Starting phenix.real_space_refine
on Fri Aug 22 14:10:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xop_33355/08_2025/7xop_33355.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xop_33355/08_2025/7xop_33355.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/7xop_33355/08_2025/7xop_33355.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xop_33355/08_2025/7xop_33355.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xop_33355/08_2025/7xop_33355.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xop_33355/08_2025/7xop_33355.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 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 0.97, per 1000 atoms: 0.25
  Number of scatterers: 3855
  At special positions: 0
  Unit cell: (72.21, 85.26, 71.34, 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: 0.23
  Conformation dependent library (CDL) restraints added in 117.0 milliseconds
  
  Enol-peptide restraints added in 238.4 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:
      18 helices and 7 sheets defined
      58.6% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'K' and resid 9 through 29
      removed outlier: 4.177A  pdb=" N   VAL K  29 " --> pdb=" O   ASP K  25 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 52 through 60
      removed outlier: 3.773A  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 110
      removed outlier: 3.575A  pdb=" N   GLY K 110 " --> pdb=" O   ALA K 106 " (cutoff:3.500A)
    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
      removed outlier: 3.558A  pdb=" N   GLY K 159 " --> pdb=" O   ASP K 155 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 201 through 205
    Processing helix  chain 'K' and resid 233 through 244
    Processing helix  chain 'K' and resid 256 through 269
    Processing helix  chain 'K' and resid 282 through 297
    Processing helix  chain 'K' and resid 338 through 355
    Processing helix  chain 'K' and resid 359 through 375
      removed outlier: 4.053A  pdb=" N   GLY K 375 " --> pdb=" O   LYS K 371 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 385 through 410
    Processing helix  chain 'K' and resid 416 through 427
      removed outlier: 3.834A  pdb=" N   ILE K 420 " --> pdb=" O   GLY K 416 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 433 through 458
      Proline residue:  K 450  - end of helix
    Processing helix  chain 'K' and resid 461 through 472
    Processing helix  chain 'K' and resid 497 through 516
    Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 5
    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
      removed outlier: 6.530A  pdb=" N   VAL K 174 " --> pdb=" O   ALA K 377 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   ILE K 379 " --> pdb=" O   VAL K 174 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   THR K 176 " --> pdb=" O   ILE K 379 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   VAL K 381 " --> pdb=" O   THR K 176 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   GLU K 178 " --> pdb=" O   VAL K 381 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 192 through 193
    Processing sheet with id=AA5, first strand: chain 'K' and resid 273 through 277
    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
      removed outlier: 3.670A  pdb=" N   GLU K 484 " --> pdb=" O   ASN K 479 " (cutoff:3.500A)

    264 hydrogen bonds defined for protein.
    762 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: 0.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1340
        1.34 -     1.46: 490
        1.46 -     1.57: 2016
        1.57 -     1.69: 0
        1.69 -     1.80: 37
  Bond restraints: 3883
  Sorted by residual:
  bond pdb=" SD  MET K 520 "
       pdb=" CE  MET K 520 "
    ideal  model  delta    sigma   weight residual
    1.791  1.759  0.032 2.50e-02 1.60e+03 1.62e+00
  bond pdb=" CA  MET K 520 "
       pdb=" CB  MET K 520 "
    ideal  model  delta    sigma   weight residual
    1.536  1.510  0.026 2.08e-02 2.31e+03 1.54e+00
  bond pdb=" CB  MET K 520 "
       pdb=" CG  MET K 520 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CA  GLY K 256 "
       pdb=" C   GLY K 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.508  0.012 1.28e-02 6.10e+03 8.15e-01
  bond pdb=" SD  MET K  16 "
       pdb=" CE  MET K  16 "
    ideal  model  delta    sigma   weight residual
    1.791  1.771  0.020 2.50e-02 1.60e+03 6.30e-01
  ... (remaining 3878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 5166
        1.55 -     3.10: 68
        3.10 -     4.65: 4
        4.65 -     6.20: 4
        6.20 -     7.75: 1
  Bond angle restraints: 5243
  Sorted by residual:
  angle pdb=" CB  MET K 520 "
        pdb=" CG  MET K 520 "
        pdb=" SD  MET K 520 "
      ideal   model   delta    sigma   weight residual
     112.70  104.95    7.75 3.00e+00 1.11e-01 6.67e+00
  angle pdb=" N   ALA K 449 "
        pdb=" CA  ALA K 449 "
        pdb=" C   ALA K 449 "
      ideal   model   delta    sigma   weight residual
     112.75  115.50   -2.75 1.36e+00 5.41e-01 4.09e+00
  angle pdb=" CB  MET K 166 "
        pdb=" CG  MET K 166 "
        pdb=" SD  MET K 166 "
      ideal   model   delta    sigma   weight residual
     112.70  118.43   -5.73 3.00e+00 1.11e-01 3.64e+00
  angle pdb=" C   GLU K 409 "
        pdb=" N   GLY K 410 "
        pdb=" CA  GLY K 410 "
      ideal   model   delta    sigma   weight residual
     121.45  118.95    2.50 1.54e+00 4.22e-01 2.63e+00
  angle pdb=" C   ASP K 490 "
        pdb=" N   MET K 491 "
        pdb=" CA  MET K 491 "
      ideal   model   delta    sigma   weight residual
     122.65  120.08    2.57 1.60e+00 3.91e-01 2.58e+00
  ... (remaining 5238 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 2262
       17.68 -    35.37: 126
       35.37 -    53.05: 20
       53.05 -    70.73: 3
       70.73 -    88.41: 1
  Dihedral angle restraints: 2412
    sinusoidal: 934
      harmonic: 1478
  Sorted by residual:
  dihedral pdb=" CA  ASP K 224 "
           pdb=" CB  ASP K 224 "
           pdb=" CG  ASP K 224 "
           pdb=" OD1 ASP K 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.40   56.40     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" CB  GLU K 102 "
           pdb=" CG  GLU K 102 "
           pdb=" CD  GLU K 102 "
           pdb=" OE1 GLU K 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.41  -88.41     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  MET K 491 "
           pdb=" C   MET K 491 "
           pdb=" N   GLY K 492 "
           pdb=" CA  GLY K 492 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.92   15.08     0      5.00e+00 4.00e-02 9.09e+00
  ... (remaining 2409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 360
       0.024 -    0.048: 159
       0.048 -    0.072: 65
       0.072 -    0.096: 34
       0.096 -    0.120: 20
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" CA  VAL K 136 "
            pdb=" N   VAL K 136 "
            pdb=" C   VAL K 136 "
            pdb=" CB  VAL K 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  PRO K 462 "
            pdb=" N   PRO K 462 "
            pdb=" C   PRO K 462 "
            pdb=" CB  PRO K 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  VAL K 412 "
            pdb=" N   VAL K 412 "
            pdb=" C   VAL K 412 "
            pdb=" CB  VAL K 412 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.43e-01
  ... (remaining 635 not shown)

  Planarity restraints: 687
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K 245 "   -0.016 5.00e-02 4.00e+02   2.43e-02 9.45e-01
        pdb=" N   PRO K 246 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO K 246 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO K 246 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER K 201 "    0.014 5.00e-02 4.00e+02   2.14e-02 7.33e-01
        pdb=" N   PRO K 202 "   -0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO K 202 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO K 202 "    0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL K 336 "    0.003 2.00e-02 2.50e+03   6.64e-03 4.41e-01
        pdb=" C   VAL K 336 "   -0.011 2.00e-02 2.50e+03
        pdb=" O   VAL K 336 "    0.004 2.00e-02 2.50e+03
        pdb=" N   GLY K 337 "    0.004 2.00e-02 2.50e+03
  ... (remaining 684 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 247
        2.73 -     3.27: 4008
        3.27 -     3.82: 6482
        3.82 -     4.36: 7028
        4.36 -     4.90: 12698
  Nonbonded interactions: 30463
  Sorted by model distance:
  nonbonded pdb=" OG1 THR K 299 "
            pdb=" OD1 ASP K 316 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" NH2 ARG K 421 "
            pdb=" O   VAL K 469 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OD1 ASP K 115 "
            pdb=" NH2 ARG K 118 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" O   GLY K  35 "
            pdb=" NZ  LYS K  51 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" OE2 GLU K 214 "
            pdb=" NH2 ARG K 322 "
     model   vdw
     2.336 3.120
  ... (remaining 30458 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:             2.850
  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:                    0.010
  Process input model:                     5.140
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
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   0.032   3883  Z= 0.136
  Angle     :  0.491   7.745   5243  Z= 0.271
  Chirality :  0.039   0.120    638
  Planarity :  0.002   0.024    687
  Dihedral  : 11.427  88.413   1464
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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 aren not related in a simple way.
  whole:  2.31 (0.36), residues: 522
  helix:  2.48 (0.29), residues: 294
  sheet:  0.33 (0.51), residues: 88
  loop :  0.38 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K 268 
 TYR   0.007   0.001   TYR K 506 
 PHE   0.007   0.001   PHE K 195 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3883)
  covalent geometry    : angle       0.49088 ( 5243)
  hydrogen bonds       : bond        0.15167 (  264)
  hydrogen bonds       : angle       5.31828 (  762)

*********************** 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
  33 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.090 
Fit side-chains
REVERT: K  191 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7343 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1009
  time to fit residues: 4.0031
Evaluate side-chains
  25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.6982

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

Flipped N/Q/H residues before XYZ refinement:
K 432 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.077511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.064089 restraints weight = 11278.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 2.94
r_work: 0.2999 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3883  Z= 0.129
  Angle     :  0.495   4.943   5243  Z= 0.268
  Chirality :  0.040   0.141    638
  Planarity :  0.003   0.025    687
  Dihedral  :  3.676  14.253    552
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.36), residues: 522
  helix:  2.31 (0.29), residues: 301
  sheet:  0.21 (0.57), residues: 72
  loop :  0.12 (0.49), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  18 
 TYR   0.009   0.001   TYR K 199 
 PHE   0.011   0.001   PHE K 195 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3883)
  covalent geometry    : angle       0.49512 ( 5243)
  hydrogen bonds       : bond        0.04602 (  264)
  hydrogen bonds       : angle       4.39790 (  762)

*********************** 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
  26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.153 
Fit side-chains
REVERT: K  193 MET cc_start: 0.8301 (ptt) cc_final: 0.7868 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0485
  time to fit residues: 1.8588
Evaluate side-chains
  26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 46 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    4.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.074892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.061585 restraints weight = 11147.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.83
r_work: 0.2931 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3883  Z= 0.242
  Angle     :  0.571   6.286   5243  Z= 0.300
  Chirality :  0.043   0.132    638
  Planarity :  0.003   0.022    687
  Dihedral  :  3.888  19.776    552
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.67 %
    Favored  : 91.34 %
  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 (0.35), residues: 522
  helix:  2.13 (0.29), residues: 299
  sheet: -0.10 (0.55), residues: 72
  loop : -0.10 (0.47), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  18 
 TYR   0.011   0.002   TYR K 199 
 PHE   0.020   0.002   PHE K  44 
 HIS   0.001   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 ( 3883)
  covalent geometry    : angle       0.57058 ( 5243)
  hydrogen bonds       : bond        0.04780 (  264)
  hydrogen bonds       : angle       4.39932 (  762)

*********************** 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
  27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.158 
Fit side-chains
REVERT: K  520 MET cc_start: 0.8637 (mtt) cc_final: 0.8195 (mtt)
  outliers start: 4
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0485
  time to fit residues: 1.8472
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  294 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3381 r_free = 0.3381 target = 0.075031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.061888 restraints weight = 11113.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.82
r_work: 0.2953 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3883  Z= 0.173
  Angle     :  0.516   6.100   5243  Z= 0.274
  Chirality :  0.041   0.137    638
  Planarity :  0.002   0.021    687
  Dihedral  :  3.812  14.037    552
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.89 %
    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:  1.69 (0.35), residues: 522
  helix:  2.11 (0.28), residues: 299
  sheet: -0.20 (0.56), residues: 69
  loop : -0.14 (0.48), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  18 
 TYR   0.010   0.001   TYR K 199 
 PHE   0.011   0.001   PHE K 195 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 3883)
  covalent geometry    : angle       0.51566 ( 5243)
  hydrogen bonds       : bond        0.04393 (  264)
  hydrogen bonds       : angle       4.29201 (  762)

*********************** 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
  25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.154 
Fit side-chains
REVERT: K  193 MET cc_start: 0.8729 (ppp) cc_final: 0.7664 (ptm)
REVERT: K  520 MET cc_start: 0.8563 (mtt) cc_final: 0.8302 (mtt)
  outliers start: 4
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0430
  time to fit residues: 1.6070
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3382 r_free = 0.3382 target = 0.075128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.061939 restraints weight = 11142.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 2.88
r_work: 0.2946 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3883  Z= 0.156
  Angle     :  0.496   6.110   5243  Z= 0.263
  Chirality :  0.040   0.133    638
  Planarity :  0.002   0.021    687
  Dihedral  :  3.755  13.955    552
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.13 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.36), residues: 522
  helix:  2.16 (0.29), residues: 299
  sheet: -0.43 (0.53), residues: 85
  loop :  0.05 (0.52), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  18 
 TYR   0.009   0.001   TYR K 199 
 PHE   0.012   0.001   PHE K 195 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3883)
  covalent geometry    : angle       0.49557 ( 5243)
  hydrogen bonds       : bond        0.04230 (  264)
  hydrogen bonds       : angle       4.21921 (  762)

*********************** 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
  28 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.137 
Fit side-chains
REVERT: K  193 MET cc_start: 0.8798 (ppp) cc_final: 0.7736 (ptm)
REVERT: K  520 MET cc_start: 0.8685 (mtt) cc_final: 0.8485 (mtt)
  outliers start: 4
  outliers final: 1
  residues processed: 27
  average time/residue: 0.0427
  time to fit residues: 1.6576
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  294 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 36 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.076174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.062637 restraints weight = 11371.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 2.98
r_work: 0.2962 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3883  Z= 0.121
  Angle     :  0.470   6.422   5243  Z= 0.251
  Chirality :  0.040   0.133    638
  Planarity :  0.002   0.020    687
  Dihedral  :  3.693  13.292    552
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 13.12 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.36), residues: 522
  helix:  2.26 (0.29), residues: 299
  sheet: -0.47 (0.53), residues: 85
  loop :  0.11 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 395 
 TYR   0.009   0.001   TYR K 199 
 PHE   0.019   0.002   PHE K  44 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3883)
  covalent geometry    : angle       0.46969 ( 5243)
  hydrogen bonds       : bond        0.03984 (  264)
  hydrogen bonds       : angle       4.14513 (  762)

*********************** 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
  25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.157 
Fit side-chains
REVERT: K  193 MET cc_start: 0.8863 (ppp) cc_final: 0.7794 (ptm)
  outliers start: 3
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0476
  time to fit residues: 1.7693
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  294 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 4 optimal weight:    0.0470
   chunk 43 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0570
   chunk 45 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.8202

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.076482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.063269 restraints weight = 11294.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.90
r_work: 0.2971 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3883  Z= 0.126
  Angle     :  0.479   7.910   5243  Z= 0.254
  Chirality :  0.040   0.140    638
  Planarity :  0.002   0.020    687
  Dihedral  :  3.673  13.045    552
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 13.61 %
    Favored  : 86.14 %
  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:  1.85 (0.36), residues: 522
  helix:  2.27 (0.29), residues: 299
  sheet: -0.51 (0.52), residues: 85
  loop :  0.16 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  18 
 TYR   0.009   0.001   TYR K 199 
 PHE   0.008   0.001   PHE K 195 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3883)
  covalent geometry    : angle       0.47937 ( 5243)
  hydrogen bonds       : bond        0.03975 (  264)
  hydrogen bonds       : angle       4.12061 (  762)

*********************** 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
  24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.112 
Fit side-chains
REVERT: K  193 MET cc_start: 0.8877 (ppp) cc_final: 0.7843 (ptm)
  outliers start: 1
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0548
  time to fit residues: 1.8582
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  294 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
K 432 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.078491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.065023 restraints weight = 11101.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 3.02
r_work: 0.3035 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3883  Z= 0.109
  Angle     :  0.478   7.781   5243  Z= 0.254
  Chirality :  0.039   0.136    638
  Planarity :  0.002   0.020    687
  Dihedral  :  3.626  12.398    552
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 13.61 %
    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:  1.77 (0.36), residues: 522
  helix:  2.15 (0.29), residues: 303
  sheet: -0.29 (0.53), residues: 80
  loop : -0.01 (0.52), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  18 
 TYR   0.008   0.001   TYR K 199 
 PHE   0.017   0.001   PHE K  44 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3883)
  covalent geometry    : angle       0.47804 ( 5243)
  hydrogen bonds       : bond        0.03880 (  264)
  hydrogen bonds       : angle       4.06378 (  762)

*********************** 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
  25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.149 
Fit side-chains
REVERT: K  193 MET cc_start: 0.8848 (ppp) cc_final: 0.7798 (ptm)
  outliers start: 2
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0581
  time to fit residues: 2.0220
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  294 THR
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:    4.9990
   chunk 8 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
K 432 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.075907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.062135 restraints weight = 11130.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 2.98
r_work: 0.2969 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3883  Z= 0.218
  Angle     :  0.579  12.861   5243  Z= 0.301
  Chirality :  0.042   0.141    638
  Planarity :  0.002   0.021    687
  Dihedral  :  3.782  13.605    552
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 13.86 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.36), residues: 522
  helix:  1.97 (0.29), residues: 302
  sheet: -0.59 (0.52), residues: 85
  loop :  0.14 (0.54), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 231 
 TYR   0.010   0.001   TYR K 199 
 PHE   0.009   0.001   PHE K 195 
 HIS   0.001   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 3883)
  covalent geometry    : angle       0.57853 ( 5243)
  hydrogen bonds       : bond        0.04526 (  264)
  hydrogen bonds       : angle       4.28441 (  762)

*********************** 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
  24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.105 
Fit side-chains
REVERT: K  193 MET cc_start: 0.8852 (ppp) cc_final: 0.7874 (ptm)
  outliers start: 2
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0420
  time to fit residues: 1.4147
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  294 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.077236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.063081 restraints weight = 11297.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 3.13
r_work: 0.2984 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3883  Z= 0.143
  Angle     :  0.537   9.872   5243  Z= 0.278
  Chirality :  0.040   0.136    638
  Planarity :  0.002   0.022    687
  Dihedral  :  3.766  13.331    552
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 13.61 %
    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:  1.57 (0.36), residues: 522
  helix:  2.00 (0.29), residues: 302
  sheet: -0.60 (0.53), residues: 85
  loop :  0.11 (0.54), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 395 
 TYR   0.009   0.001   TYR K 199 
 PHE   0.018   0.002   PHE K  44 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3883)
  covalent geometry    : angle       0.53743 ( 5243)
  hydrogen bonds       : bond        0.04155 (  264)
  hydrogen bonds       : angle       4.20675 (  762)

********************** 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
  24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.161 
Fit side-chains
REVERT: K  193 MET cc_start: 0.8913 (ppp) cc_final: 0.7873 (ptm)
  outliers start: 2
  outliers final: 1
  residues processed: 23
  average time/residue: 0.0631
  time to fit residues: 2.0440
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  294 THR
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:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 26 optimal weight:    0.0980
   overall best weight:    2.4188

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.076706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.062624 restraints weight = 11334.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 3.11
r_work: 0.2975 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3883  Z= 0.146
  Angle     :  0.522   9.834   5243  Z= 0.273
  Chirality :  0.040   0.133    638
  Planarity :  0.002   0.021    687
  Dihedral  :  3.734  14.651    552
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 13.86 %
    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:  1.66 (0.36), residues: 522
  helix:  2.12 (0.29), residues: 301
  sheet: -0.58 (0.52), residues: 85
  loop :  0.05 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  18 
 TYR   0.009   0.001   TYR K 199 
 PHE   0.009   0.001   PHE K 195 
 HIS   0.000   0.000   HIS K 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3883)
  covalent geometry    : angle       0.52248 ( 5243)
  hydrogen bonds       : bond        0.04158 (  264)
  hydrogen bonds       : angle       4.16885 (  762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 799.02 seconds
wall clock time: 14 minutes 26.13 seconds (866.13 seconds total)