Starting phenix.real_space_refine
on Wed Mar  5 21:32:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6q_50238/03_2025/9f6q_50238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6q_50238/03_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_50238/03_2025/9f6q_50238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6q_50238/03_2025/9f6q_50238.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6q_50238/03_2025/9f6q_50238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6q_50238/03_2025/9f6q_50238.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.85, per 1000 atoms: 0.79
  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: 0.91
  Conformation dependent library (CDL) restraints added in 417.2 milliseconds
  

  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: 0.36
  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: 1.04

  Time building geometry restraints manager: 1.10 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:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     13.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.020
-------------------------------------------------------------------------------
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   3706  Z= 0.226
  Angle     :  0.826   8.612   5053  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 : 16.19
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.014   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 493 
 PHE   0.030   0.002   PHE A 296 
 TYR   0.017   0.001   TYR A 362 
 ARG   0.005   0.000   ARG A 400 

*********************** 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  : 0.420 
Fit side-chains
   revert: symmetry clash
   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: 0.4650 (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: 0.7852 (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: 0.1266
  time to fit residues: 26.1513
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  : 0.389 
-------------------------------------------------------------------------------
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 38 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0270
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0010
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.4844

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.117825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.100112 restraints weight = 11192.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.102845 restraints weight = 7524.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.104811 restraints weight = 5545.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3706  Z= 0.206
  Angle     :  0.809   9.307   5053  Z= 0.413
  Chirality :  0.046   0.180    602
  Planarity :  0.006   0.058    624
  Dihedral  :  5.971  50.234    515
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 19.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 26.51 %
    Favored  : 69.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.40), residues: 467
  helix:  1.56 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.52 (0.67), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 364 
 HIS   0.003   0.001   HIS A 493 
 PHE   0.031   0.002   PHE A 199 
 TYR   0.021   0.002   TYR A 362 
 ARG   0.002   0.000   ARG A 134 

*********************** 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: 14
    poor density    : 144
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8160 (m-10) cc_final: 0.7663 (m-80)
REVERT: A   70 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8920 (mp)
REVERT: A  138 TRP cc_start: 0.9071 (t60) cc_final: 0.8760 (t60)
REVERT: A  139 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9250 (mm)
REVERT: A  142 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8384 (mm-30)
REVERT: A  199 PHE cc_start: 0.7676 (m-80) cc_final: 0.7421 (m-80)
REVERT: A  265 LYS cc_start: 0.8321 (mttp) cc_final: 0.7998 (mptt)
REVERT: A  268 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8094 (mp0)
REVERT: A  297 ILE cc_start: 0.9402 (pt) cc_final: 0.9200 (pt)
REVERT: A  384 GLN cc_start: 0.8392 (tt0) cc_final: 0.7856 (tm-30)
REVERT: A  387 MET cc_start: 0.8763 (tpp) cc_final: 0.8364 (mpp)
REVERT: A  456 MET cc_start: 0.7680 (mpp) cc_final: 0.7169 (mpp)
REVERT: A  514 LEU cc_start: 0.9384 (mm) cc_final: 0.9103 (mm)
  outliers start: 14
  outliers final: 9
  residues processed: 149
  average time/residue: 0.1107
  time to fit residues: 21.5239
Evaluate side-chains
  144 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
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 24 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 27 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0070
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.117523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.100197 restraints weight = 11029.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.102735 restraints weight = 7310.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.104783 restraints weight = 5419.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3706  Z= 0.201
  Angle     :  0.786  10.873   5053  Z= 0.394
  Chirality :  0.045   0.158    602
  Planarity :  0.006   0.058    624
  Dihedral  :  5.663  50.295    511
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 27.03 %
    Favored  : 66.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.40), residues: 467
  helix:  1.64 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.49 (0.66), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 255 
 PHE   0.042   0.002   PHE A 301 
 TYR   0.020   0.001   TYR A 362 
 ARG   0.002   0.000   ARG A 167 

*********************** 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
  161 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8166 (m-10) cc_final: 0.7675 (m-80)
REVERT: A   70 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8901 (mp)
REVERT: A  107 GLN cc_start: 0.9394 (mt0) cc_final: 0.9079 (mm110)
REVERT: A  138 TRP cc_start: 0.9043 (t60) cc_final: 0.8624 (t60)
REVERT: A  139 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9183 (mm)
REVERT: A  142 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8105 (mm-30)
REVERT: A  149 ASP cc_start: 0.9052 (m-30) cc_final: 0.8822 (m-30)
REVERT: A  167 ARG cc_start: 0.4812 (mtt180) cc_final: 0.3636 (tpt170)
REVERT: A  192 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6295 (mp)
REVERT: A  255 HIS cc_start: 0.9342 (p90) cc_final: 0.9058 (p90)
REVERT: A  268 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8109 (mp0)
REVERT: A  273 ARG cc_start: 0.9036 (tpm170) cc_final: 0.8752 (tpm170)
REVERT: A  384 GLN cc_start: 0.8395 (tt0) cc_final: 0.7856 (tm-30)
REVERT: A  456 MET cc_start: 0.7727 (mpp) cc_final: 0.7340 (mpp)
  outliers start: 23
  outliers final: 12
  residues processed: 145
  average time/residue: 0.1083
  time to fit residues: 20.7600
Evaluate side-chains
  140 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  487 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    0.1980
   chunk 26 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 14 optimal weight:    0.3980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 337 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.117107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.099223 restraints weight = 11290.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.101998 restraints weight = 7586.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.103951 restraints weight = 5515.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3706  Z= 0.221
  Angle     :  0.826   9.630   5053  Z= 0.411
  Chirality :  0.046   0.179    602
  Planarity :  0.006   0.059    624
  Dihedral  :  5.740  49.805    511
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 30.71 %
    Favored  : 64.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.40), residues: 467
  helix:  1.62 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.39 (0.65), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.045   0.002   PHE A 301 
 TYR   0.029   0.002   TYR A 362 
 ARG   0.002   0.000   ARG A 397 

*********************** 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
  158 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8161 (m-10) cc_final: 0.7665 (m-80)
REVERT: A   70 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8977 (mp)
REVERT: A  107 GLN cc_start: 0.9285 (mt0) cc_final: 0.9066 (mm110)
REVERT: A  138 TRP cc_start: 0.8924 (t60) cc_final: 0.8419 (t60)
REVERT: A  142 GLU cc_start: 0.9205 (mm-30) cc_final: 0.7715 (mm-30)
REVERT: A  149 ASP cc_start: 0.9120 (m-30) cc_final: 0.8892 (m-30)
REVERT: A  167 ARG cc_start: 0.4913 (mtt180) cc_final: 0.3612 (tpt170)
REVERT: A  192 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6487 (mp)
REVERT: A  265 LYS cc_start: 0.8442 (mttp) cc_final: 0.8010 (mptt)
REVERT: A  268 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8104 (mp0)
REVERT: A  273 ARG cc_start: 0.9068 (tpm170) cc_final: 0.8860 (tpm170)
REVERT: A  336 MET cc_start: 0.7861 (mmm) cc_final: 0.7065 (tpp)
REVERT: A  384 GLN cc_start: 0.8305 (tt0) cc_final: 0.7831 (tm-30)
REVERT: A  456 MET cc_start: 0.7950 (mpp) cc_final: 0.7687 (mpp)
  outliers start: 17
  outliers final: 13
  residues processed: 146
  average time/residue: 0.1138
  time to fit residues: 21.4323
Evaluate side-chains
  142 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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  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  463 LEU
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 35 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.117884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.099725 restraints weight = 11497.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.102545 restraints weight = 7769.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.104520 restraints weight = 5658.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3706  Z= 0.221
  Angle     :  0.851   9.502   5053  Z= 0.415
  Chirality :  0.045   0.159    602
  Planarity :  0.006   0.059    624
  Dihedral  :  5.788  48.915    511
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 32.02 %
    Favored  : 61.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.40), residues: 467
  helix:  1.62 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.17 (0.66), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.043   0.002   PHE A 301 
 TYR   0.024   0.001   TYR A 362 
 ARG   0.002   0.000   ARG A 397 

*********************** 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
  162 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8134 (m-10) cc_final: 0.7604 (m-80)
REVERT: A   70 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9006 (mp)
REVERT: A  138 TRP cc_start: 0.8913 (t60) cc_final: 0.8544 (t60)
REVERT: A  139 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9158 (mm)
REVERT: A  142 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8075 (mm-30)
REVERT: A  145 ILE cc_start: 0.9422 (pt) cc_final: 0.9068 (pt)
REVERT: A  149 ASP cc_start: 0.9169 (m-30) cc_final: 0.8919 (m-30)
REVERT: A  167 ARG cc_start: 0.5016 (mtt180) cc_final: 0.3529 (tpt170)
REVERT: A  192 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6187 (mp)
REVERT: A  265 LYS cc_start: 0.8469 (mttp) cc_final: 0.8078 (mptt)
REVERT: A  268 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8127 (mp0)
REVERT: A  273 ARG cc_start: 0.9089 (tpm170) cc_final: 0.8856 (tpm170)
REVERT: A  336 MET cc_start: 0.7741 (mmm) cc_final: 0.7344 (tpp)
REVERT: A  384 GLN cc_start: 0.8290 (tt0) cc_final: 0.7801 (tm-30)
  outliers start: 23
  outliers final: 12
  residues processed: 149
  average time/residue: 0.1083
  time to fit residues: 21.1094
Evaluate side-chains
  141 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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  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  463 LEU
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 42 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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
A 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.117717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.099212 restraints weight = 11642.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.101941 restraints weight = 7977.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.103993 restraints weight = 5895.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3706  Z= 0.228
  Angle     :  0.874  10.597   5053  Z= 0.431
  Chirality :  0.047   0.237    602
  Planarity :  0.006   0.060    624
  Dihedral  :  5.860  49.204    511
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  7.35 %
    Allowed  : 31.50 %
    Favored  : 61.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.40), residues: 467
  helix:  1.58 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.22 (0.68), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.048   0.002   PHE A 301 
 TYR   0.023   0.001   TYR A 362 
 ARG   0.002   0.000   ARG A 134 

*********************** 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
  160 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8175 (m-10) cc_final: 0.7676 (m-80)
REVERT: A   70 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8980 (mp)
REVERT: A  106 CYS cc_start: 0.9292 (m) cc_final: 0.8956 (m)
REVERT: A  138 TRP cc_start: 0.8900 (t60) cc_final: 0.8449 (t60)
REVERT: A  139 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9136 (mm)
REVERT: A  142 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8156 (mm-30)
REVERT: A  149 ASP cc_start: 0.9199 (m-30) cc_final: 0.8938 (m-30)
REVERT: A  192 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6393 (mp)
REVERT: A  265 LYS cc_start: 0.8456 (mttp) cc_final: 0.8175 (mttp)
REVERT: A  268 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8106 (mp0)
REVERT: A  273 ARG cc_start: 0.9096 (tpm170) cc_final: 0.8866 (tpm170)
REVERT: A  384 GLN cc_start: 0.8290 (tt0) cc_final: 0.7820 (tm-30)
REVERT: A  443 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.8984 (p)
  outliers start: 28
  outliers final: 17
  residues processed: 145
  average time/residue: 0.1128
  time to fit residues: 21.3141
Evaluate side-chains
  148 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  113 LEU
Chi-restraints excluded: chain A residue  121 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  433 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  463 LEU
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 36 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 21 optimal weight:    0.1980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.118584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.100425 restraints weight = 11454.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.103018 restraints weight = 7890.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.105010 restraints weight = 5875.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3706  Z= 0.234
  Angle     :  0.916  10.057   5053  Z= 0.445
  Chirality :  0.049   0.299    602
  Planarity :  0.006   0.062    624
  Dihedral  :  6.010  51.734    511
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 19.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 34.38 %
    Favored  : 58.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.39), residues: 467
  helix:  1.48 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -1.25 (0.68), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.049   0.002   PHE A 301 
 TYR   0.029   0.002   TYR A 362 
 ARG   0.002   0.000   ARG A 392 

*********************** 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
  159 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8160 (m-10) cc_final: 0.7687 (m-80)
REVERT: A   92 LEU cc_start: 0.8402 (mt) cc_final: 0.8185 (mt)
REVERT: A  106 CYS cc_start: 0.9242 (m) cc_final: 0.8932 (m)
REVERT: A  138 TRP cc_start: 0.8866 (t60) cc_final: 0.8576 (t60)
REVERT: A  139 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9092 (mm)
REVERT: A  142 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8103 (mm-30)
REVERT: A  149 ASP cc_start: 0.9172 (m-30) cc_final: 0.8903 (m-30)
REVERT: A  192 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6201 (mp)
REVERT: A  229 PHE cc_start: 0.6742 (t80) cc_final: 0.6257 (t80)
REVERT: A  265 LYS cc_start: 0.8272 (mttp) cc_final: 0.8031 (mttp)
REVERT: A  268 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8095 (mp0)
REVERT: A  273 ARG cc_start: 0.9111 (tpm170) cc_final: 0.8872 (tpm170)
REVERT: A  384 GLN cc_start: 0.8218 (tt0) cc_final: 0.7779 (tm-30)
REVERT: A  443 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9005 (p)
  outliers start: 27
  outliers final: 20
  residues processed: 143
  average time/residue: 0.1125
  time to fit residues: 20.9758
Evaluate side-chains
  151 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
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  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  438 LEU
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  487 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0570
   chunk 38 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   overall best weight:    0.7298

-------------------------------------------------------------------------------
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 = 0.3869 r_free = 0.3869 target = 0.117256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.098824 restraints weight = 11340.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.101430 restraints weight = 7770.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.103464 restraints weight = 5767.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.3556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3706  Z= 0.240
  Angle     :  0.920  10.498   5053  Z= 0.454
  Chirality :  0.048   0.218    602
  Planarity :  0.006   0.064    624
  Dihedral  :  6.049  54.633    511
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  7.35 %
    Allowed  : 34.12 %
    Favored  : 58.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.39), residues: 467
  helix:  1.39 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.24 (0.69), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.049   0.003   PHE A 301 
 TYR   0.027   0.002   TYR A 362 
 ARG   0.002   0.000   ARG A 397 

*********************** 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
  161 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8166 (m-10) cc_final: 0.7928 (m-80)
REVERT: A  106 CYS cc_start: 0.9210 (m) cc_final: 0.8909 (m)
REVERT: A  119 LYS cc_start: 0.7848 (ptpt) cc_final: 0.7313 (ptmm)
REVERT: A  138 TRP cc_start: 0.9038 (t60) cc_final: 0.8515 (t60)
REVERT: A  139 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9058 (mm)
REVERT: A  142 GLU cc_start: 0.9196 (mm-30) cc_final: 0.7970 (mm-30)
REVERT: A  149 ASP cc_start: 0.9199 (m-30) cc_final: 0.8912 (m-30)
REVERT: A  192 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.5931 (mp)
REVERT: A  229 PHE cc_start: 0.6719 (t80) cc_final: 0.6228 (t80)
REVERT: A  268 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8102 (mp0)
REVERT: A  273 ARG cc_start: 0.9121 (tpm170) cc_final: 0.8870 (tpm170)
REVERT: A  443 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9022 (p)
  outliers start: 28
  outliers final: 21
  residues processed: 143
  average time/residue: 0.1192
  time to fit residues: 22.0680
Evaluate side-chains
  157 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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  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  438 LEU
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  487 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.117695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.099816 restraints weight = 11393.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.102353 restraints weight = 7815.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.104247 restraints weight = 5837.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3706  Z= 0.240
  Angle     :  0.966  12.847   5053  Z= 0.469
  Chirality :  0.049   0.196    602
  Planarity :  0.006   0.065    624
  Dihedral  :  6.107  56.571    511
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 19.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 35.43 %
    Favored  : 58.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.39), residues: 467
  helix:  1.25 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.40 (0.67), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.051   0.003   PHE A 301 
 TYR   0.027   0.002   TYR A 362 
 ARG   0.003   0.000   ARG A 400 

*********************** 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: 24
    poor density    : 132
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 CYS cc_start: 0.9203 (m) cc_final: 0.8932 (m)
REVERT: A  119 LYS cc_start: 0.7892 (ptpt) cc_final: 0.7417 (ptmm)
REVERT: A  138 TRP cc_start: 0.8998 (t60) cc_final: 0.8519 (t60)
REVERT: A  139 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9029 (mm)
REVERT: A  142 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8032 (mm-30)
REVERT: A  149 ASP cc_start: 0.9176 (m-30) cc_final: 0.8883 (m-30)
REVERT: A  192 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.5941 (mp)
REVERT: A  229 PHE cc_start: 0.6603 (t80) cc_final: 0.6037 (t80)
REVERT: A  268 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8130 (mp0)
REVERT: A  273 ARG cc_start: 0.9097 (tpm170) cc_final: 0.8849 (tpm170)
REVERT: A  329 ASP cc_start: 0.7184 (t0) cc_final: 0.4738 (t0)
REVERT: A  384 GLN cc_start: 0.8403 (tt0) cc_final: 0.7817 (pp30)
REVERT: A  387 MET cc_start: 0.7581 (mtt) cc_final: 0.7353 (mtt)
  outliers start: 24
  outliers final: 20
  residues processed: 141
  average time/residue: 0.1134
  time to fit residues: 20.7210
Evaluate side-chains
  151 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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  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  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 30 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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
** A 435 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 = 0.3858 r_free = 0.3858 target = 0.116859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.098931 restraints weight = 11362.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.101538 restraints weight = 7795.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.103450 restraints weight = 5782.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3706  Z= 0.253
  Angle     :  0.978  11.856   5053  Z= 0.486
  Chirality :  0.050   0.199    602
  Planarity :  0.006   0.067    624
  Dihedral  :  6.216  57.022    511
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 19.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 35.96 %
    Favored  : 58.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.39), residues: 467
  helix:  1.17 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.22 (0.67), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.053   0.003   PHE A 186 
 TYR   0.026   0.002   TYR A 362 
 ARG   0.003   0.000   ARG A 400 

********************** 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
  156 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 LEU cc_start: 0.9585 (tp) cc_final: 0.9250 (tt)
REVERT: A  106 CYS cc_start: 0.9224 (m) cc_final: 0.8913 (m)
REVERT: A  119 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7587 (ptmm)
REVERT: A  138 TRP cc_start: 0.9043 (t60) cc_final: 0.8547 (t60)
REVERT: A  139 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9014 (mm)
REVERT: A  142 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8005 (mm-30)
REVERT: A  149 ASP cc_start: 0.9215 (m-30) cc_final: 0.8896 (m-30)
REVERT: A  192 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6011 (mp)
REVERT: A  229 PHE cc_start: 0.6691 (t80) cc_final: 0.6145 (t80)
REVERT: A  268 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8133 (mp0)
REVERT: A  273 ARG cc_start: 0.9103 (tpm170) cc_final: 0.8839 (tpm170)
REVERT: A  319 PHE cc_start: 0.7706 (t80) cc_final: 0.7210 (m-80)
REVERT: A  384 GLN cc_start: 0.8408 (tt0) cc_final: 0.7553 (pt0)
REVERT: A  387 MET cc_start: 0.7657 (mtt) cc_final: 0.7435 (mtt)
  outliers start: 23
  outliers final: 19
  residues processed: 142
  average time/residue: 0.1166
  time to fit residues: 21.5660
Evaluate side-chains
  148 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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  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  265 LYS
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  391 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 42 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   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**
A 255 HIS
** A 435 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 = 0.3864 r_free = 0.3864 target = 0.117023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.098604 restraints weight = 11593.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.101184 restraints weight = 7999.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.103079 restraints weight = 5963.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3706  Z= 0.249
  Angle     :  0.989  16.436   5053  Z= 0.486
  Chirality :  0.052   0.205    602
  Planarity :  0.006   0.067    624
  Dihedral  :  5.894  59.363    509
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 19.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 37.27 %
    Favored  : 57.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.39), residues: 467
  helix:  1.21 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.32 (0.66), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 255 
 PHE   0.052   0.003   PHE A 301 
 TYR   0.026   0.002   TYR A 362 
 ARG   0.003   0.000   ARG A 193 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1400.02 seconds
wall clock time: 25 minutes 5.58 seconds (1505.58 seconds total)