Starting phenix.real_space_refine
on Sun Apr 27 13:19:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jsp_61780/04_2025/9jsp_61780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jsp_61780/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jsp_61780/04_2025/9jsp_61780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jsp_61780/04_2025/9jsp_61780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jsp_61780/04_2025/9jsp_61780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jsp_61780/04_2025/9jsp_61780.cif"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.062
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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.33, per 1000 atoms: 0.74
  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: 1.60
  Conformation dependent library (CDL) restraints added in 789.1 milliseconds
  

  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: 1.83
  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: 1.52

  Time building geometry restraints manager: 1.87 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:             0.990
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.110
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:3.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.740
-------------------------------------------------------------------------------
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 : 6.91
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (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
 TRP   0.019   0.002   TRP A 366 
 HIS   0.006   0.001   HIS B 253 
 PHE   0.026   0.002   PHE A 388 
 TYR   0.017   0.002   TYR B 335 
 ARG   0.004   0.000   ARG A 333 

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

*********************** 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  : 0.645 
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: 0.2165
  time to fit residues: 21.4887
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  : 0.638 
-------------------------------------------------------------------------------
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 57 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.5086 r_free = 0.5086 target = 0.273882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.234202 restraints weight = 6650.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.4768 rms_B_bonded: 2.93
r_work: 0.4431 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6046  Z= 0.172
  Angle     :  0.656   7.930   8277  Z= 0.339
  Chirality :  0.042   0.261    897
  Planarity :  0.005   0.054    990
  Dihedral  : 14.023 174.494   1024
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 33.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.30), residues: 661
  helix:  0.34 (0.36), residues: 206
  sheet: -1.22 (0.46), residues: 123
  loop : -3.11 (0.28), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 366 
 HIS   0.005   0.001   HIS B 253 
 PHE   0.015   0.002   PHE A 342 
 TYR   0.019   0.002   TYR A 239 
 ARG   0.004   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04619 (  206)
  hydrogen bonds       : angle       4.85737 (  553)
  covalent geometry    : bond        0.00395 ( 6046)
  covalent geometry    : angle       0.65649 ( 8277)

*********************** 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
  94 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6743 (ttp-170)
REVERT: B  352 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.6406 (p90)
  outliers start: 21
  outliers final: 13
  residues processed: 90
  average time/residue: 0.3336
  time to fit residues: 37.0437
Evaluate side-chains
  84 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
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  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  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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.5085 r_free = 0.5085 target = 0.274999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.233796 restraints weight = 6684.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.4752 rms_B_bonded: 3.27
r_work: 0.4394 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.4394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6046  Z= 0.141
  Angle     :  0.604   6.858   8277  Z= 0.312
  Chirality :  0.040   0.218    897
  Planarity :  0.005   0.050    990
  Dihedral  : 13.851 177.933   1024
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.04 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 34.21 %
    Favored  : 61.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.31), residues: 661
  helix:  0.65 (0.36), residues: 208
  sheet: -1.20 (0.47), residues: 122
  loop : -3.02 (0.28), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 366 
 HIS   0.005   0.001   HIS B 253 
 PHE   0.013   0.001   PHE A 282 
 TYR   0.022   0.002   TYR A 239 
 ARG   0.004   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  206)
  hydrogen bonds       : angle       4.57454 (  553)
  covalent geometry    : bond        0.00325 ( 6046)
  covalent geometry    : angle       0.60385 ( 8277)

*********************** 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
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 HIS cc_start: 0.6649 (OUTLIER) cc_final: 0.6430 (p90)
  outliers start: 25
  outliers final: 17
  residues processed: 94
  average time/residue: 0.2638
  time to fit residues: 31.5824
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
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  159 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  231 TRP
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 B residue  205 VAL
Chi-restraints excluded: chain B residue  272 ASP
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 423 HIS
** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 379 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.266184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.223339 restraints weight = 6881.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.4654 rms_B_bonded: 3.32
r_work: 0.4298 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   6046  Z= 0.266
  Angle     :  0.754  10.842   8277  Z= 0.384
  Chirality :  0.046   0.237    897
  Planarity :  0.006   0.064    990
  Dihedral  : 14.202 173.541   1024
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.37 %
    Favored  : 85.63 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 32.64 %
    Favored  : 60.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.31), residues: 661
  helix:  0.52 (0.36), residues: 206
  sheet: -1.38 (0.46), residues: 120
  loop : -3.06 (0.28), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 366 
 HIS   0.005   0.001   HIS B 253 
 PHE   0.015   0.002   PHE A  15 
 TYR   0.025   0.002   TYR A 239 
 ARG   0.004   0.001   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05497 (  206)
  hydrogen bonds       : angle       5.01552 (  553)
  covalent geometry    : bond        0.00618 ( 6046)
  covalent geometry    : angle       0.75431 ( 8277)

*********************** 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
  112 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 71
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 TRP cc_start: 0.5772 (OUTLIER) cc_final: 0.2002 (t-100)
REVERT: A  301 ARG cc_start: 0.5736 (tpt90) cc_final: 0.5458 (tpt170)
REVERT: A  363 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7426 (m-30)
REVERT: A  462 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6731 (ttp-170)
REVERT: B  224 GLU cc_start: 0.7538 (pp20) cc_final: 0.7048 (pp20)
  outliers start: 41
  outliers final: 24
  residues processed: 103
  average time/residue: 0.2980
  time to fit residues: 38.3577
Evaluate side-chains
  96 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue    7 ILE
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  160 ASN
Chi-restraints excluded: chain A residue  221 ARG
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  387 THR
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  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  352 HIS
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  359 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 39 optimal weight:    0.4980
   chunk 59 optimal weight:    9.9990
   chunk 56 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.5048 r_free = 0.5048 target = 0.270340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.227715 restraints weight = 6686.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.4688 rms_B_bonded: 3.16
r_work: 0.4338 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.2050

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= 0.176
  Angle     :  0.668   7.796   8277  Z= 0.342
  Chirality :  0.043   0.246    897
  Planarity :  0.005   0.063    990
  Dihedral  : 14.079 175.506   1022
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 33.33 %
    Favored  : 60.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.31), residues: 661
  helix:  0.74 (0.36), residues: 206
  sheet: -1.52 (0.46), residues: 122
  loop : -3.02 (0.28), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 366 
 HIS   0.004   0.001   HIS B 253 
 PHE   0.015   0.002   PHE A 282 
 TYR   0.019   0.002   TYR A 239 
 ARG   0.004   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04615 (  206)
  hydrogen bonds       : angle       4.71671 (  553)
  covalent geometry    : bond        0.00407 ( 6046)
  covalent geometry    : angle       0.66753 ( 8277)

*********************** 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
  109 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 75
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 TRP cc_start: 0.5621 (OUTLIER) cc_final: 0.4592 (t-100)
REVERT: A  303 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.3408 (mtm-85)
REVERT: A  314 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6914 (ptmt)
REVERT: A  341 ARG cc_start: 0.6341 (ptm-80) cc_final: 0.5981 (ptm-80)
REVERT: A  363 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7382 (m-30)
REVERT: A  403 MET cc_start: 0.7347 (mtp) cc_final: 0.7113 (mtp)
REVERT: A  462 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6761 (ttp-170)
REVERT: B  171 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6255 (mp)
REVERT: B  224 GLU cc_start: 0.7593 (pp20) cc_final: 0.7333 (pp20)
REVERT: B  402 MET cc_start: 0.6945 (mmp) cc_final: 0.6636 (mpp)
  outliers start: 34
  outliers final: 21
  residues processed: 99
  average time/residue: 0.2363
  time to fit residues: 29.0489
Evaluate side-chains
  101 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
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   64 SER
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  220 SER
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  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  387 THR
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  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
Chi-restraints excluded: chain B residue  359 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 14 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
** A 446 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 = 0.5026 r_free = 0.5026 target = 0.267190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.227340 restraints weight = 6709.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.4690 rms_B_bonded: 3.21
r_work: 0.4316 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6046  Z= 0.218
  Angle     :  0.721   9.616   8277  Z= 0.369
  Chirality :  0.045   0.252    897
  Planarity :  0.006   0.065    990
  Dihedral  : 14.237 173.167   1022
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.52 %
    Favored  : 85.48 %
  Rotamer:
    Outliers :  6.46 %
    Allowed  : 33.33 %
    Favored  : 60.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.31), residues: 661
  helix:  0.66 (0.36), residues: 206
  sheet: -1.62 (0.46), residues: 122
  loop : -3.01 (0.29), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 366 
 HIS   0.006   0.001   HIS B 215 
 PHE   0.014   0.002   PHE A 282 
 TYR   0.020   0.002   TYR A 398 
 ARG   0.004   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04958 (  206)
  hydrogen bonds       : angle       4.83102 (  553)
  covalent geometry    : bond        0.00508 ( 6046)
  covalent geometry    : angle       0.72078 ( 8277)

*********************** 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
  113 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 76
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 TRP cc_start: 0.5637 (OUTLIER) cc_final: 0.4601 (t-100)
REVERT: A  303 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.3783 (mtm-85)
REVERT: A  345 GLU cc_start: 0.7868 (pm20) cc_final: 0.7662 (pm20)
REVERT: A  406 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.4153 (m-80)
REVERT: A  462 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6780 (ttp-170)
REVERT: B  171 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6198 (mp)
REVERT: B  224 GLU cc_start: 0.7604 (pp20) cc_final: 0.7346 (pp20)
REVERT: B  402 MET cc_start: 0.6906 (mmp) cc_final: 0.6662 (mpp)
  outliers start: 37
  outliers final: 26
  residues processed: 103
  average time/residue: 0.2551
  time to fit residues: 32.7790
Evaluate side-chains
  109 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 78
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
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   64 SER
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  221 ARG
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  314 LYS
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  406 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  226 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
Chi-restraints excluded: chain B residue  359 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 45 optimal weight:    0.4980
   chunk 67 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.5085 r_free = 0.5085 target = 0.274571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.233347 restraints weight = 6642.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.4747 rms_B_bonded: 3.05
r_work: 0.4430 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.4430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.2139

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= 0.120
  Angle     :  0.611   6.813   8277  Z= 0.316
  Chirality :  0.040   0.192    897
  Planarity :  0.005   0.059    990
  Dihedral  : 14.061 178.343   1022
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 34.90 %
    Favored  : 60.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.32), residues: 661
  helix:  0.91 (0.37), residues: 208
  sheet: -1.49 (0.46), residues: 122
  loop : -2.92 (0.29), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 247 
 HIS   0.004   0.001   HIS B 253 
 PHE   0.012   0.001   PHE A 342 
 TYR   0.020   0.002   TYR A 398 
 ARG   0.005   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  206)
  hydrogen bonds       : angle       4.38575 (  553)
  covalent geometry    : bond        0.00273 ( 6046)
  covalent geometry    : angle       0.61125 ( 8277)

*********************** 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
  107 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 LYS cc_start: 0.7215 (tptp) cc_final: 0.6824 (ptpt)
REVERT: A  363 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7258 (m-30)
REVERT: A  403 MET cc_start: 0.7652 (mtp) cc_final: 0.7261 (mtp)
REVERT: A  406 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.3843 (m-80)
REVERT: B  171 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6056 (mp)
REVERT: B  224 GLU cc_start: 0.7545 (pp20) cc_final: 0.7265 (pp20)
REVERT: B  260 ARG cc_start: 0.7238 (ttt-90) cc_final: 0.7031 (ttp80)
REVERT: B  402 MET cc_start: 0.6804 (mmp) cc_final: 0.6523 (mpp)
  outliers start: 28
  outliers final: 18
  residues processed: 99
  average time/residue: 0.1999
  time to fit residues: 25.4857
Evaluate side-chains
  97 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
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   64 SER
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  220 SER
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  406 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  215 HIS
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  345 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0000
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7586

-------------------------------------------------------------------------------
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 = 0.5086 r_free = 0.5086 target = 0.274904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.232586 restraints weight = 6610.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.4741 rms_B_bonded: 3.13
r_work: 0.4411 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.4411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
moved from start:          0.2144

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= 0.121
  Angle     :  0.613   8.818   8277  Z= 0.314
  Chirality :  0.041   0.245    897
  Planarity :  0.004   0.057    990
  Dihedral  : 14.039 179.829   1020
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 35.25 %
    Favored  : 60.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.32), residues: 661
  helix:  0.99 (0.37), residues: 208
  sheet: -1.40 (0.47), residues: 122
  loop : -2.86 (0.29), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 247 
 HIS   0.004   0.001   HIS B 253 
 PHE   0.016   0.001   PHE A 388 
 TYR   0.019   0.002   TYR A 239 
 ARG   0.006   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  206)
  hydrogen bonds       : angle       4.32804 (  553)
  covalent geometry    : bond        0.00278 ( 6046)
  covalent geometry    : angle       0.61312 ( 8277)

*********************** 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
  102 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  363 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7283 (m-30)
REVERT: A  406 TYR cc_start: 0.6395 (OUTLIER) cc_final: 0.3955 (m-80)
REVERT: A  462 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6765 (ttp-170)
REVERT: B  171 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6104 (mp)
REVERT: B  173 LEU cc_start: 0.6710 (mp) cc_final: 0.6413 (mt)
REVERT: B  224 GLU cc_start: 0.7542 (pp20) cc_final: 0.7270 (pp20)
REVERT: B  402 MET cc_start: 0.6735 (mmp) cc_final: 0.6514 (mpp)
  outliers start: 24
  outliers final: 19
  residues processed: 95
  average time/residue: 0.2033
  time to fit residues: 24.6208
Evaluate side-chains
  100 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
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   64 SER
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
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  406 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  215 HIS
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  345 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   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 = 0.5074 r_free = 0.5074 target = 0.273493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.231307 restraints weight = 6609.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.4724 rms_B_bonded: 3.08
r_work: 0.4391 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.4391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6046  Z= 0.137
  Angle     :  0.629   9.103   8277  Z= 0.321
  Chirality :  0.041   0.252    897
  Planarity :  0.005   0.058    990
  Dihedral  : 14.092 177.980   1020
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.65 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 35.08 %
    Favored  : 60.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.32), residues: 661
  helix:  1.03 (0.37), residues: 207
  sheet: -1.42 (0.47), residues: 122
  loop : -2.88 (0.29), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 247 
 HIS   0.004   0.001   HIS B 253 
 PHE   0.013   0.001   PHE A   8 
 TYR   0.019   0.002   TYR A 398 
 ARG   0.004   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03815 (  206)
  hydrogen bonds       : angle       4.37920 (  553)
  covalent geometry    : bond        0.00316 ( 6046)
  covalent geometry    : angle       0.62871 ( 8277)

*********************** 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
  107 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  363 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7269 (m-30)
REVERT: A  462 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6665 (ttp-170)
REVERT: B  171 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6101 (mp)
REVERT: B  173 LEU cc_start: 0.6746 (mp) cc_final: 0.6439 (mt)
REVERT: B  260 ARG cc_start: 0.7299 (ttt-90) cc_final: 0.7026 (ttp80)
  outliers start: 27
  outliers final: 22
  residues processed: 99
  average time/residue: 0.2448
  time to fit residues: 30.6123
Evaluate side-chains
  102 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
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   64 SER
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  220 SER
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  171 LEU
Chi-restraints excluded: chain B residue  215 HIS
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  272 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 58 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 207 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5097 r_free = 0.5097 target = 0.276246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.234766 restraints weight = 6752.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4752 rms_B_bonded: 3.07
r_work: 0.4411 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.4411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6046  Z= 0.122
  Angle     :  0.628   8.645   8277  Z= 0.321
  Chirality :  0.041   0.250    897
  Planarity :  0.004   0.056    990
  Dihedral  : 14.097 178.658   1020
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 35.78 %
    Favored  : 60.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.32), residues: 661
  helix:  1.08 (0.37), residues: 207
  sheet: -1.13 (0.47), residues: 130
  loop : -2.93 (0.29), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 247 
 HIS   0.004   0.001   HIS B 253 
 PHE   0.016   0.001   PHE A 265 
 TYR   0.022   0.002   TYR A 239 
 ARG   0.005   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03521 (  206)
  hydrogen bonds       : angle       4.30675 (  553)
  covalent geometry    : bond        0.00279 ( 6046)
  covalent geometry    : angle       0.62848 ( 8277)

********************** 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: 23
    poor density    : 76
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  363 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7240 (m-30)
REVERT: A  406 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.4437 (m-80)
REVERT: A  462 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6729 (ttp-170)
REVERT: B  173 LEU cc_start: 0.6770 (mp) cc_final: 0.6543 (mt)
REVERT: B  402 MET cc_start: 0.7500 (mpp) cc_final: 0.6816 (mmp)
  outliers start: 23
  outliers final: 20
  residues processed: 92
  average time/residue: 0.2100
  time to fit residues: 24.6749
Evaluate side-chains
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
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   64 SER
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  159 TRP
Chi-restraints excluded: chain A residue  220 SER
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  391 LEU
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  345 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0570
   overall best weight:    0.9900

-------------------------------------------------------------------------------
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 = 0.5084 r_free = 0.5084 target = 0.274515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.232927 restraints weight = 6675.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4740 rms_B_bonded: 3.05
r_work: 0.4403 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6046  Z= 0.134
  Angle     :  0.640   8.593   8277  Z= 0.327
  Chirality :  0.041   0.252    897
  Planarity :  0.005   0.057    990
  Dihedral  : 14.141 178.913   1020
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 36.65 %
    Favored  : 58.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.32), residues: 661
  helix:  1.10 (0.37), residues: 207
  sheet: -1.16 (0.47), residues: 129
  loop : -2.91 (0.29), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 247 
 HIS   0.004   0.001   HIS B 253 
 PHE   0.011   0.001   PHE A 282 
 TYR   0.020   0.002   TYR A 239 
 ARG   0.005   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03680 (  206)
  hydrogen bonds       : angle       4.34423 (  553)
  covalent geometry    : bond        0.00309 ( 6046)
  covalent geometry    : angle       0.64015 ( 8277)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3337.71 seconds
wall clock time: 59 minutes 58.23 seconds (3598.23 seconds total)