 531
  Sorted by residual:
  chirality pdb=" CA  PHE A 291 "
            pdb=" N   PHE A 291 "
            pdb=" C   PHE A 291 "
            pdb=" CB  PHE A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.51e-01
  chirality pdb=" CA  HIS A 257 "
            pdb=" N   HIS A 257 "
            pdb=" C   HIS A 257 "
            pdb=" CB  HIS A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  ARG A 311 "
            pdb=" N   ARG A 311 "
            pdb=" C   ARG A 311 "
            pdb=" CB  ARG A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.63   -0.12 2.00e-01 2.50e+01 3.42e-01
  ... (remaining 528 not shown)

  Planarity restraints: 579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 374 "   -0.054 5.00e-02 4.00e+02   8.13e-02 1.06e+01
        pdb=" N   PRO A 375 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 357 "    0.042 5.00e-02 4.00e+02   6.28e-02 6.32e+00
        pdb=" N   PRO A 358 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 358 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 358 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 361 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.17e+00
        pdb=" N   PRO A 362 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 362 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 362 "    0.021 5.00e-02 4.00e+02
  ... (remaining 576 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 911
        2.79 -     3.32: 3003
        3.32 -     3.84: 5226
        3.84 -     4.37: 6317
        4.37 -     4.90: 11018
  Nonbonded interactions: 26475
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 105 "
            pdb=" OE2 GLU A 109 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" O   LEU A 211 "
            pdb=" OG  SER A 215 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   GLY A 443 "
            pdb=" OG  SER A 447 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   CYS A 180 "
            pdb=" OG1 THR A 183 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" O   ASN A 300 "
            pdb=" OG  SER A 303 "
     model   vdw
     2.347 3.040
  ... (remaining 26470 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:             2.770
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.800
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
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      :  0.006   0.064   3496  Z= 0.281
  Angle     :  0.705   7.883   4781  Z= 0.405
  Chirality :  0.042   0.134    531
  Planarity :  0.006   0.081    579
  Dihedral  : 14.788  89.769   1137
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.18 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.66 (0.35), residues: 426
  helix: -1.82 (0.26), residues: 306
  sheet:  None (None), residues: 0
  loop : -3.70 (0.46), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 194 
 TYR   0.017   0.002   TYR A  69 
 PHE   0.013   0.002   PHE A 417 
 TRP   0.010   0.001   TRP A 134 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 3495)
  covalent geometry    : angle       0.70434 ( 4779)
  SS BOND              : bond        0.00297 (    1)
  SS BOND              : angle       1.51701 (    2)
  hydrogen bonds       : bond        0.18738 (  194)
  hydrogen bonds       : angle       6.23814 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.7925 (tpp) cc_final: 0.7634 (tpp)
REVERT: A  260 TRP cc_start: 0.6972 (OUTLIER) cc_final: 0.5409 (p90)
  outliers start: 10
  outliers final: 3
  residues processed: 67
  average time/residue: 0.0688
  time to fit residues: 5.7080
Evaluate side-chains
  46 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  319 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 GLN
A 241 ASN
A 321 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.163918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.122271 restraints weight = 3948.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.14
r_work: 0.3257 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3496  Z= 0.145
  Angle     :  0.568   5.875   4781  Z= 0.300
  Chirality :  0.040   0.137    531
  Planarity :  0.006   0.080    579
  Dihedral  :  6.272  63.389    467
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.88 %
    Favored  : 80.59 %
  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: -1.99 (0.39), residues: 426
  helix: -0.46 (0.29), residues: 303
  sheet:  None (None), residues: 0
  loop : -3.40 (0.49), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 352 
 TYR   0.012   0.001   TYR A 101 
 PHE   0.012   0.001   PHE A 291 
 TRP   0.012   0.001   TRP A 134 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3495)
  covalent geometry    : angle       0.56770 ( 4779)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.17970 (    2)
  hydrogen bonds       : bond        0.05356 (  194)
  hydrogen bonds       : angle       4.47542 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A   89 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7867 (mp)
REVERT: A  127 ASP cc_start: 0.8437 (t70) cc_final: 0.8116 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0508
  time to fit residues: 3.4830
Evaluate side-chains
  47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  253 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 257 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.156934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.112327 restraints weight = 3929.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.30
r_work: 0.3136 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3496  Z= 0.147
  Angle     :  0.557   6.617   4781  Z= 0.289
  Chirality :  0.040   0.126    531
  Planarity :  0.005   0.079    579
  Dihedral  :  5.322  61.143    462
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.76 %
    Favored  : 80.59 %
  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: -1.30 (0.41), residues: 426
  helix:  0.07 (0.30), residues: 305
  sheet:  None (None), residues: 0
  loop : -3.25 (0.51), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 311 
 TYR   0.014   0.001   TYR A 244 
 PHE   0.014   0.001   PHE A 145 
 TRP   0.012   0.001   TRP A 421 
 HIS   0.006   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3495)
  covalent geometry    : angle       0.55747 ( 4779)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       0.28099 (    2)
  hydrogen bonds       : bond        0.05574 (  194)
  hydrogen bonds       : angle       4.23530 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   89 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7167 (mp)
REVERT: A  127 ASP cc_start: 0.8383 (t70) cc_final: 0.7970 (t0)
REVERT: A  296 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8579 (pp)
REVERT: A  453 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7758 (mtp180)
  outliers start: 9
  outliers final: 4
  residues processed: 57
  average time/residue: 0.0660
  time to fit residues: 4.7293
Evaluate side-chains
  55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  299 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A 167 HIS
A 218 HIS
A 257 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.155465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.111516 restraints weight = 3878.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.26
r_work: 0.3070 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3496  Z= 0.144
  Angle     :  0.552   9.158   4781  Z= 0.283
  Chirality :  0.039   0.128    531
  Planarity :  0.005   0.078    579
  Dihedral  :  5.201  62.059    461
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 16.76 %
    Favored  : 79.12 %
  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: -0.86 (0.41), residues: 426
  helix:  0.40 (0.30), residues: 297
  sheet:  None (None), residues: 0
  loop : -2.89 (0.50), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 107 
 TYR   0.014   0.001   TYR A 244 
 PHE   0.010   0.001   PHE A 246 
 TRP   0.009   0.001   TRP A 134 
 HIS   0.008   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3495)
  covalent geometry    : angle       0.55234 ( 4779)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.20678 (    2)
  hydrogen bonds       : bond        0.05254 (  194)
  hydrogen bonds       : angle       4.17978 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6997 (mp)
REVERT: A  103 GLU cc_start: 0.8157 (tp30) cc_final: 0.7912 (tp30)
REVERT: A  127 ASP cc_start: 0.8427 (t70) cc_final: 0.8033 (t0)
REVERT: A  296 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8512 (pp)
REVERT: A  356 ARG cc_start: 0.7594 (mtm180) cc_final: 0.7202 (mtm180)
  outliers start: 14
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0732
  time to fit residues: 4.9449
Evaluate side-chains
  56 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0870
   chunk 24 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0970
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4356

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.157069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113443 restraints weight = 3947.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.28
r_work: 0.3156 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3496  Z= 0.113
  Angle     :  0.529   9.911   4781  Z= 0.268
  Chirality :  0.038   0.130    531
  Planarity :  0.005   0.073    579
  Dihedral  :  5.069  60.725    461
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.18 %
    Favored  : 80.29 %
  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: -0.47 (0.42), residues: 426
  helix:  0.72 (0.31), residues: 297
  sheet:  None (None), residues: 0
  loop : -2.83 (0.50), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 105 
 TYR   0.011   0.001   TYR A  69 
 PHE   0.008   0.001   PHE A 291 
 TRP   0.006   0.001   TRP A 209 
 HIS   0.002   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3495)
  covalent geometry    : angle       0.52871 ( 4779)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.06249 (    2)
  hydrogen bonds       : bond        0.04666 (  194)
  hydrogen bonds       : angle       4.03440 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7122 (mp)
REVERT: A  103 GLU cc_start: 0.8097 (tp30) cc_final: 0.7810 (tp30)
REVERT: A  127 ASP cc_start: 0.8427 (t70) cc_final: 0.8063 (t0)
REVERT: A  296 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8518 (pp)
REVERT: A  356 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7328 (mtm180)
  outliers start: 12
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0786
  time to fit residues: 5.2815
Evaluate side-chains
  57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 39 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0870
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0040
   chunk 24 optimal weight:    0.4980
   chunk 14 optimal weight:    8.9990
   overall best weight:    0.2570

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.160344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.118186 restraints weight = 3925.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.21
r_work: 0.3214 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3496  Z= 0.096
  Angle     :  0.500  10.186   4781  Z= 0.251
  Chirality :  0.037   0.130    531
  Planarity :  0.005   0.070    579
  Dihedral  :  4.764  56.023    461
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.65 %
    Favored  : 79.41 %
  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: -0.07 (0.42), residues: 426
  helix:  1.02 (0.31), residues: 297
  sheet:  None (None), residues: 0
  loop : -2.65 (0.51), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 105 
 TYR   0.009   0.001   TYR A  69 
 PHE   0.006   0.001   PHE A 291 
 TRP   0.007   0.001   TRP A  43 
 HIS   0.003   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 3495)
  covalent geometry    : angle       0.50048 ( 4779)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       0.11787 (    2)
  hydrogen bonds       : bond        0.03898 (  194)
  hydrogen bonds       : angle       3.88912 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7313 (mp)
REVERT: A  103 GLU cc_start: 0.8195 (tp30) cc_final: 0.7939 (tp30)
REVERT: A  127 ASP cc_start: 0.8450 (t70) cc_final: 0.8163 (t0)
REVERT: A  181 CYS cc_start: 0.6954 (m) cc_final: 0.6520 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 54
  average time/residue: 0.0860
  time to fit residues: 5.5539
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3745 r_free = 0.3745 target = 0.151859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.107535 restraints weight = 3993.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.30
r_work: 0.3072 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3496  Z= 0.222
  Angle     :  0.603  11.208   4781  Z= 0.312
  Chirality :  0.042   0.143    531
  Planarity :  0.006   0.081    579
  Dihedral  :  5.217  62.538    461
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 16.76 %
    Favored  : 79.12 %
  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: -0.54 (0.41), residues: 426
  helix:  0.66 (0.30), residues: 296
  sheet:  None (None), residues: 0
  loop : -2.80 (0.50), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 105 
 TYR   0.024   0.002   TYR A 244 
 PHE   0.013   0.002   PHE A 246 
 TRP   0.011   0.001   TRP A 134 
 HIS   0.003   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 3495)
  covalent geometry    : angle       0.60239 ( 4779)
  SS BOND              : bond        0.01312 (    1)
  SS BOND              : angle       1.85849 (    2)
  hydrogen bonds       : bond        0.06184 (  194)
  hydrogen bonds       : angle       4.25383 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7081 (mp)
REVERT: A  127 ASP cc_start: 0.8466 (t70) cc_final: 0.8081 (t0)
REVERT: A  181 CYS cc_start: 0.7107 (m) cc_final: 0.6598 (m)
  outliers start: 14
  outliers final: 9
  residues processed: 54
  average time/residue: 0.0902
  time to fit residues: 5.9319
Evaluate side-chains
  57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3758 r_free = 0.3758 target = 0.153198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.109084 restraints weight = 3980.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.29
r_work: 0.3107 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3496  Z= 0.132
  Angle     :  0.561  12.438   4781  Z= 0.280
  Chirality :  0.039   0.129    531
  Planarity :  0.005   0.076    579
  Dihedral  :  5.051  59.036    461
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.12 %
    Favored  : 78.24 %
  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 are not related in a simple way.
  whole: -0.28 (0.41), residues: 426
  helix:  0.85 (0.30), residues: 296
  sheet:  None (None), residues: 0
  loop : -2.66 (0.51), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 356 
 TYR   0.012   0.001   TYR A  69 
 PHE   0.008   0.001   PHE A 145 
 TRP   0.006   0.001   TRP A 122 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3495)
  covalent geometry    : angle       0.56104 ( 4779)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       1.07457 (    2)
  hydrogen bonds       : bond        0.05043 (  194)
  hydrogen bonds       : angle       4.08042 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6996 (mp)
REVERT: A  103 GLU cc_start: 0.8004 (tp30) cc_final: 0.7783 (tp30)
REVERT: A  127 ASP cc_start: 0.8390 (t70) cc_final: 0.8016 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 53
  average time/residue: 0.0678
  time to fit residues: 4.3760
Evaluate side-chains
  56 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   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 = 0.3744 r_free = 0.3744 target = 0.151922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.107809 restraints weight = 3929.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.27
r_work: 0.3102 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.4464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3496  Z= 0.150
  Angle     :  0.583  12.647   4781  Z= 0.290
  Chirality :  0.039   0.128    531
  Planarity :  0.005   0.078    579
  Dihedral  :  5.023  57.546    461
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.82 %
    Favored  : 77.94 %
  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: -0.26 (0.41), residues: 426
  helix:  0.83 (0.30), residues: 296
  sheet:  None (None), residues: 0
  loop : -2.56 (0.51), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.016   0.001   TYR A 244 
 PHE   0.009   0.001   PHE A 145 
 TRP   0.007   0.001   TRP A 134 
 HIS   0.003   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3495)
  covalent geometry    : angle       0.58256 ( 4779)
  SS BOND              : bond        0.00238 (    1)
  SS BOND              : angle       1.24313 (    2)
  hydrogen bonds       : bond        0.05440 (  194)
  hydrogen bonds       : angle       4.11327 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7008 (mp)
REVERT: A  127 ASP cc_start: 0.8410 (t70) cc_final: 0.8029 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0761
  time to fit residues: 5.0517
Evaluate side-chains
  57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0980
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0970
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    0.3980
   chunk 6 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.155718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.111601 restraints weight = 3894.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.32
r_work: 0.3146 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3496  Z= 0.107
  Angle     :  0.553  13.896   4781  Z= 0.269
  Chirality :  0.038   0.130    531
  Planarity :  0.005   0.073    579
  Dihedral  :  4.751  52.930    461
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.82 %
    Favored  : 77.94 %
  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:  0.14 (0.42), residues: 426
  helix:  1.10 (0.31), residues: 296
  sheet:  None (None), residues: 0
  loop : -2.34 (0.52), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 105 
 TYR   0.009   0.001   TYR A  69 
 PHE   0.006   0.001   PHE A 291 
 TRP   0.008   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 3495)
  covalent geometry    : angle       0.55255 ( 4779)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       0.54718 (    2)
  hydrogen bonds       : bond        0.04277 (  194)
  hydrogen bonds       : angle       3.93312 (  558)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6906 (mp)
REVERT: A  127 ASP cc_start: 0.8327 (t70) cc_final: 0.7954 (t0)
  outliers start: 11
  outliers final: 10
  residues processed: 55
  average time/residue: 0.0708
  time to fit residues: 4.7601
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0060
   chunk 21 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0970
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.155707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.111527 restraints weight = 3979.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.32
r_work: 0.3136 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.4619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3496  Z= 0.124
  Angle     :  0.568  13.616   4781  Z= 0.279
  Chirality :  0.038   0.129    531
  Planarity :  0.005   0.074    579
  Dihedral  :  4.713  51.400    461
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 18.24 %
    Favored  : 78.24 %
  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 are not related in a simple way.
  whole:  0.22 (0.42), residues: 426
  helix:  1.14 (0.31), residues: 296
  sheet:  None (None), residues: 0
  loop : -2.23 (0.54), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.012   0.001   TYR A  69 
 PHE   0.008   0.001   PHE A 291 
 TRP   0.006   0.001   TRP A 122 
 HIS   0.002   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3495)
  covalent geometry    : angle       0.56805 ( 4779)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.84979 (    2)
  hydrogen bonds       : bond        0.04692 (  194)
  hydrogen bonds       : angle       3.97561 (  558)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1163.45 seconds
wall clock time: 20 minutes 33.60 seconds (1233.60 seconds total)