Starting phenix.real_space_refine
on Thu Oct 22 17:55:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/26qf_80823/10_2026/26qf_80823.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/26qf_80823/10_2026/26qf_80823.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/26qf_80823/10_2026/26qf_80823.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/26qf_80823/10_2026/26qf_80823.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/26qf_80823/10_2026/26qf_80823.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/26qf_80823/10_2026/26qf_80823.cif"
  }
  resolution = 3.22
  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=   0.082
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      27      5.16       5
     C    1988      2.51       5
     N     497      2.21       5
     O     518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3030
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 3030
          Classifications: {'peptide': 378}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 15, 'TRANS': 362}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 0.87, per 1000 atoms: 0.29
  Number of scatterers: 3030
  At special positions: 0
  Unit cell: (62.624, 59.328, 84.872, 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      27     16.00
     O     518      8.00
     N     497      7.00
     C    1988      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 115.4 milliseconds
  

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  706

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 3 sheets defined
      60.8% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 36
    Processing helix  chain 'A' and resid 65 through 75
    Processing helix  chain 'A' and resid 93 through 105
    Processing helix  chain 'A' and resid 122 through 134
      Proline residue:  A 130  - end of helix
    Processing helix  chain 'A' and resid 152 through 160
      removed outlier: 3.726A  pdb=" N   ASP A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 204
      removed outlier: 3.560A  pdb=" N   THR A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   HIS A 193 " --> pdb=" O   PHE A 189 " (cutoff:3.500A)
      Proline residue:  A 194  - end of helix
      removed outlier: 3.713A  pdb=" N   SER A 199 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 227 through 231
      removed outlier: 4.133A  pdb=" N   GLN A 231 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 242
      removed outlier: 3.744A  pdb=" N   ALA A 240 " --> pdb=" O   ASP A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 246
    Processing helix  chain 'A' and resid 265 through 284
    Processing helix  chain 'A' and resid 286 through 294
      Proline residue:  A 292  - end of helix
    Processing helix  chain 'A' and resid 295 through 311
    Processing helix  chain 'A' and resid 314 through 339
    Processing helix  chain 'A' and resid 345 through 370
      removed outlier: 4.459A  pdb=" N   ILE A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   TYR A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASP A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114
      removed outlier: 8.468A  pdb=" N   ARG A 111 " --> pdb=" O   TYR A  81 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   VAL A  83 " --> pdb=" O   ARG A 111 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   PHE A 113 " --> pdb=" O   VAL A  83 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU A  85 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A  53 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU A  84 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU A  55 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   CYS A  86 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LYS A  57 " --> pdb=" O   CYS A  86 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   CYS A 143 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   LEU A 167 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148
      removed outlier: 3.807A  pdb=" N   MET A 258 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   TYR A 173 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 373 through 374

    166 hydrogen bonds defined for protein.
    489 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: 0.31

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 933
        1.35 -     1.46: 786
        1.46 -     1.58: 1349
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 3112
  Sorted by residual:
  bond pdb=" C   THR A 377 "
       pdb=" N   GLY A 378 "
    ideal  model  delta    sigma   weight residual
    1.329  1.319  0.010 1.24e-02 6.50e+03 6.65e-01
  bond pdb=" CB  MET A 283 "
       pdb=" CG  MET A 283 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 3.00e-02 1.11e+03 4.85e-01
  bond pdb=" C   ILE A 114 "
       pdb=" N   GLY A 115 "
    ideal  model  delta    sigma   weight residual
    1.328  1.335 -0.007 1.22e-02 6.72e+03 3.50e-01
  bond pdb=" C   MET A 129 "
       pdb=" N   PRO A 130 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.007 1.28e-02 6.10e+03 3.20e-01
  bond pdb=" CA  MET A 129 "
       pdb=" C   MET A 129 "
    ideal  model  delta    sigma   weight residual
    1.520  1.527 -0.006 1.23e-02 6.61e+03 2.76e-01
  ... (remaining 3107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 4063
        1.04 -     2.09: 130
        2.09 -     3.13: 19
        3.13 -     4.18: 2
        4.18 -     5.22: 6
  Bond angle restraints: 4220
  Sorted by residual:
  angle pdb=" N   LYS A  60 "
        pdb=" CA  LYS A  60 "
        pdb=" C   LYS A  60 "
      ideal   model   delta    sigma   weight residual
     107.49  110.28   -2.79 1.74e+00 3.30e-01 2.58e+00
  angle pdb=" CA  LEU A   3 "
        pdb=" CB  LEU A   3 "
        pdb=" CG  LEU A   3 "
      ideal   model   delta    sigma   weight residual
     116.30  121.52   -5.22 3.50e+00 8.16e-02 2.23e+00
  angle pdb=" CB  MET A 283 "
        pdb=" CG  MET A 283 "
        pdb=" SD  MET A 283 "
      ideal   model   delta    sigma   weight residual
     112.70  117.14   -4.44 3.00e+00 1.11e-01 2.19e+00
  angle pdb=" NE  ARG A 376 "
        pdb=" CZ  ARG A 376 "
        pdb=" NH1 ARG A 376 "
      ideal   model   delta    sigma   weight residual
     121.50  120.05    1.45 1.00e+00 1.00e+00 2.10e+00
  angle pdb=" NE  ARG A 280 "
        pdb=" CZ  ARG A 280 "
        pdb=" NH1 ARG A 280 "
      ideal   model   delta    sigma   weight residual
     121.50  120.06    1.44 1.00e+00 1.00e+00 2.09e+00
  ... (remaining 4215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 1655
       17.75 -    35.50: 119
       35.50 -    53.26: 37
       53.26 -    71.01: 5
       71.01 -    88.76: 2
  Dihedral angle restraints: 1818
    sinusoidal: 718
      harmonic: 1100
  Sorted by residual:
  dihedral pdb=" CA  ASP A  89 "
           pdb=" CB  ASP A  89 "
           pdb=" CG  ASP A  89 "
           pdb=" OD1 ASP A  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.37   53.37     1      2.00e+01 2.50e-03 9.68e+00
  dihedral pdb=" N   MET A 211 "
           pdb=" CA  MET A 211 "
           pdb=" CB  MET A 211 "
           pdb=" CG  MET A 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.05   56.05     3      1.50e+01 4.44e-03 9.38e+00
  dihedral pdb=" CA  ARG A 379 "
           pdb=" CB  ARG A 379 "
           pdb=" CG  ARG A 379 "
           pdb=" CD  ARG A 379 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.40   50.40     3      1.50e+01 4.44e-03 8.90e+00
  ... (remaining 1815 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 292
       0.024 -    0.048: 89
       0.048 -    0.072: 47
       0.072 -    0.096: 27
       0.096 -    0.120: 11
  Chirality restraints: 466
  Sorted by residual:
  chirality pdb=" CA  ILE A 114 "
            pdb=" N   ILE A 114 "
            pdb=" C   ILE A 114 "
            pdb=" CB  ILE A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.60e-01
  chirality pdb=" CA  ILE A 142 "
            pdb=" N   ILE A 142 "
            pdb=" C   ILE A 142 "
            pdb=" CB  ILE A 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.45e-01
  chirality pdb=" CA  PRO A 151 "
            pdb=" N   PRO A 151 "
            pdb=" C   PRO A 151 "
            pdb=" CB  PRO A 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.02e-01
  ... (remaining 463 not shown)

  Planarity restraints: 522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  92 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO A  93 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 150 "   -0.017 5.00e-02 4.00e+02   2.58e-02 1.07e+00
        pdb=" N   PRO A 151 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 151 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 151 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  78 "    0.014 5.00e-02 4.00e+02   2.17e-02 7.56e-01
        pdb=" N   PRO A  79 "   -0.038 5.00e-02 4.00e+02
        pdb=" CA  PRO A  79 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A  79 "    0.012 5.00e-02 4.00e+02
  ... (remaining 519 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1055
        2.86 -     3.37: 2892
        3.37 -     3.88: 5073
        3.88 -     4.39: 5380
        4.39 -     4.90: 9712
  Nonbonded interactions: 24112
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 178 "
            pdb=" OH  TYR A 264 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" NE2 GLN A 186 "
            pdb=" OE1 GLN A 338 "
     model   vdw
     2.414 3.120
  nonbonded pdb=" OG  SER A 300 "
            pdb=" ND1 HIS A 322 "
     model   vdw
     2.423 3.120
  nonbonded pdb=" OG  SER A 345 "
            pdb=" OD2 ASP A 348 "
     model   vdw
     2.429 3.040
  nonbonded pdb=" OG  SER A  54 "
            pdb=" OE2 GLU A  82 "
     model   vdw
     2.450 3.040
  ... (remaining 24107 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     4.150
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
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      :  0.002   0.021   3112  Z= 0.102
  Angle     :  0.467   5.223   4220  Z= 0.277
  Chirality :  0.037   0.120    466
  Planarity :  0.003   0.037    522
  Dihedral  : 13.563  88.761   1112
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.05 %
    Favored  : 91.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.40), residues: 374
  helix:  0.66 (0.33), residues: 213
  sheet: -1.43 (0.68), residues: 47
  loop : -1.88 (0.48), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 111 
 TYR   0.005   0.000   TYR A 349 
 PHE   0.012   0.001   PHE A  19 
 TRP   0.009   0.001   TRP A 375 
 HIS   0.001   0.000   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00171 /  0.10 ( 3112)
  covalent geometry    : angle       0.46708 /  0.28 ( 4220)
  hydrogen bonds       : bond        0.11741 /  7.53 (  166)
  hydrogen bonds       : angle       4.38604 /  3.07 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7034 (mm)
REVERT: A  150 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7809 (pt)
REVERT: A  232 TYR cc_start: 0.7939 (m-80) cc_final: 0.7647 (m-10)
REVERT: A  273 MET cc_start: 0.8022 (mmm) cc_final: 0.7820 (mmp)
  outliers start: 3
  outliers final: 1
  residues processed: 91
  average time/residue: 0.0496
  time to fit residues: 5.6250
Evaluate side-chains
  76 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  150 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 13]
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  65 ASN
A 107 ASN
A 178 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.168450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.126801 restraints weight = 3679.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.44
r_work: 0.3254 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3112  Z= 0.131
  Angle     :  0.524   7.834   4220  Z= 0.258
  Chirality :  0.041   0.120    466
  Planarity :  0.004   0.042    522
  Dihedral  :  3.812  27.616    416
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.41 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.42), residues: 374
  helix:  1.73 (0.34), residues: 220
  sheet: -1.66 (0.65), residues: 47
  loop : -1.69 (0.51), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 356 
 TYR   0.011   0.001   TYR A 331 
 PHE   0.022   0.002   PHE A 311 
 TRP   0.012   0.001   TRP A  23 
 HIS   0.004   0.001   HIS A  36 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 3112)
  covalent geometry    : angle       0.52433 /  0.26 ( 4220)
  hydrogen bonds       : bond        0.03381 /  2.27 (  166)
  hydrogen bonds       : angle       3.35587 /  2.39 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 PHE cc_start: 0.8557 (m-80) cc_final: 0.8058 (m-80)
REVERT: A  129 MET cc_start: 0.8021 (mmm) cc_final: 0.7479 (tpt)
REVERT: A  133 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7466 (mm-30)
REVERT: A  144 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7412 (t0)
REVERT: A  232 TYR cc_start: 0.7694 (m-80) cc_final: 0.7355 (m-10)
REVERT: A  261 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8654 (p)
REVERT: A  273 MET cc_start: 0.7920 (mmm) cc_final: 0.7557 (mmp)
REVERT: A  359 MET cc_start: 0.7031 (ttt) cc_final: 0.6767 (ttt)
  outliers start: 10
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0430
  time to fit residues: 3.4513
Evaluate side-chains
  66 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [32, 16, 35, 25, 28, 26, 10, 8, 7, 11, 30]
   chunk 32 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 28 optimal weight:    0.4980
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.5980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.167888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.126704 restraints weight = 3635.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.40
r_work: 0.3253 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3112  Z= 0.104
  Angle     :  0.481   6.269   4220  Z= 0.232
  Chirality :  0.040   0.120    466
  Planarity :  0.003   0.041    522
  Dihedral  :  3.443  25.405    412
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.96 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.43), residues: 374
  helix:  2.15 (0.35), residues: 220
  sheet: -1.66 (0.64), residues: 47
  loop : -1.46 (0.54), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 356 
 TYR   0.008   0.001   TYR A 349 
 PHE   0.011   0.001   PHE A 327 
 TRP   0.013   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.10 ( 3112)
  covalent geometry    : angle       0.48073 /  0.23 ( 4220)
  hydrogen bonds       : bond        0.03018 /  2.02 (  166)
  hydrogen bonds       : angle       3.21855 /  2.30 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 PHE cc_start: 0.8581 (m-80) cc_final: 0.8122 (m-80)
REVERT: A  133 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7677 (mm-30)
REVERT: A  232 TYR cc_start: 0.7776 (m-80) cc_final: 0.7421 (m-10)
REVERT: A  273 MET cc_start: 0.7881 (mmm) cc_final: 0.7554 (mmp)
REVERT: A  283 MET cc_start: 0.8147 (mmp) cc_final: 0.7619 (mtm)
REVERT: A  359 MET cc_start: 0.7182 (ttt) cc_final: 0.6850 (ttt)
  outliers start: 10
  outliers final: 5
  residues processed: 60
  average time/residue: 0.0432
  time to fit residues: 3.4752
Evaluate side-chains
  59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [27, 30, 20, 14, 7, 26, 5, 16, 34, 22, 9]
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0870
   chunk 20 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0870
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5736

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.178782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.140316 restraints weight = 3609.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.31
r_work: 0.3456 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3112  Z= 0.103
  Angle     :  0.479   6.660   4220  Z= 0.235
  Chirality :  0.040   0.119    466
  Planarity :  0.003   0.037    522
  Dihedral  :  3.392  24.653    412
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 21.05 %
    Favored  : 76.47 %
  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:  1.29 (0.44), residues: 374
  helix:  2.54 (0.35), residues: 209
  sheet: -1.63 (0.66), residues: 47
  loop : -1.23 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 356 
 TYR   0.008   0.001   TYR A 349 
 PHE   0.012   0.001   PHE A 327 
 TRP   0.012   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.10 ( 3112)
  covalent geometry    : angle       0.47887 /  0.23 ( 4220)
  hydrogen bonds       : bond        0.03071 /  2.05 (  166)
  hydrogen bonds       : angle       3.19004 /  2.28 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 PHE cc_start: 0.8679 (m-80) cc_final: 0.8250 (m-80)
REVERT: A  129 MET cc_start: 0.8129 (mmm) cc_final: 0.7782 (mmm)
REVERT: A  133 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7802 (mm-30)
REVERT: A  232 TYR cc_start: 0.7882 (m-80) cc_final: 0.7550 (m-10)
REVERT: A  273 MET cc_start: 0.8051 (mmm) cc_final: 0.7731 (mmp)
REVERT: A  359 MET cc_start: 0.7347 (ttt) cc_final: 0.6987 (ttt)
  outliers start: 8
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0370
  time to fit residues: 2.6570
Evaluate side-chains
  55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [36, 11, 8, 16, 18, 17, 6, 20, 7, 0, 12]
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 17 optimal weight:    0.0770
   chunk 6 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6342

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.180336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.142216 restraints weight = 3613.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.32
r_work: 0.3449 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3112  Z= 0.107
  Angle     :  0.483   7.019   4220  Z= 0.235
  Chirality :  0.040   0.119    466
  Planarity :  0.003   0.036    522
  Dihedral  :  3.382  25.203    412
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.05 %
    Favored  : 76.16 %
  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:  1.41 (0.44), residues: 374
  helix:  2.66 (0.35), residues: 209
  sheet: -1.62 (0.67), residues: 47
  loop : -1.21 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 356 
 TYR   0.008   0.001   TYR A  32 
 PHE   0.013   0.001   PHE A 327 
 TRP   0.012   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 3112)
  covalent geometry    : angle       0.48322 /  0.23 ( 4220)
  hydrogen bonds       : bond        0.03105 /  2.07 (  166)
  hydrogen bonds       : angle       3.18944 /  2.27 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6940 (mp0)
REVERT: A  113 PHE cc_start: 0.8674 (m-80) cc_final: 0.8261 (m-80)
REVERT: A  133 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7724 (mm-30)
REVERT: A  232 TYR cc_start: 0.7885 (m-80) cc_final: 0.7584 (m-10)
REVERT: A  273 MET cc_start: 0.8026 (mmm) cc_final: 0.7700 (mmp)
REVERT: A  359 MET cc_start: 0.7382 (ttt) cc_final: 0.7076 (ttt)
  outliers start: 9
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0490
  time to fit residues: 3.5413
Evaluate side-chains
  57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [1, 0, 4, 11, 23, 29, 31, 35, 6, 25, 10]
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.179582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.141342 restraints weight = 3628.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.32
r_work: 0.3435 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3112  Z= 0.115
  Angle     :  0.491   6.947   4220  Z= 0.240
  Chirality :  0.040   0.121    466
  Planarity :  0.003   0.035    522
  Dihedral  :  3.424  25.502    412
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.12 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.45), residues: 374
  helix:  2.76 (0.35), residues: 208
  sheet: -1.64 (0.68), residues: 47
  loop : -1.20 (0.55), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 280 
 TYR   0.009   0.001   TYR A 349 
 PHE   0.013   0.001   PHE A 327 
 TRP   0.013   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 3112)
  covalent geometry    : angle       0.49103 /  0.24 ( 4220)
  hydrogen bonds       : bond        0.03253 /  2.17 (  166)
  hydrogen bonds       : angle       3.23702 /  2.30 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7071 (mp0)
REVERT: A  113 PHE cc_start: 0.8651 (m-80) cc_final: 0.8253 (m-80)
REVERT: A  129 MET cc_start: 0.8198 (mmm) cc_final: 0.7855 (mmm)
REVERT: A  133 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7831 (mm-30)
REVERT: A  232 TYR cc_start: 0.7796 (m-80) cc_final: 0.7467 (m-10)
REVERT: A  273 MET cc_start: 0.8018 (mmm) cc_final: 0.7708 (mmp)
REVERT: A  359 MET cc_start: 0.7407 (ttt) cc_final: 0.7039 (ttt)
  outliers start: 14
  outliers final: 7
  residues processed: 58
  average time/residue: 0.0415
  time to fit residues: 3.1021
Evaluate side-chains
  58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [14, 29, 10, 2, 24, 35, 31, 7, 17, 21, 30]
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  88 GLN
A 270 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.174785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.136055 restraints weight = 3685.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.30
r_work: 0.3318 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3112  Z= 0.161
  Angle     :  0.539   7.094   4220  Z= 0.266
  Chirality :  0.042   0.123    466
  Planarity :  0.003   0.035    522
  Dihedral  :  3.629  26.475    412
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.36 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.45), residues: 374
  helix:  2.66 (0.36), residues: 207
  sheet: -1.73 (0.67), residues: 47
  loop : -1.21 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 356 
 TYR   0.010   0.001   TYR A 349 
 PHE   0.015   0.001   PHE A 327 
 TRP   0.014   0.001   TRP A  23 
 HIS   0.004   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.16 ( 3112)
  covalent geometry    : angle       0.53882 /  0.27 ( 4220)
  hydrogen bonds       : bond        0.03695 /  2.43 (  166)
  hydrogen bonds       : angle       3.43034 /  2.44 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7158 (mp0)
REVERT: A  113 PHE cc_start: 0.8581 (m-80) cc_final: 0.8159 (m-80)
REVERT: A  129 MET cc_start: 0.8281 (mmm) cc_final: 0.7922 (mmm)
REVERT: A  133 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7805 (mm-30)
REVERT: A  232 TYR cc_start: 0.7629 (m-80) cc_final: 0.7170 (m-10)
REVERT: A  273 MET cc_start: 0.8052 (mmm) cc_final: 0.7748 (mmp)
REVERT: A  359 MET cc_start: 0.7531 (ttt) cc_final: 0.7125 (ttt)
  outliers start: 10
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0403
  time to fit residues: 2.9810
Evaluate side-chains
  52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [6, 22, 21, 12, 28, 5, 7, 30, 9, 18, 8]
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0370
   chunk 7 optimal weight:    0.0870
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.4436

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.180505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.142705 restraints weight = 3691.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.33
r_work: 0.3452 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3112  Z= 0.095
  Angle     :  0.500   6.948   4220  Z= 0.236
  Chirality :  0.040   0.125    466
  Planarity :  0.003   0.034    522
  Dihedral  :  3.401  25.173    412
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.29 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.45), residues: 374
  helix:  2.69 (0.36), residues: 208
  sheet: -1.60 (0.70), residues: 47
  loop : -1.16 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 356 
 TYR   0.010   0.001   TYR A 349 
 PHE   0.012   0.001   PHE A 327 
 TRP   0.012   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00211 /  0.10 ( 3112)
  covalent geometry    : angle       0.50015 /  0.24 ( 4220)
  hydrogen bonds       : bond        0.03033 /  2.02 (  166)
  hydrogen bonds       : angle       3.21635 /  2.29 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 HIS cc_start: 0.8660 (t-170) cc_final: 0.8265 (t-170)
REVERT: A   75 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7028 (mp0)
REVERT: A  113 PHE cc_start: 0.8690 (m-80) cc_final: 0.8371 (m-80)
REVERT: A  129 MET cc_start: 0.8317 (mmm) cc_final: 0.7963 (mmm)
REVERT: A  133 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7833 (mm-30)
REVERT: A  220 LEU cc_start: 0.8668 (mt) cc_final: 0.8463 (mp)
REVERT: A  232 TYR cc_start: 0.7668 (m-80) cc_final: 0.7302 (m-10)
REVERT: A  273 MET cc_start: 0.8003 (mmm) cc_final: 0.7704 (mmp)
REVERT: A  359 MET cc_start: 0.7418 (ttt) cc_final: 0.7091 (ttt)
  outliers start: 7
  outliers final: 6
  residues processed: 54
  average time/residue: 0.0472
  time to fit residues: 3.3039
Evaluate side-chains
  55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [19, 16, 10, 11, 26, 29, 5, 25, 36, 21, 28]
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0070
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0970
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.5398

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.178494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.140211 restraints weight = 3710.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.35
r_work: 0.3471 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3112  Z= 0.102
  Angle     :  0.511   7.570   4220  Z= 0.241
  Chirality :  0.040   0.123    466
  Planarity :  0.003   0.034    522
  Dihedral  :  3.363  25.195    412
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 21.67 %
    Favored  : 75.85 %
  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:  1.49 (0.45), residues: 374
  helix:  2.73 (0.36), residues: 208
  sheet: -1.51 (0.70), residues: 47
  loop : -1.19 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 356 
 TYR   0.009   0.001   TYR A 349 
 PHE   0.014   0.001   PHE A 327 
 TRP   0.012   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.10 ( 3112)
  covalent geometry    : angle       0.51130 /  0.24 ( 4220)
  hydrogen bonds       : bond        0.03094 /  2.06 (  166)
  hydrogen bonds       : angle       3.18637 /  2.26 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 HIS cc_start: 0.8650 (t-170) cc_final: 0.8234 (t-170)
REVERT: A   75 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7124 (mp0)
REVERT: A  113 PHE cc_start: 0.8744 (m-80) cc_final: 0.8366 (m-80)
REVERT: A  129 MET cc_start: 0.8323 (mmm) cc_final: 0.7966 (mmm)
REVERT: A  133 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: A  232 TYR cc_start: 0.7691 (m-80) cc_final: 0.7247 (m-10)
REVERT: A  273 MET cc_start: 0.8002 (mmm) cc_final: 0.7702 (mmp)
REVERT: A  359 MET cc_start: 0.7410 (ttt) cc_final: 0.7113 (ttt)
  outliers start: 8
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0449
  time to fit residues: 3.2781
Evaluate side-chains
  57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [14, 18, 32, 0, 1, 7, 24, 20, 22, 16, 3]
   chunk 14 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 32 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0370
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.5858

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.180531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.142585 restraints weight = 3611.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.33
r_work: 0.3477 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3112  Z= 0.105
  Angle     :  0.515   7.241   4220  Z= 0.243
  Chirality :  0.040   0.121    466
  Planarity :  0.003   0.034    522
  Dihedral  :  3.360  25.236    412
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.67 %
    Favored  : 76.16 %
  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:  1.45 (0.45), residues: 374
  helix:  2.68 (0.36), residues: 208
  sheet: -1.48 (0.71), residues: 47
  loop : -1.18 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 356 
 TYR   0.009   0.001   TYR A 349 
 PHE   0.014   0.001   PHE A 327 
 TRP   0.013   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.10 ( 3112)
  covalent geometry    : angle       0.51516 /  0.24 ( 4220)
  hydrogen bonds       : bond        0.03072 /  2.04 (  166)
  hydrogen bonds       : angle       3.20211 /  2.28 (  489)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 HIS cc_start: 0.8649 (t-170) cc_final: 0.8253 (t-170)
REVERT: A   75 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7154 (mp0)
REVERT: A  113 PHE cc_start: 0.8760 (m-80) cc_final: 0.8385 (m-80)
REVERT: A  232 TYR cc_start: 0.7679 (m-80) cc_final: 0.7258 (m-10)
REVERT: A  273 MET cc_start: 0.8039 (mmm) cc_final: 0.7736 (mmp)
REVERT: A  359 MET cc_start: 0.7416 (ttt) cc_final: 0.7121 (ttt)
  outliers start: 7
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0461
  time to fit residues: 3.3330
Evaluate side-chains
  58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  355 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks: [24, 6, 29, 11, 28, 1, 5, 8, 10, 7, 35]
   chunk 24 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0470
   chunk 8 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6478

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.169663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.129075 restraints weight = 3732.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.40
r_work: 0.3370 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3112  Z= 0.111
  Angle     :  0.521   7.126   4220  Z= 0.247
  Chirality :  0.040   0.120    466
  Planarity :  0.003   0.034    522
  Dihedral  :  3.371  24.538    412
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 21.36 %
    Favored  : 76.16 %
  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:  1.48 (0.45), residues: 374
  helix:  2.69 (0.36), residues: 208
  sheet: -1.40 (0.71), residues: 47
  loop : -1.17 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 356 
 TYR   0.009   0.001   TYR A 349 
 PHE   0.014   0.001   PHE A 327 
 TRP   0.013   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 3112)
  covalent geometry    : angle       0.52092 /  0.25 ( 4220)
  hydrogen bonds       : bond        0.03168 /  2.11 (  166)
  hydrogen bonds       : angle       3.23981 /  2.31 (  489)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1007.06 seconds
wall clock time: 17 minutes 54.36 seconds (1074.36 seconds total)