Starting phenix.real_space_refine
on Tue Mar  3 11:17:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wyk_21967/03_2026/6wyk_21967.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wyk_21967/03_2026/6wyk_21967.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wyk_21967/03_2026/6wyk_21967.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wyk_21967/03_2026/6wyk_21967.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wyk_21967/03_2026/6wyk_21967.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wyk_21967/03_2026/6wyk_21967.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      18      5.16       5
     C    2029      2.51       5
     N     490      2.21       5
     O     546      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3083
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3083
          Classifications: {'peptide': 415}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 396}
          Chain breaks: 1
  Time building chain proxies: 0.71, per 1000 atoms: 0.23
  Number of scatterers: 3083
  At special positions: 0
  Unit cell: (73.95, 70.992, 76.908, 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      18     16.00
     O     546      8.00
     N     490      7.00
     C    2029      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.25
  Conformation dependent library (CDL) restraints added in 132.7 milliseconds
  

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  750

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      86.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 10
    Processing helix  chain 'A' and resid 13 through 29
      removed outlier: 4.045A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 78
      Proline residue:  A  45  - end of helix
      removed outlier: 3.508A  pdb=" N   PHE A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   MET A  59 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
      Proline residue:  A  60  - end of helix
      removed outlier: 3.530A  pdb=" N   PHE A  63 " --> pdb=" O   MET A  59 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
    Processing helix  chain 'A' and resid 79 through 108
    Processing helix  chain 'A' and resid 129 through 137
      removed outlier: 3.510A  pdb=" N   ILE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 149
      removed outlier: 3.671A  pdb=" N   GLY A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 170
      removed outlier: 4.268A  pdb=" N   ASN A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 221
      removed outlier: 4.025A  pdb=" N   GLN A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.780A  pdb=" N   GLN A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 255
      removed outlier: 3.832A  pdb=" N   GLU A 227 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 4.420A  pdb=" N   ASP A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   ALA A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 293
      removed outlier: 4.021A  pdb=" N   VAL A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      Proline residue:  A 304  - end of helix
    Processing helix  chain 'A' and resid 312 through 330
    Processing helix  chain 'A' and resid 334 through 352
    Processing helix  chain 'A' and resid 357 through 370
      removed outlier: 4.388A  pdb=" N   ILE A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   MET A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   MET A 365 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 416
      removed outlier: 3.667A  pdb=" N   GLY A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ILE A 389 " --> pdb=" O   MET A 385 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   ILE A 392 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   MET A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   MET A 399 " --> pdb=" O   MET A 395 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.46

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 946
        1.34 -     1.46: 451
        1.46 -     1.57: 1705
        1.57 -     1.69: 0
        1.69 -     1.81: 34
  Bond restraints: 3136
  Sorted by residual:
  bond pdb=" N   VAL A 225 "
       pdb=" CA  VAL A 225 "
    ideal  model  delta    sigma   weight residual
    1.459  1.507 -0.048 1.33e-02 5.65e+03 1.29e+01
  bond pdb=" N   VAL A 274 "
       pdb=" CA  VAL A 274 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.21e-02 6.83e+03 9.53e+00
  bond pdb=" N   LYS A 223 "
       pdb=" CA  LYS A 223 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.31e-02 5.83e+03 9.29e+00
  bond pdb=" N   VAL A 224 "
       pdb=" CA  VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.036 1.26e-02 6.30e+03 8.36e+00
  bond pdb=" N   ASN A 148 "
       pdb=" CA  ASN A 148 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.37e+00
  ... (remaining 3131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 3886
        1.12 -     2.24: 289
        2.24 -     3.36: 55
        3.36 -     4.48: 32
        4.48 -     5.59: 7
  Bond angle restraints: 4269
  Sorted by residual:
  angle pdb=" CA  VAL A 224 "
        pdb=" C   VAL A 224 "
        pdb=" O   VAL A 224 "
      ideal   model   delta    sigma   weight residual
     120.57  115.75    4.82 1.07e+00 8.73e-01 2.03e+01
  angle pdb=" CA  GLN A 150 "
        pdb=" C   GLN A 150 "
        pdb=" O   GLN A 150 "
      ideal   model   delta    sigma   weight residual
     120.32  115.83    4.49 1.11e+00 8.12e-01 1.64e+01
  angle pdb=" CA  VAL A 274 "
        pdb=" C   VAL A 274 "
        pdb=" O   VAL A 274 "
      ideal   model   delta    sigma   weight residual
     120.85  116.85    4.00 1.06e+00 8.90e-01 1.43e+01
  angle pdb=" CA  THR A 275 "
        pdb=" C   THR A 275 "
        pdb=" O   THR A 275 "
      ideal   model   delta    sigma   weight residual
     119.97  115.76    4.21 1.15e+00 7.56e-01 1.34e+01
  angle pdb=" CA  PHE A 273 "
        pdb=" C   PHE A 273 "
        pdb=" O   PHE A 273 "
      ideal   model   delta    sigma   weight residual
     120.82  117.24    3.58 1.05e+00 9.07e-01 1.16e+01
  ... (remaining 4264 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 1699
       15.92 -    31.83: 138
       31.83 -    47.75: 26
       47.75 -    63.66: 2
       63.66 -    79.58: 1
  Dihedral angle restraints: 1866
    sinusoidal: 685
      harmonic: 1181
  Sorted by residual:
  dihedral pdb=" CA  ILE A  73 "
           pdb=" C   ILE A  73 "
           pdb=" N   SER A  74 "
           pdb=" CA  SER A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.13  -25.87     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  PRO A 109 "
           pdb=" C   PRO A 109 "
           pdb=" N   GLY A 110 "
           pdb=" CA  GLY A 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.97  -25.03     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  GLY A 221 "
           pdb=" C   GLY A 221 "
           pdb=" N   VAL A 222 "
           pdb=" CA  VAL A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.02  -20.98     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 1863 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 411
       0.053 -    0.106: 109
       0.106 -    0.159: 13
       0.159 -    0.212: 3
       0.212 -    0.266: 2
  Chirality restraints: 538
  Sorted by residual:
  chirality pdb=" CB  VAL A 224 "
            pdb=" CA  VAL A 224 "
            pdb=" CG1 VAL A 224 "
            pdb=" CG2 VAL A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CB  VAL A 225 "
            pdb=" CA  VAL A 225 "
            pdb=" CG1 VAL A 225 "
            pdb=" CG2 VAL A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  GLN A 150 "
            pdb=" N   GLN A 150 "
            pdb=" C   GLN A 150 "
            pdb=" CB  GLN A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.45e-01
  ... (remaining 535 not shown)

  Planarity restraints: 524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 147 "    0.015 2.00e-02 2.50e+03   2.87e-02 8.23e+00
        pdb=" C   ALA A 147 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ALA A 147 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN A 148 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 299 "    0.022 2.00e-02 2.50e+03   1.80e-02 6.46e+00
        pdb=" CG  TYR A 299 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 299 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 299 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 299 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 299 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 299 "    0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 299 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 224 "    0.010 2.00e-02 2.50e+03   2.06e-02 4.25e+00
        pdb=" C   VAL A 224 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL A 224 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 225 "    0.013 2.00e-02 2.50e+03
  ... (remaining 521 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 560
        2.76 -     3.29: 3550
        3.29 -     3.83: 4990
        3.83 -     4.36: 5548
        4.36 -     4.90: 9361
  Nonbonded interactions: 24009
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  71 "
            pdb=" OG1 THR A 166 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   SER A 278 "
            pdb=" OG1 THR A 281 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   VAL A 151 "
            pdb=" OG1 THR A 154 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   LEU A 228 "
            pdb=" OG1 THR A 232 "
     model   vdw
     2.383 3.040
  nonbonded pdb=" O   VAL A 412 "
            pdb=" OG1 THR A 415 "
     model   vdw
     2.387 3.040
  ... (remaining 24004 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:             0.570
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.790
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   3136  Z= 0.335
  Angle     :  0.769   5.594   4269  Z= 0.463
  Chirality :  0.048   0.266    538
  Planarity :  0.005   0.029    524
  Dihedral  : 11.978  79.581   1116
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.28 (0.34), residues: 412
  helix: -1.19 (0.24), residues: 321
  sheet:  None (None), residues: 0
  loop : -2.03 (0.57), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 397 
 TYR   0.043   0.003   TYR A 299 
 PHE   0.015   0.002   PHE A 261 
 HIS   0.003   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00735 ( 3136)
  covalent geometry    : angle       0.76921 ( 4269)
  hydrogen bonds       : bond        0.16537 (  251)
  hydrogen bonds       : angle       7.69762 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7880 (mmmt)
REVERT: A  105 ARG cc_start: 0.7068 (mpt-90) cc_final: 0.6704 (ttt-90)
REVERT: A  108 ASN cc_start: 0.6656 (m110) cc_final: 0.5520 (t0)
REVERT: A  126 GLN cc_start: 0.7441 (tp40) cc_final: 0.6918 (mm110)
REVERT: A  273 PHE cc_start: 0.5679 (t80) cc_final: 0.5403 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0618
  time to fit residues: 8.5544
Evaluate side-chains
  82 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.165255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.136429 restraints weight = 5580.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.139107 restraints weight = 3658.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.140570 restraints weight = 2738.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.141921 restraints weight = 2310.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142669 restraints weight = 2027.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3136  Z= 0.170
  Angle     :  0.679   6.141   4269  Z= 0.345
  Chirality :  0.043   0.154    538
  Planarity :  0.004   0.026    524
  Dihedral  :  5.480  26.408    441
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.19 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.39), residues: 412
  helix:  1.05 (0.27), residues: 328
  sheet:  None (None), residues: 0
  loop : -1.85 (0.57), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 397 
 TYR   0.034   0.002   TYR A 299 
 PHE   0.016   0.002   PHE A 210 
 HIS   0.001   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3136)
  covalent geometry    : angle       0.67869 ( 4269)
  hydrogen bonds       : bond        0.06115 (  251)
  hydrogen bonds       : angle       4.90307 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ARG cc_start: 0.7148 (mpt-90) cc_final: 0.6838 (ttt-90)
REVERT: A  108 ASN cc_start: 0.6819 (m-40) cc_final: 0.5648 (t0)
REVERT: A  126 GLN cc_start: 0.7428 (tp40) cc_final: 0.6749 (mm110)
  outliers start: 7
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0443
  time to fit residues: 4.9627
Evaluate side-chains
  83 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  407 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.159111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.128249 restraints weight = 5624.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.131052 restraints weight = 3691.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.132692 restraints weight = 2767.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.134030 restraints weight = 2303.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.134737 restraints weight = 2036.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3136  Z= 0.177
  Angle     :  0.670   7.936   4269  Z= 0.336
  Chirality :  0.044   0.150    538
  Planarity :  0.003   0.023    524
  Dihedral  :  5.323  26.366    441
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.48 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.40), residues: 412
  helix:  1.42 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.74 (0.58), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 276 
 TYR   0.031   0.002   TYR A 299 
 PHE   0.017   0.002   PHE A 210 
 HIS   0.001   0.000   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 3136)
  covalent geometry    : angle       0.66992 ( 4269)
  hydrogen bonds       : bond        0.05920 (  251)
  hydrogen bonds       : angle       4.71419 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.6807 (m-40) cc_final: 0.5560 (t0)
REVERT: A  126 GLN cc_start: 0.7539 (tp40) cc_final: 0.6819 (mm110)
REVERT: A  219 GLU cc_start: 0.7785 (tt0) cc_final: 0.7531 (tt0)
REVERT: A  351 CYS cc_start: 0.7616 (p) cc_final: 0.6762 (p)
  outliers start: 10
  outliers final: 7
  residues processed: 90
  average time/residue: 0.0440
  time to fit residues: 5.1274
Evaluate side-chains
  84 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0060
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.161367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.131068 restraints weight = 5610.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.133761 restraints weight = 3671.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.135682 restraints weight = 2748.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.136882 restraints weight = 2264.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.137569 restraints weight = 1994.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3136  Z= 0.146
  Angle     :  0.649   9.978   4269  Z= 0.321
  Chirality :  0.044   0.157    538
  Planarity :  0.003   0.023    524
  Dihedral  :  5.156  28.726    441
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.10 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.41), residues: 412
  helix:  1.71 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.60 (0.61), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 397 
 TYR   0.027   0.002   TYR A 299 
 PHE   0.014   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3136)
  covalent geometry    : angle       0.64918 ( 4269)
  hydrogen bonds       : bond        0.05172 (  251)
  hydrogen bonds       : angle       4.48210 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8938 (pt) cc_final: 0.8704 (pt)
REVERT: A  103 MET cc_start: 0.8211 (ttm) cc_final: 0.7921 (ttm)
REVERT: A  126 GLN cc_start: 0.7626 (tp40) cc_final: 0.6938 (mm110)
  outliers start: 10
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0489
  time to fit residues: 5.3900
Evaluate side-chains
  90 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 4 optimal weight:    0.1980
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0270
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.166897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.137674 restraints weight = 5577.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.140222 restraints weight = 3797.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.141578 restraints weight = 2913.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.142797 restraints weight = 2482.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.143417 restraints weight = 2210.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3136  Z= 0.134
  Angle     :  0.648  11.402   4269  Z= 0.320
  Chirality :  0.042   0.150    538
  Planarity :  0.004   0.042    524
  Dihedral  :  5.104  28.327    441
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.02 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.41), residues: 412
  helix:  1.83 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.43 (0.65), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.025   0.002   TYR A 299 
 PHE   0.013   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3136)
  covalent geometry    : angle       0.64760 ( 4269)
  hydrogen bonds       : bond        0.04890 (  251)
  hydrogen bonds       : angle       4.39160 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8930 (pt) cc_final: 0.8623 (pt)
REVERT: A  103 MET cc_start: 0.8193 (ttm) cc_final: 0.7958 (ttm)
REVERT: A  105 ARG cc_start: 0.6349 (ttt90) cc_final: 0.5967 (ttt-90)
REVERT: A  126 GLN cc_start: 0.7637 (tp40) cc_final: 0.6942 (mm110)
REVERT: A  210 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7658 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 90
  average time/residue: 0.0555
  time to fit residues: 6.2310
Evaluate side-chains
  92 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    0.3980
   chunk 14 optimal weight:    0.0970
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.166667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.137301 restraints weight = 5631.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.139882 restraints weight = 3866.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.141525 restraints weight = 2965.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142446 restraints weight = 2486.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.143195 restraints weight = 2232.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3136  Z= 0.139
  Angle     :  0.658  12.053   4269  Z= 0.324
  Chirality :  0.043   0.146    538
  Planarity :  0.003   0.023    524
  Dihedral  :  5.084  27.634    441
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 21.17 %
    Favored  : 74.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.42), residues: 412
  helix:  1.85 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.48 (0.65), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.025   0.002   TYR A 299 
 PHE   0.013   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3136)
  covalent geometry    : angle       0.65763 ( 4269)
  hydrogen bonds       : bond        0.04873 (  251)
  hydrogen bonds       : angle       4.44133 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8925 (pt) cc_final: 0.8670 (pt)
REVERT: A  103 MET cc_start: 0.8178 (ttm) cc_final: 0.7873 (ttm)
REVERT: A  105 ARG cc_start: 0.6367 (ttt90) cc_final: 0.6136 (ttt-90)
REVERT: A  114 HIS cc_start: 0.8188 (p90) cc_final: 0.7764 (p90)
REVERT: A  126 GLN cc_start: 0.7606 (tp40) cc_final: 0.6904 (mm110)
REVERT: A  210 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7651 (t80)
  outliers start: 14
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0514
  time to fit residues: 6.1444
Evaluate side-chains
  91 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 6 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.164704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.135601 restraints weight = 5587.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.137938 restraints weight = 3765.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.139590 restraints weight = 2893.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140507 restraints weight = 2436.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.141214 restraints weight = 2193.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.4505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3136  Z= 0.148
  Angle     :  0.683  12.536   4269  Z= 0.334
  Chirality :  0.043   0.203    538
  Planarity :  0.004   0.049    524
  Dihedral  :  5.112  27.561    441
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.31 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.41), residues: 412
  helix:  1.81 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.52 (0.64), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 276 
 TYR   0.025   0.002   TYR A 299 
 PHE   0.014   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3136)
  covalent geometry    : angle       0.68307 ( 4269)
  hydrogen bonds       : bond        0.04972 (  251)
  hydrogen bonds       : angle       4.40509 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8923 (pt) cc_final: 0.8608 (pt)
REVERT: A   52 ARG cc_start: 0.8458 (tpp80) cc_final: 0.6367 (ttp-170)
REVERT: A  103 MET cc_start: 0.8104 (ttm) cc_final: 0.7894 (ttm)
REVERT: A  105 ARG cc_start: 0.6504 (ttt90) cc_final: 0.6127 (ttt-90)
REVERT: A  114 HIS cc_start: 0.8187 (p90) cc_final: 0.7760 (p90)
REVERT: A  126 GLN cc_start: 0.7593 (tp40) cc_final: 0.6935 (mm110)
REVERT: A  210 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7559 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0549
  time to fit residues: 6.4117
Evaluate side-chains
  94 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  399 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0070
   chunk 25 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0570
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.166491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.137336 restraints weight = 5668.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.139956 restraints weight = 3777.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.141493 restraints weight = 2855.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.142785 restraints weight = 2393.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.143456 restraints weight = 2117.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3136  Z= 0.136
  Angle     :  0.677  12.708   4269  Z= 0.330
  Chirality :  0.044   0.220    538
  Planarity :  0.003   0.024    524
  Dihedral  :  4.997  27.021    441
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 23.31 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.42), residues: 412
  helix:  1.90 (0.28), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.28 (0.68), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 276 
 TYR   0.028   0.002   TYR A 317 
 PHE   0.013   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3136)
  covalent geometry    : angle       0.67676 ( 4269)
  hydrogen bonds       : bond        0.04697 (  251)
  hydrogen bonds       : angle       4.35356 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8923 (pt) cc_final: 0.8609 (pt)
REVERT: A   52 ARG cc_start: 0.8431 (tpp80) cc_final: 0.6408 (ttp-170)
REVERT: A  105 ARG cc_start: 0.6556 (ttt90) cc_final: 0.6172 (ttt-90)
REVERT: A  114 HIS cc_start: 0.8150 (p90) cc_final: 0.7771 (p90)
REVERT: A  126 GLN cc_start: 0.7646 (tp40) cc_final: 0.7025 (mm110)
REVERT: A  210 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7607 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 92
  average time/residue: 0.0495
  time to fit residues: 5.7069
Evaluate side-chains
  94 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  399 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0270
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4638

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.166180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.137080 restraints weight = 5656.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.139476 restraints weight = 3708.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.141274 restraints weight = 2845.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.142239 restraints weight = 2396.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.143061 restraints weight = 2143.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.4907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3136  Z= 0.144
  Angle     :  0.719  13.270   4269  Z= 0.343
  Chirality :  0.044   0.216    538
  Planarity :  0.004   0.049    524
  Dihedral  :  5.010  26.982    441
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 25.15 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.42), residues: 412
  helix:  1.80 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.33 (0.68), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 397 
 TYR   0.038   0.002   TYR A 317 
 PHE   0.014   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3136)
  covalent geometry    : angle       0.71929 ( 4269)
  hydrogen bonds       : bond        0.04796 (  251)
  hydrogen bonds       : angle       4.37103 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.8426 (tpp80) cc_final: 0.6390 (ttp-170)
REVERT: A  105 ARG cc_start: 0.6551 (ttt90) cc_final: 0.6283 (ttt-90)
REVERT: A  114 HIS cc_start: 0.8110 (p90) cc_final: 0.7773 (p90)
REVERT: A  126 GLN cc_start: 0.7638 (tp40) cc_final: 0.7045 (mm110)
REVERT: A  210 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7524 (t80)
REVERT: A  327 ASN cc_start: 0.6661 (t0) cc_final: 0.6373 (t0)
  outliers start: 10
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0583
  time to fit residues: 6.7570
Evaluate side-chains
  97 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  399 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0000
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 25 optimal weight:    0.0770
   chunk 31 optimal weight:    0.0470
   overall best weight:    0.2240

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.168765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.138860 restraints weight = 5590.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.142012 restraints weight = 3457.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144105 restraints weight = 2496.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145496 restraints weight = 2007.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.146282 restraints weight = 1737.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.5173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3136  Z= 0.143
  Angle     :  0.742  13.817   4269  Z= 0.349
  Chirality :  0.045   0.222    538
  Planarity :  0.004   0.042    524
  Dihedral  :  5.022  28.858    441
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.99 %
    Favored  : 70.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.42), residues: 412
  helix:  1.86 (0.29), residues: 328
  sheet:  None (None), residues: 0
  loop : -1.29 (0.68), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 397 
 TYR   0.054   0.002   TYR A 317 
 PHE   0.013   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3136)
  covalent geometry    : angle       0.74245 ( 4269)
  hydrogen bonds       : bond        0.04566 (  251)
  hydrogen bonds       : angle       4.30032 (  753)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.8389 (tpp80) cc_final: 0.6296 (ttp-170)
REVERT: A  126 GLN cc_start: 0.7661 (tp40) cc_final: 0.7089 (mm110)
REVERT: A  210 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7743 (t80)
REVERT: A  276 ARG cc_start: 0.6752 (mtp85) cc_final: 0.6367 (ttp-170)
REVERT: A  327 ASN cc_start: 0.6719 (t0) cc_final: 0.6415 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0562
  time to fit residues: 6.3913
Evaluate side-chains
  96 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  399 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0980
   chunk 21 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.167264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.137332 restraints weight = 5631.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.140348 restraints weight = 3482.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.142429 restraints weight = 2531.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.143894 restraints weight = 2040.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144663 restraints weight = 1775.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.5279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3136  Z= 0.156
  Angle     :  0.756  13.527   4269  Z= 0.360
  Chirality :  0.045   0.219    538
  Planarity :  0.004   0.037    524
  Dihedral  :  5.000  27.256    441
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 26.38 %
    Favored  : 70.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.43), residues: 412
  helix:  1.86 (0.29), residues: 328
  sheet:  None (None), residues: 0
  loop : -1.34 (0.68), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 397 
 TYR   0.025   0.002   TYR A 299 
 PHE   0.013   0.001   PHE A 210 
 HIS   0.001   0.000   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 3136)
  covalent geometry    : angle       0.75587 ( 4269)
  hydrogen bonds       : bond        0.04789 (  251)
  hydrogen bonds       : angle       4.39525 (  753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 702.40 seconds
wall clock time: 12 minutes 43.31 seconds (763.31 seconds total)