Starting phenix.real_space_refine
on Tue Feb  3 14:33:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9okg_70563/02_2026/9okg_70563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9okg_70563/02_2026/9okg_70563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9okg_70563/02_2026/9okg_70563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9okg_70563/02_2026/9okg_70563.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9okg_70563/02_2026/9okg_70563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9okg_70563/02_2026/9okg_70563.map"
  }
  resolution = 2.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
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      31      5.16       5
     C    2453      2.51       5
     N     618      2.21       5
     O     633      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3735
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 475, 3723
          Classifications: {'peptide': 475}
          Link IDs: {'PTRANS': 13, 'TRANS': 461}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'UKX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.98, per 1000 atoms: 0.26
  Number of scatterers: 3735
  At special positions: 0
  Unit cell: (77.88, 72.039, 85.668, 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      31     16.00
     O     633      8.00
     N     618      7.00
     C    2453      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: 0.34
  Conformation dependent library (CDL) restraints added in 137.2 milliseconds
  

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  862

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      85.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 139 through 160
    Processing helix  chain 'A' and resid 162 through 189
      removed outlier: 3.881A  pdb=" N   ALA A 175 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 230
      removed outlier: 4.397A  pdb=" N   VAL A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   TYR A 212 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A 213 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ASP A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ARG A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 252
      removed outlier: 3.554A  pdb=" N   SER A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   PHE A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 270
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 288 through 295
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.541A  pdb=" N   MET A 301 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 340
      removed outlier: 3.750A  pdb=" N   VAL A 335 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 352
    Processing helix  chain 'A' and resid 357 through 364
    Processing helix  chain 'A' and resid 366 through 385
    Processing helix  chain 'A' and resid 416 through 438
    Processing helix  chain 'A' and resid 443 through 482
      Proline residue:  A 469  - end of helix
    Processing helix  chain 'A' and resid 595 through 607
    Processing helix  chain 'A' and resid 607 through 623
      removed outlier: 4.533A  pdb=" N   GLY A 611 " --> pdb=" O   ALA A 607 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   ASP A 620 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   LYS A 621 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 641
      removed outlier: 3.585A  pdb=" N   PHE A 640 " --> pdb=" O   CYS A 636 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE A 641 " --> pdb=" O   VAL A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 645
    Processing helix  chain 'A' and resid 647 through 677
      removed outlier: 4.666A  pdb=" N   ALA A 664 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   SER A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TRP A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   TYR A 677 " --> pdb=" O   THR A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 708
      removed outlier: 3.679A  pdb=" N   SER A 706 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A 707 " --> pdb=" O   ILE A 703 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A 708 " --> pdb=" O   PHE A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 731

    296 hydrogen bonds defined for protein.
    885 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: 0.57

  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: 1144
        1.34 -     1.46: 814
        1.46 -     1.58: 1827
        1.58 -     1.69: 0
        1.69 -     1.81: 51
  Bond restraints: 3836
  Sorted by residual:
  bond pdb=" N   ILE A 237 "
       pdb=" CA  ILE A 237 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.21e-02 6.83e+03 8.20e+00
  bond pdb=" CA  ILE A 273 "
       pdb=" CB  ILE A 273 "
    ideal  model  delta    sigma   weight residual
    1.539  1.552 -0.013 5.40e-03 3.43e+04 5.65e+00
  bond pdb=" C   ILE A 273 "
       pdb=" O   ILE A 273 "
    ideal  model  delta    sigma   weight residual
    1.242  1.222  0.020 8.60e-03 1.35e+04 5.53e+00
  bond pdb=" N   SER A 238 "
       pdb=" CA  SER A 238 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 5.00e+00
  bond pdb=" N   LEU A 239 "
       pdb=" CA  LEU A 239 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.23e-02 6.61e+03 4.47e+00
  ... (remaining 3831 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 5058
        1.39 -     2.78: 111
        2.78 -     4.17: 21
        4.17 -     5.55: 0
        5.55 -     6.94: 1
  Bond angle restraints: 5191
  Sorted by residual:
  angle pdb=" CA  ILE A 273 "
        pdb=" C   ILE A 273 "
        pdb=" N   PRO A 274 "
      ideal   model   delta    sigma   weight residual
     120.83  118.56    2.27 6.10e-01 2.69e+00 1.39e+01
  angle pdb=" N   ILE A 273 "
        pdb=" CA  ILE A 273 "
        pdb=" C   ILE A 273 "
      ideal   model   delta    sigma   weight residual
     112.35  116.25   -3.90 1.20e+00 6.94e-01 1.06e+01
  angle pdb=" CA  ILE A 237 "
        pdb=" C   ILE A 237 "
        pdb=" O   ILE A 237 "
      ideal   model   delta    sigma   weight residual
     120.85  117.88    2.97 1.06e+00 8.90e-01 7.86e+00
  angle pdb=" C   ILE A 273 "
        pdb=" CA  ILE A 273 "
        pdb=" CB  ILE A 273 "
      ideal   model   delta    sigma   weight residual
     114.00  110.45    3.55 1.31e+00 5.83e-01 7.35e+00
  angle pdb=" CA  LEU A 239 "
        pdb=" C   LEU A 239 "
        pdb=" O   LEU A 239 "
      ideal   model   delta    sigma   weight residual
     120.42  117.58    2.84 1.06e+00 8.90e-01 7.20e+00
  ... (remaining 5186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.04: 2164
       32.04 -    64.07: 28
       64.07 -    96.10: 2
       96.10 -   128.14: 0
      128.14 -   160.17: 2
  Dihedral angle restraints: 2196
    sinusoidal: 848
      harmonic: 1348
  Sorted by residual:
  dihedral pdb=" CA  GLU A 194 "
           pdb=" C   GLU A 194 "
           pdb=" N   LYS A 195 "
           pdb=" CA  LYS A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.38  -23.62     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" N1  UKX A 801 "
           pdb=" C5  UKX A 801 "
           pdb=" C6  UKX A 801 "
           pdb=" O2  UKX A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      85.40 -114.43 -160.17     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" C7  UKX A 801 "
           pdb=" C5  UKX A 801 "
           pdb=" C6  UKX A 801 "
           pdb=" O2  UKX A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -39.21  118.74 -157.95     1      3.00e+01 1.11e-03 2.06e+01
  ... (remaining 2193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 383
       0.028 -    0.056: 115
       0.056 -    0.084: 51
       0.084 -    0.112: 17
       0.112 -    0.140: 3
  Chirality restraints: 569
  Sorted by residual:
  chirality pdb=" CA  ILE A 237 "
            pdb=" N   ILE A 237 "
            pdb=" C   ILE A 237 "
            pdb=" CB  ILE A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  LEU A 239 "
            pdb=" N   LEU A 239 "
            pdb=" C   LEU A 239 "
            pdb=" CB  LEU A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  ILE A 397 "
            pdb=" N   ILE A 397 "
            pdb=" C   ILE A 397 "
            pdb=" CB  ILE A 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 566 not shown)

  Planarity restraints: 641
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 190 "    0.044 5.00e-02 4.00e+02   6.67e-02 7.13e+00
        pdb=" N   PRO A 191 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 191 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 191 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  UKX A 801 "    0.012 2.00e-02 2.50e+03   1.34e-02 2.70e+00
        pdb=" C2  UKX A 801 "   -0.020 2.00e-02 2.50e+03
        pdb=" C4  UKX A 801 "    0.010 2.00e-02 2.50e+03
        pdb=" C6  UKX A 801 "   -0.017 2.00e-02 2.50e+03
        pdb=" N1  UKX A 801 "    0.009 2.00e-02 2.50e+03
        pdb=" O1  UKX A 801 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 315 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO A 316 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 316 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 316 "    0.016 5.00e-02 4.00e+02
  ... (remaining 638 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 784
        2.78 -     3.31: 3793
        3.31 -     3.84: 6537
        3.84 -     4.37: 7547
        4.37 -     4.90: 13069
  Nonbonded interactions: 31730
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" O   PRO A 355 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OE1 GLU A 675 "
            pdb=" OG1 THR A 736 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" OE1 GLU A 282 "
            pdb=" OG  SER A 357 "
     model   vdw
     2.384 3.040
  nonbonded pdb=" O   ASP A 479 "
            pdb=" OG  SER A 482 "
     model   vdw
     2.427 3.040
  nonbonded pdb=" OD2 ASP A 227 "
            pdb=" OG1 THR A 684 "
     model   vdw
     2.439 3.040
  ... (remaining 31725 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:             7.110
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.710
  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:7.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
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   0.035   3836  Z= 0.166
  Angle     :  0.525   6.942   5191  Z= 0.317
  Chirality :  0.035   0.140    569
  Planarity :  0.004   0.067    641
  Dihedral  : 12.994 160.169   1334
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 1.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.86 %
    Favored  : 95.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.94 (0.38), residues: 467
  helix:  2.48 (0.26), residues: 371
  sheet:  None (None), residues: 0
  loop : -0.19 (0.68), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 626 
 TYR   0.008   0.001   TYR A 169 
 PHE   0.012   0.001   PHE A 245 
 TRP   0.005   0.001   TRP A 300 
 HIS   0.002   0.000   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3836)
  covalent geometry    : angle       0.52535 ( 5191)
  hydrogen bonds       : bond        0.10954 (  296)
  hydrogen bonds       : angle       5.29785 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  147 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7363 (mm-30)
REVERT: A  206 MET cc_start: 0.7523 (tpp) cc_final: 0.6982 (tpp)
REVERT: A  445 ARG cc_start: 0.8310 (ttt90) cc_final: 0.8070 (ttt90)
  outliers start: 1
  outliers final: 0
  residues processed: 66
  average time/residue: 0.6449
  time to fit residues: 43.7562
Evaluate side-chains
  58 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0050
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.168391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.133594 restraints weight = 3828.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.45
r_work: 0.3572 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3836  Z= 0.145
  Angle     :  0.526   5.413   5191  Z= 0.280
  Chirality :  0.038   0.128    569
  Planarity :  0.004   0.069    641
  Dihedral  : 10.318 151.242    525
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  7.20 %
    Favored  : 90.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.38 (0.38), residues: 467
  helix:  2.77 (0.25), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.08 (0.69), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 444 
 TYR   0.010   0.002   TYR A 169 
 PHE   0.016   0.002   PHE A 245 
 TRP   0.010   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3836)
  covalent geometry    : angle       0.52599 ( 5191)
  hydrogen bonds       : bond        0.05248 (  296)
  hydrogen bonds       : angle       4.24937 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  147 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7463 (mm-30)
REVERT: A  158 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6450 (tm-30)
REVERT: A  206 MET cc_start: 0.7522 (tpp) cc_final: 0.6906 (tpp)
REVERT: A  445 ARG cc_start: 0.8378 (ttt90) cc_final: 0.8133 (ttp80)
REVERT: A  621 LYS cc_start: 0.8318 (mttt) cc_final: 0.8117 (mttt)
REVERT: A  716 ILE cc_start: 0.7273 (mm) cc_final: 0.6933 (mt)
REVERT: A  718 PHE cc_start: 0.7757 (m-80) cc_final: 0.7545 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 65
  average time/residue: 0.5339
  time to fit residues: 35.8124
Evaluate side-chains
  57 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  674 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   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 = 0.3947 r_free = 0.3947 target = 0.162185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.125403 restraints weight = 3731.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.50
r_work: 0.3462 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3836  Z= 0.166
  Angle     :  0.530   5.629   5191  Z= 0.281
  Chirality :  0.039   0.133    569
  Planarity :  0.005   0.070    641
  Dihedral  : 10.571 154.785    525
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  :  8.48 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.30 (0.38), residues: 467
  helix:  2.73 (0.25), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.24 (0.68), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 444 
 TYR   0.009   0.001   TYR A 417 
 PHE   0.017   0.002   PHE A 245 
 TRP   0.012   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3836)
  covalent geometry    : angle       0.53017 ( 5191)
  hydrogen bonds       : bond        0.05641 (  296)
  hydrogen bonds       : angle       4.16264 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  142 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7600 (ttm170)
REVERT: A  147 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7389 (mm-30)
REVERT: A  158 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6567 (tm-30)
REVERT: A  197 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4682 (mpp)
REVERT: A  206 MET cc_start: 0.7533 (tpp) cc_final: 0.6866 (tpp)
REVERT: A  445 ARG cc_start: 0.8312 (ttt90) cc_final: 0.8088 (ttp80)
REVERT: A  681 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8105 (mtpm)
REVERT: A  716 ILE cc_start: 0.7157 (mm) cc_final: 0.6868 (mt)
REVERT: A  718 PHE cc_start: 0.7744 (m-80) cc_final: 0.7523 (m-80)
  outliers start: 11
  outliers final: 5
  residues processed: 58
  average time/residue: 0.5658
  time to fit residues: 33.8540
Evaluate side-chains
  58 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  681 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.166913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.132688 restraints weight = 3783.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.40
r_work: 0.3560 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3836  Z= 0.149
  Angle     :  0.505   5.190   5191  Z= 0.266
  Chirality :  0.038   0.126    569
  Planarity :  0.005   0.070    641
  Dihedral  : 10.462 153.713    525
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  :  9.25 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.39 (0.38), residues: 467
  helix:  2.82 (0.25), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.35 (0.67), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 444 
 TYR   0.008   0.001   TYR A 417 
 PHE   0.016   0.002   PHE A 245 
 TRP   0.010   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3836)
  covalent geometry    : angle       0.50495 ( 5191)
  hydrogen bonds       : bond        0.05267 (  296)
  hydrogen bonds       : angle       4.06920 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  142 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7639 (ttm170)
REVERT: A  143 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7575 (tttp)
REVERT: A  147 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7497 (mm-30)
REVERT: A  158 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6421 (tm-30)
REVERT: A  197 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4753 (mpp)
REVERT: A  206 MET cc_start: 0.7516 (tpp) cc_final: 0.6870 (tpp)
REVERT: A  445 ARG cc_start: 0.8386 (ttt90) cc_final: 0.8166 (ttp80)
REVERT: A  681 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8148 (mtpm)
REVERT: A  716 ILE cc_start: 0.7191 (mm) cc_final: 0.6901 (mt)
  outliers start: 11
  outliers final: 5
  residues processed: 62
  average time/residue: 0.6207
  time to fit residues: 39.6360
Evaluate side-chains
  60 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  681 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0050
   chunk 42 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.167750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.133751 restraints weight = 3743.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.39
r_work: 0.3567 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3836  Z= 0.134
  Angle     :  0.482   5.021   5191  Z= 0.253
  Chirality :  0.037   0.124    569
  Planarity :  0.004   0.071    641
  Dihedral  : 10.177 150.093    525
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 10.54 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.51 (0.39), residues: 467
  helix:  2.91 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.34 (0.67), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 444 
 TYR   0.008   0.001   TYR A 417 
 PHE   0.015   0.001   PHE A 245 
 TRP   0.009   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3836)
  covalent geometry    : angle       0.48168 ( 5191)
  hydrogen bonds       : bond        0.04921 (  296)
  hydrogen bonds       : angle       3.98312 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  143 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7527 (tttp)
REVERT: A  147 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7492 (mm-30)
REVERT: A  158 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6486 (tm-30)
REVERT: A  197 MET cc_start: 0.4998 (OUTLIER) cc_final: 0.4100 (pp-130)
REVERT: A  206 MET cc_start: 0.7543 (tpp) cc_final: 0.6849 (tpp)
REVERT: A  445 ARG cc_start: 0.8352 (ttt90) cc_final: 0.8134 (ttp80)
REVERT: A  681 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8161 (mtpm)
REVERT: A  716 ILE cc_start: 0.7102 (mm) cc_final: 0.6809 (mt)
  outliers start: 11
  outliers final: 4
  residues processed: 62
  average time/residue: 0.6257
  time to fit residues: 39.8884
Evaluate side-chains
  60 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  681 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.165855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.131497 restraints weight = 3806.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 1.43
r_work: 0.3550 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3836  Z= 0.167
  Angle     :  0.521   5.898   5191  Z= 0.274
  Chirality :  0.039   0.129    569
  Planarity :  0.005   0.071    641
  Dihedral  : 10.601 155.291    525
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 10.54 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.25 (0.38), residues: 467
  helix:  2.74 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.48 (0.65), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 444 
 TYR   0.009   0.001   TYR A 417 
 PHE   0.018   0.002   PHE A 245 
 TRP   0.010   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 3836)
  covalent geometry    : angle       0.52125 ( 5191)
  hydrogen bonds       : bond        0.05557 (  296)
  hydrogen bonds       : angle       4.08161 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  143 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7582 (tttp)
REVERT: A  147 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7490 (mm-30)
REVERT: A  158 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6659 (tm-30)
REVERT: A  197 MET cc_start: 0.4945 (OUTLIER) cc_final: 0.4078 (pp-130)
REVERT: A  206 MET cc_start: 0.7590 (tpp) cc_final: 0.6868 (tpp)
REVERT: A  445 ARG cc_start: 0.8395 (ttt90) cc_final: 0.8165 (ttp80)
REVERT: A  681 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8174 (mtpm)
REVERT: A  716 ILE cc_start: 0.7116 (mm) cc_final: 0.6787 (mt)
REVERT: A  739 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7577 (mt0)
  outliers start: 15
  outliers final: 9
  residues processed: 62
  average time/residue: 0.5954
  time to fit residues: 38.0053
Evaluate side-chains
  64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  681 LYS
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain A residue  720 SER
Chi-restraints excluded: chain A residue  739 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 46 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.166594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.132569 restraints weight = 3820.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 1.41
r_work: 0.3557 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3836  Z= 0.148
  Angle     :  0.501   5.145   5191  Z= 0.263
  Chirality :  0.038   0.126    569
  Planarity :  0.005   0.069    641
  Dihedral  : 10.490 154.202    525
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 10.80 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.33 (0.38), residues: 467
  helix:  2.80 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.46 (0.66), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 444 
 TYR   0.008   0.001   TYR A 417 
 PHE   0.016   0.002   PHE A 245 
 TRP   0.010   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3836)
  covalent geometry    : angle       0.50076 ( 5191)
  hydrogen bonds       : bond        0.05207 (  296)
  hydrogen bonds       : angle       4.02576 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  143 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7538 (tttp)
REVERT: A  147 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7483 (mm-30)
REVERT: A  158 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6465 (tm-30)
REVERT: A  197 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4057 (pp-130)
REVERT: A  206 MET cc_start: 0.7581 (tpp) cc_final: 0.6810 (mmp)
REVERT: A  445 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8107 (ttt90)
REVERT: A  681 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8171 (mtpm)
REVERT: A  716 ILE cc_start: 0.7103 (mm) cc_final: 0.6771 (mt)
REVERT: A  739 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7592 (mt0)
  outliers start: 14
  outliers final: 9
  residues processed: 60
  average time/residue: 0.5548
  time to fit residues: 34.3103
Evaluate side-chains
  65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  681 LYS
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain A residue  720 SER
Chi-restraints excluded: chain A residue  739 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.167641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.133425 restraints weight = 3883.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 1.44
r_work: 0.3565 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3836  Z= 0.140
  Angle     :  0.495   5.005   5191  Z= 0.258
  Chirality :  0.037   0.123    569
  Planarity :  0.004   0.064    641
  Dihedral  : 10.339 152.208    525
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 11.05 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.40 (0.39), residues: 467
  helix:  2.84 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.41 (0.67), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 444 
 TYR   0.008   0.001   TYR A 417 
 PHE   0.016   0.001   PHE A 245 
 TRP   0.009   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3836)
  covalent geometry    : angle       0.49456 ( 5191)
  hydrogen bonds       : bond        0.05046 (  296)
  hydrogen bonds       : angle       3.99619 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  142 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7646 (ttm170)
REVERT: A  143 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7530 (tttp)
REVERT: A  147 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7497 (mm-30)
REVERT: A  158 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6465 (tm-30)
REVERT: A  197 MET cc_start: 0.4915 (OUTLIER) cc_final: 0.4117 (pp-130)
REVERT: A  206 MET cc_start: 0.7577 (tpp) cc_final: 0.6811 (mmp)
REVERT: A  445 ARG cc_start: 0.8389 (ttt90) cc_final: 0.8127 (ttt90)
REVERT: A  681 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8172 (mtpm)
REVERT: A  739 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7628 (mt0)
  outliers start: 14
  outliers final: 8
  residues processed: 60
  average time/residue: 0.5996
  time to fit residues: 37.0652
Evaluate side-chains
  61 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  681 LYS
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain A residue  720 SER
Chi-restraints excluded: chain A residue  739 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.165808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.131821 restraints weight = 3801.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.41
r_work: 0.3555 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3836  Z= 0.164
  Angle     :  0.523   5.887   5191  Z= 0.274
  Chirality :  0.038   0.128    569
  Planarity :  0.005   0.064    641
  Dihedral  : 10.621 155.673    525
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 11.31 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.26 (0.38), residues: 467
  helix:  2.74 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.41 (0.66), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 444 
 TYR   0.008   0.001   TYR A 417 
 PHE   0.018   0.002   PHE A 245 
 TRP   0.010   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 3836)
  covalent geometry    : angle       0.52322 ( 5191)
  hydrogen bonds       : bond        0.05456 (  296)
  hydrogen bonds       : angle       4.07310 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  143 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7578 (tttp)
REVERT: A  158 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6654 (tm-30)
REVERT: A  197 MET cc_start: 0.4951 (OUTLIER) cc_final: 0.4114 (pp-130)
REVERT: A  206 MET cc_start: 0.7599 (tpp) cc_final: 0.6833 (mmp)
REVERT: A  445 ARG cc_start: 0.8411 (ttt90) cc_final: 0.8144 (ttt90)
REVERT: A  681 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8185 (mtpm)
REVERT: A  739 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7636 (mt0)
  outliers start: 15
  outliers final: 9
  residues processed: 58
  average time/residue: 0.5272
  time to fit residues: 31.4675
Evaluate side-chains
  60 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  681 LYS
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain A residue  720 SER
Chi-restraints excluded: chain A residue  739 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0050
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.4394

-------------------------------------------------------------------------------
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 = 0.4038 r_free = 0.4038 target = 0.167771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.133717 restraints weight = 3855.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 1.43
r_work: 0.3578 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3836  Z= 0.124
  Angle     :  0.482   5.197   5191  Z= 0.253
  Chirality :  0.036   0.119    569
  Planarity :  0.004   0.065    641
  Dihedral  : 10.124 149.590    525
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.88 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.52 (0.39), residues: 467
  helix:  2.91 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.28 (0.67), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 444 
 TYR   0.007   0.001   TYR A 462 
 PHE   0.014   0.001   PHE A 245 
 TRP   0.009   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3836)
  covalent geometry    : angle       0.48240 ( 5191)
  hydrogen bonds       : bond        0.04690 (  296)
  hydrogen bonds       : angle       3.95319 (  885)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  143 LYS cc_start: 0.8012 (ttpp) cc_final: 0.7541 (tttp)
REVERT: A  197 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.4047 (pp-130)
REVERT: A  206 MET cc_start: 0.7579 (tpp) cc_final: 0.6823 (mmp)
REVERT: A  445 ARG cc_start: 0.8347 (ttt90) cc_final: 0.8084 (ttt90)
  outliers start: 8
  outliers final: 6
  residues processed: 54
  average time/residue: 0.4905
  time to fit residues: 27.4067
Evaluate side-chains
  55 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  693 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0770
   chunk 34 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.167058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.133372 restraints weight = 3776.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.39
r_work: 0.3579 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3836  Z= 0.137
  Angle     :  0.500   5.407   5191  Z= 0.261
  Chirality :  0.037   0.120    569
  Planarity :  0.004   0.065    641
  Dihedral  : 10.103 148.915    525
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.37 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.43 (0.39), residues: 467
  helix:  2.85 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.32 (0.67), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 444 
 TYR   0.008   0.001   TYR A 462 
 PHE   0.015   0.001   PHE A 245 
 TRP   0.009   0.001   TRP A 166 
 HIS   0.001   0.000   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3836)
  covalent geometry    : angle       0.49973 ( 5191)
  hydrogen bonds       : bond        0.04923 (  296)
  hydrogen bonds       : angle       3.97701 (  885)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1641.42 seconds
wall clock time: 28 minutes 41.31 seconds (1721.31 seconds total)