Starting phenix.real_space_refine
on Tue Mar  3 13:43:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ugv_26497/03_2026/7ugv_26497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ugv_26497/03_2026/7ugv_26497.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ugv_26497/03_2026/7ugv_26497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ugv_26497/03_2026/7ugv_26497.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ugv_26497/03_2026/7ugv_26497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ugv_26497/03_2026/7ugv_26497.map"
  }
  resolution = 2.94
  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=   0.003 sd=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2846 atoms to isotropic.
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      16      5.16       5
     Na      3      4.78       5
     C    2038      2.51       5
     N     506      2.21       5
     O     543      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 3107
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3104
          Classifications: {'peptide': 418}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 399}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'EFC:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' NA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 0.71, per 1000 atoms: 0.23
  Number of scatterers: 3107
  At special positions: 0
  Unit cell: (69.012, 74.976, 74.124, 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)
     S      16     16.00
     Na      3     11.00
     F       1      9.00
     O     543      8.00
     N     506      7.00
     C    2038      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: 0.26
  Conformation dependent library (CDL) restraints added in 111.0 milliseconds
  

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  750

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 0 sheets defined
      89.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
      removed outlier: 4.147A  pdb=" N   LYS A   6 " --> pdb=" O   GLY A   2 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR A   7 " --> pdb=" O   LEU A   3 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE A   8 " --> pdb=" O   TYR A   4 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLU A   9 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 32
    Processing helix  chain 'A' and resid 35 through 42
    Processing helix  chain 'A' and resid 43 through 57
      removed outlier: 3.803A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 71
      removed outlier: 3.555A  pdb=" N   ILE A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 78
    Processing helix  chain 'A' and resid 79 through 108
      removed outlier: 3.597A  pdb=" N   LYS A  84 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
    Processing helix  chain 'A' and resid 141 through 149
      removed outlier: 3.661A  pdb=" N   LEU A 146 " --> pdb=" O   PRO A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 169
      removed outlier: 3.519A  pdb=" N   THR A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A 166 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 220
      removed outlier: 3.504A  pdb=" N   LYS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.519A  pdb=" N   HIS A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 246
      removed outlier: 4.081A  pdb=" N   GLY A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 255
    Processing helix  chain 'A' and resid 257 through 265
    Processing helix  chain 'A' and resid 265 through 276
    Processing helix  chain 'A' and resid 277 through 292
      Proline residue:  A 283  - end of helix
      removed outlier: 3.517A  pdb=" N   ALA A 289 " --> pdb=" O   THR A 285 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LYS A 290 " --> pdb=" O   MET A 286 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLU A 291 " --> pdb=" O   ARG A 287 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   MET A 292 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 300
    Processing helix  chain 'A' and resid 301 through 310
      removed outlier: 4.173A  pdb=" N   THR A 308 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 330
      removed outlier: 3.624A  pdb=" N   PHE A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 352
      removed outlier: 3.604A  pdb=" N   VAL A 342 " --> pdb=" O   GLN A 338 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 343 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 370
      removed outlier: 4.323A  pdb=" N   ILE A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   MET A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ALA A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   MET A 365 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   VAL A 366 " --> pdb=" O   MET A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 389
      removed outlier: 3.811A  pdb=" N   EFC A 385 " --> pdb=" O   ALA A 381 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A 389 " --> pdb=" O   EFC A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 417
      removed outlier: 3.554A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ARG A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   MET A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A 400 " --> pdb=" O   GLY A 396 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ASP A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 411 " --> pdb=" O   THR A 407 " (cutoff:3.500A)

    234 hydrogen bonds defined for protein.
    696 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: 0.41

  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:
        1.18 -     1.37: 986
        1.37 -     1.55: 2147
        1.55 -     1.73: 1
        1.73 -     1.92: 30
        1.92 -     2.10: 1
  Bond restraints: 3165
  Sorted by residual:
  bond pdb=" N   ILE A 309 "
       pdb=" CA  ILE A 309 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.036 1.19e-02 7.06e+03 8.97e+00
  bond pdb=" N   LEU A 305 "
       pdb=" CA  LEU A 305 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.20e+00
  bond pdb=" N   ASP A 312 "
       pdb=" CA  ASP A 312 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.10e+00
  bond pdb=" N   LEU A 316 "
       pdb=" CA  LEU A 316 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.72e+00
  bond pdb=" N   THR A 308 "
       pdb=" CA  THR A 308 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.28e-02 6.10e+03 5.65e+00
  ... (remaining 3160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 4212
        1.72 -     3.43: 88
        3.43 -     5.15: 11
        5.15 -     6.87: 3
        6.87 -     8.58: 1
  Bond angle restraints: 4315
  Sorted by residual:
  angle pdb=" CA  ILE A 309 "
        pdb=" C   ILE A 309 "
        pdb=" O   ILE A 309 "
      ideal   model   delta    sigma   weight residual
     120.95  117.68    3.27 1.04e+00 9.25e-01 9.87e+00
  angle pdb=" CB  EFC A 385 "
        pdb=" SG  EFC A 385 "
        pdb=" SD  EFC A 385 "
      ideal   model   delta    sigma   weight residual
     101.65  110.23   -8.58 3.00e+00 1.11e-01 8.19e+00
  angle pdb=" N   LEU A 316 "
        pdb=" CA  LEU A 316 "
        pdb=" C   LEU A 316 "
      ideal   model   delta    sigma   weight residual
     111.28  108.43    2.85 1.09e+00 8.42e-01 6.83e+00
  angle pdb=" CA  ALA A 307 "
        pdb=" C   ALA A 307 "
        pdb=" O   ALA A 307 "
      ideal   model   delta    sigma   weight residual
     120.55  117.93    2.62 1.06e+00 8.90e-01 6.10e+00
  angle pdb=" O   GLY A 313 "
        pdb=" C   GLY A 313 "
        pdb=" N   THR A 314 "
      ideal   model   delta    sigma   weight residual
     122.19  124.55   -2.36 9.60e-01 1.09e+00 6.04e+00
  ... (remaining 4310 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.18: 1773
       15.18 -    30.36: 64
       30.36 -    45.54: 11
       45.54 -    60.73: 2
       60.73 -    75.91: 3
  Dihedral angle restraints: 1853
    sinusoidal: 670
      harmonic: 1183
  Sorted by residual:
  dihedral pdb=" CB  MET A 362 "
           pdb=" CG  MET A 362 "
           pdb=" SD  MET A 362 "
           pdb=" CE  MET A 362 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  102.25  -42.25     3      1.50e+01 4.44e-03 7.58e+00
  dihedral pdb=" N   LEU A  91 "
           pdb=" CA  LEU A  91 "
           pdb=" CB  LEU A  91 "
           pdb=" CG  LEU A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -94.69   34.69     3      1.50e+01 4.44e-03 5.89e+00
  dihedral pdb=" N   LEU A  78 "
           pdb=" CA  LEU A  78 "
           pdb=" CB  LEU A  78 "
           pdb=" CG  LEU A  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -145.57  -34.43     3      1.50e+01 4.44e-03 5.83e+00
  ... (remaining 1850 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 368
       0.034 -    0.068: 134
       0.068 -    0.101: 29
       0.101 -    0.135: 7
       0.135 -    0.169: 2
  Chirality restraints: 540
  Sorted by residual:
  chirality pdb=" CA  LEU A 305 "
            pdb=" N   LEU A 305 "
            pdb=" C   LEU A 305 "
            pdb=" CB  LEU A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CA  LEU A 316 "
            pdb=" N   LEU A 316 "
            pdb=" C   LEU A 316 "
            pdb=" CB  LEU A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  MET A 311 "
            pdb=" N   MET A 311 "
            pdb=" C   MET A 311 "
            pdb=" CB  MET A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.13 2.00e-01 2.50e+01 4.55e-01
  ... (remaining 537 not shown)

  Planarity restraints: 532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 376 "    0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO A 377 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 377 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 377 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 205 "   -0.020 5.00e-02 4.00e+02   2.96e-02 1.41e+00
        pdb=" N   PRO A 206 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 206 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 206 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  10 "   -0.018 5.00e-02 4.00e+02   2.78e-02 1.23e+00
        pdb=" N   PRO A  11 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A  11 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A  11 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 529 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 31
        2.67 -     3.23: 3207
        3.23 -     3.78: 4555
        3.78 -     4.34: 6229
        4.34 -     4.90: 10179
  Nonbonded interactions: 24201
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 310 "
            pdb="NA    NA A 502 "
     model   vdw
     2.111 2.470
  nonbonded pdb=" O   THR A 308 "
            pdb="NA    NA A 503 "
     model   vdw
     2.229 2.470
  nonbonded pdb=" OD1 ASP A 312 "
            pdb="NA    NA A 504 "
     model   vdw
     2.238 2.470
  nonbonded pdb=" N   GLY A 359 "
            pdb=" OD2 ASP A 501 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   ALA A 348 "
            pdb=" OG1 THR A 352 "
     model   vdw
     2.389 3.040
  ... (remaining 24196 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:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.650
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3165  Z= 0.206
  Angle     :  0.566   8.583   4315  Z= 0.326
  Chirality :  0.039   0.169    540
  Planarity :  0.004   0.030    532
  Dihedral  :  9.131  75.906   1103
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  2.34 (0.40), residues: 412
  helix:  1.83 (0.27), residues: 328
  sheet:  None (None), residues: 0
  loop :  0.64 (0.76), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 287 
 TYR   0.017   0.001   TYR A  89 
 PHE   0.006   0.001   PHE A 122 
 HIS   0.002   0.000   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3165)
  covalent geometry    : angle       0.56555 ( 4315)
  hydrogen bonds       : bond        0.28275 (  234)
  hydrogen bonds       : angle       6.28178 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7573 (mmt-90)
REVERT: A  121 GLN cc_start: 0.9068 (mt0) cc_final: 0.8747 (mt0)
REVERT: A  291 GLU cc_start: 0.8584 (mp0) cc_final: 0.8340 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.6261
  time to fit residues: 36.4952
Evaluate side-chains
  40 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.090924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.063575 restraints weight = 6151.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 2.64
r_work: 0.2674 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3165  Z= 0.207
  Angle     :  0.624   7.585   4315  Z= 0.330
  Chirality :  0.042   0.130    540
  Planarity :  0.005   0.039    532
  Dihedral  :  4.489  45.904    445
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  :  9.26 %
    Favored  : 87.35 %
  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:  3.06 (0.41), residues: 412
  helix:  2.26 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop :  1.21 (0.77), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  80 
 TYR   0.021   0.002   TYR A  89 
 PHE   0.014   0.002   PHE A  50 
 HIS   0.002   0.001   HIS A 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 3165)
  covalent geometry    : angle       0.62381 ( 4315)
  hydrogen bonds       : bond        0.08030 (  234)
  hydrogen bonds       : angle       4.60654 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7537 (mmt90) cc_final: 0.6675 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8518 (mp0) cc_final: 0.7823 (mp0)
REVERT: A  125 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.8713 (t-90)
REVERT: A  291 GLU cc_start: 0.8645 (mp0) cc_final: 0.8356 (mp0)
REVERT: A  296 GLU cc_start: 0.8992 (tp30) cc_final: 0.8655 (tp30)
  outliers start: 11
  outliers final: 6
  residues processed: 41
  average time/residue: 0.6588
  time to fit residues: 27.6301
Evaluate side-chains
  37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  390 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0970
   chunk 37 optimal weight:    0.0270
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.5036

-------------------------------------------------------------------------------
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 = 0.3375 r_free = 0.3375 target = 0.094913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.068330 restraints weight = 6075.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 2.58
r_work: 0.2766 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3165  Z= 0.131
  Angle     :  0.511   7.924   4315  Z= 0.263
  Chirality :  0.037   0.136    540
  Planarity :  0.004   0.035    532
  Dihedral  :  4.153  30.527    445
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.11 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.47 (0.42), residues: 412
  helix:  2.59 (0.28), residues: 337
  sheet:  None (None), residues: 0
  loop :  1.00 (0.79), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 177 
 TYR   0.016   0.001   TYR A 299 
 PHE   0.009   0.001   PHE A 156 
 HIS   0.001   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 3165)
  covalent geometry    : angle       0.51114 ( 4315)
  hydrogen bonds       : bond        0.05373 (  234)
  hydrogen bonds       : angle       4.07707 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7581 (mmt90) cc_final: 0.6759 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8564 (mp0) cc_final: 0.7847 (mp0)
REVERT: A  291 GLU cc_start: 0.8703 (mp0) cc_final: 0.8339 (mp0)
REVERT: A  296 GLU cc_start: 0.8959 (tp30) cc_final: 0.8689 (tp30)
  outliers start: 7
  outliers final: 2
  residues processed: 40
  average time/residue: 0.6026
  time to fit residues: 24.7293
Evaluate side-chains
  34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  113 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 28 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0870
   overall best weight:    0.7358

-------------------------------------------------------------------------------
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 = 0.3358 r_free = 0.3358 target = 0.093614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.066532 restraints weight = 6097.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 2.63
r_work: 0.2730 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3165  Z= 0.132
  Angle     :  0.526   8.405   4315  Z= 0.264
  Chirality :  0.038   0.119    540
  Planarity :  0.004   0.034    532
  Dihedral  :  3.975  26.464    445
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.35 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.57 (0.41), residues: 412
  helix:  2.66 (0.28), residues: 337
  sheet:  None (None), residues: 0
  loop :  1.01 (0.77), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  80 
 TYR   0.015   0.001   TYR A 299 
 PHE   0.010   0.001   PHE A 301 
 HIS   0.001   0.000   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3165)
  covalent geometry    : angle       0.52613 ( 4315)
  hydrogen bonds       : bond        0.05358 (  234)
  hydrogen bonds       : angle       4.00448 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7606 (mmt90) cc_final: 0.6820 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8558 (mp0) cc_final: 0.7838 (mp0)
REVERT: A  291 GLU cc_start: 0.8693 (mp0) cc_final: 0.8290 (mp0)
REVERT: A  296 GLU cc_start: 0.8968 (tp30) cc_final: 0.8693 (tp30)
  outliers start: 5
  outliers final: 1
  residues processed: 38
  average time/residue: 0.6311
  time to fit residues: 24.5355
Evaluate side-chains
  32 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.093711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.066604 restraints weight = 6105.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.63
r_work: 0.2733 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3165  Z= 0.129
  Angle     :  0.519   8.641   4315  Z= 0.260
  Chirality :  0.037   0.118    540
  Planarity :  0.004   0.033    532
  Dihedral  :  3.971  27.753    445
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 11.11 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.48 (0.41), residues: 412
  helix:  2.62 (0.28), residues: 343
  sheet:  None (None), residues: 0
  loop :  0.69 (0.77), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  80 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.009   0.001   PHE A 156 
 HIS   0.001   0.000   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3165)
  covalent geometry    : angle       0.51878 ( 4315)
  hydrogen bonds       : bond        0.05125 (  234)
  hydrogen bonds       : angle       3.91078 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7597 (mmt90) cc_final: 0.6818 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8476 (mp0) cc_final: 0.7735 (mp0)
REVERT: A  291 GLU cc_start: 0.8735 (mp0) cc_final: 0.8404 (mp0)
REVERT: A  296 GLU cc_start: 0.8942 (tp30) cc_final: 0.8658 (tp30)
  outliers start: 9
  outliers final: 4
  residues processed: 37
  average time/residue: 0.6878
  time to fit residues: 26.0717
Evaluate side-chains
  34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  292 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3334 r_free = 0.3334 target = 0.092072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.064960 restraints weight = 6100.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.61
r_work: 0.2698 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3165  Z= 0.154
  Angle     :  0.548   8.673   4315  Z= 0.275
  Chirality :  0.038   0.121    540
  Planarity :  0.004   0.034    532
  Dihedral  :  3.965  27.193    445
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.65 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.41 (0.41), residues: 412
  helix:  2.59 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop :  0.71 (0.73), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  80 
 TYR   0.016   0.001   TYR A 383 
 PHE   0.016   0.002   PHE A 261 
 HIS   0.001   0.000   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3165)
  covalent geometry    : angle       0.54846 ( 4315)
  hydrogen bonds       : bond        0.05738 (  234)
  hydrogen bonds       : angle       3.96731 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7662 (mmt90) cc_final: 0.6961 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8376 (mp0) cc_final: 0.7627 (mp0)
REVERT: A  120 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8569 (tp-100)
REVERT: A  291 GLU cc_start: 0.8730 (mp0) cc_final: 0.8367 (mp0)
REVERT: A  296 GLU cc_start: 0.8946 (tp30) cc_final: 0.8656 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 35
  average time/residue: 0.7485
  time to fit residues: 26.7169
Evaluate side-chains
  33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  245 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0270
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.094548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.067561 restraints weight = 6167.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 2.63
r_work: 0.2751 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3165  Z= 0.119
  Angle     :  0.509   8.927   4315  Z= 0.256
  Chirality :  0.037   0.120    540
  Planarity :  0.004   0.033    532
  Dihedral  :  3.938  28.146    445
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.65 %
    Favored  : 84.88 %
  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:  3.64 (0.41), residues: 412
  helix:  2.74 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop :  0.84 (0.71), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  80 
 TYR   0.012   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 156 
 HIS   0.001   0.000   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3165)
  covalent geometry    : angle       0.50935 ( 4315)
  hydrogen bonds       : bond        0.04661 (  234)
  hydrogen bonds       : angle       3.80615 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7670 (mmt90) cc_final: 0.6976 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8326 (mp0) cc_final: 0.7608 (mp0)
REVERT: A  120 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8593 (tp-100)
REVERT: A  287 ARG cc_start: 0.9012 (tmm-80) cc_final: 0.8711 (tmm-80)
REVERT: A  291 GLU cc_start: 0.8756 (mp0) cc_final: 0.8366 (mp0)
REVERT: A  296 GLU cc_start: 0.8974 (tp30) cc_final: 0.8669 (tp30)
  outliers start: 8
  outliers final: 4
  residues processed: 40
  average time/residue: 0.6883
  time to fit residues: 28.2177
Evaluate side-chains
  36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  374 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.091323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.063926 restraints weight = 6236.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.64
r_work: 0.2685 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3165  Z= 0.174
  Angle     :  0.573   8.845   4315  Z= 0.287
  Chirality :  0.040   0.197    540
  Planarity :  0.004   0.034    532
  Dihedral  :  3.959  28.567    445
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.27 %
    Favored  : 84.26 %
  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:  3.47 (0.41), residues: 412
  helix:  2.60 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop :  0.88 (0.71), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  80 
 TYR   0.017   0.001   TYR A 383 
 PHE   0.015   0.002   PHE A 261 
 HIS   0.002   0.000   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 3165)
  covalent geometry    : angle       0.57333 ( 4315)
  hydrogen bonds       : bond        0.05847 (  234)
  hydrogen bonds       : angle       3.98809 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7706 (mmt90) cc_final: 0.7015 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8269 (mp0) cc_final: 0.7531 (mp0)
REVERT: A   77 ARG cc_start: 0.8138 (ptp-170) cc_final: 0.7875 (ptp-170)
REVERT: A  120 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8572 (tp-100)
REVERT: A  291 GLU cc_start: 0.8753 (mp0) cc_final: 0.8444 (mp0)
REVERT: A  296 GLU cc_start: 0.8972 (tp30) cc_final: 0.8679 (tp30)
  outliers start: 8
  outliers final: 1
  residues processed: 38
  average time/residue: 0.6995
  time to fit residues: 27.1885
Evaluate side-chains
  32 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0170
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.3367 r_free = 0.3367 target = 0.094125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.067270 restraints weight = 6202.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 2.64
r_work: 0.2750 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3165  Z= 0.123
  Angle     :  0.542   8.962   4315  Z= 0.270
  Chirality :  0.039   0.277    540
  Planarity :  0.004   0.033    532
  Dihedral  :  3.916  26.678    445
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 14.81 %
    Favored  : 84.26 %
  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:  3.58 (0.41), residues: 412
  helix:  2.69 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop :  0.85 (0.71), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  80 
 TYR   0.013   0.001   TYR A 299 
 PHE   0.014   0.001   PHE A 261 
 HIS   0.001   0.000   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3165)
  covalent geometry    : angle       0.54244 ( 4315)
  hydrogen bonds       : bond        0.04771 (  234)
  hydrogen bonds       : angle       3.85760 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7689 (mmt90) cc_final: 0.6974 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8240 (mp0) cc_final: 0.7497 (mp0)
REVERT: A  120 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8576 (tp-100)
REVERT: A  287 ARG cc_start: 0.9011 (tmm-80) cc_final: 0.8733 (tmm-80)
REVERT: A  291 GLU cc_start: 0.8782 (mp0) cc_final: 0.8433 (mp0)
REVERT: A  296 GLU cc_start: 0.8987 (tp30) cc_final: 0.8675 (tp30)
  outliers start: 3
  outliers final: 2
  residues processed: 37
  average time/residue: 0.7252
  time to fit residues: 27.4210
Evaluate side-chains
  36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    0.4980
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0010
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 242 GLN
A 338 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.095332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.068762 restraints weight = 6149.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.64
r_work: 0.2774 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3165  Z= 0.120
  Angle     :  0.556   9.007   4315  Z= 0.271
  Chirality :  0.039   0.264    540
  Planarity :  0.004   0.032    532
  Dihedral  :  3.793  25.681    445
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.12 %
    Favored  : 83.64 %
  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:  3.72 (0.41), residues: 412
  helix:  2.76 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop :  1.05 (0.74), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  80 
 TYR   0.012   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3165)
  covalent geometry    : angle       0.55605 ( 4315)
  hydrogen bonds       : bond        0.04384 (  234)
  hydrogen bonds       : angle       3.76600 (  696)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7696 (mmt90) cc_final: 0.7001 (mmt-90)
REVERT: A    9 GLU cc_start: 0.8237 (mp0) cc_final: 0.7529 (mp0)
REVERT: A   77 ARG cc_start: 0.8098 (ptp-170) cc_final: 0.7804 (ptm160)
REVERT: A  120 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8565 (tp-100)
REVERT: A  287 ARG cc_start: 0.9038 (tmm-80) cc_final: 0.8738 (tmm-80)
REVERT: A  291 GLU cc_start: 0.8800 (mp0) cc_final: 0.8385 (mp0)
  outliers start: 4
  outliers final: 2
  residues processed: 42
  average time/residue: 0.7016
  time to fit residues: 30.1091
Evaluate side-chains
  38 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3365 r_free = 0.3365 target = 0.093789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.066685 restraints weight = 6296.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 2.64
r_work: 0.2753 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3165  Z= 0.136
  Angle     :  0.561   8.979   4315  Z= 0.280
  Chirality :  0.039   0.265    540
  Planarity :  0.004   0.033    532
  Dihedral  :  3.754  24.258    445
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 15.74 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.72 (0.41), residues: 412
  helix:  2.74 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop :  1.15 (0.73), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  80 
 TYR   0.012   0.001   TYR A 299 
 PHE   0.015   0.001   PHE A 261 
 HIS   0.001   0.000   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3165)
  covalent geometry    : angle       0.56118 ( 4315)
  hydrogen bonds       : bond        0.04864 (  234)
  hydrogen bonds       : angle       3.82070 (  696)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1182.46 seconds
wall clock time: 20 minutes 49.72 seconds (1249.72 seconds total)