Starting phenix.real_space_refine
on Wed Sep 17 04:12:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xos_33358/09_2025/7xos_33358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xos_33358/09_2025/7xos_33358.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xos_33358/09_2025/7xos_33358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xos_33358/09_2025/7xos_33358.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xos_33358/09_2025/7xos_33358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xos_33358/09_2025/7xos_33358.cif"
  }
  resolution = 3.2
  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=   0.006
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      20      5.16       5
     C    2397      2.51       5
     N     665      2.21       5
     O     773      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3855
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "K"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
  Time building chain proxies: 1.09, per 1000 atoms: 0.28
  Number of scatterers: 3855
  At special positions: 0
  Unit cell: (73.08, 88.74, 69.6, 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      20     16.00
     O     773      8.00
     N     665      7.00
     C    2397      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: 0.29
  Conformation dependent library (CDL) restraints added in 166.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  948

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 7 sheets defined
      59.2% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'K' and resid 9 through 28
    Processing helix  chain 'K' and resid 29 through 31
      No H-bonds generated for 'chain 'K' and resid 29 through 31'
    Processing helix  chain 'K' and resid 52 through 59
      removed outlier: 3.805A  pdb=" N   VAL K  56 " --> pdb=" O   ASP K  52 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 64 through 86
    Processing helix  chain 'K' and resid 88 through 109
    Processing helix  chain 'K' and resid 112 through 135
    Processing helix  chain 'K' and resid 140 through 152
    Processing helix  chain 'K' and resid 155 through 170
    Processing helix  chain 'K' and resid 201 through 205
      removed outlier: 3.700A  pdb=" N   ILE K 205 " --> pdb=" O   PRO K 202 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 233 through 244
      removed outlier: 3.630A  pdb=" N   LEU K 237 " --> pdb=" O   MET K 233 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 256 through 268
      removed outlier: 4.086A  pdb=" N   ALA K 260 " --> pdb=" O   GLY K 256 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 283 through 297
    Processing helix  chain 'K' and resid 338 through 355
      removed outlier: 3.863A  pdb=" N   ILE K 342 " --> pdb=" O   GLU K 338 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 358 through 375
      removed outlier: 4.299A  pdb=" N   GLY K 375 " --> pdb=" O   LYS K 371 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 385 through 409
    Processing helix  chain 'K' and resid 416 through 426
    Processing helix  chain 'K' and resid 433 through 459
      Proline residue:  K 450  - end of helix
    Processing helix  chain 'K' and resid 461 through 472
      removed outlier: 4.131A  pdb=" N   VAL K 465 " --> pdb=" O   GLU K 461 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 488 through 492
    Processing helix  chain 'K' and resid 497 through 516
    Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 8
    Processing sheet with id=AA2, first strand: chain 'K' and resid 38 through 40
    Processing sheet with id=AA3, first strand: chain 'K' and resid 174 through 179
    Processing sheet with id=AA4, first strand: chain 'K' and resid 193 through 195
    Processing sheet with id=AA5, first strand: chain 'K' and resid 219 through 222
      removed outlier: 6.268A  pdb=" N   PHE K 219 " --> pdb=" O   LEU K 248 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   ILE K 250 " --> pdb=" O   PHE K 219 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   LEU K 221 " --> pdb=" O   ILE K 250 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA K 251 " --> pdb=" O   VAL K 276 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 411 through 413
    Processing sheet with id=AA7, first strand: chain 'K' and resid 476 through 479

    262 hydrogen bonds defined for protein.
    756 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: 0.74

  Time building geometry restraints manager: 0.39 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: 1312
        1.34 -     1.45: 243
        1.45 -     1.57: 2291
        1.57 -     1.69: 0
        1.69 -     1.81: 37
  Bond restraints: 3883
  Sorted by residual:
  bond pdb=" CG1 ILE K 353 "
       pdb=" CD1 ILE K 353 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.14e+00
  bond pdb=" CA  ALA K 449 "
       pdb=" C   ALA K 449 "
    ideal  model  delta    sigma   weight residual
    1.520  1.530 -0.010 1.23e-02 6.61e+03 6.60e-01
  bond pdb=" N   GLU K 354 "
       pdb=" CA  GLU K 354 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.40e-02 5.10e+03 5.32e-01
  bond pdb=" C   VAL K 169 "
       pdb=" O   VAL K 169 "
    ideal  model  delta    sigma   weight residual
    1.230  1.242 -0.013 1.78e-02 3.16e+03 5.14e-01
  bond pdb=" C   VAL K  27 "
       pdb=" O   VAL K  27 "
    ideal  model  delta    sigma   weight residual
    1.241  1.233  0.007 1.03e-02 9.43e+03 5.09e-01
  ... (remaining 3878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 5071
        1.41 -     2.81: 139
        2.81 -     4.22: 25
        4.22 -     5.62: 6
        5.62 -     7.03: 2
  Bond angle restraints: 5243
  Sorted by residual:
  angle pdb=" N   ILE K 305 "
        pdb=" CA  ILE K 305 "
        pdb=" C   ILE K 305 "
      ideal   model   delta    sigma   weight residual
     112.80  109.43    3.37 1.15e+00 7.56e-01 8.58e+00
  angle pdb=" N   GLN K 351 "
        pdb=" CA  GLN K 351 "
        pdb=" CB  GLN K 351 "
      ideal   model   delta    sigma   weight residual
     110.22  114.64   -4.42 1.54e+00 4.22e-01 8.24e+00
  angle pdb=" N   GLU K 164 "
        pdb=" CA  GLU K 164 "
        pdb=" CB  GLU K 164 "
      ideal   model   delta    sigma   weight residual
     110.39  114.81   -4.42 1.66e+00 3.63e-01 7.10e+00
  angle pdb=" C   VAL K 169 "
        pdb=" CA  VAL K 169 "
        pdb=" CB  VAL K 169 "
      ideal   model   delta    sigma   weight residual
     112.46  109.49    2.97 1.33e+00 5.65e-01 4.99e+00
  angle pdb=" CA  LEU K 234 "
        pdb=" C   LEU K 234 "
        pdb=" N   PRO K 235 "
      ideal   model   delta    sigma   weight residual
     118.44  121.95   -3.51 1.59e+00 3.96e-01 4.87e+00
  ... (remaining 5238 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 2135
       15.94 -    31.89: 224
       31.89 -    47.83: 48
       47.83 -    63.78: 2
       63.78 -    79.72: 3
  Dihedral angle restraints: 2412
    sinusoidal: 934
      harmonic: 1478
  Sorted by residual:
  dihedral pdb=" CA  GLU K 354 "
           pdb=" C   GLU K 354 "
           pdb=" N   GLU K 355 "
           pdb=" CA  GLU K 355 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.33   24.67     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  PHE K 219 "
           pdb=" C   PHE K 219 "
           pdb=" N   ILE K 220 "
           pdb=" CA  ILE K 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.83  -16.17     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" N   LYS K 321 "
           pdb=" CA  LYS K 321 "
           pdb=" CB  LYS K 321 "
           pdb=" CG  LYS K 321 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -112.99   52.99     3      1.50e+01 4.44e-03 9.17e+00
  ... (remaining 2409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 394
       0.028 -    0.057: 154
       0.057 -    0.085: 49
       0.085 -    0.113: 31
       0.113 -    0.142: 10
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" CA  GLU K 164 "
            pdb=" N   GLU K 164 "
            pdb=" C   GLU K 164 "
            pdb=" CB  GLU K 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  GLN K  72 "
            pdb=" N   GLN K  72 "
            pdb=" C   GLN K  72 "
            pdb=" CB  GLN K  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  GLU K 354 "
            pdb=" N   GLU K 354 "
            pdb=" C   GLU K 354 "
            pdb=" CB  GLU K 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 635 not shown)

  Planarity restraints: 687
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS K 160 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.95e+00
        pdb=" C   LYS K 160 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   LYS K 160 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU K 161 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU K 161 "    0.006 2.00e-02 2.50e+03   1.23e-02 1.51e+00
        pdb=" C   LEU K 161 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   LEU K 161 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ILE K 162 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU K 234 "   -0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO K 235 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO K 235 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO K 235 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 684 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 65
        2.67 -     3.23: 3838
        3.23 -     3.78: 6356
        3.78 -     4.34: 7900
        4.34 -     4.90: 13141
  Nonbonded interactions: 31300
  Sorted by model distance:
  nonbonded pdb=" OG1 THR K 385 "
            pdb=" OE1 GLU K 388 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" O   VAL K 147 "
            pdb=" OG  SER K 151 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" O   GLY K 173 "
            pdb=" NH2 ARG K 404 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" OG  SER K 228 "
            pdb=" OE2 GLU K 255 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG1 THR K 296 "
            pdb=" O   GLN K 319 "
     model   vdw
     2.249 3.040
  ... (remaining 31295 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.720
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     5.860
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
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   0.042   3883  Z= 0.147
  Angle     :  0.578   7.027   5243  Z= 0.344
  Chirality :  0.041   0.142    638
  Planarity :  0.003   0.027    687
  Dihedral  : 13.124  79.720   1464
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.36), residues: 522
  helix:  1.78 (0.30), residues: 295
  sheet:  0.83 (0.65), residues: 70
  loop : -0.72 (0.43), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 322 
 TYR   0.006   0.001   TYR K 478 
 PHE   0.010   0.001   PHE K 195 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3883)
  covalent geometry    : angle       0.57783 ( 5243)
  hydrogen bonds       : bond        0.15039 (  262)
  hydrogen bonds       : angle       5.82843 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.4353 (pp20) cc_final: 0.3516 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0591
  time to fit residues: 3.9157
Evaluate side-chains
  38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:   30.0000
   chunk 25 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    8.9990
   overall best weight:    4.5988

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.097749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.069325 restraints weight = 11778.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.88
r_work: 0.3161 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3883  Z= 0.210
  Angle     :  0.642  10.846   5243  Z= 0.336
  Chirality :  0.044   0.145    638
  Planarity :  0.004   0.047    687
  Dihedral  :  4.183  19.549    552
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.15 %
    Favored  : 88.12 %
  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:  1.29 (0.36), residues: 522
  helix:  1.83 (0.29), residues: 297
  sheet:  0.59 (0.59), residues: 78
  loop : -1.01 (0.44), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 404 
 TYR   0.006   0.001   TYR K 478 
 PHE   0.015   0.002   PHE K 195 
 HIS   0.001   0.001   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 3883)
  covalent geometry    : angle       0.64224 ( 5243)
  hydrogen bonds       : bond        0.04847 (  262)
  hydrogen bonds       : angle       4.65092 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5095 (pp20) cc_final: 0.4182 (pt0)
REVERT: K  518 GLU cc_start: 0.5436 (pt0) cc_final: 0.5208 (pt0)
  outliers start: 7
  outliers final: 2
  residues processed: 43
  average time/residue: 0.0583
  time to fit residues: 3.3926
Evaluate side-chains
  37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  281 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 22 optimal weight:   40.0000
   chunk 48 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 26 optimal weight:    9.9990
   chunk 23 optimal weight:   30.0000
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.098124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.069848 restraints weight = 11482.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.83
r_work: 0.3177 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3883  Z= 0.136
  Angle     :  0.560  10.193   5243  Z= 0.289
  Chirality :  0.041   0.143    638
  Planarity :  0.003   0.033    687
  Dihedral  :  3.976  16.673    552
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 10.40 %
    Favored  : 87.13 %
  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:  1.48 (0.36), residues: 522
  helix:  1.99 (0.29), residues: 297
  sheet:  0.63 (0.59), residues: 78
  loop : -0.93 (0.45), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 404 
 TYR   0.007   0.001   TYR K 478 
 PHE   0.014   0.001   PHE K 195 
 HIS   0.001   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3883)
  covalent geometry    : angle       0.56018 ( 5243)
  hydrogen bonds       : bond        0.04343 (  262)
  hydrogen bonds       : angle       4.41199 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5245 (pp20) cc_final: 0.4156 (pt0)
REVERT: K  267 MET cc_start: 0.5479 (mmt) cc_final: 0.5176 (mmt)
REVERT: K  351 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7758 (pp30)
REVERT: K  518 GLU cc_start: 0.5526 (pt0) cc_final: 0.5304 (pt0)
  outliers start: 10
  outliers final: 5
  residues processed: 44
  average time/residue: 0.0630
  time to fit residues: 3.6709
Evaluate side-chains
  40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   60 ILE
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  281 PHE
Chi-restraints excluded: chain K residue  351 GLN
Chi-restraints excluded: chain K residue  355 GLU
Chi-restraints excluded: chain K residue  401 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 37 optimal weight:   30.0000
   chunk 33 optimal weight:   20.0000
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 18 optimal weight:   30.0000
   chunk 36 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   overall best weight:    6.7988

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

Flipped N/Q/H residues before XYZ refinement:
K  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.095335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.066946 restraints weight = 11690.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.86
r_work: 0.3103 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3883  Z= 0.278
  Angle     :  0.664  10.087   5243  Z= 0.343
  Chirality :  0.044   0.159    638
  Planarity :  0.004   0.040    687
  Dihedral  :  4.320  16.968    552
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 10.64 %
    Favored  : 85.89 %
  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 aren not related in a simple way.
  whole:  1.15 (0.35), residues: 522
  helix:  1.70 (0.28), residues: 297
  sheet:  0.58 (0.61), residues: 70
  loop : -0.98 (0.42), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 404 
 TYR   0.008   0.001   TYR K 199 
 PHE   0.013   0.002   PHE K 195 
 HIS   0.001   0.001   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 3883)
  covalent geometry    : angle       0.66403 ( 5243)
  hydrogen bonds       : bond        0.05145 (  262)
  hydrogen bonds       : angle       4.51128 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5755 (pp20) cc_final: 0.4655 (pt0)
REVERT: K  200 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6785 (tt)
REVERT: K  351 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8171 (pm20)
REVERT: K  518 GLU cc_start: 0.5848 (pt0) cc_final: 0.5569 (pt0)
  outliers start: 14
  outliers final: 9
  residues processed: 43
  average time/residue: 0.0699
  time to fit residues: 3.8818
Evaluate side-chains
  44 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   60 ILE
Chi-restraints excluded: chain K residue   72 GLN
Chi-restraints excluded: chain K residue   73 MET
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  200 LEU
Chi-restraints excluded: chain K residue  234 LEU
Chi-restraints excluded: chain K residue  247 LEU
Chi-restraints excluded: chain K residue  281 PHE
Chi-restraints excluded: chain K residue  351 GLN
Chi-restraints excluded: chain K residue  401 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:   20.0000
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.097387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.069435 restraints weight = 11691.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.87
r_work: 0.3163 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3883  Z= 0.128
  Angle     :  0.572  10.718   5243  Z= 0.291
  Chirality :  0.041   0.151    638
  Planarity :  0.003   0.032    687
  Dihedral  :  4.058  16.519    552
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 11.88 %
    Favored  : 84.41 %
  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:  1.48 (0.35), residues: 522
  helix:  2.03 (0.29), residues: 297
  sheet:  0.61 (0.62), residues: 70
  loop : -0.90 (0.43), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 404 
 TYR   0.008   0.001   TYR K 478 
 PHE   0.014   0.002   PHE K 195 
 HIS   0.001   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3883)
  covalent geometry    : angle       0.57205 ( 5243)
  hydrogen bonds       : bond        0.04362 (  262)
  hydrogen bonds       : angle       4.28481 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5400 (pp20) cc_final: 0.4273 (pt0)
REVERT: K  267 MET cc_start: 0.5797 (mmt) cc_final: 0.5518 (mmt)
REVERT: K  351 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7510 (pp30)
REVERT: K  518 GLU cc_start: 0.5468 (pt0) cc_final: 0.5256 (pt0)
  outliers start: 15
  outliers final: 6
  residues processed: 45
  average time/residue: 0.0784
  time to fit residues: 4.4713
Evaluate side-chains
  39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   39 VAL
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  247 LEU
Chi-restraints excluded: chain K residue  281 PHE
Chi-restraints excluded: chain K residue  351 GLN
Chi-restraints excluded: chain K residue  401 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    3.7188

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.096659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.068590 restraints weight = 12065.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.95
r_work: 0.3140 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3883  Z= 0.173
  Angle     :  0.597   9.946   5243  Z= 0.302
  Chirality :  0.041   0.146    638
  Planarity :  0.003   0.022    687
  Dihedral  :  4.083  16.801    552
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.60 %
    Favored  : 82.92 %
  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 aren not related in a simple way.
  whole:  1.47 (0.36), residues: 522
  helix:  2.04 (0.29), residues: 297
  sheet:  0.49 (0.62), residues: 70
  loop : -0.92 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 404 
 TYR   0.008   0.001   TYR K 476 
 PHE   0.014   0.002   PHE K 195 
 HIS   0.001   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3883)
  covalent geometry    : angle       0.59691 ( 5243)
  hydrogen bonds       : bond        0.04432 (  262)
  hydrogen bonds       : angle       4.28910 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5487 (pp20) cc_final: 0.4371 (pt0)
REVERT: K  267 MET cc_start: 0.5869 (mmt) cc_final: 0.5576 (mmt)
REVERT: K  351 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8152 (pm20)
REVERT: K  518 GLU cc_start: 0.5630 (pt0) cc_final: 0.5414 (pt0)
  outliers start: 10
  outliers final: 7
  residues processed: 41
  average time/residue: 0.0628
  time to fit residues: 3.4492
Evaluate side-chains
  40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   73 MET
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  247 LEU
Chi-restraints excluded: chain K residue  281 PHE
Chi-restraints excluded: chain K residue  351 GLN
Chi-restraints excluded: chain K residue  388 GLU
Chi-restraints excluded: chain K residue  401 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 4 optimal weight:    0.0980
   chunk 43 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 23 optimal weight:   30.0000
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 27 optimal weight:   40.0000
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.0188

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.097711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.069945 restraints weight = 11979.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.92
r_work: 0.3172 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3883  Z= 0.127
  Angle     :  0.584  10.860   5243  Z= 0.293
  Chirality :  0.041   0.146    638
  Planarity :  0.002   0.020    687
  Dihedral  :  3.986  18.691    552
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.35 %
    Favored  : 81.93 %
  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:  1.58 (0.36), residues: 522
  helix:  2.12 (0.29), residues: 297
  sheet:  0.50 (0.63), residues: 70
  loop : -0.83 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 404 
 TYR   0.009   0.001   TYR K 476 
 PHE   0.014   0.002   PHE K 195 
 HIS   0.001   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3883)
  covalent geometry    : angle       0.58392 ( 5243)
  hydrogen bonds       : bond        0.04148 (  262)
  hydrogen bonds       : angle       4.17468 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5249 (pp20) cc_final: 0.4210 (pt0)
REVERT: K  267 MET cc_start: 0.5850 (mmt) cc_final: 0.5547 (mmt)
REVERT: K  351 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7787 (pp30)
REVERT: K  518 GLU cc_start: 0.5491 (pt0) cc_final: 0.5283 (pt0)
  outliers start: 11
  outliers final: 8
  residues processed: 45
  average time/residue: 0.0619
  time to fit residues: 3.7294
Evaluate side-chains
  41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   39 VAL
Chi-restraints excluded: chain K residue   72 GLN
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  234 LEU
Chi-restraints excluded: chain K residue  247 LEU
Chi-restraints excluded: chain K residue  281 PHE
Chi-restraints excluded: chain K residue  351 GLN
Chi-restraints excluded: chain K residue  388 GLU
Chi-restraints excluded: chain K residue  401 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    0.3980
   chunk 29 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0570
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0670
   chunk 30 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.1040

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

Flipped N/Q/H residues before XYZ refinement:
** K 505 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 = 0.3901 r_free = 0.3901 target = 0.098445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.070859 restraints weight = 11794.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.91
r_work: 0.3190 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3883  Z= 0.115
  Angle     :  0.599  12.160   5243  Z= 0.297
  Chirality :  0.041   0.146    638
  Planarity :  0.002   0.019    687
  Dihedral  :  3.902  21.432    552
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.10 %
    Favored  : 81.93 %
  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:  1.75 (0.36), residues: 522
  helix:  2.27 (0.29), residues: 297
  sheet:  0.53 (0.64), residues: 70
  loop : -0.74 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 404 
 TYR   0.009   0.001   TYR K 476 
 PHE   0.014   0.002   PHE K 195 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3883)
  covalent geometry    : angle       0.59850 ( 5243)
  hydrogen bonds       : bond        0.03909 (  262)
  hydrogen bonds       : angle       4.07114 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5087 (pp20) cc_final: 0.3970 (pt0)
REVERT: K  267 MET cc_start: 0.5828 (mmt) cc_final: 0.5533 (mmt)
REVERT: K  351 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8201 (pm20)
  outliers start: 12
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0608
  time to fit residues: 3.7183
Evaluate side-chains
  41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   72 GLN
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  234 LEU
Chi-restraints excluded: chain K residue  247 LEU
Chi-restraints excluded: chain K residue  281 PHE
Chi-restraints excluded: chain K residue  342 ILE
Chi-restraints excluded: chain K residue  351 GLN
Chi-restraints excluded: chain K residue  388 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 41 optimal weight:    9.9990
   overall best weight:    2.4988

-------------------------------------------------------------------------------
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 = 0.3886 r_free = 0.3886 target = 0.097741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.070001 restraints weight = 11889.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.92
r_work: 0.3169 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3883  Z= 0.141
  Angle     :  0.631  12.433   5243  Z= 0.310
  Chirality :  0.042   0.150    638
  Planarity :  0.003   0.021    687
  Dihedral  :  3.995  21.529    552
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.84 %
    Favored  : 81.44 %
  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:  1.66 (0.36), residues: 522
  helix:  2.24 (0.29), residues: 297
  sheet:  0.41 (0.64), residues: 70
  loop : -0.87 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 404 
 TYR   0.009   0.001   TYR K 476 
 PHE   0.012   0.001   PHE K 195 
 HIS   0.001   0.001   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3883)
  covalent geometry    : angle       0.63069 ( 5243)
  hydrogen bonds       : bond        0.04095 (  262)
  hydrogen bonds       : angle       4.07451 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5245 (pp20) cc_final: 0.4237 (pt0)
REVERT: K  267 MET cc_start: 0.5859 (mmt) cc_final: 0.5570 (mmt)
REVERT: K  351 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7768 (pp30)
  outliers start: 11
  outliers final: 8
  residues processed: 43
  average time/residue: 0.0592
  time to fit residues: 3.4132
Evaluate side-chains
  41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   72 GLN
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  232 GLU
Chi-restraints excluded: chain K residue  234 LEU
Chi-restraints excluded: chain K residue  247 LEU
Chi-restraints excluded: chain K residue  281 PHE
Chi-restraints excluded: chain K residue  351 GLN
Chi-restraints excluded: chain K residue  388 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:   20.0000
   chunk 40 optimal weight:    5.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.097763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.069759 restraints weight = 11888.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.93
r_work: 0.3167 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3883  Z= 0.134
  Angle     :  0.654  12.533   5243  Z= 0.319
  Chirality :  0.042   0.158    638
  Planarity :  0.003   0.020    687
  Dihedral  :  4.002  21.903    552
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.09 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.36), residues: 522
  helix:  2.27 (0.29), residues: 297
  sheet:  0.29 (0.64), residues: 70
  loop : -0.85 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 285 
 TYR   0.009   0.001   TYR K 476 
 PHE   0.014   0.002   PHE K 195 
 HIS   0.001   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3883)
  covalent geometry    : angle       0.65428 ( 5243)
  hydrogen bonds       : bond        0.04052 (  262)
  hydrogen bonds       : angle       4.10098 (  756)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   61 GLU cc_start: 0.5281 (pp20) cc_final: 0.4216 (pt0)
REVERT: K  267 MET cc_start: 0.5945 (mmt) cc_final: 0.5656 (mmt)
REVERT: K  351 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7572 (pp30)
  outliers start: 11
  outliers final: 8
  residues processed: 42
  average time/residue: 0.0620
  time to fit residues: 3.4304
Evaluate side-chains
  43 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   39 VAL
Chi-restraints excluded: chain K residue   72 GLN
Chi-restraints excluded: chain K residue  164 GLU
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  232 GLU
Chi-restraints excluded: chain K residue  247 LEU
Chi-restraints excluded: chain K residue  281 PHE
Chi-restraints excluded: chain K residue  351 GLN
Chi-restraints excluded: chain K residue  388 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    0.1980
   chunk 36 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:   10.0000
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.097927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.070019 restraints weight = 11826.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.90
r_work: 0.3169 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3883  Z= 0.130
  Angle     :  0.637  12.578   5243  Z= 0.315
  Chirality :  0.041   0.147    638
  Planarity :  0.003   0.020    687
  Dihedral  :  4.004  21.591    552
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.09 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.36), residues: 522
  helix:  2.30 (0.29), residues: 297
  sheet:  0.24 (0.61), residues: 78
  loop : -0.96 (0.46), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 404 
 TYR   0.009   0.001   TYR K 476 
 PHE   0.013   0.001   PHE K 195 
 HIS   0.001   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3883)
  covalent geometry    : angle       0.63670 ( 5243)
  hydrogen bonds       : bond        0.04021 (  262)
  hydrogen bonds       : angle       4.11726 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1167.53 seconds
wall clock time: 20 minutes 45.73 seconds (1245.73 seconds total)