Starting phenix.real_space_refine
on Mon Feb 10 22:20:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wyk_21967/02_2025/6wyk_21967.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wyk_21967/02_2025/6wyk_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_21967/02_2025/6wyk_21967.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wyk_21967/02_2025/6wyk_21967.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wyk_21967/02_2025/6wyk_21967.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wyk_21967/02_2025/6wyk_21967.cif"
  }
  resolution = 4.0
  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=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 2.72, per 1000 atoms: 0.88
  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: 1.01
  Conformation dependent library (CDL) restraints added in 386.3 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: 0.21
  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: 0.85

  Time building geometry restraints manager: 1.04 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:             0.670
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.760
  Find NCS groups from input model:        0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.500
-------------------------------------------------------------------------------
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= 0.471
  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 (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: -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
 HIS   0.003   0.001   HIS A 114 
 PHE   0.015   0.002   PHE A 261 
 TYR   0.043   0.003   TYR A 299 
 ARG   0.008   0.001   ARG A 397 

*********************** 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  : 0.344 
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: 0.1562
  time to fit residues: 21.3953
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  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0000
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
A 108 ASN
A 318 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.167605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.138120 restraints weight = 5501.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.141094 restraints weight = 3396.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.143255 restraints weight = 2441.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3136  Z= 0.224
  Angle     :  0.665   5.908   4269  Z= 0.339
  Chirality :  0.043   0.157    538
  Planarity :  0.004   0.026    524
  Dihedral  :  5.427  26.228    441
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.80 %
    Favored  : 84.36 %
  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:  0.72 (0.39), residues: 412
  helix:  1.09 (0.27), residues: 328
  sheet:  None (None), residues: 0
  loop : -1.83 (0.57), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A 114 
 PHE   0.015   0.002   PHE A 210 
 TYR   0.034   0.002   TYR A 299 
 ARG   0.003   0.000   ARG A 397 

*********************** 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
  92 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.6769 (m-40) cc_final: 0.5609 (t0)
REVERT: A  126 GLN cc_start: 0.7491 (tp40) cc_final: 0.6754 (mm110)
  outliers start: 6
  outliers final: 4
  residues processed: 88
  average time/residue: 0.1197
  time to fit residues: 13.4059
Evaluate side-chains
  81 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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  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 29 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0980
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.164189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.134695 restraints weight = 5501.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.137469 restraints weight = 3608.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.139247 restraints weight = 2711.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3136  Z= 0.208
  Angle     :  0.639   8.110   4269  Z= 0.319
  Chirality :  0.043   0.152    538
  Planarity :  0.003   0.022    524
  Dihedral  :  5.171  25.597    441
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.18 %
    Favored  : 80.37 %
  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:  1.47 (0.40), residues: 412
  helix:  1.63 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.71 (0.58), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A 332 
 PHE   0.015   0.001   PHE A 210 
 TYR   0.030   0.002   TYR A 299 
 ARG   0.004   0.001   ARG A 397 

*********************** 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
  96 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  105 ARG cc_start: 0.6350 (ttt-90) cc_final: 0.5660 (ttt-90)
REVERT: A  108 ASN cc_start: 0.7003 (m-40) cc_final: 0.5794 (t0)
REVERT: A  114 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.8069 (p-80)
REVERT: A  126 GLN cc_start: 0.7574 (tp40) cc_final: 0.6875 (mm110)
REVERT: A  202 MET cc_start: 0.8494 (mmm) cc_final: 0.8054 (tpp)
REVERT: A  273 PHE cc_start: 0.5993 (t80) cc_final: 0.5373 (t80)
REVERT: A  351 CYS cc_start: 0.7623 (p) cc_final: 0.6652 (p)
  outliers start: 8
  outliers final: 5
  residues processed: 90
  average time/residue: 0.1152
  time to fit residues: 13.1287
Evaluate side-chains
  85 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
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  114 HIS
Chi-restraints excluded: chain A residue  198 VAL
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 27 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0670
   chunk 31 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
** A 338 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 = 0.4022 r_free = 0.4022 target = 0.170400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.140713 restraints weight = 5495.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.143365 restraints weight = 3531.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.145331 restraints weight = 2629.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3136  Z= 0.223
  Angle     :  0.661   9.823   4269  Z= 0.324
  Chirality :  0.042   0.159    538
  Planarity :  0.004   0.044    524
  Dihedral  :  5.163  28.017    441
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.56 %
    Favored  : 80.37 %
  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:  1.68 (0.41), residues: 412
  helix:  1.72 (0.28), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.55 (0.62), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.014   0.002   PHE A 210 
 TYR   0.027   0.002   TYR A 299 
 ARG   0.004   0.001   ARG A 397 

*********************** 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
  96 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  126 GLN cc_start: 0.7634 (tp40) cc_final: 0.6925 (mm110)
REVERT: A  202 MET cc_start: 0.8588 (mmm) cc_final: 0.8271 (tpp)
REVERT: A  210 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7656 (t80)
REVERT: A  219 GLU cc_start: 0.7736 (tp30) cc_final: 0.7437 (mm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1267
  time to fit residues: 14.5854
Evaluate side-chains
  89 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
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  198 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    0.0870
   chunk 12 optimal weight:    0.0570
   chunk 20 optimal weight:    0.3980
   chunk 22 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0060
   chunk 8 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   overall best weight:    0.1292

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.169891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140826 restraints weight = 5530.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.143615 restraints weight = 3615.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.145484 restraints weight = 2709.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.4215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3136  Z= 0.175
  Angle     :  0.634  10.630   4269  Z= 0.309
  Chirality :  0.043   0.169    538
  Planarity :  0.003   0.021    524
  Dihedral  :  4.942  27.481    441
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 20.86 %
    Favored  : 76.99 %
  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:  1.99 (0.42), residues: 412
  helix:  1.96 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.53 (0.64), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.011   0.001   PHE A 210 
 TYR   0.025   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 105 

*********************** 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
  98 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8981 (pt) cc_final: 0.8717 (pt)
REVERT: A  103 MET cc_start: 0.8281 (ttm) cc_final: 0.7897 (ttm)
REVERT: A  105 ARG cc_start: 0.6501 (ttt-90) cc_final: 0.6141 (ttt-90)
REVERT: A  114 HIS cc_start: 0.8116 (p90) cc_final: 0.7699 (p90)
REVERT: A  126 GLN cc_start: 0.7615 (tp40) cc_final: 0.6920 (mm110)
REVERT: A  210 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7602 (t80)
  outliers start: 7
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1302
  time to fit residues: 14.8909
Evaluate side-chains
  91 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0170
   chunk 23 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6420

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 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 = 0.3963 r_free = 0.3963 target = 0.165641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.135894 restraints weight = 5654.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.138369 restraints weight = 3758.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.140206 restraints weight = 2871.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3136  Z= 0.217
  Angle     :  0.701  12.026   4269  Z= 0.339
  Chirality :  0.046   0.205    538
  Planarity :  0.004   0.044    524
  Dihedral  :  4.974  26.205    441
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.39 %
    Favored  : 73.93 %
  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:  2.01 (0.42), residues: 412
  helix:  1.95 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.41 (0.65), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.015   0.002   PHE A 210 
 TYR   0.024   0.002   TYR A 299 
 ARG   0.003   0.000   ARG A 397 

*********************** 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
  100 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8989 (pt) cc_final: 0.8719 (pt)
REVERT: A  103 MET cc_start: 0.8228 (ttm) cc_final: 0.8027 (ttm)
REVERT: A  105 ARG cc_start: 0.6551 (ttt-90) cc_final: 0.6161 (ttt-90)
REVERT: A  114 HIS cc_start: 0.8150 (p90) cc_final: 0.7721 (p90)
REVERT: A  126 GLN cc_start: 0.7626 (tp40) cc_final: 0.6923 (mm110)
REVERT: A  210 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7586 (t80)
REVERT: A  269 MET cc_start: 0.7467 (tpp) cc_final: 0.7099 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 93
  average time/residue: 0.1194
  time to fit residues: 14.1266
Evaluate side-chains
  93 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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   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 35 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   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 318 GLN
** A 338 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 = 0.3963 r_free = 0.3963 target = 0.165545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.135793 restraints weight = 5546.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.138011 restraints weight = 3816.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.139714 restraints weight = 2991.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3136  Z= 0.216
  Angle     :  0.694  12.453   4269  Z= 0.337
  Chirality :  0.046   0.209    538
  Planarity :  0.003   0.025    524
  Dihedral  :  4.931  26.074    441
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.01 %
    Favored  : 72.70 %
  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:  1.89 (0.42), residues: 412
  helix:  1.87 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.43 (0.65), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.015   0.001   PHE A 210 
 TYR   0.025   0.002   TYR A 317 
 ARG   0.003   0.000   ARG A 397 

*********************** 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: 14
    poor density    : 87
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8981 (pt) cc_final: 0.8697 (pt)
REVERT: A   52 ARG cc_start: 0.8478 (tpp80) cc_final: 0.6447 (ttp-170)
REVERT: A  103 MET cc_start: 0.8130 (ttm) cc_final: 0.7926 (ttm)
REVERT: A  105 ARG cc_start: 0.6630 (ttt-90) cc_final: 0.6263 (ttt-90)
REVERT: A  114 HIS cc_start: 0.8207 (p90) cc_final: 0.7783 (p90)
REVERT: A  126 GLN cc_start: 0.7693 (tp40) cc_final: 0.6993 (mm110)
REVERT: A  210 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7601 (t80)
REVERT: A  269 MET cc_start: 0.7361 (tpp) cc_final: 0.6942 (mmm)
REVERT: A  276 ARG cc_start: 0.6751 (mtp85) cc_final: 0.6384 (ttp-170)
  outliers start: 14
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1202
  time to fit residues: 14.3286
Evaluate side-chains
  93 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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   56 MET
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  339 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0020
   chunk 10 optimal weight:    0.0870
   chunk 35 optimal weight:    3.9990
   chunk 11 optimal weight:    0.1980
   chunk 13 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.3166

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 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 = 0.3993 r_free = 0.3993 target = 0.168688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.139771 restraints weight = 5570.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.142175 restraints weight = 3801.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.143612 restraints weight = 2978.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3136  Z= 0.182
  Angle     :  0.674  12.685   4269  Z= 0.331
  Chirality :  0.046   0.229    538
  Planarity :  0.004   0.047    524
  Dihedral  :  4.905  26.039    441
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.54 %
    Favored  : 72.09 %
  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:  2.01 (0.42), residues: 412
  helix:  1.98 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.25 (0.67), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 332 
 PHE   0.013   0.001   PHE A 210 
 TYR   0.033   0.002   TYR A 317 
 ARG   0.001   0.000   ARG A 105 

*********************** 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
  97 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.8432 (tpp80) cc_final: 0.6422 (ttp-170)
REVERT: A  114 HIS cc_start: 0.8111 (p90) cc_final: 0.7752 (p90)
REVERT: A  126 GLN cc_start: 0.7642 (tp40) cc_final: 0.6967 (mm110)
REVERT: A  210 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7592 (t80)
REVERT: A  269 MET cc_start: 0.7564 (tpp) cc_final: 0.7352 (mmm)
REVERT: A  276 ARG cc_start: 0.6816 (mtp85) cc_final: 0.6465 (ttp-170)
  outliers start: 11
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1315
  time to fit residues: 14.8501
Evaluate side-chains
  91 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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  222 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  400 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0670
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0170
   chunk 37 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.3354

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 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 = 0.3998 r_free = 0.3998 target = 0.168832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.139549 restraints weight = 5510.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.141986 restraints weight = 3713.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.143818 restraints weight = 2869.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.5068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3136  Z= 0.181
  Angle     :  0.701  13.686   4269  Z= 0.337
  Chirality :  0.046   0.225    538
  Planarity :  0.003   0.024    524
  Dihedral  :  4.887  26.100    441
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.85 %
    Favored  : 72.39 %
  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:  2.05 (0.42), residues: 412
  helix:  2.01 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.27 (0.67), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.014   0.001   PHE A 210 
 TYR   0.048   0.002   TYR A 317 
 ARG   0.002   0.000   ARG A 105 

*********************** 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
  97 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.8418 (tpp80) cc_final: 0.6392 (ttp-170)
REVERT: A  103 MET cc_start: 0.8201 (ttm) cc_final: 0.7885 (ttm)
REVERT: A  114 HIS cc_start: 0.8078 (p90) cc_final: 0.7753 (p90)
REVERT: A  126 GLN cc_start: 0.7658 (tp40) cc_final: 0.7009 (mm110)
REVERT: A  269 MET cc_start: 0.7455 (tpp) cc_final: 0.7074 (tpp)
REVERT: A  276 ARG cc_start: 0.6796 (mtp85) cc_final: 0.6377 (ttp-170)
  outliers start: 9
  outliers final: 8
  residues processed: 92
  average time/residue: 0.1324
  time to fit residues: 14.9979
Evaluate side-chains
  92 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
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  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  400 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 20 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3974 r_free = 0.3974 target = 0.167141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.136591 restraints weight = 5506.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.139597 restraints weight = 3462.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.141528 restraints weight = 2545.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.5176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3136  Z= 0.235
  Angle     :  0.729  13.079   4269  Z= 0.360
  Chirality :  0.046   0.228    538
  Planarity :  0.004   0.049    524
  Dihedral  :  4.976  26.056    441
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 25.77 %
    Favored  : 71.47 %
  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:  1.87 (0.42), residues: 412
  helix:  1.87 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.27 (0.67), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.015   0.002   PHE A 210 
 TYR   0.043   0.002   TYR A 317 
 ARG   0.006   0.001   ARG A 397 

********************** 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
  98 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8455 (tpp80) cc_final: 0.6414 (ttp-170)
REVERT: A  103 MET cc_start: 0.8230 (ttm) cc_final: 0.7903 (ttm)
REVERT: A  114 HIS cc_start: 0.8109 (p90) cc_final: 0.7763 (p90)
REVERT: A  126 GLN cc_start: 0.7675 (tp40) cc_final: 0.7006 (mm110)
REVERT: A  269 MET cc_start: 0.7401 (tpp) cc_final: 0.7020 (tpp)
  outliers start: 9
  outliers final: 7
  residues processed: 93
  average time/residue: 0.1498
  time to fit residues: 16.8603
Evaluate side-chains
  94 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  222 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  399 MET
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3946 r_free = 0.3946 target = 0.164444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.134504 restraints weight = 5568.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.136949 restraints weight = 3788.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.138496 restraints weight = 2952.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.5269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3136  Z= 0.256
  Angle     :  0.751  12.948   4269  Z= 0.369
  Chirality :  0.048   0.226    538
  Planarity :  0.006   0.090    524
  Dihedral  :  5.125  26.278    441
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 25.77 %
    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 (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:  1.63 (0.42), residues: 412
  helix:  1.71 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.37 (0.67), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A  32 
 PHE   0.015   0.002   PHE A 210 
 TYR   0.041   0.002   TYR A 317 
 ARG   0.014   0.001   ARG A 397 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1347.29 seconds
wall clock time: 24 minutes 47.15 seconds (1487.15 seconds total)