Starting phenix.real_space_refine
on Wed Sep 17 04:04:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6q_50238/09_2025/9f6q_50238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6q_50238/09_2025/9f6q_50238.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6q_50238/09_2025/9f6q_50238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6q_50238/09_2025/9f6q_50238.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6q_50238/09_2025/9f6q_50238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6q_50238/09_2025/9f6q_50238.cif"
  }
  resolution = 3.9
  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=   0.022
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    2392      2.51       5
     N     589      2.21       5
     O     615      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3618
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3618
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 19, 'TRANS': 449}
  Time building chain proxies: 1.24, per 1000 atoms: 0.34
  Number of scatterers: 3618
  At special positions: 0
  Unit cell: (84.63, 69.006, 71.61, 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     615      8.00
     N     589      7.00
     C    2392      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 354 " 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: 0.32
  Conformation dependent library (CDL) restraints added in 153.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  864

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      87.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 62
    Processing helix  chain 'A' and resid 63 through 73
      removed outlier: 3.887A  pdb=" N   LEU A  67 " --> pdb=" O   GLY A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 88
    Processing helix  chain 'A' and resid 89 through 91
      No H-bonds generated for 'chain 'A' and resid 89 through 91'
    Processing helix  chain 'A' and resid 92 through 118
    Processing helix  chain 'A' and resid 120 through 129
    Processing helix  chain 'A' and resid 130 through 165
    Processing helix  chain 'A' and resid 169 through 187
    Processing helix  chain 'A' and resid 188 through 191
      removed outlier: 3.747A  pdb=" N   GLY A 191 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 188 through 191'
    Processing helix  chain 'A' and resid 195 through 218
    Processing helix  chain 'A' and resid 220 through 230
      removed outlier: 4.182A  pdb=" N   LEU A 224 " --> pdb=" O   GLU A 220 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ARG A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 252
      removed outlier: 3.733A  pdb=" N   ILE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 264
      removed outlier: 4.517A  pdb=" N   TYR A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 273 through 311
      removed outlier: 3.525A  pdb=" N   ILE A 277 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 322
    Processing helix  chain 'A' and resid 344 through 357
    Processing helix  chain 'A' and resid 357 through 391
      removed outlier: 3.756A  pdb=" N   LEU A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 419
      Proline residue:  A 411  - end of helix
    Processing helix  chain 'A' and resid 420 through 439
    Processing helix  chain 'A' and resid 439 through 452
      Proline residue:  A 445  - end of helix
      removed outlier: 3.557A  pdb=" N   MET A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 488
    Processing helix  chain 'A' and resid 489 through 491
      No H-bonds generated for 'chain 'A' and resid 489 through 491'
    Processing helix  chain 'A' and resid 495 through 522
      removed outlier: 4.521A  pdb=" N   LEU A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)

    302 hydrogen bonds defined for protein.
    906 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: 0.63

  Time building geometry restraints manager: 0.42 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: 1121
        1.34 -     1.46: 905
        1.46 -     1.58: 1646
        1.58 -     1.70: 0
        1.70 -     1.82: 34
  Bond restraints: 3706
  Sorted by residual:
  bond pdb=" N   LEU A 361 "
       pdb=" CA  LEU A 361 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.20e-02 6.94e+03 4.32e+00
  bond pdb=" CG1 ILE A 141 "
       pdb=" CD1 ILE A 141 "
    ideal  model  delta    sigma   weight residual
    1.513  1.446  0.067 3.90e-02 6.57e+02 2.93e+00
  bond pdb=" CG  MET A  68 "
       pdb=" SD  MET A  68 "
    ideal  model  delta    sigma   weight residual
    1.803  1.771  0.032 2.50e-02 1.60e+03 1.61e+00
  bond pdb=" CB  GLU A 268 "
       pdb=" CG  GLU A 268 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CB  PRO A 335 "
       pdb=" CG  PRO A 335 "
    ideal  model  delta    sigma   weight residual
    1.492  1.543 -0.051 5.00e-02 4.00e+02 1.04e+00
  ... (remaining 3701 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 4849
        1.72 -     3.45: 149
        3.45 -     5.17: 31
        5.17 -     6.89: 14
        6.89 -     8.61: 10
  Bond angle restraints: 5053
  Sorted by residual:
  angle pdb=" CA  MET A  68 "
        pdb=" CB  MET A  68 "
        pdb=" CG  MET A  68 "
      ideal   model   delta    sigma   weight residual
     114.10  121.17   -7.07 2.00e+00 2.50e-01 1.25e+01
  angle pdb=" N   ILE A 141 "
        pdb=" CA  ILE A 141 "
        pdb=" CB  ILE A 141 "
      ideal   model   delta    sigma   weight residual
     110.65  116.54   -5.89 1.71e+00 3.42e-01 1.19e+01
  angle pdb=" N   MET A  68 "
        pdb=" CA  MET A  68 "
        pdb=" CB  MET A  68 "
      ideal   model   delta    sigma   weight residual
     110.16  114.90   -4.74 1.48e+00 4.57e-01 1.03e+01
  angle pdb=" CA  MET A 473 "
        pdb=" CB  MET A 473 "
        pdb=" CG  MET A 473 "
      ideal   model   delta    sigma   weight residual
     114.10  120.43   -6.33 2.00e+00 2.50e-01 1.00e+01
  angle pdb=" CA  ILE A 141 "
        pdb=" CB  ILE A 141 "
        pdb=" CG1 ILE A 141 "
      ideal   model   delta    sigma   weight residual
     110.40  115.68   -5.28 1.70e+00 3.46e-01 9.66e+00
  ... (remaining 5048 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 1830
       15.99 -    31.98: 233
       31.98 -    47.97: 75
       47.97 -    63.96: 14
       63.96 -    79.95: 5
  Dihedral angle restraints: 2157
    sinusoidal: 808
      harmonic: 1349
  Sorted by residual:
  dihedral pdb=" CB  CYS A 233 "
           pdb=" SG  CYS A 233 "
           pdb=" SG  CYS A 236 "
           pdb=" CB  CYS A 236 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.71  -73.71     1      1.00e+01 1.00e-02 6.91e+01
  dihedral pdb=" CB  CYS A 322 "
           pdb=" SG  CYS A 322 "
           pdb=" SG  CYS A 354 "
           pdb=" CB  CYS A 354 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -45.81  -40.19     1      1.00e+01 1.00e-02 2.27e+01
  dihedral pdb=" CA  PHE A 334 "
           pdb=" C   PHE A 334 "
           pdb=" N   PRO A 335 "
           pdb=" CA  PRO A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.04   17.96     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 2154 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 407
       0.037 -    0.075: 133
       0.075 -    0.112: 48
       0.112 -    0.150: 12
       0.150 -    0.187: 2
  Chirality restraints: 602
  Sorted by residual:
  chirality pdb=" CB  THR A 209 "
            pdb=" CA  THR A 209 "
            pdb=" OG1 THR A 209 "
            pdb=" CG2 THR A 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.75e-01
  chirality pdb=" CB  THR A 412 "
            pdb=" CA  THR A 412 "
            pdb=" OG1 THR A 412 "
            pdb=" CG2 THR A 412 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.00e-01
  chirality pdb=" CA  MET A  68 "
            pdb=" N   MET A  68 "
            pdb=" C   MET A  68 "
            pdb=" CB  MET A  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.53e-01
  ... (remaining 599 not shown)

  Planarity restraints: 624
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  63 "   -0.033 5.00e-02 4.00e+02   5.06e-02 4.09e+00
        pdb=" N   PRO A  64 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A  64 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  64 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 296 "   -0.006 2.00e-02 2.50e+03   1.42e-02 3.52e+00
        pdb=" CG  PHE A 296 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 296 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 296 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 296 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 296 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 296 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 230 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO A 231 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 231 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 231 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 621 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 568
        2.76 -     3.29: 3996
        3.29 -     3.83: 6369
        3.83 -     4.36: 6782
        4.36 -     4.90: 11324
  Nonbonded interactions: 29039
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  58 "
            pdb=" OG1 THR A  62 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG1 THR A 450 "
            pdb=" OD1 ASN A 461 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   GLY A 372 "
            pdb=" OG1 THR A 376 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   MET A 377 "
            pdb=" OG1 THR A 380 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OE2 GLU A 142 "
            pdb=" NH2 ARG A 400 "
     model   vdw
     2.334 3.120
  ... (remaining 29034 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.100
  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:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
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   0.067   3708  Z= 0.160
  Angle     :  0.827   8.612   5057  Z= 0.414
  Chirality :  0.044   0.187    602
  Planarity :  0.005   0.051    624
  Dihedral  : 15.985  79.954   1287
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 23.10 %
    Favored  : 74.28 %
  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:  1.22 (0.40), residues: 467
  helix:  1.47 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.83 (0.67), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 400 
 TYR   0.017   0.001   TYR A 362 
 PHE   0.030   0.002   PHE A 296 
 TRP   0.014   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3706)
  covalent geometry    : angle       0.82629 ( 5053)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       1.29047 (    4)
  hydrogen bonds       : bond        0.08942 (  302)
  hydrogen bonds       : angle       5.26630 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8201 (m-10) cc_final: 0.7573 (m-10)
REVERT: A  120 ASP cc_start: 0.7306 (p0) cc_final: 0.6729 (p0)
REVERT: A  138 TRP cc_start: 0.8426 (t60) cc_final: 0.7959 (t60)
REVERT: A  167 ARG cc_start: 0.5113 (mtt90) cc_final: 0.4651 (tpt170)
REVERT: A  268 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8208 (mp0)
REVERT: A  297 ILE cc_start: 0.9518 (pt) cc_final: 0.8929 (pt)
REVERT: A  319 PHE cc_start: 0.7102 (t80) cc_final: 0.6724 (t80)
REVERT: A  346 TYR cc_start: 0.7927 (t80) cc_final: 0.7288 (t80)
REVERT: A  384 GLN cc_start: 0.8102 (tt0) cc_final: 0.7851 (tm-30)
REVERT: A  394 ARG cc_start: 0.7880 (tpt-90) cc_final: 0.7209 (tpt90)
  outliers start: 10
  outliers final: 5
  residues processed: 163
  average time/residue: 0.0541
  time to fit residues: 11.4116
Evaluate side-chains
  142 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 137
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.116001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.098569 restraints weight = 11536.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.101280 restraints weight = 7768.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.103175 restraints weight = 5645.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.104610 restraints weight = 4379.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.105733 restraints weight = 3564.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3708  Z= 0.170
  Angle     :  0.810   9.675   5057  Z= 0.420
  Chirality :  0.047   0.189    602
  Planarity :  0.006   0.057    624
  Dihedral  :  6.004  49.974    515
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 19.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 27.03 %
    Favored  : 68.77 %
  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:  1.36 (0.40), residues: 467
  helix:  1.46 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop : -1.50 (0.69), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 397 
 TYR   0.017   0.002   TYR A 362 
 PHE   0.030   0.002   PHE A 199 
 TRP   0.012   0.001   TRP A 364 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3706)
  covalent geometry    : angle       0.80936 ( 5053)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       1.31948 (    4)
  hydrogen bonds       : bond        0.04586 (  302)
  hydrogen bonds       : angle       4.76123 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8144 (m-10) cc_final: 0.7674 (m-10)
REVERT: A   70 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8913 (mp)
REVERT: A  138 TRP cc_start: 0.8982 (t60) cc_final: 0.8660 (t60)
REVERT: A  139 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9288 (mm)
REVERT: A  142 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8355 (mm-30)
REVERT: A  265 LYS cc_start: 0.8386 (mttp) cc_final: 0.8051 (mptt)
REVERT: A  268 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8117 (mp0)
REVERT: A  297 ILE cc_start: 0.9408 (pt) cc_final: 0.9176 (pt)
REVERT: A  384 GLN cc_start: 0.8380 (tt0) cc_final: 0.7866 (tm-30)
REVERT: A  387 MET cc_start: 0.8626 (tpp) cc_final: 0.8249 (mpp)
REVERT: A  391 LEU cc_start: 0.8832 (tp) cc_final: 0.8543 (tt)
  outliers start: 16
  outliers final: 9
  residues processed: 147
  average time/residue: 0.0411
  time to fit residues: 8.0628
Evaluate side-chains
  143 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  330 TYR
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 18 optimal weight:    0.4980
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 40 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
** A 243 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.116347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.098922 restraints weight = 11304.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.101496 restraints weight = 7533.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.103517 restraints weight = 5576.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.105101 restraints weight = 4295.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.106102 restraints weight = 3445.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3708  Z= 0.150
  Angle     :  0.778   8.214   5057  Z= 0.396
  Chirality :  0.046   0.179    602
  Planarity :  0.006   0.060    624
  Dihedral  :  5.668  50.150    511
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 27.82 %
    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 aren not related in a simple way.
  whole:  1.49 (0.40), residues: 467
  helix:  1.57 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.43 (0.66), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 405 
 TYR   0.020   0.002   TYR A 362 
 PHE   0.039   0.002   PHE A 301 
 TRP   0.010   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3706)
  covalent geometry    : angle       0.77742 ( 5053)
  SS BOND              : bond        0.00127 (    2)
  SS BOND              : angle       1.24525 (    4)
  hydrogen bonds       : bond        0.04309 (  302)
  hydrogen bonds       : angle       4.64401 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8139 (m-10) cc_final: 0.7697 (m-80)
REVERT: A   70 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8956 (mp)
REVERT: A  107 GLN cc_start: 0.9440 (mt0) cc_final: 0.9104 (mm110)
REVERT: A  138 TRP cc_start: 0.9053 (t60) cc_final: 0.8682 (t60)
REVERT: A  139 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9183 (mm)
REVERT: A  142 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8118 (mm-30)
REVERT: A  167 ARG cc_start: 0.4706 (mtt180) cc_final: 0.3573 (tpt170)
REVERT: A  192 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6323 (mp)
REVERT: A  255 HIS cc_start: 0.9374 (p90) cc_final: 0.9070 (p90)
REVERT: A  268 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8122 (mp0)
REVERT: A  384 GLN cc_start: 0.8373 (tt0) cc_final: 0.7863 (tm-30)
REVERT: A  391 LEU cc_start: 0.8852 (tp) cc_final: 0.8553 (tt)
REVERT: A  456 MET cc_start: 0.7818 (mpp) cc_final: 0.7367 (mpp)
REVERT: A  514 LEU cc_start: 0.9424 (mm) cc_final: 0.9212 (mm)
  outliers start: 21
  outliers final: 13
  residues processed: 149
  average time/residue: 0.0476
  time to fit residues: 9.3629
Evaluate side-chains
  144 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.117425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.099832 restraints weight = 11406.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.102572 restraints weight = 7763.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.104463 restraints weight = 5676.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.106004 restraints weight = 4419.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.107094 restraints weight = 3576.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3708  Z= 0.154
  Angle     :  0.803   9.405   5057  Z= 0.405
  Chirality :  0.045   0.163    602
  Planarity :  0.006   0.058    624
  Dihedral  :  5.754  49.725    511
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 30.18 %
    Favored  : 64.30 %
  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 aren not related in a simple way.
  whole:  1.53 (0.40), residues: 467
  helix:  1.61 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.43 (0.66), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.028   0.002   TYR A 362 
 PHE   0.041   0.002   PHE A 301 
 TRP   0.009   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3706)
  covalent geometry    : angle       0.80272 ( 5053)
  SS BOND              : bond        0.00139 (    2)
  SS BOND              : angle       1.24198 (    4)
  hydrogen bonds       : bond        0.04330 (  302)
  hydrogen bonds       : angle       4.68019 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8159 (m-10) cc_final: 0.7640 (m-80)
REVERT: A   70 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8943 (mp)
REVERT: A  107 GLN cc_start: 0.9339 (mt0) cc_final: 0.9102 (mm110)
REVERT: A  138 TRP cc_start: 0.8964 (t60) cc_final: 0.8471 (t60)
REVERT: A  139 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9114 (mm)
REVERT: A  142 GLU cc_start: 0.9209 (mm-30) cc_final: 0.7832 (mm-30)
REVERT: A  167 ARG cc_start: 0.4698 (mtt180) cc_final: 0.3483 (tpt170)
REVERT: A  192 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6383 (mp)
REVERT: A  255 HIS cc_start: 0.9379 (p90) cc_final: 0.9059 (p90)
REVERT: A  265 LYS cc_start: 0.8405 (mttp) cc_final: 0.7982 (mptt)
REVERT: A  268 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8136 (mp0)
REVERT: A  384 GLN cc_start: 0.8293 (tt0) cc_final: 0.7817 (tm-30)
REVERT: A  391 LEU cc_start: 0.8858 (tp) cc_final: 0.8500 (tt)
REVERT: A  456 MET cc_start: 0.7789 (mpp) cc_final: 0.7502 (mpp)
  outliers start: 21
  outliers final: 15
  residues processed: 150
  average time/residue: 0.0451
  time to fit residues: 9.1298
Evaluate side-chains
  146 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.117763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.100124 restraints weight = 11456.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.102846 restraints weight = 7751.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.104669 restraints weight = 5665.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.106244 restraints weight = 4431.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.107413 restraints weight = 3594.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3708  Z= 0.153
  Angle     :  0.846   8.982   5057  Z= 0.415
  Chirality :  0.048   0.271    602
  Planarity :  0.006   0.059    624
  Dihedral  :  5.776  48.666    511
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 32.55 %
    Favored  : 61.68 %
  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:  1.55 (0.40), residues: 467
  helix:  1.59 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.19 (0.66), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 193 
 TYR   0.024   0.001   TYR A 362 
 PHE   0.044   0.002   PHE A 301 
 TRP   0.008   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3706)
  covalent geometry    : angle       0.84535 ( 5053)
  SS BOND              : bond        0.00123 (    2)
  SS BOND              : angle       1.24212 (    4)
  hydrogen bonds       : bond        0.04342 (  302)
  hydrogen bonds       : angle       4.75116 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8125 (m-10) cc_final: 0.7610 (m-80)
REVERT: A   70 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8986 (mp)
REVERT: A  120 ASP cc_start: 0.7722 (p0) cc_final: 0.6727 (p0)
REVERT: A  138 TRP cc_start: 0.8855 (t60) cc_final: 0.8541 (t60)
REVERT: A  142 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8002 (mm-30)
REVERT: A  167 ARG cc_start: 0.4812 (mtt180) cc_final: 0.3399 (tpt170)
REVERT: A  192 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6259 (mp)
REVERT: A  265 LYS cc_start: 0.8456 (mttp) cc_final: 0.8026 (mptt)
REVERT: A  268 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8127 (mp0)
REVERT: A  336 MET cc_start: 0.7700 (mmm) cc_final: 0.7046 (tpp)
REVERT: A  384 GLN cc_start: 0.8273 (tt0) cc_final: 0.7797 (tm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 150
  average time/residue: 0.0412
  time to fit residues: 8.2496
Evaluate side-chains
  145 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  330 TYR
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.117660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.099887 restraints weight = 11315.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.102555 restraints weight = 7758.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.104420 restraints weight = 5730.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.105937 restraints weight = 4496.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.107050 restraints weight = 3673.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3708  Z= 0.157
  Angle     :  0.871   9.003   5057  Z= 0.429
  Chirality :  0.047   0.175    602
  Planarity :  0.006   0.060    624
  Dihedral  :  5.788  47.813    511
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 19.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  7.35 %
    Allowed  : 33.33 %
    Favored  : 59.32 %
  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:  1.42 (0.40), residues: 467
  helix:  1.51 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop : -1.42 (0.67), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 134 
 TYR   0.024   0.002   TYR A 362 
 PHE   0.045   0.002   PHE A 301 
 TRP   0.008   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3706)
  covalent geometry    : angle       0.87092 ( 5053)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       1.15385 (    4)
  hydrogen bonds       : bond        0.04347 (  302)
  hydrogen bonds       : angle       4.73352 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8153 (m-10) cc_final: 0.7609 (m-80)
REVERT: A   70 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8993 (mp)
REVERT: A  106 CYS cc_start: 0.9329 (m) cc_final: 0.8973 (m)
REVERT: A  138 TRP cc_start: 0.8917 (t60) cc_final: 0.8549 (t60)
REVERT: A  139 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9155 (mm)
REVERT: A  142 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8138 (mm-30)
REVERT: A  192 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6218 (mp)
REVERT: A  265 LYS cc_start: 0.8522 (mttp) cc_final: 0.8287 (mptt)
REVERT: A  268 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8125 (mp0)
REVERT: A  384 GLN cc_start: 0.8265 (tt0) cc_final: 0.7751 (tm-30)
REVERT: A  387 MET cc_start: 0.8761 (mmm) cc_final: 0.8331 (mtp)
REVERT: A  424 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8464 (mt)
REVERT: A  443 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9021 (p)
  outliers start: 28
  outliers final: 20
  residues processed: 147
  average time/residue: 0.0448
  time to fit residues: 8.8554
Evaluate side-chains
  152 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  330 TYR
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    0.0470
   chunk 6 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.117574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.099839 restraints weight = 11581.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.102536 restraints weight = 7882.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.104456 restraints weight = 5796.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.105974 restraints weight = 4543.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.106821 restraints weight = 3709.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3708  Z= 0.161
  Angle     :  0.902   8.553   5057  Z= 0.442
  Chirality :  0.048   0.158    602
  Planarity :  0.006   0.063    624
  Dihedral  :  5.901  47.791    511
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 20.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 34.91 %
    Favored  : 57.48 %
  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:  1.35 (0.40), residues: 467
  helix:  1.45 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.35 (0.67), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.030   0.002   TYR A 362 
 PHE   0.045   0.002   PHE A 301 
 TRP   0.008   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3706)
  covalent geometry    : angle       0.90166 ( 5053)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       1.07986 (    4)
  hydrogen bonds       : bond        0.04367 (  302)
  hydrogen bonds       : angle       4.86963 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8146 (m-10) cc_final: 0.7629 (m-80)
REVERT: A   92 LEU cc_start: 0.8415 (mt) cc_final: 0.8193 (mt)
REVERT: A  106 CYS cc_start: 0.9290 (m) cc_final: 0.8946 (m)
REVERT: A  138 TRP cc_start: 0.8871 (t60) cc_final: 0.8518 (t60)
REVERT: A  139 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9115 (mm)
REVERT: A  142 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8166 (mm-30)
REVERT: A  192 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.5959 (mp)
REVERT: A  229 PHE cc_start: 0.6696 (t80) cc_final: 0.6192 (t80)
REVERT: A  265 LYS cc_start: 0.8327 (mttp) cc_final: 0.8073 (mttp)
REVERT: A  268 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8109 (mp0)
REVERT: A  384 GLN cc_start: 0.8147 (tt0) cc_final: 0.7798 (tm-30)
REVERT: A  443 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9005 (p)
  outliers start: 29
  outliers final: 20
  residues processed: 147
  average time/residue: 0.0360
  time to fit residues: 7.1985
Evaluate side-chains
  154 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  330 TYR
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0010
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.117130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.099083 restraints weight = 11537.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.101693 restraints weight = 7901.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.103693 restraints weight = 5880.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.105153 restraints weight = 4602.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.106360 restraints weight = 3782.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3708  Z= 0.166
  Angle     :  0.935  11.460   5057  Z= 0.459
  Chirality :  0.049   0.176    602
  Planarity :  0.006   0.064    624
  Dihedral  :  5.966  47.139    511
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  7.35 %
    Allowed  : 34.91 %
    Favored  : 57.74 %
  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:  1.18 (0.40), residues: 467
  helix:  1.32 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.34 (0.67), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.028   0.002   TYR A 362 
 PHE   0.051   0.003   PHE A 301 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3706)
  covalent geometry    : angle       0.93469 ( 5053)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       0.98132 (    4)
  hydrogen bonds       : bond        0.04438 (  302)
  hydrogen bonds       : angle       4.94790 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8237 (m-10) cc_final: 0.7971 (m-80)
REVERT: A  106 CYS cc_start: 0.9262 (m) cc_final: 0.8942 (m)
REVERT: A  138 TRP cc_start: 0.8958 (t60) cc_final: 0.8682 (t60)
REVERT: A  139 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9074 (mm)
REVERT: A  142 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8152 (mm-30)
REVERT: A  192 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.5888 (mp)
REVERT: A  229 PHE cc_start: 0.6673 (t80) cc_final: 0.6130 (t80)
REVERT: A  265 LYS cc_start: 0.8291 (mttp) cc_final: 0.8053 (mptt)
REVERT: A  268 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8116 (mp0)
REVERT: A  384 GLN cc_start: 0.8234 (tt0) cc_final: 0.7841 (tm-30)
REVERT: A  387 MET cc_start: 0.8878 (mmm) cc_final: 0.8542 (mtt)
REVERT: A  443 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.9048 (p)
  outliers start: 28
  outliers final: 22
  residues processed: 148
  average time/residue: 0.0463
  time to fit residues: 9.1479
Evaluate side-chains
  157 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  330 TYR
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0670
   chunk 16 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7718

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.117413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.099499 restraints weight = 11299.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.101981 restraints weight = 7766.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.103963 restraints weight = 5848.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.105468 restraints weight = 4614.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.106614 restraints weight = 3754.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3708  Z= 0.169
  Angle     :  0.966   9.890   5057  Z= 0.477
  Chirality :  0.050   0.230    602
  Planarity :  0.006   0.066    624
  Dihedral  :  6.005  46.220    511
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 20.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 36.75 %
    Favored  : 56.17 %
  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:  1.09 (0.39), residues: 467
  helix:  1.26 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.37 (0.68), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 273 
 TYR   0.027   0.002   TYR A 362 
 PHE   0.053   0.003   PHE A 301 
 TRP   0.007   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3706)
  covalent geometry    : angle       0.96561 ( 5053)
  SS BOND              : bond        0.00046 (    2)
  SS BOND              : angle       0.81522 (    4)
  hydrogen bonds       : bond        0.04478 (  302)
  hydrogen bonds       : angle       4.99671 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 CYS cc_start: 0.9265 (m) cc_final: 0.8961 (m)
REVERT: A  138 TRP cc_start: 0.9005 (t60) cc_final: 0.8646 (t60)
REVERT: A  139 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9200 (mm)
REVERT: A  142 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8050 (mm-30)
REVERT: A  192 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.5838 (mp)
REVERT: A  229 PHE cc_start: 0.6573 (t80) cc_final: 0.5999 (t80)
REVERT: A  265 LYS cc_start: 0.8352 (mttp) cc_final: 0.8017 (mptt)
REVERT: A  268 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8126 (mp0)
REVERT: A  329 ASP cc_start: 0.6460 (t0) cc_final: 0.3840 (t0)
REVERT: A  334 PHE cc_start: 0.7283 (p90) cc_final: 0.6994 (p90)
REVERT: A  336 MET cc_start: 0.7546 (mmm) cc_final: 0.7294 (mmp)
REVERT: A  384 GLN cc_start: 0.8176 (tt0) cc_final: 0.7825 (tm-30)
  outliers start: 27
  outliers final: 22
  residues processed: 139
  average time/residue: 0.0427
  time to fit residues: 8.0068
Evaluate side-chains
  153 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  330 TYR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0370
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0010
   overall best weight:    0.5266

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 HIS
** A 435 GLN ** 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 = 0.3875 r_free = 0.3875 target = 0.118157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.099848 restraints weight = 11458.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.102485 restraints weight = 7881.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.104486 restraints weight = 5862.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.106068 restraints weight = 4611.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.107279 restraints weight = 3758.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3708  Z= 0.169
  Angle     :  0.992  10.368   5057  Z= 0.489
  Chirality :  0.051   0.254    602
  Planarity :  0.006   0.065    624
  Dihedral  :  5.733  46.636    509
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 21.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 37.80 %
    Favored  : 56.43 %
  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:  1.12 (0.39), residues: 467
  helix:  1.29 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop : -1.21 (0.64), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 193 
 TYR   0.027   0.002   TYR A 362 
 PHE   0.053   0.003   PHE A 301 
 TRP   0.009   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3706)
  covalent geometry    : angle       0.99178 ( 5053)
  SS BOND              : bond        0.00029 (    2)
  SS BOND              : angle       0.67858 (    4)
  hydrogen bonds       : bond        0.04528 (  302)
  hydrogen bonds       : angle       4.99974 (  906)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 CYS cc_start: 0.9272 (m) cc_final: 0.8964 (m)
REVERT: A  138 TRP cc_start: 0.9021 (t60) cc_final: 0.8704 (t60)
REVERT: A  139 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9180 (mm)
REVERT: A  142 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8120 (mm-30)
REVERT: A  192 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.5803 (mp)
REVERT: A  229 PHE cc_start: 0.6606 (t80) cc_final: 0.6059 (t80)
REVERT: A  265 LYS cc_start: 0.8336 (mttp) cc_final: 0.8012 (mptt)
REVERT: A  268 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8114 (mp0)
REVERT: A  336 MET cc_start: 0.7878 (mmm) cc_final: 0.7461 (mmp)
REVERT: A  384 GLN cc_start: 0.8123 (tt0) cc_final: 0.7772 (tm-30)
REVERT: A  387 MET cc_start: 0.8858 (mmm) cc_final: 0.8325 (mmm)
REVERT: A  514 LEU cc_start: 0.9332 (mm) cc_final: 0.9113 (mm)
  outliers start: 22
  outliers final: 18
  residues processed: 138
  average time/residue: 0.0477
  time to fit residues: 8.8845
Evaluate side-chains
  148 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  330 TYR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.116309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.098990 restraints weight = 11370.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.101549 restraints weight = 7736.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.103557 restraints weight = 5735.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.105065 restraints weight = 4458.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.106009 restraints weight = 3606.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3708  Z= 0.175
  Angle     :  0.982  10.790   5057  Z= 0.488
  Chirality :  0.051   0.247    602
  Planarity :  0.006   0.067    624
  Dihedral  :  5.675  44.947    509
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 21.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 37.80 %
    Favored  : 56.69 %
  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:  0.90 (0.40), residues: 467
  helix:  1.12 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop : -1.51 (0.70), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 193 
 TYR   0.026   0.002   TYR A 362 
 PHE   0.050   0.003   PHE A 301 
 TRP   0.009   0.001   TRP A 171 
 HIS   0.003   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3706)
  covalent geometry    : angle       0.98258 ( 5053)
  SS BOND              : bond        0.00112 (    2)
  SS BOND              : angle       0.80125 (    4)
  hydrogen bonds       : bond        0.04483 (  302)
  hydrogen bonds       : angle       5.04035 (  906)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 756.15 seconds
wall clock time: 13 minutes 48.06 seconds (828.06 seconds total)