Starting phenix.real_space_refine
on Tue Feb  3 14:45:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wn1_32619/02_2026/7wn1_32619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wn1_32619/02_2026/7wn1_32619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wn1_32619/02_2026/7wn1_32619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wn1_32619/02_2026/7wn1_32619.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wn1_32619/02_2026/7wn1_32619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wn1_32619/02_2026/7wn1_32619.cif"
  }
  resolution = 3.11
  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=   0.033
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      26      5.16       5
     C    2572      2.51       5
     N     616      2.21       5
     O     687      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3901
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2953
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 11, 'TRANS': 359}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 929
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'NOS%rna2p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna2p': 1}
  Time building chain proxies: 0.68, per 1000 atoms: 0.17
  Number of scatterers: 3901
  At special positions: 0
  Unit cell: (110.39, 60.59, 64.74, 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      26     16.00
     O     687      8.00
     N     616      7.00
     C    2572      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.19
  Conformation dependent library (CDL) restraints added in 89.2 milliseconds
  

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  914

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 3 sheets defined
      64.3% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 59
      removed outlier: 4.331A  pdb=" N   VAL A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   TRP A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 83
      removed outlier: 3.547A  pdb=" N   ASN A  66 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE A  82 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 88
      No H-bonds generated for 'chain 'A' and resid 86 through 88'
    Processing helix  chain 'A' and resid 89 through 111
    Processing helix  chain 'A' and resid 112 through 144
    Processing helix  chain 'A' and resid 149 through 175
      removed outlier: 3.802A  pdb=" N   GLN A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   PHE A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 210
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 239 through 257
      removed outlier: 3.734A  pdb=" N   ILE A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN A 250 " --> pdb=" O   MET A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 270
      removed outlier: 3.674A  pdb=" N   GLN A 266 " --> pdb=" O   HIS A 262 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 290
      removed outlier: 3.759A  pdb=" N   THR A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ILE A 278 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A 283 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   PHE A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
      removed outlier: 3.967A  pdb=" N   ASN A 295 " --> pdb=" O   ARG A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 319
    Processing helix  chain 'A' and resid 321 through 332
      removed outlier: 3.538A  pdb=" N   TRP A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA A 330 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 369
      removed outlier: 3.804A  pdb=" N   LEU A 350 " --> pdb=" O   CYS A 346 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      Proline residue:  A 361  - end of helix
      removed outlier: 5.181A  pdb=" N   VAL A 366 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   LYS A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU A 368 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 400
      removed outlier: 3.655A  pdb=" N   ILE A 378 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR A 400 " --> pdb=" O   GLY A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
    Processing helix  chain 'C' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.193A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   ARG C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   LEU C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.193A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN C 109 " --> pdb=" O   THR C  99 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    750 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: 0.44

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 823
        1.33 -     1.45: 929
        1.45 -     1.57: 2205
        1.57 -     1.69: 2
        1.69 -     1.81: 39
  Bond restraints: 3998
  Sorted by residual:
  bond pdb=" C1' NOS A 501 "
       pdb=" O4' NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.600 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C1' NOS A 501 "
       pdb=" C2' NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.528  1.346  0.182 2.00e-02 2.50e+03 8.30e+01
  bond pdb=" C2  NOS A 501 "
       pdb=" N3  NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.293  1.444 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C4  NOS A 501 "
       pdb=" N3  NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.347  1.497 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" C4' NOS A 501 "
       pdb=" O4' NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.432  1.309  0.123 2.00e-02 2.50e+03 3.77e+01
  ... (remaining 3993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 5331
        2.00 -     4.00: 75
        4.00 -     6.00: 17
        6.00 -     8.00: 4
        8.00 -    10.00: 2
  Bond angle restraints: 5429
  Sorted by residual:
  angle pdb=" C5  NOS A 501 "
        pdb=" C6  NOS A 501 "
        pdb=" O6  NOS A 501 "
      ideal   model   delta    sigma   weight residual
     128.65  118.65   10.00 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" N   SER A 308 "
        pdb=" CA  SER A 308 "
        pdb=" C   SER A 308 "
      ideal   model   delta    sigma   weight residual
     107.88  112.42   -4.54 1.41e+00 5.03e-01 1.04e+01
  angle pdb=" C3' NOS A 501 "
        pdb=" C2' NOS A 501 "
        pdb=" O2' NOS A 501 "
      ideal   model   delta    sigma   weight residual
     116.89  107.68    9.21 3.00e+00 1.11e-01 9.42e+00
  angle pdb=" C   TYR C  37 "
        pdb=" N   ARG C  38 "
        pdb=" CA  ARG C  38 "
      ideal   model   delta    sigma   weight residual
     122.65  118.88    3.77 1.49e+00 4.50e-01 6.40e+00
  angle pdb=" C2  NOS A 501 "
        pdb=" N3  NOS A 501 "
        pdb=" C4  NOS A 501 "
      ideal   model   delta    sigma   weight residual
     112.58  119.70   -7.12 3.00e+00 1.11e-01 5.63e+00
  ... (remaining 5424 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.24: 2048
       15.24 -    30.48: 199
       30.48 -    45.71: 56
       45.71 -    60.95: 17
       60.95 -    76.19: 3
  Dihedral angle restraints: 2323
    sinusoidal: 899
      harmonic: 1424
  Sorted by residual:
  dihedral pdb=" CA  LEU A 256 "
           pdb=" C   LEU A 256 "
           pdb=" N   PHE A 257 "
           pdb=" CA  PHE A 257 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.88  -18.12     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  MET A 145 "
           pdb=" C   MET A 145 "
           pdb=" N   GLU A 146 "
           pdb=" CA  GLU A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.85   17.15     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  VAL A 332 "
           pdb=" C   VAL A 332 "
           pdb=" N   ASP A 333 "
           pdb=" CA  ASP A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.41  -15.59     0      5.00e+00 4.00e-02 9.72e+00
  ... (remaining 2320 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 372
       0.031 -    0.061: 174
       0.061 -    0.092: 56
       0.092 -    0.122: 20
       0.122 -    0.153: 8
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CB  ILE A 193 "
            pdb=" CA  ILE A 193 "
            pdb=" CG1 ILE A 193 "
            pdb=" CG2 ILE A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" C1' NOS A 501 "
            pdb=" C2' NOS A 501 "
            pdb=" N9  NOS A 501 "
            pdb=" O4' NOS A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.50   -0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  ASP A 147 "
            pdb=" N   ASP A 147 "
            pdb=" C   ASP A 147 "
            pdb=" CB  ASP A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 627 not shown)

  Planarity restraints: 665
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 257 "   -0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO A 258 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 258 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 258 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 334 "   -0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO A 335 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 335 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 335 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 412 "   -0.020 5.00e-02 4.00e+02   3.08e-02 1.51e+00
        pdb=" N   PRO A 413 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 413 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 413 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 662 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 835
        2.78 -     3.31: 3841
        3.31 -     3.84: 6568
        3.84 -     4.37: 7875
        4.37 -     4.90: 13686
  Nonbonded interactions: 32805
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  65 "
            pdb=" OD1 ASP A 117 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG1 THR A  41 "
            pdb=" OD1 ASN A 209 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   CYS A 395 "
            pdb=" OG1 THR A 399 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   LEU A 256 "
            pdb=" N   GLY A 261 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NE2 GLN C  81 "
            pdb=" OD1 ASN C  83 "
     model   vdw
     2.320 3.120
  ... (remaining 32800 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             1.300
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.570
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
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      :  0.007   0.203   3999  Z= 0.360
  Angle     :  0.651  10.003   5431  Z= 0.333
  Chirality :  0.042   0.153    630
  Planarity :  0.004   0.035    665
  Dihedral  : 13.871  76.187   1406
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.38), residues: 487
  helix:  1.09 (0.30), residues: 285
  sheet:  0.84 (0.64), residues: 58
  loop : -0.10 (0.58), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 319 
 TYR   0.018   0.001   TYR C 102 
 PHE   0.016   0.001   PHE C  27 
 TRP   0.009   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00727 ( 3998)
  covalent geometry    : angle       0.65079 ( 5429)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       0.17564 (    2)
  hydrogen bonds       : bond        0.18087 (  256)
  hydrogen bonds       : angle       6.16735 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A  175 VAL cc_start: 0.8097 (t) cc_final: 0.7828 (m)
REVERT: A  303 LYS cc_start: 0.8628 (tppt) cc_final: 0.8418 (tppt)
REVERT: A  407 ASN cc_start: 0.8197 (t0) cc_final: 0.7963 (t0)
REVERT: C   94 TYR cc_start: 0.8213 (m-10) cc_final: 0.8003 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0414
  time to fit residues: 3.9045
Evaluate side-chains
  62 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 209 ASN
C  58 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.113197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.099941 restraints weight = 5220.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.61
r_work: 0.3052 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3999  Z= 0.156
  Angle     :  0.570   6.524   5431  Z= 0.308
  Chirality :  0.043   0.144    630
  Planarity :  0.004   0.033    665
  Dihedral  :  5.672  35.770    540
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  5.35 %
    Favored  : 92.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.38), residues: 487
  helix:  1.49 (0.29), residues: 289
  sheet:  0.96 (0.64), residues: 58
  loop : -0.17 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 319 
 TYR   0.015   0.001   TYR C 102 
 PHE   0.017   0.001   PHE C  27 
 TRP   0.012   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3998)
  covalent geometry    : angle       0.57057 ( 5429)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.30316 (    2)
  hydrogen bonds       : bond        0.05767 (  256)
  hydrogen bonds       : angle       4.66742 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  303 LYS cc_start: 0.8769 (tppt) cc_final: 0.8551 (tppt)
REVERT: A  407 ASN cc_start: 0.8453 (t0) cc_final: 0.8097 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 64
  average time/residue: 0.0751
  time to fit residues: 6.0458
Evaluate side-chains
  59 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   39 GLN
Chi-restraints excluded: chain C residue   82 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 42 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.112554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.098906 restraints weight = 5091.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.65
r_work: 0.3067 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3999  Z= 0.138
  Angle     :  0.535   6.531   5431  Z= 0.288
  Chirality :  0.042   0.146    630
  Planarity :  0.004   0.034    665
  Dihedral  :  5.270  31.851    540
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  9.07 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.38), residues: 487
  helix:  1.76 (0.29), residues: 288
  sheet:  1.14 (0.64), residues: 58
  loop : -0.04 (0.59), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 319 
 TYR   0.018   0.001   TYR C 102 
 PHE   0.016   0.001   PHE C  27 
 TRP   0.013   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3998)
  covalent geometry    : angle       0.53534 ( 5429)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.32927 (    2)
  hydrogen bonds       : bond        0.04993 (  256)
  hydrogen bonds       : angle       4.37091 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.8778 (tppt) cc_final: 0.8552 (tppt)
  outliers start: 10
  outliers final: 7
  residues processed: 63
  average time/residue: 0.0682
  time to fit residues: 5.5532
Evaluate side-chains
  63 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 25 optimal weight:    0.3980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** 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 = 0.3346 r_free = 0.3346 target = 0.113117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.099804 restraints weight = 5121.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.59
r_work: 0.3072 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3999  Z= 0.138
  Angle     :  0.528   6.805   5431  Z= 0.283
  Chirality :  0.042   0.142    630
  Planarity :  0.004   0.035    665
  Dihedral  :  5.075  29.008    540
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 11.63 %
    Favored  : 85.12 %
  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 are not related in a simple way.
  whole:  1.87 (0.38), residues: 487
  helix:  1.87 (0.29), residues: 288
  sheet:  1.19 (0.65), residues: 58
  loop :  0.01 (0.59), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C  66 
 TYR   0.020   0.001   TYR C 102 
 PHE   0.015   0.001   PHE C  27 
 TRP   0.011   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3998)
  covalent geometry    : angle       0.52813 ( 5429)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.33217 (    2)
  hydrogen bonds       : bond        0.04791 (  256)
  hydrogen bonds       : angle       4.26594 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8225 (m-30)
REVERT: A  303 LYS cc_start: 0.8794 (tppt) cc_final: 0.8567 (tppt)
  outliers start: 14
  outliers final: 8
  residues processed: 61
  average time/residue: 0.0594
  time to fit residues: 4.8016
Evaluate side-chains
  65 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 6 optimal weight:    0.1980
   chunk 17 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 358 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.113106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.099739 restraints weight = 5130.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.60
r_work: 0.3072 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3999  Z= 0.138
  Angle     :  0.528   7.205   5431  Z= 0.282
  Chirality :  0.042   0.147    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.962  26.930    540
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 12.56 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.38), residues: 487
  helix:  1.82 (0.29), residues: 294
  sheet:  1.12 (0.65), residues: 58
  loop :  0.10 (0.60), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  66 
 TYR   0.018   0.001   TYR C 102 
 PHE   0.014   0.001   PHE C  27 
 TRP   0.011   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3998)
  covalent geometry    : angle       0.52780 ( 5429)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.32694 (    2)
  hydrogen bonds       : bond        0.04745 (  256)
  hydrogen bonds       : angle       4.21580 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8245 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0399
  time to fit residues: 3.3061
Evaluate side-chains
  65 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.111584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.097710 restraints weight = 5150.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.65
r_work: 0.3050 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3999  Z= 0.146
  Angle     :  0.535   6.368   5431  Z= 0.286
  Chirality :  0.042   0.150    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.950  26.428    540
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 13.72 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.38), residues: 487
  helix:  1.81 (0.29), residues: 294
  sheet:  1.05 (0.65), residues: 58
  loop :  0.19 (0.59), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  66 
 TYR   0.018   0.001   TYR C 102 
 PHE   0.014   0.001   PHE C  27 
 TRP   0.009   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3998)
  covalent geometry    : angle       0.53505 ( 5429)
  SS BOND              : bond        0.00181 (    1)
  SS BOND              : angle       0.40435 (    2)
  hydrogen bonds       : bond        0.04822 (  256)
  hydrogen bonds       : angle       4.21179 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8250 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0456
  time to fit residues: 3.6427
Evaluate side-chains
  67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3340 r_free = 0.3340 target = 0.112348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.098427 restraints weight = 5193.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.66
r_work: 0.3065 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3999  Z= 0.136
  Angle     :  0.528   7.537   5431  Z= 0.281
  Chirality :  0.042   0.152    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.871  26.785    540
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.19 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.38), residues: 487
  helix:  1.86 (0.29), residues: 294
  sheet:  1.12 (0.65), residues: 58
  loop :  0.21 (0.60), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  66 
 TYR   0.017   0.001   TYR C 102 
 PHE   0.013   0.001   PHE C  27 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3998)
  covalent geometry    : angle       0.52795 ( 5429)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.32439 (    2)
  hydrogen bonds       : bond        0.04673 (  256)
  hydrogen bonds       : angle       4.16584 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  113 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8232 (m-30)
REVERT: C   64 LYS cc_start: 0.7870 (tppp) cc_final: 0.7668 (tppt)
  outliers start: 13
  outliers final: 11
  residues processed: 68
  average time/residue: 0.0642
  time to fit residues: 5.5776
Evaluate side-chains
  69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 40 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3359 r_free = 0.3359 target = 0.114069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.100544 restraints weight = 5109.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.60
r_work: 0.3068 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3999  Z= 0.139
  Angle     :  0.528   7.115   5431  Z= 0.281
  Chirality :  0.042   0.158    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.841  27.302    540
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 14.65 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.38), residues: 487
  helix:  1.87 (0.29), residues: 294
  sheet:  1.20 (0.65), residues: 59
  loop :  0.11 (0.59), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  66 
 TYR   0.017   0.001   TYR C 102 
 PHE   0.013   0.001   PHE C  27 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3998)
  covalent geometry    : angle       0.52761 ( 5429)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.36892 (    2)
  hydrogen bonds       : bond        0.04698 (  256)
  hydrogen bonds       : angle       4.13016 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  113 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8247 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 67
  average time/residue: 0.0672
  time to fit residues: 5.7632
Evaluate side-chains
  69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0020
   chunk 7 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.4988

-------------------------------------------------------------------------------
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 = 0.3363 r_free = 0.3363 target = 0.114057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.100089 restraints weight = 5133.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.67
r_work: 0.3096 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3999  Z= 0.126
  Angle     :  0.524   7.823   5431  Z= 0.278
  Chirality :  0.042   0.161    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.741  27.908    540
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.12 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.38), residues: 487
  helix:  2.01 (0.29), residues: 293
  sheet:  1.27 (0.66), residues: 58
  loop :  0.19 (0.61), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 319 
 TYR   0.017   0.001   TYR C 102 
 PHE   0.012   0.001   PHE C  27 
 TRP   0.013   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3998)
  covalent geometry    : angle       0.52408 ( 5429)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.41074 (    2)
  hydrogen bonds       : bond        0.04470 (  256)
  hydrogen bonds       : angle       4.06045 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  113 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8241 (m-30)
REVERT: C   19 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8361 (mtp85)
REVERT: C   64 LYS cc_start: 0.7505 (tppt) cc_final: 0.7171 (mttp)
  outliers start: 12
  outliers final: 10
  residues processed: 63
  average time/residue: 0.0684
  time to fit residues: 5.4656
Evaluate side-chains
  67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0570
   chunk 29 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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 = 0.3379 r_free = 0.3379 target = 0.115250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.101133 restraints weight = 5139.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.68
r_work: 0.3105 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3999  Z= 0.124
  Angle     :  0.520   7.713   5431  Z= 0.276
  Chirality :  0.041   0.166    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.661  28.670    540
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.35 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.38), residues: 487
  helix:  2.08 (0.29), residues: 293
  sheet:  1.35 (0.67), residues: 58
  loop :  0.22 (0.61), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  19 
 TYR   0.015   0.001   TYR C 102 
 PHE   0.013   0.001   PHE C  27 
 TRP   0.014   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3998)
  covalent geometry    : angle       0.52025 ( 5429)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.40388 (    2)
  hydrogen bonds       : bond        0.04370 (  256)
  hydrogen bonds       : angle       4.03329 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  113 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8246 (m-30)
REVERT: A  303 LYS cc_start: 0.8753 (tppt) cc_final: 0.8141 (pttt)
REVERT: C   64 LYS cc_start: 0.7484 (tppt) cc_final: 0.7178 (mttp)
  outliers start: 11
  outliers final: 8
  residues processed: 67
  average time/residue: 0.0616
  time to fit residues: 5.3577
Evaluate side-chains
  66 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3339 r_free = 0.3339 target = 0.112379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.098377 restraints weight = 5168.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.66
r_work: 0.3061 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3999  Z= 0.150
  Angle     :  0.540   7.215   5431  Z= 0.288
  Chirality :  0.043   0.160    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.765  27.187    540
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.05 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.38), residues: 487
  helix:  1.97 (0.29), residues: 294
  sheet:  1.23 (0.65), residues: 59
  loop :  0.09 (0.59), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  66 
 TYR   0.019   0.001   TYR C 102 
 PHE   0.013   0.001   PHE C  27 
 TRP   0.008   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3998)
  covalent geometry    : angle       0.54027 ( 5429)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.44942 (    2)
  hydrogen bonds       : bond        0.04771 (  256)
  hydrogen bonds       : angle       4.09641 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1028.70 seconds
wall clock time: 18 minutes 25.95 seconds (1105.95 seconds total)