Starting phenix.real_space_refine
on Wed Sep 17 03:43:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lva_63417/09_2025/9lva_63417.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lva_63417/09_2025/9lva_63417.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lva_63417/09_2025/9lva_63417.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lva_63417/09_2025/9lva_63417.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lva_63417/09_2025/9lva_63417.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lva_63417/09_2025/9lva_63417.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.157
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      18      5.16       5
     C    2233      2.51       5
     N     524      2.21       5
     O     548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3323
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3310
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 15, 'TRANS': 399}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'IAC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.16, per 1000 atoms: 0.35
  Number of scatterers: 3323
  At special positions: 0
  Unit cell: (80.7975, 67.8699, 70.0245, 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      18     16.00
     O     548      8.00
     N     524      7.00
     C    2233      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 131.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      79.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 60
      removed outlier: 4.189A  pdb=" N   VAL A  60 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 75
    Processing helix  chain 'A' and resid 75 through 112
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 132 through 162
    Processing helix  chain 'A' and resid 169 through 183
      removed outlier: 3.876A  pdb=" N   ALA A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   CYS A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 186
      No H-bonds generated for 'chain 'A' and resid 184 through 186'
    Processing helix  chain 'A' and resid 192 through 219
      removed outlier: 4.216A  pdb=" N   TRP A 196 " --> pdb=" O   ASN A 192 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ILE A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   ILE A 217 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLY A 219 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 245
      removed outlier: 4.012A  pdb=" N   LEU A 243 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TYR A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   THR A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 4.033A  pdb=" N   MET A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 292
      Proline residue:  A 282  - end of helix
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 308 through 342
      Proline residue:  A 332  - end of helix
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 3.828A  pdb=" N   VAL A 360 " --> pdb=" O   ARG A 356 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 373 through 384
      removed outlier: 3.781A  pdb=" N   ASN A 377 " --> pdb=" O   PHE A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 389
    Processing helix  chain 'A' and resid 390 through 401
    Processing helix  chain 'A' and resid 403 through 409
      removed outlier: 3.807A  pdb=" N   ARG A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 439
      removed outlier: 4.030A  pdb=" N   MET A 424 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 459
      removed outlier: 4.187A  pdb=" N   THR A 449 " --> pdb=" O   TRP A 445 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    663 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: 0.61

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 963
        1.34 -     1.46: 816
        1.46 -     1.57: 1631
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 3438
  Sorted by residual:
  bond pdb=" CA  GLN A 454 "
       pdb=" C   GLN A 454 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.026 1.27e-02 6.20e+03 4.24e+00
  bond pdb=" CA  ALA A 258 "
       pdb=" CB  ALA A 258 "
    ideal  model  delta    sigma   weight residual
    1.541  1.523  0.018 1.20e-02 6.94e+03 2.18e+00
  bond pdb=" CA  GLN A 454 "
       pdb=" CB  GLN A 454 "
    ideal  model  delta    sigma   weight residual
    1.529  1.513  0.016 1.55e-02 4.16e+03 1.05e+00
  bond pdb=" C   ALA A 272 "
       pdb=" O   ALA A 272 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.012 1.15e-02 7.56e+03 1.02e+00
  bond pdb=" N   ALA A 258 "
       pdb=" CA  ALA A 258 "
    ideal  model  delta    sigma   weight residual
    1.456  1.468 -0.012 1.23e-02 6.61e+03 1.01e+00
  ... (remaining 3433 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 4575
        1.46 -     2.91: 96
        2.91 -     4.37: 17
        4.37 -     5.82: 3
        5.82 -     7.28: 2
  Bond angle restraints: 4693
  Sorted by residual:
  angle pdb=" C   LYS A 261 "
        pdb=" N   PRO A 262 "
        pdb=" CA  PRO A 262 "
      ideal   model   delta    sigma   weight residual
     119.28  116.09    3.19 1.10e+00 8.26e-01 8.43e+00
  angle pdb=" C   HIS A 257 "
        pdb=" N   ALA A 258 "
        pdb=" CA  ALA A 258 "
      ideal   model   delta    sigma   weight residual
     126.45  121.50    4.95 1.77e+00 3.19e-01 7.81e+00
  angle pdb=" C   GLN A 454 "
        pdb=" CA  GLN A 454 "
        pdb=" CB  GLN A 454 "
      ideal   model   delta    sigma   weight residual
     110.88  106.50    4.38 1.57e+00 4.06e-01 7.77e+00
  angle pdb=" N   TYR A 275 "
        pdb=" CA  TYR A 275 "
        pdb=" C   TYR A 275 "
      ideal   model   delta    sigma   weight residual
     111.28  108.63    2.65 1.09e+00 8.42e-01 5.91e+00
  angle pdb=" CB  MET A 256 "
        pdb=" CG  MET A 256 "
        pdb=" SD  MET A 256 "
      ideal   model   delta    sigma   weight residual
     112.70  119.98   -7.28 3.00e+00 1.11e-01 5.88e+00
  ... (remaining 4688 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 1625
       17.82 -    35.63: 219
       35.63 -    53.45: 57
       53.45 -    71.26: 4
       71.26 -    89.08: 3
  Dihedral angle restraints: 1908
    sinusoidal: 702
      harmonic: 1206
  Sorted by residual:
  dihedral pdb=" CB  CYS A 464 "
           pdb=" SG  CYS A 464 "
           pdb=" SG  CYS A 467 "
           pdb=" CB  CYS A 467 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.93   75.93     1      1.00e+01 1.00e-02 7.27e+01
  dihedral pdb=" CA  LYS A 231 "
           pdb=" C   LYS A 231 "
           pdb=" N   LEU A 232 "
           pdb=" CA  LEU A 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.42  -17.58     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CB  GLU A 111 "
           pdb=" CG  GLU A 111 "
           pdb=" CD  GLU A 111 "
           pdb=" OE1 GLU A 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.08  -89.08     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 1905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 381
       0.034 -    0.068: 93
       0.068 -    0.101: 35
       0.101 -    0.135: 7
       0.135 -    0.168: 1
  Chirality restraints: 517
  Sorted by residual:
  chirality pdb=" CB  VAL A 315 "
            pdb=" CA  VAL A 315 "
            pdb=" CG1 VAL A 315 "
            pdb=" CG2 VAL A 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CB  ILE A 161 "
            pdb=" CA  ILE A 161 "
            pdb=" CG1 ILE A 161 "
            pdb=" CG2 ILE A 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.13 2.00e-01 2.50e+01 4.50e-01
  chirality pdb=" CA  ILE A 120 "
            pdb=" N   ILE A 120 "
            pdb=" C   ILE A 120 "
            pdb=" CB  ILE A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.16e-01
  ... (remaining 514 not shown)

  Planarity restraints: 566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 198 "    0.008 2.00e-02 2.50e+03   1.08e-02 2.02e+00
        pdb=" CG  PHE A 198 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 198 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 198 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 198 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 198 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 198 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 418 "   -0.023 5.00e-02 4.00e+02   3.46e-02 1.91e+00
        pdb=" N   PRO A 419 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 419 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 419 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 414 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 415 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 415 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 415 "    0.018 5.00e-02 4.00e+02
  ... (remaining 563 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 1338
        2.88 -     3.38: 3509
        3.38 -     3.89: 5507
        3.89 -     4.39: 6001
        4.39 -     4.90: 9883
  Nonbonded interactions: 26238
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 246 "
            pdb=" OH  TYR A 390 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OD1 ASP A  50 "
            pdb=" NE  ARG A 194 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" SD  MET A 256 "
            pdb=" O   PRO A 262 "
     model   vdw
     2.400 3.400
  nonbonded pdb=" OD2 ASP A 169 "
            pdb=" NZ  LYS A 463 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" O   ASN A 300 "
            pdb=" OG  SER A 303 "
     model   vdw
     2.409 3.040
  ... (remaining 26233 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 group one per residue
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:             0.600
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.940
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5808
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   0.026   3439  Z= 0.140
  Angle     :  0.527   7.277   4695  Z= 0.297
  Chirality :  0.036   0.168    517
  Planarity :  0.004   0.035    566
  Dihedral  : 16.844  89.079   1135
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 26.32 %
    Favored  : 71.35 %
  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 aren not related in a simple way.
  whole:  2.10 (0.43), residues: 411
  helix:  2.29 (0.31), residues: 298
  sheet:  None (None), residues: 0
  loop : -1.14 (0.59), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 453 
 TYR   0.014   0.001   TYR A 104 
 PHE   0.024   0.001   PHE A 198 
 TRP   0.008   0.001   TRP A 260 
 HIS   0.002   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3438)
  covalent geometry    : angle       0.52682 ( 4693)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.04114 (    2)
  hydrogen bonds       : bond        0.12812 (  223)
  hydrogen bonds       : angle       5.69934 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0626
  time to fit residues: 7.5166
Evaluate side-chains
  89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  454 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0070
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.7000

-------------------------------------------------------------------------------
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 = 0.4518 r_free = 0.4518 target = 0.240788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.214711 restraints weight = 4947.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.219926 restraints weight = 3094.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.223710 restraints weight = 2188.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.226087 restraints weight = 1665.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.228167 restraints weight = 1355.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5899
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3439  Z= 0.129
  Angle     :  0.549  11.696   4695  Z= 0.292
  Chirality :  0.040   0.123    517
  Planarity :  0.005   0.044    566
  Dihedral  :  6.560  51.564    461
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 25.73 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.42), residues: 411
  helix:  2.31 (0.30), residues: 295
  sheet:  None (None), residues: 0
  loop : -1.60 (0.55), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 311 
 TYR   0.018   0.001   TYR A 269 
 PHE   0.024   0.001   PHE A 177 
 TRP   0.010   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 298 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3438)
  covalent geometry    : angle       0.54909 ( 4693)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.09762 (    2)
  hydrogen bonds       : bond        0.04059 (  223)
  hydrogen bonds       : angle       4.70574 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 LYS cc_start: 0.6681 (tptp) cc_final: 0.6205 (ttmt)
REVERT: A  307 LYS cc_start: 0.5615 (tppt) cc_final: 0.4465 (ttpt)
  outliers start: 16
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0663
  time to fit residues: 7.3712
Evaluate side-chains
  89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4521 r_free = 0.4521 target = 0.241485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.215618 restraints weight = 4980.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.220696 restraints weight = 3147.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.224229 restraints weight = 2257.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.226830 restraints weight = 1749.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.228537 restraints weight = 1424.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5949
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3439  Z= 0.130
  Angle     :  0.529  10.298   4695  Z= 0.282
  Chirality :  0.040   0.135    517
  Planarity :  0.005   0.048    566
  Dihedral  :  5.812  52.240    453
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 25.15 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.42), residues: 411
  helix:  2.29 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.50 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 107 
 TYR   0.015   0.001   TYR A 269 
 PHE   0.025   0.001   PHE A 177 
 TRP   0.007   0.001   TRP A 445 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3438)
  covalent geometry    : angle       0.52897 ( 4693)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.05036 (    2)
  hydrogen bonds       : bond        0.03934 (  223)
  hydrogen bonds       : angle       4.49584 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  307 LYS cc_start: 0.5478 (tppt) cc_final: 0.4364 (ttpt)
  outliers start: 21
  outliers final: 13
  residues processed: 96
  average time/residue: 0.0615
  time to fit residues: 7.3315
Evaluate side-chains
  90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0020
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0870
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4966

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.243001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.216996 restraints weight = 4917.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.222328 restraints weight = 3096.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.226016 restraints weight = 2194.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.228708 restraints weight = 1679.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.230666 restraints weight = 1351.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.4437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5894
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3439  Z= 0.114
  Angle     :  0.557  10.861   4695  Z= 0.284
  Chirality :  0.040   0.132    517
  Planarity :  0.005   0.048    566
  Dihedral  :  5.305  52.339    449
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 28.07 %
    Favored  : 67.54 %
  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 aren not related in a simple way.
  whole:  2.03 (0.43), residues: 411
  helix:  2.33 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.28 (0.59), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 107 
 TYR   0.013   0.001   TYR A 269 
 PHE   0.028   0.001   PHE A 177 
 TRP   0.007   0.001   TRP A  92 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3438)
  covalent geometry    : angle       0.55729 ( 4693)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.01768 (    2)
  hydrogen bonds       : bond        0.03722 (  223)
  hydrogen bonds       : angle       4.37517 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 TYR cc_start: 0.2421 (OUTLIER) cc_final: 0.1750 (m-10)
REVERT: A  281 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6701 (mm)
REVERT: A  307 LYS cc_start: 0.5410 (tppt) cc_final: 0.4360 (ttpt)
  outliers start: 15
  outliers final: 10
  residues processed: 90
  average time/residue: 0.0599
  time to fit residues: 6.6577
Evaluate side-chains
  87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.0470
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.2084

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
A 249 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.238891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.212730 restraints weight = 5037.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.217667 restraints weight = 3263.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.221065 restraints weight = 2373.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.223279 restraints weight = 1865.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.225355 restraints weight = 1559.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.4375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6014
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3439  Z= 0.153
  Angle     :  0.575  10.666   4695  Z= 0.303
  Chirality :  0.042   0.146    517
  Planarity :  0.005   0.050    566
  Dihedral  :  5.606  52.761    449
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  7.02 %
    Allowed  : 25.44 %
    Favored  : 67.54 %
  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 aren not related in a simple way.
  whole:  1.72 (0.42), residues: 411
  helix:  2.14 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.53 (0.54), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 107 
 TYR   0.015   0.001   TYR A 269 
 PHE   0.027   0.002   PHE A 177 
 TRP   0.008   0.001   TRP A 260 
 HIS   0.004   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3438)
  covalent geometry    : angle       0.57469 ( 4693)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.11235 (    2)
  hydrogen bonds       : bond        0.04184 (  223)
  hydrogen bonds       : angle       4.48169 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 TYR cc_start: 0.2368 (OUTLIER) cc_final: 0.1742 (m-10)
REVERT: A  281 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.6961 (mm)
REVERT: A  307 LYS cc_start: 0.5551 (tppt) cc_final: 0.4423 (ttpt)
  outliers start: 24
  outliers final: 16
  residues processed: 98
  average time/residue: 0.0565
  time to fit residues: 6.9775
Evaluate side-chains
  95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.240268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.214271 restraints weight = 4997.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.219399 restraints weight = 3211.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.222888 restraints weight = 2315.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.225356 restraints weight = 1801.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.227145 restraints weight = 1478.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5973
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3439  Z= 0.126
  Angle     :  0.562  10.683   4695  Z= 0.292
  Chirality :  0.040   0.126    517
  Planarity :  0.005   0.050    566
  Dihedral  :  5.628  54.537    449
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 26.90 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.42), residues: 411
  helix:  2.12 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.43 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 171 
 TYR   0.013   0.001   TYR A 269 
 PHE   0.027   0.001   PHE A 177 
 TRP   0.008   0.001   TRP A 260 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3438)
  covalent geometry    : angle       0.56176 ( 4693)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.07726 (    2)
  hydrogen bonds       : bond        0.03927 (  223)
  hydrogen bonds       : angle       4.40654 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 TYR cc_start: 0.2444 (OUTLIER) cc_final: 0.1713 (m-10)
REVERT: A  281 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6848 (mm)
  outliers start: 18
  outliers final: 16
  residues processed: 94
  average time/residue: 0.0605
  time to fit residues: 7.0926
Evaluate side-chains
  95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0870
   chunk 24 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0050
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.5372

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.240394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.214304 restraints weight = 5045.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.219695 restraints weight = 3204.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.223431 restraints weight = 2277.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.225868 restraints weight = 1738.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.227885 restraints weight = 1417.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.4414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5934
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3439  Z= 0.115
  Angle     :  0.566  12.715   4695  Z= 0.286
  Chirality :  0.041   0.173    517
  Planarity :  0.005   0.051    566
  Dihedral  :  5.543  55.864    449
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 27.19 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.42), residues: 411
  helix:  2.16 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.44 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 107 
 TYR   0.012   0.001   TYR A 269 
 PHE   0.030   0.001   PHE A 177 
 TRP   0.009   0.001   TRP A 260 
 HIS   0.002   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 3438)
  covalent geometry    : angle       0.56646 ( 4693)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.05050 (    2)
  hydrogen bonds       : bond        0.03721 (  223)
  hydrogen bonds       : angle       4.32731 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 TYR cc_start: 0.2252 (OUTLIER) cc_final: 0.1657 (m-10)
REVERT: A  281 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6849 (mm)
REVERT: A  307 LYS cc_start: 0.5472 (tppt) cc_final: 0.4766 (tmtt)
  outliers start: 19
  outliers final: 15
  residues processed: 92
  average time/residue: 0.0606
  time to fit residues: 6.9549
Evaluate side-chains
  94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.240571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.214426 restraints weight = 5084.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.219601 restraints weight = 3262.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.223140 restraints weight = 2344.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.225684 restraints weight = 1821.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.227612 restraints weight = 1492.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5968
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3439  Z= 0.128
  Angle     :  0.586  12.893   4695  Z= 0.299
  Chirality :  0.041   0.131    517
  Planarity :  0.005   0.051    566
  Dihedral  :  5.555  56.264    449
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 27.19 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.42), residues: 411
  helix:  2.12 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.49 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 107 
 TYR   0.014   0.001   TYR A 269 
 PHE   0.032   0.001   PHE A 198 
 TRP   0.019   0.001   TRP A 122 
 HIS   0.002   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3438)
  covalent geometry    : angle       0.58631 ( 4693)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.11579 (    2)
  hydrogen bonds       : bond        0.03815 (  223)
  hydrogen bonds       : angle       4.34590 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 TYR cc_start: 0.2466 (OUTLIER) cc_final: 0.1739 (m-10)
REVERT: A  281 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6866 (mm)
REVERT: A  307 LYS cc_start: 0.5538 (tppt) cc_final: 0.4836 (tmtt)
REVERT: A  310 TRP cc_start: 0.5329 (m-10) cc_final: 0.4209 (m-10)
  outliers start: 20
  outliers final: 16
  residues processed: 93
  average time/residue: 0.0615
  time to fit residues: 7.0933
Evaluate side-chains
  94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0010
   chunk 21 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.4764

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.243527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.217622 restraints weight = 5079.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.223031 restraints weight = 3175.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.226902 restraints weight = 2237.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.229260 restraints weight = 1700.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.231417 restraints weight = 1388.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.4437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5911
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3439  Z= 0.113
  Angle     :  0.580  12.827   4695  Z= 0.289
  Chirality :  0.041   0.224    517
  Planarity :  0.005   0.051    566
  Dihedral  :  5.463  57.715    449
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 28.36 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.42), residues: 411
  helix:  2.20 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.44 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 107 
 TYR   0.015   0.001   TYR A 244 
 PHE   0.030   0.001   PHE A 177 
 TRP   0.026   0.001   TRP A 122 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3438)
  covalent geometry    : angle       0.58024 ( 4693)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.09528 (    2)
  hydrogen bonds       : bond        0.03607 (  223)
  hydrogen bonds       : angle       4.25456 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 VAL cc_start: 0.8715 (t) cc_final: 0.8477 (p)
REVERT: A   84 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7250 (pt)
REVERT: A  175 TYR cc_start: 0.2253 (OUTLIER) cc_final: 0.1650 (m-10)
REVERT: A  281 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.6796 (mm)
REVERT: A  307 LYS cc_start: 0.5514 (tppt) cc_final: 0.4894 (tmtt)
REVERT: A  310 TRP cc_start: 0.5233 (m-10) cc_final: 0.4138 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0622
  time to fit residues: 6.7833
Evaluate side-chains
  90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0980
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0670
   overall best weight:    0.5118

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.242717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.216746 restraints weight = 5058.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.222020 restraints weight = 3216.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.225798 restraints weight = 2299.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.228334 restraints weight = 1760.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.230202 restraints weight = 1438.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.4429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5902
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3439  Z= 0.115
  Angle     :  0.605  12.941   4695  Z= 0.299
  Chirality :  0.042   0.316    517
  Planarity :  0.005   0.052    566
  Dihedral  :  5.393  57.796    449
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 29.53 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.42), residues: 411
  helix:  2.23 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.49 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 171 
 TYR   0.016   0.001   TYR A 104 
 PHE   0.030   0.001   PHE A 177 
 TRP   0.023   0.001   TRP A 122 
 HIS   0.002   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3438)
  covalent geometry    : angle       0.60522 ( 4693)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.14390 (    2)
  hydrogen bonds       : bond        0.03565 (  223)
  hydrogen bonds       : angle       4.25182 (  663)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 VAL cc_start: 0.8718 (t) cc_final: 0.8479 (p)
REVERT: A   84 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7232 (pt)
REVERT: A  175 TYR cc_start: 0.2467 (OUTLIER) cc_final: 0.1741 (m-10)
REVERT: A  271 MET cc_start: 0.6677 (tpt) cc_final: 0.6082 (tpt)
REVERT: A  281 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.6799 (mm)
REVERT: A  307 LYS cc_start: 0.5509 (tppt) cc_final: 0.4961 (tmtt)
REVERT: A  310 TRP cc_start: 0.5205 (m-10) cc_final: 0.4107 (m-10)
  outliers start: 16
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0630
  time to fit residues: 6.8454
Evaluate side-chains
  92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0770
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.7540

-------------------------------------------------------------------------------
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 = 0.4517 r_free = 0.4517 target = 0.240439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.213737 restraints weight = 5213.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.219102 restraints weight = 3312.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.222913 restraints weight = 2363.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.225568 restraints weight = 1815.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.227456 restraints weight = 1479.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5941
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      :  0.003   0.026   3439  Z= 0.122
  Angle     :  0.591  12.990   4695  Z= 0.296
  Chirality :  0.043   0.301    517
  Planarity :  0.005   0.052    566
  Dihedral  :  5.441  57.893    449
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 28.95 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.42), residues: 411
  helix:  2.20 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.55 (0.54), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 171 
 TYR   0.015   0.001   TYR A 104 
 PHE   0.029   0.001   PHE A 177 
 TRP   0.022   0.001   TRP A 122 
 HIS   0.002   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3438)
  covalent geometry    : angle       0.59064 ( 4693)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.07396 (    2)
  hydrogen bonds       : bond        0.03734 (  223)
  hydrogen bonds       : angle       4.28350 (  663)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 794.29 seconds
wall clock time: 14 minutes 30.74 seconds (870.74 seconds total)