Starting phenix.real_space_refine
on Wed Sep 17 03:56:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y65_38966/09_2025/8y65_38966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y65_38966/09_2025/8y65_38966.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y65_38966/09_2025/8y65_38966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y65_38966/09_2025/8y65_38966.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y65_38966/09_2025/8y65_38966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y65_38966/09_2025/8y65_38966.map"
  }
  resolution = 3.51
  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=   0.007 sd=   0.171
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      13      5.16       5
     C    2355      2.51       5
     N     574      2.21       5
     O     623      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3565
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 3553
          Classifications: {'peptide': 467}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 24, 'TRANS': 442}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'URC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.01, per 1000 atoms: 0.28
  Number of scatterers: 3565
  At special positions: 0
  Unit cell: (84.5383, 62.5803, 69.1677, 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      13     16.00
     O     623      8.00
     N     574      7.00
     C    2355      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: 0.31
  Conformation dependent library (CDL) restraints added in 136.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  848

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      86.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 76
      removed outlier: 4.372A  pdb=" N   PHE A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   LEU A  70 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 98
    Processing helix  chain 'A' and resid 102 through 132
      removed outlier: 4.794A  pdb=" N   PHE A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   ALA A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LYS A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   MET A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 157
    Processing helix  chain 'A' and resid 157 through 162
      removed outlier: 4.116A  pdb=" N   ALA A 161 " --> pdb=" O   CYS A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 193
      removed outlier: 3.742A  pdb=" N   LEU A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      Proline residue:  A 186  - end of helix
      removed outlier: 3.848A  pdb=" N   GLU A 191 " --> pdb=" O   MET A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 3.625A  pdb=" N   LEU A 201 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ALA A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ILE A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 237
      removed outlier: 4.096A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 249
      removed outlier: 3.589A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 252
      No H-bonds generated for 'chain 'A' and resid 250 through 252'
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 3.799A  pdb=" N   LEU A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLU A 262 " --> pdb=" O   TYR A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 282 through 299
      removed outlier: 3.501A  pdb=" N   ILE A 299 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 310
    Processing helix  chain 'A' and resid 313 through 331
      removed outlier: 4.333A  pdb=" N   GLY A 331 " --> pdb=" O   TYR A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 338
    Processing helix  chain 'A' and resid 338 through 345
    Processing helix  chain 'A' and resid 352 through 379
      removed outlier: 4.064A  pdb=" N   LEU A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   GLU A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   HIS A 377 " --> pdb=" O   LEU A 373 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLY A 379 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 404
    Processing helix  chain 'A' and resid 410 through 412
      No H-bonds generated for 'chain 'A' and resid 410 through 412'
    Processing helix  chain 'A' and resid 413 through 428
      removed outlier: 4.043A  pdb=" N   VAL A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 442
      removed outlier: 4.708A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE A 442 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 476
      Proline residue:  A 470  - end of helix
    Processing helix  chain 'A' and resid 481 through 499
    Processing helix  chain 'A' and resid 506 through 518

    271 hydrogen bonds defined for protein.
    801 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: 0.49

  Time building geometry restraints manager: 0.41 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: 1101
        1.34 -     1.46: 872
        1.46 -     1.58: 1664
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3655
  Sorted by residual:
  bond pdb=" C4  URC A 601 "
       pdb=" C5  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.358  1.470 -0.112 2.00e-02 2.50e+03 3.15e+01
  bond pdb=" C6  URC A 601 "
       pdb=" N1  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.398  1.317  0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" C8  URC A 601 "
       pdb=" N9  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.396  1.316  0.080 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" N   ILE A 335 "
       pdb=" CA  ILE A 335 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.10e+01
  bond pdb=" C2  URC A 601 "
       pdb=" N3  URC A 601 "
    ideal  model  delta    sigma   weight residual
    1.376  1.311  0.065 2.00e-02 2.50e+03 1.06e+01
  ... (remaining 3650 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 4930
        2.81 -     5.62: 44
        5.62 -     8.42: 11
        8.42 -    11.23: 3
       11.23 -    14.04: 1
  Bond angle restraints: 4989
  Sorted by residual:
  angle pdb=" N7  URC A 601 "
        pdb=" C8  URC A 601 "
        pdb=" N9  URC A 601 "
      ideal   model   delta    sigma   weight residual
     104.73  118.77  -14.04 3.00e+00 1.11e-01 2.19e+01
  angle pdb=" N   ILE A 436 "
        pdb=" CA  ILE A 436 "
        pdb=" C   ILE A 436 "
      ideal   model   delta    sigma   weight residual
     112.96  108.33    4.63 1.00e+00 1.00e+00 2.15e+01
  angle pdb=" CA  ILE A 335 "
        pdb=" C   ILE A 335 "
        pdb=" N   TRP A 336 "
      ideal   model   delta    sigma   weight residual
     118.13  123.44   -5.31 1.37e+00 5.33e-01 1.50e+01
  angle pdb=" N1  URC A 601 "
        pdb=" C2  URC A 601 "
        pdb=" N3  URC A 601 "
      ideal   model   delta    sigma   weight residual
     114.62  124.69  -10.07 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" N   ILE A 335 "
        pdb=" CA  ILE A 335 "
        pdb=" C   ILE A 335 "
      ideal   model   delta    sigma   weight residual
     113.00  108.67    4.33 1.30e+00 5.92e-01 1.11e+01
  ... (remaining 4984 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 1911
       17.37 -    34.73: 166
       34.73 -    52.10: 26
       52.10 -    69.46: 4
       69.46 -    86.83: 4
  Dihedral angle restraints: 2111
    sinusoidal: 781
      harmonic: 1330
  Sorted by residual:
  dihedral pdb=" CA  GLY A 331 "
           pdb=" C   GLY A 331 "
           pdb=" N   LEU A 332 "
           pdb=" CA  LEU A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.26   16.74     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CB  GLU A 223 "
           pdb=" CG  GLU A 223 "
           pdb=" CD  GLU A 223 "
           pdb=" OE1 GLU A 223 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.83   86.83     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU A 287 "
           pdb=" CG  GLU A 287 "
           pdb=" CD  GLU A 287 "
           pdb=" OE1 GLU A 287 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.24  -86.24     1      3.00e+01 1.11e-03 9.97e+00
  ... (remaining 2108 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 425
       0.039 -    0.079: 125
       0.079 -    0.118: 37
       0.118 -    0.158: 3
       0.158 -    0.197: 2
  Chirality restraints: 592
  Sorted by residual:
  chirality pdb=" CB  ILE A 335 "
            pdb=" CA  ILE A 335 "
            pdb=" CG1 ILE A 335 "
            pdb=" CG2 ILE A 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.70e-01
  chirality pdb=" CB  ILE A 197 "
            pdb=" CA  ILE A 197 "
            pdb=" CG1 ILE A 197 "
            pdb=" CG2 ILE A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.33e-01
  chirality pdb=" CA  ILE A 348 "
            pdb=" N   ILE A 348 "
            pdb=" C   ILE A 348 "
            pdb=" CB  ILE A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 589 not shown)

  Planarity restraints: 618
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 381 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 382 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 382 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 382 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 255 "    0.038 5.00e-02 4.00e+02   5.83e-02 5.44e+00
        pdb=" N   PRO A 256 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 256 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 256 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 335 "    0.012 2.00e-02 2.50e+03   2.31e-02 5.32e+00
        pdb=" C   ILE A 335 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A 335 "    0.014 2.00e-02 2.50e+03
        pdb=" N   TRP A 336 "    0.014 2.00e-02 2.50e+03
  ... (remaining 615 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 673
        2.76 -     3.30: 3548
        3.30 -     3.83: 6129
        3.83 -     4.37: 6408
        4.37 -     4.90: 11451
  Nonbonded interactions: 28209
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  96 "
            pdb=" O   GLY A 162 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" NE2 GLN A 328 "
            pdb=" OD1 ASN A 458 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OE1 GLN A 328 "
            pdb=" ND2 ASN A 333 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" NZ  LYS A 195 "
            pdb=" OE2 GLU A 288 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   GLY A 136 "
            pdb=" OG1 THR A 140 "
     model   vdw
     2.353 3.040
  ... (remaining 28204 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.140
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5316
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   3655  Z= 0.224
  Angle     :  0.734  14.038   4989  Z= 0.355
  Chirality :  0.041   0.197    592
  Planarity :  0.005   0.063    618
  Dihedral  : 13.646  86.828   1263
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.27 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.42), residues: 465
  helix:  1.61 (0.29), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.14 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  95 
 TYR   0.007   0.001   TYR A 327 
 PHE   0.012   0.001   PHE A 208 
 TRP   0.012   0.001   TRP A  93 
 HIS   0.002   0.000   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 3655)
  covalent geometry    : angle       0.73422 ( 4989)
  hydrogen bonds       : bond        0.09191 (  271)
  hydrogen bonds       : angle       4.71183 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  400 ILE cc_start: 0.7317 (tp) cc_final: 0.6686 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0621
  time to fit residues: 2.3835
Evaluate side-chains
  23 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0000
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.277335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.254366 restraints weight = 4036.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.258725 restraints weight = 2405.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.261482 restraints weight = 1622.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.263633 restraints weight = 1217.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.264592 restraints weight = 990.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.4712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5391
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3655  Z= 0.126
  Angle     :  0.588   7.576   4989  Z= 0.291
  Chirality :  0.041   0.138    592
  Planarity :  0.005   0.044    618
  Dihedral  :  4.120  20.522    500
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.32 %
    Favored  : 94.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.41), residues: 465
  helix:  1.66 (0.28), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.33 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  96 
 TYR   0.005   0.001   TYR A 338 
 PHE   0.017   0.001   PHE A 276 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.002   0.000   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3655)
  covalent geometry    : angle       0.58781 ( 4989)
  hydrogen bonds       : bond        0.03523 (  271)
  hydrogen bonds       : angle       3.95290 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.096 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 26
  average time/residue: 0.0393
  time to fit residues: 1.5638
Evaluate side-chains
  24 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 38 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 144 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 = 0.4798 r_free = 0.4798 target = 0.272308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.248505 restraints weight = 3998.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.252527 restraints weight = 2430.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.255054 restraints weight = 1674.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.257367 restraints weight = 1292.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.258316 restraints weight = 1060.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.4701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5530
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3655  Z= 0.153
  Angle     :  0.614   7.190   4989  Z= 0.306
  Chirality :  0.042   0.140    592
  Planarity :  0.004   0.035    618
  Dihedral  :  4.160  16.447    498
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.84 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.40), residues: 465
  helix:  1.45 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.72 (0.67), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  96 
 TYR   0.009   0.001   TYR A 233 
 PHE   0.010   0.001   PHE A 276 
 TRP   0.010   0.002   TRP A 315 
 HIS   0.003   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3655)
  covalent geometry    : angle       0.61410 ( 4989)
  hydrogen bonds       : bond        0.04075 (  271)
  hydrogen bonds       : angle       3.95911 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A  324 MET cc_start: 0.7257 (mmm) cc_final: 0.7044 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0349
  time to fit residues: 1.4616
Evaluate side-chains
  25 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0170
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
** A 144 ASN ** 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 = 0.4808 r_free = 0.4808 target = 0.273979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.250514 restraints weight = 3986.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.254640 restraints weight = 2401.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.257613 restraints weight = 1637.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.259017 restraints weight = 1249.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.260519 restraints weight = 1057.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.4726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5497
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3655  Z= 0.128
  Angle     :  0.570   5.448   4989  Z= 0.285
  Chirality :  0.041   0.161    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.064  15.472    498
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.50 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.40), residues: 465
  helix:  1.53 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.87 (0.65), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.006   0.001   TYR A 258 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3655)
  covalent geometry    : angle       0.56975 ( 4989)
  hydrogen bonds       : bond        0.03636 (  271)
  hydrogen bonds       : angle       3.84164 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0308 (OUTLIER) cc_final: -0.1085 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0338
  time to fit residues: 1.4394
Evaluate side-chains
  23 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.273633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.249869 restraints weight = 3970.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.254040 restraints weight = 2432.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.256980 restraints weight = 1670.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.258970 restraints weight = 1270.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.259830 restraints weight = 1047.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.4655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5481
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3655  Z= 0.127
  Angle     :  0.559   5.380   4989  Z= 0.280
  Chirality :  0.041   0.157    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.058  15.326    498
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.16 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.40), residues: 465
  helix:  1.54 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.91 (0.65), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.006   0.001   TYR A 258 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3655)
  covalent geometry    : angle       0.55932 ( 4989)
  hydrogen bonds       : bond        0.03636 (  271)
  hydrogen bonds       : angle       3.83243 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.075 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 28
  average time/residue: 0.0308
  time to fit residues: 1.3536
Evaluate side-chains
  25 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 34 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   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 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 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 = 0.4786 r_free = 0.4786 target = 0.271563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.247513 restraints weight = 4038.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.251897 restraints weight = 2400.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.254879 restraints weight = 1631.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.256488 restraints weight = 1235.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.257752 restraints weight = 1036.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.4687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5564
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3655  Z= 0.134
  Angle     :  0.590   8.178   4989  Z= 0.294
  Chirality :  0.042   0.174    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.145  15.282    498
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.63 %
    Favored  : 83.78 %
  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 aren not related in a simple way.
  whole:  1.46 (0.40), residues: 465
  helix:  1.51 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.01 (0.64), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 268 
 TYR   0.006   0.001   TYR A 258 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3655)
  covalent geometry    : angle       0.59005 ( 4989)
  hydrogen bonds       : bond        0.03750 (  271)
  hydrogen bonds       : angle       3.84466 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0320 (OUTLIER) cc_final: -0.1099 (tp30)
  outliers start: 6
  outliers final: 4
  residues processed: 26
  average time/residue: 0.0327
  time to fit residues: 1.3572
Evaluate side-chains
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 7 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 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 = 0.4766 r_free = 0.4766 target = 0.269112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.245504 restraints weight = 4087.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.249852 restraints weight = 2480.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.252263 restraints weight = 1704.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.254439 restraints weight = 1324.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.255549 restraints weight = 1096.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.4640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5584
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3655  Z= 0.145
  Angle     :  0.591   6.217   4989  Z= 0.299
  Chirality :  0.043   0.161    592
  Planarity :  0.004   0.030    618
  Dihedral  :  4.256  15.742    498
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.43 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.40), residues: 465
  helix:  1.37 (0.28), residues: 368
  sheet:  None (None), residues: 0
  loop : -1.12 (0.65), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.007   0.001   TYR A 258 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.010   0.001   TRP A 315 
 HIS   0.003   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3655)
  covalent geometry    : angle       0.59110 ( 4989)
  hydrogen bonds       : bond        0.04064 (  271)
  hydrogen bonds       : angle       3.92367 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0328 (OUTLIER) cc_final: -0.1174 (tp30)
  outliers start: 7
  outliers final: 5
  residues processed: 27
  average time/residue: 0.0326
  time to fit residues: 1.4437
Evaluate side-chains
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  480 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0170
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 38 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 44 optimal weight:    0.1980
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 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 = 0.4791 r_free = 0.4791 target = 0.272613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.249343 restraints weight = 4079.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.253803 restraints weight = 2475.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.256694 restraints weight = 1689.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.258356 restraints weight = 1290.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.259761 restraints weight = 1072.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.4674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5506
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3655  Z= 0.118
  Angle     :  0.577   9.788   4989  Z= 0.285
  Chirality :  0.041   0.192    592
  Planarity :  0.004   0.033    618
  Dihedral  :  4.082  14.894    498
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.22 %
    Favored  : 81.91 %
  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 aren not related in a simple way.
  whole:  1.45 (0.41), residues: 465
  helix:  1.48 (0.28), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.02 (0.66), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.007   0.001   TYR A 258 
 PHE   0.013   0.001   PHE A 276 
 TRP   0.009   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3655)
  covalent geometry    : angle       0.57741 ( 4989)
  hydrogen bonds       : bond        0.03419 (  271)
  hydrogen bonds       : angle       3.79684 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0378 (OUTLIER) cc_final: -0.1168 (tp30)
REVERT: A  324 MET cc_start: 0.7259 (mmm) cc_final: 0.7014 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 27
  average time/residue: 0.0343
  time to fit residues: 1.3319
Evaluate side-chains
  29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  480 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0170
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 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 = 0.4783 r_free = 0.4783 target = 0.271394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.248464 restraints weight = 4029.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.252591 restraints weight = 2465.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.255422 restraints weight = 1705.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.257308 restraints weight = 1305.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.258387 restraints weight = 1075.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5537
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3655  Z= 0.127
  Angle     :  0.588   9.194   4989  Z= 0.289
  Chirality :  0.042   0.180    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.130  15.708    498
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.43 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.40), residues: 465
  helix:  1.45 (0.28), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.06 (0.66), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.007   0.001   TYR A 258 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3655)
  covalent geometry    : angle       0.58815 ( 4989)
  hydrogen bonds       : bond        0.03600 (  271)
  hydrogen bonds       : angle       3.83102 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0326 (OUTLIER) cc_final: -0.1159 (tp30)
REVERT: A  324 MET cc_start: 0.7311 (mmm) cc_final: 0.7007 (mmm)
REVERT: A  427 CYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7291 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 27
  average time/residue: 0.0349
  time to fit residues: 1.5419
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  480 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0020
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.269730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.246468 restraints weight = 4083.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.250789 restraints weight = 2507.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.253622 restraints weight = 1725.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.255208 restraints weight = 1320.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.256764 restraints weight = 1104.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5569
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3655  Z= 0.137
  Angle     :  0.603   8.972   4989  Z= 0.298
  Chirality :  0.042   0.180    592
  Planarity :  0.004   0.032    618
  Dihedral  :  4.209  15.661    498
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.69 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.40), residues: 465
  helix:  1.38 (0.28), residues: 369
  sheet:  None (None), residues: 0
  loop : -1.01 (0.66), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.007   0.001   TYR A 258 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3655)
  covalent geometry    : angle       0.60315 ( 4989)
  hydrogen bonds       : bond        0.03855 (  271)
  hydrogen bonds       : angle       3.88616 (  801)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 20
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  262 GLU cc_start: -0.0360 (OUTLIER) cc_final: -0.1037 (tp30)
REVERT: A  324 MET cc_start: 0.7273 (mmm) cc_final: 0.7043 (mmm)
REVERT: A  427 CYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7272 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 26
  average time/residue: 0.0323
  time to fit residues: 1.3602
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 20
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  488 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 8 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   chunk 14 optimal weight:    0.0020
   chunk 27 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0270
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0170
   overall best weight:    0.1684

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
** A 265 ASN ** 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 = 0.4811 r_free = 0.4811 target = 0.275521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.252863 restraints weight = 4058.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.257291 restraints weight = 2437.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.259834 restraints weight = 1645.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.262136 restraints weight = 1260.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.263273 restraints weight = 1022.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.4681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5434
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3655  Z= 0.111
  Angle     :  0.564   8.387   4989  Z= 0.278
  Chirality :  0.040   0.208    592
  Planarity :  0.004   0.035    618
  Dihedral  :  4.000  14.313    498
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.49 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.41), residues: 465
  helix:  1.72 (0.28), residues: 365
  sheet:  None (None), residues: 0
  loop : -0.76 (0.64), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.007   0.001   TYR A 258 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.009   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 3655)
  covalent geometry    : angle       0.56421 ( 4989)
  hydrogen bonds       : bond        0.02979 (  271)
  hydrogen bonds       : angle       3.70687 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 703.79 seconds
wall clock time: 12 minutes 47.86 seconds (767.86 seconds total)