Starting phenix.real_space_refine
on Tue Mar  3 11:26:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xpz_33386/03_2026/7xpz_33386.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xpz_33386/03_2026/7xpz_33386.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xpz_33386/03_2026/7xpz_33386.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xpz_33386/03_2026/7xpz_33386.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xpz_33386/03_2026/7xpz_33386.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xpz_33386/03_2026/7xpz_33386.cif"
  }
  resolution = 3.4
  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=   0.003
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      10      5.16       5
     C    2148      2.51       5
     N     530      2.21       5
     O     539      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3227
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3227
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 14, 'TRANS': 387}
          Chain breaks: 1
  Time building chain proxies: 0.73, per 1000 atoms: 0.23
  Number of scatterers: 3227
  At special positions: 0
  Unit cell: (81, 75, 63, 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      10     16.00
     O     539      8.00
     N     530      7.00
     C    2148      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.24
  Conformation dependent library (CDL) restraints added in 128.8 milliseconds
  

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  762

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      76.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 39
      removed outlier: 3.576A  pdb=" N   PHE A  34 " --> pdb=" O   CYS A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 67
      removed outlier: 3.550A  pdb=" N   THR A  65 " --> pdb=" O   ARG A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 79
      removed outlier: 3.672A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LEU A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
      removed outlier: 3.937A  pdb=" N   ASP A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 110
      removed outlier: 3.540A  pdb=" N   GLY A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.623A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 4.340A  pdb=" N   TYR A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   SER A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 140 " --> pdb=" O   TYR A 136 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   PHE A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 177
      removed outlier: 3.820A  pdb=" N   VAL A 152 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA A 159 " --> pdb=" O   TYR A 155 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 161 " --> pdb=" O   ARG A 157 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU A 162 " --> pdb=" O   ALA A 158 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 192
      removed outlier: 3.577A  pdb=" N   ALA A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 202
      removed outlier: 3.735A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 257
    Processing helix  chain 'A' and resid 260 through 264
    Processing helix  chain 'A' and resid 266 through 277
      removed outlier: 3.642A  pdb=" N   SER A 271 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 286
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.600A  pdb=" N   ASN A 293 " --> pdb=" O   HIS A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 323
      removed outlier: 3.919A  pdb=" N   SER A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   SER A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 333
      removed outlier: 3.853A  pdb=" N   ALA A 332 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ARG A 333 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 333'
    Processing helix  chain 'A' and resid 334 through 354
      removed outlier: 3.915A  pdb=" N   THR A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 361
    Processing helix  chain 'A' and resid 362 through 377
      removed outlier: 3.594A  pdb=" N   ALA A 367 " --> pdb=" O   TRP A 363 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   PHE A 369 " --> pdb=" O   CYS A 365 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 387
    Processing helix  chain 'A' and resid 392 through 400
      removed outlier: 3.881A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LEU A 398 " --> pdb=" O   GLU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 419
    Processing helix  chain 'A' and resid 427 through 442
      removed outlier: 3.868A  pdb=" N   LEU A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL A 437 " --> pdb=" O   GLN A 433 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TYR A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    480 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: 0.28

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 962
        1.34 -     1.46: 827
        1.46 -     1.57: 1511
        1.57 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3316
  Sorted by residual:
  bond pdb=" C   THR A  93 "
       pdb=" N   PRO A  94 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.23e-02 6.61e+03 1.38e+00
  bond pdb=" CB  PRO A  70 "
       pdb=" CG  PRO A  70 "
    ideal  model  delta    sigma   weight residual
    1.492  1.437  0.055 5.00e-02 4.00e+02 1.19e+00
  bond pdb=" CB  PRO A 381 "
       pdb=" CG  PRO A 381 "
    ideal  model  delta    sigma   weight residual
    1.492  1.439  0.053 5.00e-02 4.00e+02 1.11e+00
  bond pdb=" CB  PRO A  94 "
       pdb=" CG  PRO A  94 "
    ideal  model  delta    sigma   weight residual
    1.492  1.440  0.052 5.00e-02 4.00e+02 1.08e+00
  bond pdb=" CB  PRO A  50 "
       pdb=" CG  PRO A  50 "
    ideal  model  delta    sigma   weight residual
    1.492  1.443  0.049 5.00e-02 4.00e+02 9.47e-01
  ... (remaining 3311 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 4266
        1.40 -     2.79: 206
        2.79 -     4.19: 31
        4.19 -     5.58: 12
        5.58 -     6.98: 5
  Bond angle restraints: 4520
  Sorted by residual:
  angle pdb=" C   VAL A 250 "
        pdb=" N   LEU A 251 "
        pdb=" CA  LEU A 251 "
      ideal   model   delta    sigma   weight residual
     123.05  128.86   -5.81 1.57e+00 4.06e-01 1.37e+01
  angle pdb=" N   ALA A 252 "
        pdb=" CA  ALA A 252 "
        pdb=" C   ALA A 252 "
      ideal   model   delta    sigma   weight residual
     113.18  108.52    4.66 1.33e+00 5.65e-01 1.23e+01
  angle pdb=" N   SER A 301 "
        pdb=" CA  SER A 301 "
        pdb=" C   SER A 301 "
      ideal   model   delta    sigma   weight residual
     110.80  117.03   -6.23 2.13e+00 2.20e-01 8.57e+00
  angle pdb=" CA  THR A  69 "
        pdb=" C   THR A  69 "
        pdb=" N   PRO A  70 "
      ideal   model   delta    sigma   weight residual
     118.44  122.92   -4.48 1.59e+00 3.96e-01 7.94e+00
  angle pdb=" C   VAL A 418 "
        pdb=" N   SER A 419 "
        pdb=" CA  SER A 419 "
      ideal   model   delta    sigma   weight residual
     121.54  116.19    5.35 1.91e+00 2.74e-01 7.85e+00
  ... (remaining 4515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.48: 1743
       15.48 -    30.95: 132
       30.95 -    46.42: 27
       46.42 -    61.90: 6
       61.90 -    77.37: 2
  Dihedral angle restraints: 1910
    sinusoidal: 725
      harmonic: 1185
  Sorted by residual:
  dihedral pdb=" CA  ASN A 300 "
           pdb=" C   ASN A 300 "
           pdb=" N   SER A 301 "
           pdb=" CA  SER A 301 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.80  -25.20     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  THR A 298 "
           pdb=" C   THR A 298 "
           pdb=" N   THR A 299 "
           pdb=" CA  THR A 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.29   21.71     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.01   20.99     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 1907 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 302
       0.037 -    0.073: 170
       0.073 -    0.110: 46
       0.110 -    0.146: 8
       0.146 -    0.183: 2
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  THR A  49 "
            pdb=" N   THR A  49 "
            pdb=" C   THR A  49 "
            pdb=" CB  THR A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.37e-01
  chirality pdb=" CA  THR A  93 "
            pdb=" N   THR A  93 "
            pdb=" C   THR A  93 "
            pdb=" CB  THR A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CA  THR A  69 "
            pdb=" N   THR A  69 "
            pdb=" C   THR A  69 "
            pdb=" CB  THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.16e-01
  ... (remaining 525 not shown)

  Planarity restraints: 546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  81 "    0.050 5.00e-02 4.00e+02   7.45e-02 8.89e+00
        pdb=" N   PRO A  82 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  69 "    0.049 5.00e-02 4.00e+02   7.26e-02 8.43e+00
        pdb=" N   PRO A  70 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 380 "   -0.047 5.00e-02 4.00e+02   7.07e-02 8.00e+00
        pdb=" N   PRO A 381 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 381 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 381 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 543 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1104
        2.83 -     3.35: 2879
        3.35 -     3.86: 5331
        3.86 -     4.38: 6586
        4.38 -     4.90: 10693
  Nonbonded interactions: 26593
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 304 "
            pdb=" OH  TYR A 366 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   THR A 404 "
            pdb=" OG1 THR A 408 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OD2 ASP A  56 "
            pdb=" OG  SER A 183 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OH  TYR A 139 "
            pdb=" O   LYS A 204 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG  SER A 271 "
            pdb=" OD1 ASN A 403 "
     model   vdw
     2.337 3.040
  ... (remaining 26588 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:             1.910
  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:                     4.430
  Find NCS groups from input model:        0.010
  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:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
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      :  0.005   0.055   3316  Z= 0.229
  Angle     :  0.732   6.979   4520  Z= 0.426
  Chirality :  0.046   0.183    528
  Planarity :  0.008   0.075    546
  Dihedral  : 12.260  77.370   1148
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.51 %
    Favored  : 89.91 %
  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: -6.77 (0.22), residues: 398
  helix: -4.54 (0.11), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.98 (0.52), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 264 
 TYR   0.010   0.002   TYR A  92 
 PHE   0.009   0.001   PHE A 276 
 TRP   0.011   0.002   TRP A 274 
 HIS   0.001   0.000   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 3316)
  covalent geometry    : angle       0.73163 ( 4520)
  hydrogen bonds       : bond        0.28787 (  163)
  hydrogen bonds       : angle      11.19046 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A   22 LEU cc_start: 0.6860 (tp) cc_final: 0.6364 (pp)
REVERT: A   26 ARG cc_start: 0.6911 (tpt-90) cc_final: 0.6414 (ttm170)
REVERT: A   40 GLN cc_start: 0.7794 (mm110) cc_final: 0.7520 (mm-40)
REVERT: A   92 TYR cc_start: 0.8170 (m-80) cc_final: 0.7871 (m-80)
REVERT: A  122 MET cc_start: 0.8952 (tmm) cc_final: 0.8715 (tmm)
REVERT: A  310 ASP cc_start: 0.7621 (t0) cc_final: 0.7286 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.0769
  time to fit residues: 5.2333
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   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 118 HIS
A 289 HIS
A 377 GLN
A 433 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.110908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.093579 restraints weight = 4604.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.11
r_work: 0.2961 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3316  Z= 0.166
  Angle     :  0.588   5.563   4520  Z= 0.312
  Chirality :  0.039   0.120    528
  Planarity :  0.006   0.047    546
  Dihedral  :  5.543  34.665    451
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 11.82 %
    Favored  : 85.88 %
  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: -4.58 (0.32), residues: 398
  helix: -2.95 (0.21), residues: 310
  sheet:  None (None), residues: 0
  loop : -2.32 (0.59), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 263 
 TYR   0.013   0.001   TYR A  35 
 PHE   0.009   0.001   PHE A 447 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 3316)
  covalent geometry    : angle       0.58780 ( 4520)
  hydrogen bonds       : bond        0.03391 (  163)
  hydrogen bonds       : angle       5.02312 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6913 (tpt-90) cc_final: 0.6049 (ttm170)
REVERT: A   38 MET cc_start: 0.8594 (mmt) cc_final: 0.8316 (tpp)
REVERT: A  122 MET cc_start: 0.8970 (tmm) cc_final: 0.8728 (tmm)
REVERT: A  126 TYR cc_start: 0.8211 (t80) cc_final: 0.7981 (t80)
REVERT: A  277 ASN cc_start: 0.8975 (t0) cc_final: 0.8596 (t0)
REVERT: A  310 ASP cc_start: 0.7724 (t0) cc_final: 0.7417 (t0)
REVERT: A  413 ILE cc_start: 0.8350 (mm) cc_final: 0.8117 (mt)
  outliers start: 8
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0624
  time to fit residues: 4.1714
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   chunk 30 optimal weight:    0.2980
   chunk 26 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
A  66 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.112097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.095444 restraints weight = 4401.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 2.00
r_work: 0.2983 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3316  Z= 0.137
  Angle     :  0.546   5.922   4520  Z= 0.280
  Chirality :  0.038   0.117    528
  Planarity :  0.004   0.034    546
  Dihedral  :  4.894  18.861    449
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.70 %
    Favored  : 83.29 %
  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: -3.14 (0.37), residues: 398
  helix: -1.87 (0.26), residues: 313
  sheet:  None (None), residues: 0
  loop : -2.02 (0.65), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 263 
 TYR   0.011   0.001   TYR A  92 
 PHE   0.025   0.001   PHE A  84 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3316)
  covalent geometry    : angle       0.54600 ( 4520)
  hydrogen bonds       : bond        0.02933 (  163)
  hydrogen bonds       : angle       4.32989 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6902 (tpt-90) cc_final: 0.6045 (ttm170)
REVERT: A   38 MET cc_start: 0.8481 (mmt) cc_final: 0.8247 (tpp)
REVERT: A  277 ASN cc_start: 0.8982 (t0) cc_final: 0.8609 (t0)
REVERT: A  357 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7793 (mpt-90)
REVERT: A  434 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7747 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0550
  time to fit residues: 3.3321
Evaluate side-chains
  46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   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 = 0.3298 r_free = 0.3298 target = 0.110913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.094609 restraints weight = 4444.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.00
r_work: 0.2975 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3316  Z= 0.159
  Angle     :  0.553   6.009   4520  Z= 0.280
  Chirality :  0.039   0.120    528
  Planarity :  0.003   0.028    546
  Dihedral  :  4.785  17.697    449
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.14 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.40), residues: 398
  helix: -1.35 (0.27), residues: 313
  sheet:  None (None), residues: 0
  loop : -1.76 (0.68), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 263 
 TYR   0.014   0.001   TYR A 446 
 PHE   0.009   0.001   PHE A 447 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3316)
  covalent geometry    : angle       0.55286 ( 4520)
  hydrogen bonds       : bond        0.02911 (  163)
  hydrogen bonds       : angle       4.14156 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6953 (tpt-90) cc_final: 0.6089 (ttm170)
REVERT: A  277 ASN cc_start: 0.8952 (t0) cc_final: 0.8541 (t0)
REVERT: A  306 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8408 (t0)
REVERT: A  310 ASP cc_start: 0.7650 (t0) cc_final: 0.7449 (t0)
REVERT: A  357 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7783 (mpt-90)
REVERT: A  434 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7692 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 48
  average time/residue: 0.0565
  time to fit residues: 3.4496
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   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 = 0.3300 r_free = 0.3300 target = 0.111441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.095055 restraints weight = 4439.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.00
r_work: 0.2978 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3316  Z= 0.143
  Angle     :  0.532   6.030   4520  Z= 0.269
  Chirality :  0.038   0.119    528
  Planarity :  0.003   0.027    546
  Dihedral  :  4.680  17.354    449
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.41 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.41), residues: 398
  helix: -1.03 (0.28), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.59 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 263 
 TYR   0.015   0.001   TYR A 446 
 PHE   0.018   0.001   PHE A  84 
 TRP   0.008   0.001   TRP A 273 
 HIS   0.001   0.000   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3316)
  covalent geometry    : angle       0.53172 ( 4520)
  hydrogen bonds       : bond        0.02803 (  163)
  hydrogen bonds       : angle       3.98114 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6940 (tpt-90) cc_final: 0.6062 (ttm170)
REVERT: A  211 PHE cc_start: 0.8503 (m-80) cc_final: 0.8296 (m-80)
REVERT: A  277 ASN cc_start: 0.8997 (t0) cc_final: 0.8584 (t0)
REVERT: A  306 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8435 (t0)
REVERT: A  357 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7801 (mpt-90)
REVERT: A  434 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7533 (tt)
  outliers start: 11
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0671
  time to fit residues: 4.6292
Evaluate side-chains
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.3319 r_free = 0.3319 target = 0.112927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.096423 restraints weight = 4440.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.06
r_work: 0.3066 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3316  Z= 0.123
  Angle     :  0.533   6.028   4520  Z= 0.268
  Chirality :  0.038   0.117    528
  Planarity :  0.003   0.025    546
  Dihedral  :  4.584  19.889    449
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.71 %
    Favored  : 80.69 %
  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: -1.62 (0.42), residues: 398
  helix: -0.78 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.60 (0.72), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 263 
 TYR   0.011   0.001   TYR A  92 
 PHE   0.011   0.001   PHE A 447 
 TRP   0.008   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3316)
  covalent geometry    : angle       0.53267 ( 4520)
  hydrogen bonds       : bond        0.02697 (  163)
  hydrogen bonds       : angle       3.89935 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6957 (tpt-90) cc_final: 0.6069 (ttm170)
REVERT: A  211 PHE cc_start: 0.8442 (m-80) cc_final: 0.8159 (m-80)
REVERT: A  277 ASN cc_start: 0.9005 (t0) cc_final: 0.8638 (t0)
REVERT: A  306 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8400 (t0)
REVERT: A  434 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7570 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 52
  average time/residue: 0.0664
  time to fit residues: 4.3451
Evaluate side-chains
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.109878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.093380 restraints weight = 4554.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.01
r_work: 0.2956 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3316  Z= 0.186
  Angle     :  0.573   6.087   4520  Z= 0.286
  Chirality :  0.040   0.126    528
  Planarity :  0.003   0.025    546
  Dihedral  :  4.645  20.986    449
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.71 %
    Favored  : 80.40 %
  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: -1.59 (0.42), residues: 398
  helix: -0.74 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -1.64 (0.73), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 373 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.019   0.001   PHE A  84 
 TRP   0.010   0.001   TRP A 273 
 HIS   0.001   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 3316)
  covalent geometry    : angle       0.57312 ( 4520)
  hydrogen bonds       : bond        0.02924 (  163)
  hydrogen bonds       : angle       4.05551 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6961 (tpt-90) cc_final: 0.6065 (ttm170)
REVERT: A   92 TYR cc_start: 0.8563 (m-80) cc_final: 0.8320 (m-80)
REVERT: A  277 ASN cc_start: 0.8969 (t0) cc_final: 0.8568 (t0)
REVERT: A  306 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8486 (t0)
REVERT: A  434 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7477 (tt)
  outliers start: 10
  outliers final: 7
  residues processed: 54
  average time/residue: 0.0627
  time to fit residues: 4.2915
Evaluate side-chains
  55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.4980
   chunk 1 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.112372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.096247 restraints weight = 4438.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.97
r_work: 0.2998 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3316  Z= 0.136
  Angle     :  0.546   6.137   4520  Z= 0.276
  Chirality :  0.039   0.141    528
  Planarity :  0.003   0.024    546
  Dihedral  :  4.533  19.833    449
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.58 %
    Favored  : 79.83 %
  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: -1.32 (0.42), residues: 398
  helix: -0.57 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.47 (0.73), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 263 
 TYR   0.012   0.001   TYR A  92 
 PHE   0.015   0.001   PHE A 447 
 TRP   0.009   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3316)
  covalent geometry    : angle       0.54621 ( 4520)
  hydrogen bonds       : bond        0.02766 (  163)
  hydrogen bonds       : angle       3.91963 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6954 (tpt-90) cc_final: 0.6060 (ttm170)
REVERT: A  277 ASN cc_start: 0.8956 (t0) cc_final: 0.8555 (t0)
REVERT: A  306 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8447 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 47
  average time/residue: 0.0570
  time to fit residues: 3.4884
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.1980
   chunk 14 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3317 r_free = 0.3317 target = 0.112907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.096749 restraints weight = 4409.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.95
r_work: 0.3001 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3316  Z= 0.132
  Angle     :  0.555   6.273   4520  Z= 0.278
  Chirality :  0.039   0.153    528
  Planarity :  0.003   0.024    546
  Dihedral  :  4.492  19.231    449
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.43 %
    Favored  : 80.40 %
  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: -1.20 (0.43), residues: 398
  helix: -0.49 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.40 (0.74), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 253 
 TYR   0.012   0.001   TYR A  92 
 PHE   0.016   0.001   PHE A 447 
 TRP   0.009   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3316)
  covalent geometry    : angle       0.55546 ( 4520)
  hydrogen bonds       : bond        0.02729 (  163)
  hydrogen bonds       : angle       3.88437 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7024 (tpt-90) cc_final: 0.6119 (ttm170)
REVERT: A  277 ASN cc_start: 0.8960 (t0) cc_final: 0.8570 (t0)
REVERT: A  306 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8447 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0545
  time to fit residues: 3.5353
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0030
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5990

-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.113102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.096805 restraints weight = 4397.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.92
r_work: 0.3004 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3316  Z= 0.141
  Angle     :  0.561   6.324   4520  Z= 0.280
  Chirality :  0.039   0.155    528
  Planarity :  0.003   0.024    546
  Dihedral  :  4.485  19.276    449
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.14 %
    Favored  : 80.98 %
  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: -1.19 (0.43), residues: 398
  helix: -0.47 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.47 (0.73), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 253 
 TYR   0.011   0.001   TYR A  92 
 PHE   0.023   0.001   PHE A  84 
 TRP   0.010   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3316)
  covalent geometry    : angle       0.56067 ( 4520)
  hydrogen bonds       : bond        0.02795 (  163)
  hydrogen bonds       : angle       3.87955 (  480)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7012 (tpt-90) cc_final: 0.6093 (ttm170)
REVERT: A  255 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7002 (pp)
REVERT: A  306 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8419 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 48
  average time/residue: 0.0636
  time to fit residues: 3.8773
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  334 TRP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0470
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.4878

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.115142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.098529 restraints weight = 4415.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.95
r_work: 0.3028 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3316  Z= 0.125
  Angle     :  0.555   6.585   4520  Z= 0.277
  Chirality :  0.038   0.163    528
  Planarity :  0.003   0.024    546
  Dihedral  :  4.418  18.453    449
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.00 %
    Favored  : 80.40 %
  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: -1.00 (0.43), residues: 398
  helix: -0.34 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.43 (0.73), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 253 
 TYR   0.012   0.001   TYR A  92 
 PHE   0.018   0.001   PHE A 447 
 TRP   0.009   0.001   TRP A 273 
 HIS   0.000   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3316)
  covalent geometry    : angle       0.55481 ( 4520)
  hydrogen bonds       : bond        0.02707 (  163)
  hydrogen bonds       : angle       3.81612 (  480)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 945.54 seconds
wall clock time: 16 minutes 55.28 seconds (1015.28 seconds total)