Starting phenix.real_space_refine
on Fri Aug 22 14:08:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx5_37901/08_2025/8wx5_37901.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx5_37901/08_2025/8wx5_37901.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx5_37901/08_2025/8wx5_37901.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx5_37901/08_2025/8wx5_37901.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx5_37901/08_2025/8wx5_37901.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx5_37901/08_2025/8wx5_37901.cif"
  }
  resolution = 3.91
  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=   0.052
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      22      5.16       5
     C    2552      2.51       5
     N     619      2.21       5
     O     664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3857
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 490, 3741
          Classifications: {'peptide': 490}
          Link IDs: {'PTRANS': 22, 'TRANS': 467}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 116
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Time building chain proxies: 1.16, per 1000 atoms: 0.30
  Number of scatterers: 3857
  At special positions: 0
  Unit cell: (80.51, 77.19, 73.87, 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      22     16.00
     O     664      8.00
     N     619      7.00
     C    2552      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 141 " - pdb=" SG  CYS A 152 " 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: 0.35
  Conformation dependent library (CDL) restraints added in 155.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  922

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      83.7% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 57
      removed outlier: 3.927A  pdb=" N   ASN A  57 " --> pdb=" O   GLY A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 65
      removed outlier: 3.539A  pdb=" N   ASN A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 97
      Proline residue:  A  90  - end of helix
    Processing helix  chain 'A' and resid 101 through 125
      Proline residue:  A 121  - end of helix
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 146 through 185
      removed outlier: 3.514A  pdb=" N   ALA A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      Proline residue:  A 155  - end of helix
      removed outlier: 4.443A  pdb=" N   THR A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
      removed outlier: 4.049A  pdb=" N   ASP A 185 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 220
    Processing helix  chain 'A' and resid 221 through 245
      Proline residue:  A 229  - end of helix
      removed outlier: 4.111A  pdb=" N   SER A 245 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 310 through 349
      Proline residue:  A 323  - end of helix
      Proline residue:  A 330  - end of helix
    Processing helix  chain 'A' and resid 354 through 358
      removed outlier: 4.283A  pdb=" N   ILE A 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 394
      Proline residue:  A 382  - end of helix
      Proline residue:  A 390  - end of helix
      removed outlier: 3.897A  pdb=" N   ARG A 394 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 431
    Processing helix  chain 'A' and resid 450 through 452
      No H-bonds generated for 'chain 'A' and resid 450 through 452'
    Processing helix  chain 'A' and resid 453 through 479
      removed outlier: 4.550A  pdb=" N   GLN A 457 " --> pdb=" O   TRP A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 512
    Processing helix  chain 'A' and resid 526 through 530
    Processing helix  chain 'A' and resid 531 through 556
      removed outlier: 4.067A  pdb=" N   TYR A 535 " --> pdb=" O   TYR A 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 14
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437
      removed outlier: 3.715A  pdb=" N   GLN A 437 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    930 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: 0.65

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 588
        1.31 -     1.43: 1104
        1.43 -     1.56: 2230
        1.56 -     1.69: 0
        1.69 -     1.82: 33
  Bond restraints: 3955
  Sorted by residual:
  bond pdb=" C   SER B   8 "
       pdb=" O   SER B   8 "
    ideal  model  delta    sigma   weight residual
    1.236  1.307 -0.070 1.24e-02 6.50e+03 3.21e+01
  bond pdb=" C   LEU B   7 "
       pdb=" O   LEU B   7 "
    ideal  model  delta    sigma   weight residual
    1.236  1.294 -0.058 1.19e-02 7.06e+03 2.34e+01
  bond pdb=" CA  SER B   8 "
       pdb=" CB  SER B   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.452  0.078 1.69e-02 3.50e+03 2.11e+01
  bond pdb=" C   TYR B   6 "
       pdb=" O   TYR B   6 "
    ideal  model  delta    sigma   weight residual
    1.235  1.181  0.054 1.26e-02 6.30e+03 1.84e+01
  bond pdb=" C   GLY B   9 "
       pdb=" O   GLY B   9 "
    ideal  model  delta    sigma   weight residual
    1.235  1.179  0.056 1.35e-02 5.49e+03 1.72e+01
  ... (remaining 3950 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 5238
        2.18 -     4.37: 114
        4.37 -     6.55: 23
        6.55 -     8.73: 5
        8.73 -    10.92: 4
  Bond angle restraints: 5384
  Sorted by residual:
  angle pdb=" N   GLU B   4 "
        pdb=" CA  GLU B   4 "
        pdb=" C   GLU B   4 "
      ideal   model   delta    sigma   weight residual
     112.34  102.39    9.95 1.30e+00 5.92e-01 5.86e+01
  angle pdb=" N   LEU B  10 "
        pdb=" CA  LEU B  10 "
        pdb=" C   LEU B  10 "
      ideal   model   delta    sigma   weight residual
     111.37  100.45   10.92 1.64e+00 3.72e-01 4.43e+01
  angle pdb=" N   TRP B  13 "
        pdb=" CA  TRP B  13 "
        pdb=" C   TRP B  13 "
      ideal   model   delta    sigma   weight residual
     111.37  102.04    9.33 1.65e+00 3.67e-01 3.20e+01
  angle pdb=" N   SER B   8 "
        pdb=" CA  SER B   8 "
        pdb=" C   SER B   8 "
      ideal   model   delta    sigma   weight residual
     111.75  104.52    7.23 1.28e+00 6.10e-01 3.19e+01
  angle pdb=" N   TYR B  12 "
        pdb=" CA  TYR B  12 "
        pdb=" C   TYR B  12 "
      ideal   model   delta    sigma   weight residual
     111.36  117.06   -5.70 1.09e+00 8.42e-01 2.73e+01
  ... (remaining 5379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2037
       17.98 -    35.95: 206
       35.95 -    53.93: 43
       53.93 -    71.91: 3
       71.91 -    89.89: 2
  Dihedral angle restraints: 2291
    sinusoidal: 849
      harmonic: 1442
  Sorted by residual:
  dihedral pdb=" N   SER B   8 "
           pdb=" C   SER B   8 "
           pdb=" CA  SER B   8 "
           pdb=" CB  SER B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.32   10.48     0      2.50e+00 1.60e-01 1.76e+01
  dihedral pdb=" N   LEU B  10 "
           pdb=" C   LEU B  10 "
           pdb=" CA  LEU B  10 "
           pdb=" CB  LEU B  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.37   10.43     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" C   TRP B  13 "
           pdb=" N   TRP B  13 "
           pdb=" CA  TRP B  13 "
           pdb=" CB  TRP B  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.16   -9.44     0      2.50e+00 1.60e-01 1.42e+01
  ... (remaining 2288 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 564
       0.064 -    0.128: 57
       0.128 -    0.192: 3
       0.192 -    0.256: 1
       0.256 -    0.319: 3
  Chirality restraints: 628
  Sorted by residual:
  chirality pdb=" CA  TRP B  13 "
            pdb=" N   TRP B  13 "
            pdb=" C   TRP B  13 "
            pdb=" CB  TRP B  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  TYR B  12 "
            pdb=" N   TYR B  12 "
            pdb=" C   TYR B  12 "
            pdb=" CB  TYR B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  LEU B  10 "
            pdb=" N   LEU B  10 "
            pdb=" C   LEU B  10 "
            pdb=" CB  LEU B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 625 not shown)

  Planarity restraints: 664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B   9 "    0.020 2.00e-02 2.50e+03   4.12e-02 1.70e+01
        pdb=" C   GLY B   9 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   GLY B   9 "    0.027 2.00e-02 2.50e+03
        pdb=" N   LEU B  10 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  10 "    0.013 2.00e-02 2.50e+03   2.64e-02 6.99e+00
        pdb=" C   LEU B  10 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LEU B  10 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU B  11 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 228 "   -0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO A 229 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 229 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 229 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 661 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 215
        2.73 -     3.27: 4249
        3.27 -     3.81: 6741
        3.81 -     4.36: 7416
        4.36 -     4.90: 12796
  Nonbonded interactions: 31417
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 349 "
            pdb=" NE2 GLN A 437 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" O   GLN A 337 "
            pdb=" OG1 THR A 341 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER A 355 "
            pdb=" O   THR A 358 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   GLY A 499 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   LEU A 380 "
            pdb=" N   LYS A 384 "
     model   vdw
     2.280 3.120
  ... (remaining 31412 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:             1.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.950
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
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      :  0.004   0.078   3957  Z= 0.280
  Angle     :  0.867  10.916   5388  Z= 0.555
  Chirality :  0.044   0.319    628
  Planarity :  0.005   0.051    664
  Dihedral  : 14.579  89.886   1363
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.63 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  6.98 %
    Favored  : 92.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.34), residues: 498
  helix: -0.26 (0.24), residues: 389
  sheet: -4.91 (0.87), residues: 10
  loop : -4.00 (0.45), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 102 
 TYR   0.022   0.002   TYR B  12 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.032   0.001   TRP B  13 
 HIS   0.002   0.000   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 3955)
  covalent geometry    : angle       0.86662 ( 5384)
  SS BOND              : bond        0.00010 (    2)
  SS BOND              : angle       0.96190 (    4)
  hydrogen bonds       : bond        0.10382 (  315)
  hydrogen bonds       : angle       5.18068 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 157
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 LEU cc_start: 0.9316 (mt) cc_final: 0.9044 (mt)
REVERT: A   63 ASN cc_start: 0.7813 (m110) cc_final: 0.7512 (t0)
REVERT: A  259 ASP cc_start: 0.9094 (m-30) cc_final: 0.8872 (m-30)
REVERT: A  310 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8282 (mm-30)
REVERT: A  409 MET cc_start: 0.9073 (mtt) cc_final: 0.8799 (mtt)
REVERT: A  453 TRP cc_start: 0.7998 (m100) cc_final: 0.7208 (m100)
REVERT: A  465 GLU cc_start: 0.9358 (tp30) cc_final: 0.9097 (tp30)
REVERT: A  470 ILE cc_start: 0.8834 (mm) cc_final: 0.8583 (mm)
REVERT: A  474 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7222 (mt-10)
  outliers start: 2
  outliers final: 1
  residues processed: 158
  average time/residue: 0.0591
  time to fit residues: 12.0244
Evaluate side-chains
  129 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   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 140 ASN
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
A 356 ASN
A 441 ASN
A 454 GLN
B  14 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.147705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.122989 restraints weight = 7655.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.126827 restraints weight = 4323.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.129541 restraints weight = 2887.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.131231 restraints weight = 2166.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.132608 restraints weight = 1782.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3957  Z= 0.160
  Angle     :  0.659   7.922   5388  Z= 0.339
  Chirality :  0.041   0.165    628
  Planarity :  0.005   0.050    664
  Dihedral  :  4.691  16.158    538
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 16.21 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.38), residues: 498
  helix:  0.80 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -3.31 (0.50), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 426 
 TYR   0.034   0.002   TYR B  12 
 PHE   0.017   0.001   PHE A 194 
 TRP   0.026   0.002   TRP B  13 
 HIS   0.003   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3955)
  covalent geometry    : angle       0.65881 ( 5384)
  SS BOND              : bond        0.00096 (    2)
  SS BOND              : angle       0.57693 (    4)
  hydrogen bonds       : bond        0.04713 (  315)
  hydrogen bonds       : angle       4.69941 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LEU cc_start: 0.9515 (mt) cc_final: 0.9109 (mp)
REVERT: A  120 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8229 (t80)
REVERT: A  259 ASP cc_start: 0.9105 (m-30) cc_final: 0.8886 (m-30)
REVERT: A  409 MET cc_start: 0.9156 (mtt) cc_final: 0.8790 (mtt)
REVERT: A  423 GLU cc_start: 0.8539 (tp30) cc_final: 0.8175 (tp30)
REVERT: A  453 TRP cc_start: 0.8114 (m100) cc_final: 0.7435 (m100)
REVERT: A  465 GLU cc_start: 0.9427 (tp30) cc_final: 0.9047 (tp30)
REVERT: A  470 ILE cc_start: 0.8764 (mm) cc_final: 0.8488 (mm)
REVERT: A  474 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7334 (mt-10)
REVERT: A  501 PHE cc_start: 0.8647 (m-80) cc_final: 0.7562 (t80)
REVERT: A  543 GLN cc_start: 0.9527 (tp40) cc_final: 0.9034 (tp-100)
REVERT: B   13 TRP cc_start: 0.5854 (OUTLIER) cc_final: 0.4581 (t-100)
  outliers start: 15
  outliers final: 8
  residues processed: 146
  average time/residue: 0.0524
  time to fit residues: 10.1463
Evaluate side-chains
  139 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0030
   chunk 11 optimal weight:    0.0770
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.4348

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 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 = 0.3799 r_free = 0.3799 target = 0.147479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.123850 restraints weight = 7461.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.127394 restraints weight = 4227.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.130040 restraints weight = 2834.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.131725 restraints weight = 2119.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.133032 restraints weight = 1736.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3957  Z= 0.146
  Angle     :  0.655   8.122   5388  Z= 0.332
  Chirality :  0.042   0.148    628
  Planarity :  0.005   0.059    664
  Dihedral  :  4.685  16.621    537
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.45 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.38), residues: 498
  helix:  1.12 (0.27), residues: 390
  sheet:  None (None), residues: 0
  loop : -2.86 (0.55), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 426 
 TYR   0.029   0.002   TYR B  12 
 PHE   0.013   0.001   PHE A 194 
 TRP   0.021   0.001   TRP B  13 
 HIS   0.002   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3955)
  covalent geometry    : angle       0.65559 ( 5384)
  SS BOND              : bond        0.00057 (    2)
  SS BOND              : angle       0.50300 (    4)
  hydrogen bonds       : bond        0.04562 (  315)
  hydrogen bonds       : angle       4.70419 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 TRP cc_start: 0.8967 (m-10) cc_final: 0.8574 (m-10)
REVERT: A  120 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8016 (t80)
REVERT: A  310 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8704 (mm-30)
REVERT: A  426 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8578 (ttp80)
REVERT: A  453 TRP cc_start: 0.8046 (m100) cc_final: 0.7361 (m100)
REVERT: A  465 GLU cc_start: 0.9341 (tp30) cc_final: 0.9061 (tp30)
REVERT: A  470 ILE cc_start: 0.8673 (mm) cc_final: 0.8363 (mm)
REVERT: A  474 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7337 (mt-10)
REVERT: A  501 PHE cc_start: 0.8642 (m-80) cc_final: 0.7595 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 133
  average time/residue: 0.0490
  time to fit residues: 8.7639
Evaluate side-chains
  131 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.145032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120279 restraints weight = 7601.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123888 restraints weight = 4395.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.126194 restraints weight = 2986.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.128090 restraints weight = 2297.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.128901 restraints weight = 1905.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3957  Z= 0.160
  Angle     :  0.649   9.246   5388  Z= 0.332
  Chirality :  0.041   0.133    628
  Planarity :  0.005   0.052    664
  Dihedral  :  4.562  16.833    537
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 24.69 %
    Favored  : 71.07 %
  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 aren not related in a simple way.
  whole:  0.59 (0.39), residues: 498
  helix:  1.16 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.67 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 426 
 TYR   0.025   0.002   TYR B  12 
 PHE   0.010   0.001   PHE A 195 
 TRP   0.018   0.001   TRP B  13 
 HIS   0.002   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3955)
  covalent geometry    : angle       0.64935 ( 5384)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       0.41966 (    4)
  hydrogen bonds       : bond        0.04700 (  315)
  hydrogen bonds       : angle       4.74531 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7265 (m100) cc_final: 0.6926 (m100)
REVERT: A  203 ASN cc_start: 0.8697 (m-40) cc_final: 0.8347 (m-40)
REVERT: A  316 LYS cc_start: 0.8898 (tttt) cc_final: 0.8671 (ttmt)
REVERT: A  426 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8569 (ttp80)
REVERT: A  453 TRP cc_start: 0.8113 (m100) cc_final: 0.7444 (m100)
REVERT: A  465 GLU cc_start: 0.9300 (tp30) cc_final: 0.9044 (tp30)
REVERT: A  470 ILE cc_start: 0.8701 (mm) cc_final: 0.8368 (mm)
REVERT: A  474 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7365 (mt-10)
REVERT: A  501 PHE cc_start: 0.8672 (m-80) cc_final: 0.7702 (t80)
REVERT: B   13 TRP cc_start: 0.5818 (OUTLIER) cc_final: 0.5180 (m100)
  outliers start: 17
  outliers final: 12
  residues processed: 132
  average time/residue: 0.0445
  time to fit residues: 8.0530
Evaluate side-chains
  133 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  417 PHE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0060
   chunk 31 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 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 = 0.3782 r_free = 0.3782 target = 0.146397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121811 restraints weight = 7546.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.125386 restraints weight = 4307.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.127998 restraints weight = 2916.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.129683 restraints weight = 2207.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.131031 restraints weight = 1818.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3957  Z= 0.148
  Angle     :  0.653   9.743   5388  Z= 0.329
  Chirality :  0.040   0.155    628
  Planarity :  0.005   0.048    664
  Dihedral  :  4.542  16.579    537
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 28.43 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.39), residues: 498
  helix:  1.17 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.51 (0.62), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 426 
 TYR   0.024   0.002   TYR B  12 
 PHE   0.011   0.001   PHE A 194 
 TRP   0.016   0.001   TRP B  13 
 HIS   0.002   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3955)
  covalent geometry    : angle       0.65343 ( 5384)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.37874 (    4)
  hydrogen bonds       : bond        0.04578 (  315)
  hydrogen bonds       : angle       4.71324 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7235 (m100) cc_final: 0.6961 (m100)
REVERT: A  203 ASN cc_start: 0.8622 (m-40) cc_final: 0.8255 (m-40)
REVERT: A  310 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8562 (mm-30)
REVERT: A  423 GLU cc_start: 0.8441 (tp30) cc_final: 0.8143 (tp30)
REVERT: A  426 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8585 (ttp80)
REVERT: A  453 TRP cc_start: 0.8121 (m100) cc_final: 0.7446 (m100)
REVERT: A  465 GLU cc_start: 0.9270 (tp30) cc_final: 0.9056 (tp30)
REVERT: A  470 ILE cc_start: 0.8633 (mm) cc_final: 0.8315 (mm)
REVERT: A  474 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7374 (mt-10)
REVERT: A  501 PHE cc_start: 0.8665 (m-80) cc_final: 0.7694 (t80)
REVERT: B   13 TRP cc_start: 0.5682 (OUTLIER) cc_final: 0.5177 (m100)
  outliers start: 16
  outliers final: 12
  residues processed: 131
  average time/residue: 0.0440
  time to fit residues: 7.8426
Evaluate side-chains
  138 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 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 = 0.3756 r_free = 0.3756 target = 0.144145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119960 restraints weight = 7600.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.123454 restraints weight = 4344.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.125858 restraints weight = 2923.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127694 restraints weight = 2237.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.128760 restraints weight = 1845.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3957  Z= 0.159
  Angle     :  0.663  10.834   5388  Z= 0.336
  Chirality :  0.040   0.132    628
  Planarity :  0.005   0.044    664
  Dihedral  :  4.489  17.181    537
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.18 %
    Favored  : 66.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.39), residues: 498
  helix:  1.25 (0.27), residues: 396
  sheet:  None (None), residues: 0
  loop : -2.44 (0.62), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 426 
 TYR   0.021   0.002   TYR B  12 
 PHE   0.008   0.001   PHE A 492 
 TRP   0.017   0.001   TRP B  13 
 HIS   0.002   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3955)
  covalent geometry    : angle       0.66312 ( 5384)
  SS BOND              : bond        0.00058 (    2)
  SS BOND              : angle       0.27655 (    4)
  hydrogen bonds       : bond        0.04634 (  315)
  hydrogen bonds       : angle       4.75992 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ASP cc_start: 0.8474 (m-30) cc_final: 0.7176 (t0)
REVERT: A  316 LYS cc_start: 0.8882 (tttt) cc_final: 0.8650 (ttmt)
REVERT: A  423 GLU cc_start: 0.8432 (tp30) cc_final: 0.8127 (tp30)
REVERT: A  426 ARG cc_start: 0.8796 (ttp80) cc_final: 0.8565 (ttp80)
REVERT: A  453 TRP cc_start: 0.8146 (m100) cc_final: 0.7487 (m100)
REVERT: A  465 GLU cc_start: 0.9282 (tp30) cc_final: 0.9035 (tp30)
REVERT: A  470 ILE cc_start: 0.8677 (mm) cc_final: 0.8414 (mm)
REVERT: A  474 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7399 (mt-10)
REVERT: A  501 PHE cc_start: 0.8676 (m-80) cc_final: 0.7746 (t80)
REVERT: B   13 TRP cc_start: 0.5715 (OUTLIER) cc_final: 0.5204 (m100)
  outliers start: 16
  outliers final: 13
  residues processed: 129
  average time/residue: 0.0488
  time to fit residues: 8.3814
Evaluate side-chains
  131 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 44 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 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 = 0.3766 r_free = 0.3766 target = 0.145786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.120512 restraints weight = 7687.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124401 restraints weight = 4393.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126985 restraints weight = 2968.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.128377 restraints weight = 2249.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.129977 restraints weight = 1893.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3957  Z= 0.156
  Angle     :  0.682  11.251   5388  Z= 0.340
  Chirality :  0.040   0.130    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.488  17.164    537
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.93 %
    Favored  : 66.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.39), residues: 498
  helix:  1.23 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.33 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 426 
 TYR   0.021   0.002   TYR B  12 
 PHE   0.008   0.001   PHE A 336 
 TRP   0.017   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3955)
  covalent geometry    : angle       0.68216 ( 5384)
  SS BOND              : bond        0.00039 (    2)
  SS BOND              : angle       0.30775 (    4)
  hydrogen bonds       : bond        0.04624 (  315)
  hydrogen bonds       : angle       4.77300 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ASP cc_start: 0.8449 (m-30) cc_final: 0.7143 (t0)
REVERT: A  453 TRP cc_start: 0.8182 (m100) cc_final: 0.7512 (m100)
REVERT: A  470 ILE cc_start: 0.8665 (mm) cc_final: 0.8401 (mm)
REVERT: A  474 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7413 (mt-10)
REVERT: A  501 PHE cc_start: 0.8701 (m-80) cc_final: 0.7771 (t80)
REVERT: B   13 TRP cc_start: 0.5733 (OUTLIER) cc_final: 0.5271 (m100)
  outliers start: 16
  outliers final: 13
  residues processed: 134
  average time/residue: 0.0445
  time to fit residues: 7.9816
Evaluate side-chains
  133 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   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 203 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 = 0.3761 r_free = 0.3761 target = 0.145145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120467 restraints weight = 7604.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124216 restraints weight = 4307.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126845 restraints weight = 2902.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.128551 restraints weight = 2192.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.129757 restraints weight = 1806.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3957  Z= 0.158
  Angle     :  0.695  11.625   5388  Z= 0.348
  Chirality :  0.041   0.150    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.487  17.586    537
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 31.42 %
    Favored  : 65.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.39), residues: 498
  helix:  1.21 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.38 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 426 
 TYR   0.020   0.002   TYR B  12 
 PHE   0.009   0.001   PHE A 411 
 TRP   0.019   0.002   TRP A  94 
 HIS   0.002   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3955)
  covalent geometry    : angle       0.69544 ( 5384)
  SS BOND              : bond        0.00042 (    2)
  SS BOND              : angle       0.30210 (    4)
  hydrogen bonds       : bond        0.04712 (  315)
  hydrogen bonds       : angle       4.78520 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8600 (ttp80)
REVERT: A  453 TRP cc_start: 0.8218 (m100) cc_final: 0.7367 (m100)
REVERT: A  470 ILE cc_start: 0.8654 (mm) cc_final: 0.8323 (mm)
REVERT: A  474 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7423 (mt-10)
REVERT: A  501 PHE cc_start: 0.8703 (m-80) cc_final: 0.7750 (t80)
REVERT: B   13 TRP cc_start: 0.5739 (OUTLIER) cc_final: 0.5270 (m100)
  outliers start: 13
  outliers final: 11
  residues processed: 126
  average time/residue: 0.0456
  time to fit residues: 7.8384
Evaluate side-chains
  135 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 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 = 0.3757 r_free = 0.3757 target = 0.144820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.120008 restraints weight = 7630.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.123751 restraints weight = 4318.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.126362 restraints weight = 2907.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.128187 restraints weight = 2200.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.129557 restraints weight = 1806.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3957  Z= 0.165
  Angle     :  0.733  12.250   5388  Z= 0.367
  Chirality :  0.041   0.149    628
  Planarity :  0.005   0.041    664
  Dihedral  :  4.558  17.672    537
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 30.67 %
    Favored  : 65.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.39), residues: 498
  helix:  1.15 (0.26), residues: 398
  sheet:  None (None), residues: 0
  loop : -2.48 (0.63), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 426 
 TYR   0.019   0.002   TYR B  12 
 PHE   0.011   0.001   PHE A 494 
 TRP   0.020   0.001   TRP B  13 
 HIS   0.002   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3955)
  covalent geometry    : angle       0.73301 ( 5384)
  SS BOND              : bond        0.00039 (    2)
  SS BOND              : angle       0.29096 (    4)
  hydrogen bonds       : bond        0.04810 (  315)
  hydrogen bonds       : angle       4.86771 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8390 (mm-30)
REVERT: A  453 TRP cc_start: 0.8244 (m100) cc_final: 0.7403 (m100)
REVERT: A  470 ILE cc_start: 0.8641 (mm) cc_final: 0.8319 (mm)
REVERT: A  474 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7402 (mt-10)
REVERT: A  501 PHE cc_start: 0.8697 (m-80) cc_final: 0.7759 (t80)
REVERT: B   13 TRP cc_start: 0.5765 (OUTLIER) cc_final: 0.5213 (m100)
  outliers start: 14
  outliers final: 12
  residues processed: 123
  average time/residue: 0.0389
  time to fit residues: 6.4968
Evaluate side-chains
  136 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 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 = 0.3766 r_free = 0.3766 target = 0.145528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.120824 restraints weight = 7713.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.124650 restraints weight = 4334.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.127297 restraints weight = 2888.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.128964 restraints weight = 2168.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.130457 restraints weight = 1786.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3957  Z= 0.162
  Angle     :  0.744  12.062   5388  Z= 0.371
  Chirality :  0.041   0.145    628
  Planarity :  0.005   0.041    664
  Dihedral  :  4.531  17.517    537
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 31.92 %
    Favored  : 64.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.39), residues: 498
  helix:  1.16 (0.26), residues: 398
  sheet:  None (None), residues: 0
  loop : -2.47 (0.63), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 426 
 TYR   0.020   0.002   TYR B  12 
 PHE   0.009   0.001   PHE A 411 
 TRP   0.021   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3955)
  covalent geometry    : angle       0.74424 ( 5384)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       0.30630 (    4)
  hydrogen bonds       : bond        0.04811 (  315)
  hydrogen bonds       : angle       4.86004 (  930)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8416 (mm-30)
REVERT: A  453 TRP cc_start: 0.8197 (m100) cc_final: 0.7367 (m100)
REVERT: A  470 ILE cc_start: 0.8631 (mm) cc_final: 0.8306 (mm)
REVERT: A  474 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7409 (mt-10)
REVERT: A  501 PHE cc_start: 0.8681 (m-80) cc_final: 0.7754 (t80)
REVERT: B   13 TRP cc_start: 0.5727 (OUTLIER) cc_final: 0.5289 (m100)
  outliers start: 15
  outliers final: 13
  residues processed: 129
  average time/residue: 0.0404
  time to fit residues: 6.9588
Evaluate side-chains
  135 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 47 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    0.1980
   chunk 38 optimal weight:    0.1980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 203 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 = 0.3788 r_free = 0.3788 target = 0.147060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.122356 restraints weight = 7634.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.126216 restraints weight = 4300.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.128891 restraints weight = 2872.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.130839 restraints weight = 2150.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.132010 restraints weight = 1742.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3957  Z= 0.159
  Angle     :  0.741  12.083   5388  Z= 0.370
  Chirality :  0.041   0.146    628
  Planarity :  0.005   0.042    664
  Dihedral  :  4.519  16.920    537
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 31.42 %
    Favored  : 64.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.38), residues: 498
  helix:  1.16 (0.26), residues: 398
  sheet:  None (None), residues: 0
  loop : -2.36 (0.65), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 426 
 TYR   0.019   0.002   TYR B  12 
 PHE   0.009   0.001   PHE A 178 
 TRP   0.023   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3955)
  covalent geometry    : angle       0.74079 ( 5384)
  SS BOND              : bond        0.00052 (    2)
  SS BOND              : angle       0.30444 (    4)
  hydrogen bonds       : bond        0.04760 (  315)
  hydrogen bonds       : angle       4.81446 (  930)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 811.87 seconds
wall clock time: 14 minutes 40.47 seconds (880.47 seconds total)