Starting phenix.real_space_refine
on Wed Sep 17 06:03:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jsp_61780/09_2025/9jsp_61780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jsp_61780/09_2025/9jsp_61780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jsp_61780/09_2025/9jsp_61780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jsp_61780/09_2025/9jsp_61780.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jsp_61780/09_2025/9jsp_61780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jsp_61780/09_2025/9jsp_61780.map"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.062
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: 6
    Type Number    sf(0)   Gaussians
     P      22      5.49       5
     Mg      1      5.21       5
     S      20      5.16       5
     C    3650      2.51       5
     N    1030      2.21       5
     O    1139      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  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: 5862
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3693
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 26, 'TRANS': 438}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1705
          Classifications: {'peptide': 208}
          Link IDs: {'PTRANS': 11, 'TRANS': 196}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 255
          Classifications: {'RNA': 12}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 1, 'rna3p': 10}
    Chain: "T"
      Number of atoms: 208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 208
          Classifications: {'DNA': 10}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 9}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.84, per 1000 atoms: 0.31
  Number of scatterers: 5862
  At special positions: 0
  Unit cell: (73.95, 74.8, 108.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P      22     15.00
     Mg      1     11.99
     O    1139      8.00
     N    1030      7.00
     C    3650      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: 0.60
  Conformation dependent library (CDL) restraints added in 362.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1248

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 9 sheets defined
      34.0% alpha, 10.4% beta
      10 base pairs and 15 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 30
    Processing helix  chain 'A' and resid 49 through 63
    Processing helix  chain 'A' and resid 105 through 113
      removed outlier: 3.560A  pdb=" N   LEU A 109 " --> pdb=" O   THR A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 139
    Processing helix  chain 'A' and resid 151 through 160
    Processing helix  chain 'A' and resid 181 through 191
      removed outlier: 3.649A  pdb=" N   MET A 185 " --> pdb=" O   ASN A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 206
      removed outlier: 3.522A  pdb=" N   ASP A 206 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 242
    Processing helix  chain 'A' and resid 311 through 328
    Processing helix  chain 'A' and resid 343 through 357
    Processing helix  chain 'A' and resid 429 through 441
      removed outlier: 3.531A  pdb=" N   LEU A 433 " --> pdb=" O   THR A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 469
      removed outlier: 4.304A  pdb=" N   ALA A 461 " --> pdb=" O   PRO A 457 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ARG A 462 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   LYS A 463 " --> pdb=" O   ARG A 459 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL A 467 " --> pdb=" O   LYS A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 4.468A  pdb=" N   TYR A 484 " --> pdb=" O   ASP A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 195
    Processing helix  chain 'B' and resid 216 through 220
      removed outlier: 3.576A  pdb=" N   THR B 219 " --> pdb=" O   ASP B 216 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B 220 " --> pdb=" O   PRO B 217 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 216 through 220'
    Processing helix  chain 'B' and resid 227 through 229
      No H-bonds generated for 'chain 'B' and resid 227 through 229'
    Processing helix  chain 'B' and resid 236 through 241
    Processing helix  chain 'B' and resid 245 through 263
    Processing helix  chain 'B' and resid 355 through 364
    Processing helix  chain 'B' and resid 371 through 384
      removed outlier: 3.818A  pdb=" N   GLN B 384 " --> pdb=" O   ARG B 380 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
      removed outlier: 4.338A  pdb=" N   GLU A   4 " --> pdb=" O   ASP A 390 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR A 387 " --> pdb=" O   TYR A 398 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A 389 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY A 395 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU A 420 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU A 419 " --> pdb=" O   GLN A 368 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL A 334 " --> pdb=" O   ASP A 363 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   VAL A 365 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ILE A 336 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   VAL A 367 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   LYS A 338 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   PHE A 335 " --> pdb=" O   CYS A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96
      removed outlier: 6.009A  pdb=" N   ASP A  40 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   GLU A  95 " --> pdb=" O   ASP A  40 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   ILE A  42 " --> pdb=" O   GLU A  95 " (cutoff:3.500A)
      removed outlier: 9.021A  pdb=" N   VAL A 145 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   LYS A  43 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   ILE A 147 " --> pdb=" O   LYS A  43 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLY A  45 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262
    Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 266
    Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172
      removed outlier: 3.642A  pdb=" N   MET B 402 " --> pdb=" O   THR B 172 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 211 through 213
    Processing sheet with id=AA7, first strand: chain 'B' and resid 268 through 269
    Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 323
    Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 330

    180 hydrogen bonds defined for protein.
    501 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      26 hydrogen bonds
      52 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      15 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 0.68 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: 1752
        1.34 -     1.46: 1295
        1.46 -     1.58: 2921
        1.58 -     1.70: 42
        1.70 -     1.82: 36
  Bond restraints: 6046
  Sorted by residual:
  bond pdb=" CB  TYR A 239 "
       pdb=" CG  TYR A 239 "
    ideal  model  delta    sigma   weight residual
    1.512  1.556 -0.044 2.20e-02 2.07e+03 4.04e+00
  bond pdb=" N   LYS A 328 "
       pdb=" CA  LYS A 328 "
    ideal  model  delta    sigma   weight residual
    1.457  1.480 -0.023 1.29e-02 6.01e+03 3.15e+00
  bond pdb=" C   HIS A 304 "
       pdb=" N   PRO A 305 "
    ideal  model  delta    sigma   weight residual
    1.331  1.345 -0.014 7.90e-03 1.60e+04 3.00e+00
  bond pdb=" CB  PHE B 251 "
       pdb=" CG  PHE B 251 "
    ideal  model  delta    sigma   weight residual
    1.502  1.537 -0.035 2.30e-02 1.89e+03 2.29e+00
  bond pdb=" C   ILE A 456 "
       pdb=" N   PRO A 457 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.25e-02 6.40e+03 2.14e+00
  ... (remaining 6041 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 7966
        1.98 -     3.97: 261
        3.97 -     5.95: 40
        5.95 -     7.93: 6
        7.93 -     9.92: 4
  Bond angle restraints: 8277
  Sorted by residual:
  angle pdb=" CA  TYR A 239 "
        pdb=" CB  TYR A 239 "
        pdb=" CG  TYR A 239 "
      ideal   model   delta    sigma   weight residual
     113.90  120.13   -6.23 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" N   PRO A 305 "
        pdb=" CA  PRO A 305 "
        pdb=" C   PRO A 305 "
      ideal   model   delta    sigma   weight residual
     114.92  111.06    3.86 1.19e+00 7.06e-01 1.05e+01
  angle pdb=" CA  ILE A 456 "
        pdb=" C   ILE A 456 "
        pdb=" N   PRO A 457 "
      ideal   model   delta    sigma   weight residual
     118.88  123.78   -4.90 1.54e+00 4.22e-01 1.01e+01
  angle pdb=" CA  LYS A 328 "
        pdb=" CB  LYS A 328 "
        pdb=" CG  LYS A 328 "
      ideal   model   delta    sigma   weight residual
     114.10  120.43   -6.33 2.00e+00 2.50e-01 1.00e+01
  angle pdb=" CA  GLU B 232 "
        pdb=" CB  GLU B 232 "
        pdb=" CG  GLU B 232 "
      ideal   model   delta    sigma   weight residual
     114.10  120.37   -6.27 2.00e+00 2.50e-01 9.82e+00
  ... (remaining 8272 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.53: 3329
       32.53 -    65.05: 244
       65.05 -    97.58: 18
       97.58 -   130.10: 0
      130.10 -   162.63: 1
  Dihedral angle restraints: 3592
    sinusoidal: 1648
      harmonic: 1944
  Sorted by residual:
  dihedral pdb=" O4'   U G   2 "
           pdb=" C1'   U G   2 "
           pdb=" N1    U G   2 "
           pdb=" C2    U G   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   37.37  162.63     1      1.50e+01 4.44e-03 8.34e+01
  dihedral pdb=" CA  HIS A 304 "
           pdb=" C   HIS A 304 "
           pdb=" N   PRO A 305 "
           pdb=" CA  PRO A 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.07   24.93     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  ASP B 244 "
           pdb=" C   ASP B 244 "
           pdb=" N   ILE B 245 "
           pdb=" CA  ILE B 245 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.16  -20.84     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 3589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 748
       0.060 -    0.120: 125
       0.120 -    0.180: 19
       0.180 -    0.240: 3
       0.240 -    0.301: 2
  Chirality restraints: 897
  Sorted by residual:
  chirality pdb=" CB  ILE A 456 "
            pdb=" CA  ILE A 456 "
            pdb=" CG1 ILE A 456 "
            pdb=" CG2 ILE A 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CG  LEU B 267 "
            pdb=" CB  LEU B 267 "
            pdb=" CD1 LEU B 267 "
            pdb=" CD2 LEU B 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CB  ILE A  96 "
            pdb=" CA  ILE A  96 "
            pdb=" CG1 ILE A  96 "
            pdb=" CG2 ILE A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 894 not shown)

  Planarity restraints: 990
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 304 "   -0.044 5.00e-02 4.00e+02   6.59e-02 6.96e+00
        pdb=" N   PRO A 305 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 305 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 305 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 198 "   -0.011 2.00e-02 2.50e+03   2.19e-02 4.78e+00
        pdb=" C   GLN A 198 "    0.038 2.00e-02 2.50e+03
        pdb=" O   GLN A 198 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE A 199 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 185 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO B 186 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 186 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 186 "    0.029 5.00e-02 4.00e+02
  ... (remaining 987 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1172
        2.78 -     3.31: 5119
        3.31 -     3.84: 9706
        3.84 -     4.37: 10662
        4.37 -     4.90: 18460
  Nonbonded interactions: 45119
  Sorted by model distance:
  nonbonded pdb=" O   LYS A  58 "
            pdb=" OG1 THR A  62 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   HIS B 379 "
            pdb=" OG1 THR B 383 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   THR A  52 "
            pdb=" OG1 THR A  56 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ARG A 301 "
            pdb=" NH1 ARG A 301 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" OG  SER A 370 "
            pdb=" OP2  DC T  10 "
     model   vdw
     2.317 3.040
  ... (remaining 45114 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
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:             1.120
  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:             0.020
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.880
  Find NCS groups from input model:        0.020
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6017
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   0.044   6046  Z= 0.182
  Angle     :  0.825   9.918   8277  Z= 0.443
  Chirality :  0.049   0.301    897
  Planarity :  0.006   0.066    990
  Dihedral  : 20.396 162.627   2344
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.80 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 35.08 %
    Favored  : 64.05 %
  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: -2.83 (0.29), residues: 661
  helix: -0.58 (0.33), residues: 203
  sheet: -0.76 (0.47), residues: 119
  loop : -3.26 (0.27), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.017   0.002   TYR B 335 
 PHE   0.026   0.002   PHE A 388 
 TRP   0.019   0.002   TRP A 366 
 HIS   0.006   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6046)
  covalent geometry    : angle       0.82451 ( 8277)
  hydrogen bonds       : bond        0.11996 (  206)
  hydrogen bonds       : angle       5.74979 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 ASN cc_start: 0.5683 (m110) cc_final: 0.5354 (t0)
REVERT: B  215 HIS cc_start: 0.6235 (p90) cc_final: 0.5977 (p90)
REVERT: B  352 HIS cc_start: 0.5295 (OUTLIER) cc_final: 0.4156 (p90)
  outliers start: 5
  outliers final: 1
  residues processed: 78
  average time/residue: 0.1019
  time to fit residues: 10.0435
Evaluate side-chains
  73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain B residue  352 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0470
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.1684

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

Flipped N/Q/H residues before XYZ refinement:
A 424 HIS
B 215 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5108 r_free = 0.5108 target = 0.276592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.236771 restraints weight = 6744.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.4790 rms_B_bonded: 3.03
r_work: 0.4462 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.4462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6046  Z= 0.143
  Angle     :  0.623   7.122   8277  Z= 0.323
  Chirality :  0.041   0.241    897
  Planarity :  0.005   0.051    990
  Dihedral  : 14.003 177.132   1024
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 33.33 %
    Favored  : 63.35 %
  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: -2.31 (0.30), residues: 661
  helix:  0.37 (0.36), residues: 206
  sheet: -1.13 (0.46), residues: 123
  loop : -3.08 (0.28), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 341 
 TYR   0.015   0.001   TYR A 239 
 PHE   0.014   0.001   PHE A 282 
 TRP   0.023   0.002   TRP A 366 
 HIS   0.004   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6046)
  covalent geometry    : angle       0.62275 ( 8277)
  hydrogen bonds       : bond        0.04298 (  206)
  hydrogen bonds       : angle       4.74651 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASN cc_start: 0.7075 (m110) cc_final: 0.6079 (t0)
REVERT: B  352 HIS cc_start: 0.6642 (OUTLIER) cc_final: 0.6381 (p90)
  outliers start: 19
  outliers final: 12
  residues processed: 89
  average time/residue: 0.1122
  time to fit residues: 12.3982
Evaluate side-chains
  82 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  352 HIS
Chi-restraints excluded: chain B residue  358 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0010
   chunk 67 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.2590

-------------------------------------------------------------------------------
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 = 0.5088 r_free = 0.5088 target = 0.275271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4777 r_free = 0.4777 target = 0.234189 restraints weight = 6708.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.4758 rms_B_bonded: 3.29
r_work: 0.4401 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6891
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6046  Z= 0.145
  Angle     :  0.610   6.907   8277  Z= 0.314
  Chirality :  0.040   0.225    897
  Planarity :  0.005   0.050    990
  Dihedral  : 13.860 177.696   1024
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.89 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 33.51 %
    Favored  : 62.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.15 (0.31), residues: 661
  helix:  0.63 (0.36), residues: 208
  sheet: -1.15 (0.47), residues: 122
  loop : -3.04 (0.28), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.021   0.001   TYR A 239 
 PHE   0.014   0.001   PHE A 342 
 TRP   0.025   0.002   TRP A 366 
 HIS   0.005   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6046)
  covalent geometry    : angle       0.61037 ( 8277)
  hydrogen bonds       : bond        0.04131 (  206)
  hydrogen bonds       : angle       4.54709 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6795 (ttp-170)
REVERT: B  352 HIS cc_start: 0.6588 (OUTLIER) cc_final: 0.6370 (p90)
  outliers start: 24
  outliers final: 16
  residues processed: 90
  average time/residue: 0.1047
  time to fit residues: 11.8930
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  352 HIS
Chi-restraints excluded: chain B residue  358 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 47 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0980
   chunk 18 optimal weight:    0.0570
   chunk 50 optimal weight:    0.6980
   overall best weight:    1.1100

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

Flipped N/Q/H residues before XYZ refinement:
A 424 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5086 r_free = 0.5086 target = 0.275000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.232264 restraints weight = 6666.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4730 rms_B_bonded: 3.31
r_work: 0.4385 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6046  Z= 0.136
  Angle     :  0.609   8.317   8277  Z= 0.311
  Chirality :  0.041   0.239    897
  Planarity :  0.004   0.053    990
  Dihedral  : 13.830 178.930   1024
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 32.98 %
    Favored  : 62.13 %
  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: -2.08 (0.31), residues: 661
  helix:  0.64 (0.36), residues: 209
  sheet: -1.12 (0.47), residues: 122
  loop : -2.97 (0.28), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.019   0.001   TYR A 239 
 PHE   0.012   0.001   PHE A 342 
 TRP   0.021   0.001   TRP A 366 
 HIS   0.005   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6046)
  covalent geometry    : angle       0.60945 ( 8277)
  hydrogen bonds       : bond        0.03977 (  206)
  hydrogen bonds       : angle       4.48295 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.6908 (ptmt)
REVERT: A  363 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7251 (m-30)
REVERT: A  462 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6771 (ttp-170)
REVERT: B  402 MET cc_start: 0.6851 (mmp) cc_final: 0.6509 (mpp)
  outliers start: 28
  outliers final: 21
  residues processed: 93
  average time/residue: 0.1026
  time to fit residues: 12.0760
Evaluate side-chains
  93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  363 ASP
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  358 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 48 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.5082 r_free = 0.5082 target = 0.274775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4761 r_free = 0.4761 target = 0.233017 restraints weight = 6810.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.4751 rms_B_bonded: 3.17
r_work: 0.4411 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.4411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6046  Z= 0.133
  Angle     :  0.601   7.330   8277  Z= 0.308
  Chirality :  0.041   0.232    897
  Planarity :  0.004   0.056    990
  Dihedral  : 13.735 179.206   1022
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 31.41 %
    Favored  : 62.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.31), residues: 661
  helix:  0.75 (0.37), residues: 209
  sheet: -1.17 (0.47), residues: 123
  loop : -2.98 (0.28), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.020   0.001   TYR A 239 
 PHE   0.011   0.001   PHE A 282 
 TRP   0.021   0.001   TRP A 366 
 HIS   0.004   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6046)
  covalent geometry    : angle       0.60070 ( 8277)
  hydrogen bonds       : bond        0.03880 (  206)
  hydrogen bonds       : angle       4.38780 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 70
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  314 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6909 (ptmt)
REVERT: A  341 ARG cc_start: 0.5650 (ptm-80) cc_final: 0.5278 (ptm-80)
REVERT: A  363 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7272 (m-30)
REVERT: A  462 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6771 (ttp-170)
REVERT: B  402 MET cc_start: 0.6843 (mmp) cc_final: 0.6468 (mpp)
  outliers start: 36
  outliers final: 21
  residues processed: 98
  average time/residue: 0.1069
  time to fit residues: 13.0914
Evaluate side-chains
  94 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  363 ASP
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  352 HIS
Chi-restraints excluded: chain B residue  358 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0570
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5103 r_free = 0.5103 target = 0.277148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.236929 restraints weight = 6697.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.4772 rms_B_bonded: 3.22
r_work (final): 0.4772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6460
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6046  Z= 0.116
  Angle     :  0.589   6.976   8277  Z= 0.304
  Chirality :  0.040   0.209    897
  Planarity :  0.004   0.054    990
  Dihedral  : 13.710 177.823   1020
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 32.29 %
    Favored  : 62.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.92 (0.31), residues: 661
  helix:  0.92 (0.37), residues: 209
  sheet: -1.11 (0.48), residues: 122
  loop : -2.94 (0.28), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.017   0.001   TYR A 239 
 PHE   0.009   0.001   PHE A 265 
 TRP   0.014   0.001   TRP A 366 
 HIS   0.006   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6046)
  covalent geometry    : angle       0.58867 ( 8277)
  hydrogen bonds       : bond        0.03571 (  206)
  hydrogen bonds       : angle       4.26887 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  341 ARG cc_start: 0.5181 (ptm-80) cc_final: 0.4930 (ptm-80)
REVERT: A  363 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7312 (m-30)
REVERT: A  462 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6640 (ttp-170)
REVERT: B  171 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6492 (mp)
REVERT: B  190 ILE cc_start: 0.7481 (pt) cc_final: 0.7133 (mt)
  outliers start: 28
  outliers final: 20
  residues processed: 92
  average time/residue: 0.1128
  time to fit residues: 12.8815
Evaluate side-chains
  91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  247 TRP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  363 ASP
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  345 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 60 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.5098 r_free = 0.5098 target = 0.277216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4781 r_free = 0.4781 target = 0.235665 restraints weight = 6692.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.4768 rms_B_bonded: 3.12
r_work: 0.4432 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.4432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6046  Z= 0.116
  Angle     :  0.595   7.612   8277  Z= 0.304
  Chirality :  0.040   0.204    897
  Planarity :  0.004   0.056    990
  Dihedral  : 13.764 178.035   1020
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 32.81 %
    Favored  : 62.65 %
  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: -1.90 (0.32), residues: 661
  helix:  0.97 (0.37), residues: 208
  sheet: -1.02 (0.46), residues: 132
  loop : -3.03 (0.28), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.018   0.001   TYR A 239 
 PHE   0.009   0.001   PHE A 282 
 TRP   0.015   0.001   TRP A 366 
 HIS   0.004   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6046)
  covalent geometry    : angle       0.59501 ( 8277)
  hydrogen bonds       : bond        0.03568 (  206)
  hydrogen bonds       : angle       4.29881 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.6015 (mtt) cc_final: 0.5207 (ptt)
REVERT: A  341 ARG cc_start: 0.5432 (ptm-80) cc_final: 0.5218 (ptm-80)
REVERT: A  363 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7179 (m-30)
REVERT: A  462 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6731 (ttp-170)
REVERT: B  215 HIS cc_start: 0.6873 (p-80) cc_final: 0.6606 (p-80)
REVERT: B  402 MET cc_start: 0.7518 (mpp) cc_final: 0.6886 (mmp)
  outliers start: 26
  outliers final: 22
  residues processed: 92
  average time/residue: 0.0995
  time to fit residues: 11.7104
Evaluate side-chains
  94 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  363 ASP
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  359 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0570
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.9902

-------------------------------------------------------------------------------
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 = 0.5094 r_free = 0.5094 target = 0.276482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.234621 restraints weight = 6648.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.4758 rms_B_bonded: 3.17
r_work: 0.4423 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.4423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6046  Z= 0.133
  Angle     :  0.615   6.898   8277  Z= 0.317
  Chirality :  0.040   0.205    897
  Planarity :  0.004   0.056    990
  Dihedral  : 13.851 179.886   1020
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 32.46 %
    Favored  : 62.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.32), residues: 661
  helix:  1.01 (0.38), residues: 207
  sheet: -1.09 (0.46), residues: 132
  loop : -3.03 (0.28), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 333 
 TYR   0.020   0.001   TYR A 239 
 PHE   0.010   0.001   PHE A 282 
 TRP   0.018   0.001   TRP A 366 
 HIS   0.004   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6046)
  covalent geometry    : angle       0.61489 ( 8277)
  hydrogen bonds       : bond        0.03965 (  206)
  hydrogen bonds       : angle       4.35001 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 71
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 ARG cc_start: 0.4916 (OUTLIER) cc_final: 0.2914 (mtm-85)
REVERT: A  341 ARG cc_start: 0.5455 (ptm-80) cc_final: 0.5226 (ptm-80)
REVERT: A  363 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7238 (m-30)
REVERT: A  462 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6735 (ttp-170)
REVERT: B  215 HIS cc_start: 0.6840 (p-80) cc_final: 0.6570 (p-80)
REVERT: B  402 MET cc_start: 0.7433 (mpp) cc_final: 0.6664 (mmp)
  outliers start: 27
  outliers final: 22
  residues processed: 91
  average time/residue: 0.1078
  time to fit residues: 12.2351
Evaluate side-chains
  95 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  363 ASP
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  359 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 47 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5086 r_free = 0.5086 target = 0.274740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.233350 restraints weight = 6815.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.4736 rms_B_bonded: 3.14
r_work: 0.4390 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6046  Z= 0.151
  Angle     :  0.640   8.182   8277  Z= 0.328
  Chirality :  0.041   0.208    897
  Planarity :  0.004   0.055    990
  Dihedral  : 13.932 178.220   1020
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.04 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 32.81 %
    Favored  : 62.65 %
  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: -1.97 (0.32), residues: 661
  helix:  0.96 (0.38), residues: 207
  sheet: -1.14 (0.46), residues: 133
  loop : -3.06 (0.28), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 333 
 TYR   0.023   0.002   TYR A 239 
 PHE   0.011   0.001   PHE A 282 
 TRP   0.023   0.002   TRP A 366 
 HIS   0.004   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6046)
  covalent geometry    : angle       0.64028 ( 8277)
  hydrogen bonds       : bond        0.04136 (  206)
  hydrogen bonds       : angle       4.46906 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.3137 (mtm-85)
REVERT: A  341 ARG cc_start: 0.5486 (ptm-80) cc_final: 0.5267 (ptm-80)
REVERT: A  462 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6667 (ttp-170)
REVERT: B  215 HIS cc_start: 0.6915 (p-80) cc_final: 0.6689 (p-80)
REVERT: B  402 MET cc_start: 0.7371 (mpp) cc_final: 0.6718 (mmp)
  outliers start: 26
  outliers final: 22
  residues processed: 91
  average time/residue: 0.0960
  time to fit residues: 10.8855
Evaluate side-chains
  96 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  359 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 28 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0370
   chunk 55 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.4864

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.273136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.231827 restraints weight = 6809.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.4722 rms_B_bonded: 3.05
r_work: 0.4385 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6046  Z= 0.166
  Angle     :  0.666   9.126   8277  Z= 0.342
  Chirality :  0.042   0.212    897
  Planarity :  0.005   0.058    990
  Dihedral  : 14.065 176.814   1020
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 32.64 %
    Favored  : 62.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.31), residues: 661
  helix:  0.85 (0.37), residues: 207
  sheet: -1.27 (0.46), residues: 133
  loop : -3.06 (0.28), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.024   0.002   TYR A 239 
 PHE   0.011   0.002   PHE A 282 
 TRP   0.025   0.002   TRP A 366 
 HIS   0.004   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6046)
  covalent geometry    : angle       0.66563 ( 8277)
  hydrogen bonds       : bond        0.04398 (  206)
  hydrogen bonds       : angle       4.57211 (  553)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 ARG cc_start: 0.5480 (OUTLIER) cc_final: 0.3443 (mtm-85)
REVERT: A  341 ARG cc_start: 0.5613 (ptm-80) cc_final: 0.5359 (ptm-80)
REVERT: A  363 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7291 (m-30)
REVERT: A  462 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6692 (ttp-170)
REVERT: B  215 HIS cc_start: 0.6921 (p-80) cc_final: 0.6707 (p-80)
REVERT: B  402 MET cc_start: 0.7313 (mpp) cc_final: 0.6644 (mmp)
  outliers start: 26
  outliers final: 21
  residues processed: 91
  average time/residue: 0.0996
  time to fit residues: 11.4564
Evaluate side-chains
  96 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  363 ASP
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  359 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 39 optimal weight:    0.2980
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.5111 r_free = 0.5111 target = 0.278273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4785 r_free = 0.4785 target = 0.236315 restraints weight = 6694.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.4756 rms_B_bonded: 3.17
r_work: 0.4441 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.4441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6796
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6046  Z= 0.118
  Angle     :  0.613   8.379   8277  Z= 0.316
  Chirality :  0.040   0.200    897
  Planarity :  0.004   0.060    990
  Dihedral  : 13.989 176.837   1020
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.83 %
    Favored  : 90.17 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 33.68 %
    Favored  : 62.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.99 (0.32), residues: 661
  helix:  0.94 (0.38), residues: 207
  sheet: -1.23 (0.47), residues: 131
  loop : -3.03 (0.28), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.020   0.001   TYR A 239 
 PHE   0.009   0.001   PHE A 342 
 TRP   0.014   0.001   TRP A 366 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6046)
  covalent geometry    : angle       0.61271 ( 8277)
  hydrogen bonds       : bond        0.03648 (  206)
  hydrogen bonds       : angle       4.33815 (  553)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1528.91 seconds
wall clock time: 26 minutes 58.31 seconds (1618.31 seconds total)