Starting phenix.real_space_refine
on Tue Mar  3 12:07:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wn0_32618/03_2026/7wn0_32618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wn0_32618/03_2026/7wn0_32618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wn0_32618/03_2026/7wn0_32618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wn0_32618/03_2026/7wn0_32618.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wn0_32618/03_2026/7wn0_32618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wn0_32618/03_2026/7wn0_32618.map"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.028
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    2553      2.51       5
     N     617      2.21       5
     O     683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3879
  Number of models: 1
  Model: ""
    Number of chains: 2
    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: "B"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 926
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
  Time building chain proxies: 0.98, per 1000 atoms: 0.25
  Number of scatterers: 3879
  At special positions: 0
  Unit cell: (112.05, 57.27, 61.42, 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     683      8.00
     N     617      7.00
     C    2553      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  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: 0.20
  Conformation dependent library (CDL) restraints added in 118.3 milliseconds
  

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  920

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 3 sheets defined
      61.7% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 59
      removed outlier: 4.516A  pdb=" N   VAL A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   TRP A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 83
      removed outlier: 3.887A  pdb=" N   PHE A  82 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
    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 173
      removed outlier: 4.389A  pdb=" N   GLN A 173 " --> pdb=" O   LEU A 169 " (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: 3.802A  pdb=" N   ILE A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL A 249 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 270
    Processing helix  chain 'A' and resid 272 through 282
      removed outlier: 3.752A  pdb=" N   ILE A 278 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
      removed outlier: 4.284A  pdb=" N   PHE A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
      removed outlier: 3.678A  pdb=" N   VAL A 314 " --> pdb=" O   ASN A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 329
      removed outlier: 3.769A  pdb=" N   TRP A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 369
      removed outlier: 3.519A  pdb=" N   LEU A 350 " --> pdb=" O   CYS A 346 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   PHE A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 360 " --> pdb=" O   TRP A 356 " (cutoff:3.500A)
      Proline residue:  A 361  - end of helix
      removed outlier: 5.247A  pdb=" N   VAL A 366 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   LYS A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 368 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 399
      removed outlier: 3.611A  pdb=" N   GLU A 379 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   TRP A 398 " --> pdb=" O   PHE A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 4.005A  pdb=" N   LEU A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE A 406 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 401 through 406'
    Processing helix  chain 'B' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.716A  pdb=" N   SER B 122 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   VAL B  33 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   ARG B  38 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   LEU B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.716A  pdb=" N   SER B 122 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    753 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: 0.59

  Time building geometry restraints manager: 0.29 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: 1176
        1.34 -     1.46: 999
        1.46 -     1.58: 1757
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 3971
  Sorted by residual:
  bond pdb=" N   TYR B 103 "
       pdb=" CA  TYR B 103 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.35e-02 5.49e+03 8.72e+00
  bond pdb=" CG  PRO A 258 "
       pdb=" CD  PRO A 258 "
    ideal  model  delta    sigma   weight residual
    1.503  1.539 -0.036 3.40e-02 8.65e+02 1.11e+00
  bond pdb=" CA  VAL B  48 "
       pdb=" CB  VAL B  48 "
    ideal  model  delta    sigma   weight residual
    1.545  1.538  0.007 9.10e-03 1.21e+04 6.63e-01
  bond pdb=" CB  ASP A 333 "
       pdb=" CG  ASP A 333 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 2.50e-02 1.60e+03 5.84e-01
  bond pdb=" CB  LEU A  44 "
       pdb=" CG  LEU A  44 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.015 2.00e-02 2.50e+03 5.74e-01
  ... (remaining 3966 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 5317
        1.91 -     3.83: 56
        3.83 -     5.74: 12
        5.74 -     7.65: 5
        7.65 -     9.56: 1
  Bond angle restraints: 5391
  Sorted by residual:
  angle pdb=" CA  PRO A 258 "
        pdb=" N   PRO A 258 "
        pdb=" CD  PRO A 258 "
      ideal   model   delta    sigma   weight residual
     112.00  107.92    4.08 1.40e+00 5.10e-01 8.51e+00
  angle pdb=" CA  LEU A 201 "
        pdb=" CB  LEU A 201 "
        pdb=" CG  LEU A 201 "
      ideal   model   delta    sigma   weight residual
     116.30  125.86   -9.56 3.50e+00 8.16e-02 7.47e+00
  angle pdb=" N   TYR B 103 "
        pdb=" CA  TYR B 103 "
        pdb=" C   TYR B 103 "
      ideal   model   delta    sigma   weight residual
     112.87  110.07    2.80 1.20e+00 6.94e-01 5.43e+00
  angle pdb=" CB  MET A 233 "
        pdb=" CG  MET A 233 "
        pdb=" SD  MET A 233 "
      ideal   model   delta    sigma   weight residual
     112.70  119.59   -6.89 3.00e+00 1.11e-01 5.27e+00
  angle pdb=" N   SER A 308 "
        pdb=" CA  SER A 308 "
        pdb=" C   SER A 308 "
      ideal   model   delta    sigma   weight residual
     107.88  110.66   -2.78 1.41e+00 5.03e-01 3.87e+00
  ... (remaining 5386 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 1943
       17.13 -    34.27: 278
       34.27 -    51.40: 74
       51.40 -    68.54: 8
       68.54 -    85.67: 2
  Dihedral angle restraints: 2305
    sinusoidal: 875
      harmonic: 1430
  Sorted by residual:
  dihedral pdb=" CA  HIS A 334 "
           pdb=" C   HIS A 334 "
           pdb=" N   PRO A 335 "
           pdb=" CA  PRO A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.76  -20.24     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  ASN A 148 "
           pdb=" CB  ASN A 148 "
           pdb=" CG  ASN A 148 "
           pdb=" OD1 ASN A 148 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -163.46   73.46     2      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CG  ARG B  66 "
           pdb=" CD  ARG B  66 "
           pdb=" NE  ARG B  66 "
           pdb=" CZ  ARG B  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.39  -44.61     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 2302 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 354
       0.028 -    0.056: 174
       0.056 -    0.085: 69
       0.085 -    0.113: 27
       0.113 -    0.141: 4
  Chirality restraints: 628
  Sorted by residual:
  chirality pdb=" CA  PRO A 335 "
            pdb=" N   PRO A 335 "
            pdb=" C   PRO A 335 "
            pdb=" CB  PRO A 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  TYR B 105 "
            pdb=" N   TYR B 105 "
            pdb=" C   TYR B 105 "
            pdb=" CB  TYR B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL A 183 "
            pdb=" N   VAL A 183 "
            pdb=" C   VAL A 183 "
            pdb=" CB  VAL A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 625 not shown)

  Planarity restraints: 663
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 257 "   -0.065 5.00e-02 4.00e+02   9.76e-02 1.52e+01
        pdb=" N   PRO A 258 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO A 258 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 258 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 293 "    0.035 5.00e-02 4.00e+02   5.24e-02 4.40e+00
        pdb=" N   PRO A 294 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 294 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 294 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 119 "    0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" C   TYR A 119 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   TYR A 119 "    0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 120 "    0.011 2.00e-02 2.50e+03
  ... (remaining 660 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1043
        2.80 -     3.32: 3846
        3.32 -     3.85: 6520
        3.85 -     4.37: 7483
        4.37 -     4.90: 13006
  Nonbonded interactions: 31898
  Sorted by model distance:
  nonbonded pdb=" N   GLU B  88 "
            pdb=" OE1 GLU B  88 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" N   GLU A 146 "
            pdb=" OE1 GLU A 146 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OG1 THR A 253 "
            pdb=" NH2 ARG A 319 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" N   GLN B  44 "
            pdb=" OE1 GLN B  44 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" O   SER B 102 "
            pdb=" OG  SER B 102 "
     model   vdw
     2.325 3.040
  ... (remaining 31893 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.260
  Find NCS groups from input model:        0.010
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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   0.040   3972  Z= 0.144
  Angle     :  0.572   9.565   5393  Z= 0.296
  Chirality :  0.041   0.141    628
  Planarity :  0.005   0.098    663
  Dihedral  : 16.818  85.672   1382
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 28.44 %
    Favored  : 71.10 %
  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:  1.10 (0.39), residues: 488
  helix:  1.00 (0.32), residues: 278
  sheet:  1.61 (0.73), residues: 56
  loop :  0.07 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.015   0.001   TYR A 119 
 PHE   0.012   0.001   PHE A  82 
 TRP   0.005   0.001   TRP A 356 
 HIS   0.010   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3971)
  covalent geometry    : angle       0.57208 ( 5391)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.10138 (    2)
  hydrogen bonds       : bond        0.20741 (  254)
  hydrogen bonds       : angle       7.36356 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 76
  average time/residue: 0.0556
  time to fit residues: 5.4262
Evaluate side-chains
  77 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0040
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A  66 ASN
A 135 GLN
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 GLN
A 284 GLN
A 316 ASN
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.121171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.098723 restraints weight = 5541.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.101404 restraints weight = 3312.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.103279 restraints weight = 2424.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.104179 restraints weight = 1985.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.104997 restraints weight = 1771.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3972  Z= 0.142
  Angle     :  0.575   7.882   5393  Z= 0.299
  Chirality :  0.042   0.129    628
  Planarity :  0.005   0.056    663
  Dihedral  :  4.416  33.984    521
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 26.34 %
    Favored  : 69.46 %
  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:  1.43 (0.39), residues: 488
  helix:  1.37 (0.31), residues: 285
  sheet:  1.14 (0.62), residues: 69
  loop :  0.11 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.014   0.002   TYR A 119 
 PHE   0.016   0.001   PHE A  36 
 TRP   0.007   0.001   TRP B 109 
 HIS   0.007   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3971)
  covalent geometry    : angle       0.57455 ( 5391)
  SS BOND              : bond        0.00182 (    1)
  SS BOND              : angle       0.50992 (    2)
  hydrogen bonds       : bond        0.05485 (  254)
  hydrogen bonds       : angle       5.04037 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 ASP cc_start: 0.7473 (t0) cc_final: 0.7161 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 89
  average time/residue: 0.0555
  time to fit residues: 6.4496
Evaluate side-chains
  87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  123 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.118916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.095790 restraints weight = 5483.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.098450 restraints weight = 3406.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.100030 restraints weight = 2534.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.101241 restraints weight = 2122.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.101903 restraints weight = 1885.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3972  Z= 0.148
  Angle     :  0.562   7.876   5393  Z= 0.290
  Chirality :  0.042   0.123    628
  Planarity :  0.004   0.053    663
  Dihedral  :  4.190  33.435    519
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 26.57 %
    Favored  : 68.07 %
  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:  1.50 (0.39), residues: 488
  helix:  1.48 (0.31), residues: 285
  sheet:  0.97 (0.58), residues: 71
  loop :  0.11 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.018   0.001   TYR B  37 
 PHE   0.009   0.001   PHE A  82 
 TRP   0.006   0.001   TRP A 356 
 HIS   0.006   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3971)
  covalent geometry    : angle       0.56258 ( 5391)
  SS BOND              : bond        0.00066 (    1)
  SS BOND              : angle       0.21016 (    2)
  hydrogen bonds       : bond        0.05065 (  254)
  hydrogen bonds       : angle       4.71882 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6606 (mt)
REVERT: A  141 ILE cc_start: 0.9385 (mm) cc_final: 0.9183 (mt)
REVERT: B   55 ASP cc_start: 0.7586 (t0) cc_final: 0.7231 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 94
  average time/residue: 0.0576
  time to fit residues: 6.8301
Evaluate side-chains
  94 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  123 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0370
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.126376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.104056 restraints weight = 5329.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.107140 restraints weight = 3069.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.109102 restraints weight = 2191.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.110464 restraints weight = 1769.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.111133 restraints weight = 1525.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3972  Z= 0.143
  Angle     :  0.579   7.738   5393  Z= 0.297
  Chirality :  0.042   0.124    628
  Planarity :  0.004   0.052    663
  Dihedral  :  4.161  33.104    519
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 26.34 %
    Favored  : 68.53 %
  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 are not related in a simple way.
  whole:  1.51 (0.39), residues: 488
  helix:  1.50 (0.31), residues: 285
  sheet:  0.85 (0.56), residues: 71
  loop :  0.18 (0.59), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.013   0.001   TYR A 119 
 PHE   0.008   0.001   PHE A  42 
 TRP   0.006   0.001   TRP A 251 
 HIS   0.005   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3971)
  covalent geometry    : angle       0.57886 ( 5391)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.10599 (    2)
  hydrogen bonds       : bond        0.04841 (  254)
  hydrogen bonds       : angle       4.59178 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6564 (mt)
REVERT: B   55 ASP cc_start: 0.7589 (t0) cc_final: 0.7186 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 93
  average time/residue: 0.0568
  time to fit residues: 6.8334
Evaluate side-chains
  95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 39 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0980
   chunk 38 optimal weight:    0.0970
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 ASN
B 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.127808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.106133 restraints weight = 5295.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.108988 restraints weight = 3144.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.110983 restraints weight = 2282.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.112150 restraints weight = 1846.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.112163 restraints weight = 1611.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3972  Z= 0.132
  Angle     :  0.593   9.731   5393  Z= 0.295
  Chirality :  0.041   0.121    628
  Planarity :  0.004   0.052    663
  Dihedral  :  4.141  32.811    519
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 25.64 %
    Favored  : 68.30 %
  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:  1.43 (0.39), residues: 488
  helix:  1.46 (0.31), residues: 287
  sheet:  0.84 (0.56), residues: 71
  loop :  0.03 (0.59), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.016   0.001   TYR B  37 
 PHE   0.009   0.001   PHE A  42 
 TRP   0.007   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3971)
  covalent geometry    : angle       0.59308 ( 5391)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.17130 (    2)
  hydrogen bonds       : bond        0.04659 (  254)
  hydrogen bonds       : angle       4.52708 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6518 (mt)
REVERT: B   55 ASP cc_start: 0.7647 (t0) cc_final: 0.7248 (t0)
REVERT: B  105 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.5614 (p90)
  outliers start: 26
  outliers final: 16
  residues processed: 95
  average time/residue: 0.0483
  time to fit residues: 6.0548
Evaluate side-chains
  97 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0970
   chunk 17 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.126961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.104768 restraints weight = 5376.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.107907 restraints weight = 3066.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.109752 restraints weight = 2174.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.111236 restraints weight = 1761.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.112156 restraints weight = 1499.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3972  Z= 0.145
  Angle     :  0.613   8.155   5393  Z= 0.302
  Chirality :  0.042   0.123    628
  Planarity :  0.004   0.051    663
  Dihedral  :  4.112  33.597    519
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 24.01 %
    Favored  : 69.46 %
  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:  1.39 (0.39), residues: 488
  helix:  1.44 (0.31), residues: 292
  sheet:  0.88 (0.56), residues: 71
  loop : -0.12 (0.60), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.014   0.001   TYR A 240 
 PHE   0.008   0.001   PHE A  82 
 TRP   0.007   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3971)
  covalent geometry    : angle       0.61333 ( 5391)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.07774 (    2)
  hydrogen bonds       : bond        0.04651 (  254)
  hydrogen bonds       : angle       4.48304 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 86
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6549 (mt)
REVERT: B   55 ASP cc_start: 0.7683 (t0) cc_final: 0.7222 (t0)
REVERT: B  105 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.5688 (p90)
  outliers start: 28
  outliers final: 20
  residues processed: 102
  average time/residue: 0.0533
  time to fit residues: 7.1165
Evaluate side-chains
  102 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  117 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0030
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.0794

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
A 135 GLN
A 148 ASN
A 209 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 118 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.124124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.101581 restraints weight = 5460.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.104640 restraints weight = 3126.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.106484 restraints weight = 2236.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.107782 restraints weight = 1822.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.107782 restraints weight = 1580.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3972  Z= 0.185
  Angle     :  0.642   7.802   5393  Z= 0.325
  Chirality :  0.044   0.131    628
  Planarity :  0.004   0.051    663
  Dihedral  :  4.300  33.331    519
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 26.11 %
    Favored  : 68.07 %
  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:  1.36 (0.38), residues: 488
  helix:  1.43 (0.31), residues: 285
  sheet:  0.92 (0.56), residues: 71
  loop : -0.13 (0.57), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 319 
 TYR   0.026   0.002   TYR B  37 
 PHE   0.013   0.001   PHE A 116 
 TRP   0.007   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 3971)
  covalent geometry    : angle       0.64205 ( 5391)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.06589 (    2)
  hydrogen bonds       : bond        0.04935 (  254)
  hydrogen bonds       : angle       4.56992 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6686 (mt)
REVERT: B   55 ASP cc_start: 0.7745 (t0) cc_final: 0.7277 (t0)
REVERT: B  105 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.5696 (p90)
  outliers start: 25
  outliers final: 19
  residues processed: 91
  average time/residue: 0.0551
  time to fit residues: 6.5478
Evaluate side-chains
  95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  209 ASN
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    0.0050
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 28 optimal weight:    0.2980
   chunk 42 optimal weight:    0.2980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.127170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.104832 restraints weight = 5351.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.107780 restraints weight = 3068.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.109954 restraints weight = 2209.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.111169 restraints weight = 1771.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.111840 restraints weight = 1538.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3972  Z= 0.135
  Angle     :  0.614   7.918   5393  Z= 0.309
  Chirality :  0.042   0.125    628
  Planarity :  0.004   0.051    663
  Dihedral  :  4.214  32.989    519
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 28.44 %
    Favored  : 66.90 %
  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 (0.39), residues: 488
  helix:  1.48 (0.31), residues: 286
  sheet:  0.91 (0.57), residues: 71
  loop : -0.20 (0.58), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.021   0.001   TYR B  37 
 PHE   0.009   0.001   PHE A 116 
 TRP   0.005   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3971)
  covalent geometry    : angle       0.61450 ( 5391)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       0.09364 (    2)
  hydrogen bonds       : bond        0.04668 (  254)
  hydrogen bonds       : angle       4.46689 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.8109 (tpp) cc_final: 0.7859 (tpp)
REVERT: A   93 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6529 (mt)
REVERT: B   55 ASP cc_start: 0.7731 (t0) cc_final: 0.7278 (t0)
REVERT: B  105 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.5687 (p90)
  outliers start: 20
  outliers final: 16
  residues processed: 87
  average time/residue: 0.0558
  time to fit residues: 6.3254
Evaluate side-chains
  94 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   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 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.125728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.103479 restraints weight = 5370.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.106446 restraints weight = 3082.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.108467 restraints weight = 2223.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.109398 restraints weight = 1789.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.110549 restraints weight = 1591.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3972  Z= 0.153
  Angle     :  0.630   7.982   5393  Z= 0.317
  Chirality :  0.042   0.128    628
  Planarity :  0.004   0.050    663
  Dihedral  :  4.194  32.775    519
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 27.97 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.38), residues: 488
  helix:  1.50 (0.31), residues: 285
  sheet:  0.78 (0.56), residues: 71
  loop : -0.22 (0.57), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.020   0.002   TYR B  37 
 PHE   0.009   0.001   PHE A 116 
 TRP   0.006   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3971)
  covalent geometry    : angle       0.62979 ( 5391)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.10562 (    2)
  hydrogen bonds       : bond        0.04721 (  254)
  hydrogen bonds       : angle       4.46030 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6570 (mt)
REVERT: B    3 GLN cc_start: 0.7578 (pm20) cc_final: 0.7320 (mp10)
REVERT: B   55 ASP cc_start: 0.7782 (t0) cc_final: 0.7283 (t0)
REVERT: B  105 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.5700 (p90)
  outliers start: 21
  outliers final: 17
  residues processed: 86
  average time/residue: 0.0526
  time to fit residues: 5.8131
Evaluate side-chains
  95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    0.0000
   chunk 37 optimal weight:    0.0070
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0270
   overall best weight:    0.2860

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.125256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.102684 restraints weight = 5520.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.105622 restraints weight = 3171.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.107610 restraints weight = 2271.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.108684 restraints weight = 1844.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.108684 restraints weight = 1625.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3972  Z= 0.130
  Angle     :  0.623   7.926   5393  Z= 0.312
  Chirality :  0.041   0.126    628
  Planarity :  0.004   0.049    663
  Dihedral  :  4.153  32.479    519
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 28.67 %
    Favored  : 66.67 %
  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:  1.40 (0.39), residues: 488
  helix:  1.58 (0.31), residues: 285
  sheet:  0.90 (0.57), residues: 69
  loop : -0.39 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  19 
 TYR   0.018   0.001   TYR B  37 
 PHE   0.008   0.001   PHE A 116 
 TRP   0.005   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3971)
  covalent geometry    : angle       0.62287 ( 5391)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.13168 (    2)
  hydrogen bonds       : bond        0.04495 (  254)
  hydrogen bonds       : angle       4.40278 (  753)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   93 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6479 (mt)
REVERT: B    3 GLN cc_start: 0.7547 (pm20) cc_final: 0.7308 (mp10)
REVERT: B   55 ASP cc_start: 0.7747 (t0) cc_final: 0.7296 (t0)
REVERT: B  105 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.5486 (p90)
  outliers start: 20
  outliers final: 17
  residues processed: 87
  average time/residue: 0.0511
  time to fit residues: 5.9040
Evaluate side-chains
  96 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 30 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 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.124870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.102258 restraints weight = 5451.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.105057 restraints weight = 3174.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.107048 restraints weight = 2317.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.108350 restraints weight = 1881.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.108957 restraints weight = 1645.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3972  Z= 0.147
  Angle     :  0.629   8.002   5393  Z= 0.317
  Chirality :  0.042   0.127    628
  Planarity :  0.004   0.049    663
  Dihedral  :  4.108  32.392    519
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 28.44 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.39), residues: 488
  helix:  1.56 (0.31), residues: 284
  sheet:  0.88 (0.57), residues: 69
  loop : -0.31 (0.57), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.016   0.002   TYR B  37 
 PHE   0.010   0.001   PHE A  42 
 TRP   0.006   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3971)
  covalent geometry    : angle       0.62869 ( 5391)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.09990 (    2)
  hydrogen bonds       : bond        0.04590 (  254)
  hydrogen bonds       : angle       4.41269 (  753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 767.98 seconds
wall clock time: 13 minutes 57.88 seconds (837.88 seconds total)