Starting phenix.real_space_refine
on Tue Aug  4 18:02:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jsp_61780/08_2026/9jsp_61780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jsp_61780/08_2026/9jsp_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_61780/08_2026/9jsp_61780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jsp_61780/08_2026/9jsp_61780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jsp_61780/08_2026/9jsp_61780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jsp_61780/08_2026/9jsp_61780.cif"
  }
  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-2.2rc3-6140/lib/python3.11/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: 1.61, per 1000 atoms: 0.27
  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 384.9 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: 0.70
  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: 1.02

  Time building geometry restraints manager: 0.78 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=" C3'  DG T  17 "
       pdb=" C2'  DG T  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.41e+00
  bond pdb=" C3'  DG T  14 "
       pdb=" C2'  DG T  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 8.00e-03 1.56e+04 5.53e+00
  bond pdb=" C1'  DT T  13 "
       pdb=" N1   DT T  13 "
    ideal  model  delta    sigma   weight residual
    1.468  1.498 -0.030 1.40e-02 5.10e+03 4.60e+00
  bond pdb=" C3'  DG T   9 "
       pdb=" C2'  DG T   9 "
    ideal  model  delta    sigma   weight residual
    1.516  1.532 -0.016 8.00e-03 1.56e+04 4.16e+00
  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
  ... (remaining 6041 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 7936
        1.98 -     3.97: 291
        3.97 -     5.95: 40
        5.95 -     7.93: 6
        7.93 -     9.92: 4
  Bond angle restraints: 8277
  Sorted by residual:
  angle pdb=" N3   DT T  18 "
        pdb=" C4   DT T  18 "
        pdb=" O4   DT T  18 "
      ideal   model   delta    sigma   weight residual
     119.90  122.51   -2.61 6.00e-01 2.78e+00 1.90e+01
  angle pdb=" N3   DT T  11 "
        pdb=" C4   DT T  11 "
        pdb=" O4   DT T  11 "
      ideal   model   delta    sigma   weight residual
     119.90  122.46   -2.56 6.00e-01 2.78e+00 1.83e+01
  angle pdb=" O4   DT T  11 "
        pdb=" C4   DT T  11 "
        pdb=" C5   DT T  11 "
      ideal   model   delta    sigma   weight residual
     124.90  122.08    2.82 7.00e-01 2.04e+00 1.63e+01
  angle pdb=" N3   DT T  13 "
        pdb=" C4   DT T  13 "
        pdb=" O4   DT T  13 "
      ideal   model   delta    sigma   weight residual
     119.90  122.32   -2.42 6.00e-01 2.78e+00 1.62e+01
  angle pdb=" O4   DT T  18 "
        pdb=" C4   DT T  18 "
        pdb=" C5   DT T  18 "
      ideal   model   delta    sigma   weight residual
     124.90  122.13    2.77 7.00e-01 2.04e+00 1.57e+01
  ... (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: 733
       0.060 -    0.120: 132
       0.120 -    0.180: 27
       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:             1.150
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.430
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6128
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= 0.232
  Angle     :  0.844   9.918   8277  Z= 0.503
  Chirality :  0.051   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 are 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/Z
  covalent geometry    : bond        0.00389 /  0.23 ( 6046)
  covalent geometry    : angle       0.84423 /  0.50 ( 8277)
  hydrogen bonds       : bond        0.11996 /  9.06 (  206)
  hydrogen bonds       : angle       5.74979 /  4.18 (  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  : 0.174 
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: 0.0857
  time to fit residues: 8.5723
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  : 0.148 
-------------------------------------------------------------------------------
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...
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 = 0.5123 r_free = 0.5123 target = 0.278455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4830 r_free = 0.4830 target = 0.238944 restraints weight = 6733.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.4810 rms_B_bonded: 3.14
r_work: 0.4485 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.4485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.0770

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= 0.146
  Angle     :  0.629   7.094   8277  Z= 0.337
  Chirality :  0.042   0.215    897
  Planarity :  0.005   0.048    990
  Dihedral  : 14.178 178.628   1024
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 34.03 %
    Favored  : 63.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.30), residues: 661
  helix:  0.17 (0.35), residues: 207
  sheet: -0.87 (0.46), residues: 130
  loop : -3.21 (0.27), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 333 
 TYR   0.010   0.001   TYR A 266 
 PHE   0.015   0.001   PHE A 342 
 TRP   0.019   0.002   TRP A 366 
 HIS   0.004   0.001   HIS B 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 ( 6046)
  covalent geometry    : angle       0.62903 /  0.34 ( 8277)
  hydrogen bonds       : bond        0.05001 /  3.45 (  206)
  hydrogen bonds       : angle       4.85575 /  3.34 (  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
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 VAL cc_start: 0.7487 (t) cc_final: 0.7241 (t)
REVERT: A   76 ASN cc_start: 0.7004 (m110) cc_final: 0.6089 (t0)
REVERT: A  123 GLU cc_start: 0.7609 (pp20) cc_final: 0.7404 (pt0)
REVERT: B  352 HIS cc_start: 0.6561 (OUTLIER) cc_final: 0.6190 (p90)
  outliers start: 14
  outliers final: 9
  residues processed: 85
  average time/residue: 0.0998
  time to fit residues: 10.6399
Evaluate side-chains
  82 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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  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 B residue  272 ASP
Chi-restraints excluded: chain B residue  352 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0870
   chunk 14 optimal weight:    0.0470
   overall best weight:    1.4060

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5086 r_free = 0.5086 target = 0.275227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.232876 restraints weight = 6702.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.4746 rms_B_bonded: 3.12
r_work: 0.4414 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.4414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.1176

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= 0.155
  Angle     :  0.619   7.025   8277  Z= 0.328
  Chirality :  0.041   0.245    897
  Planarity :  0.005   0.057    990
  Dihedral  : 13.955 174.489   1024
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.35 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 32.98 %
    Favored  : 63.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.31), residues: 661
  helix:  0.58 (0.36), residues: 207
  sheet: -1.14 (0.47), residues: 123
  loop : -3.05 (0.28), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.016   0.002   TYR A 239 
 PHE   0.014   0.002   PHE A 282 
 TRP   0.025   0.002   TRP A 366 
 HIS   0.005   0.001   HIS B 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 6046)
  covalent geometry    : angle       0.61926 /  0.33 ( 8277)
  hydrogen bonds       : bond        0.04677 /  3.23 (  206)
  hydrogen bonds       : angle       4.71747 /  3.21 (  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
  92 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 GLU cc_start: 0.7791 (pm20) cc_final: 0.7526 (pm20)
REVERT: A  361 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7045 (tt)
REVERT: A  462 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6754 (ttp-170)
REVERT: B  352 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.6418 (p90)
  outliers start: 23
  outliers final: 16
  residues processed: 88
  average time/residue: 0.0947
  time to fit residues: 10.5113
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  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   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  342 PHE
Chi-restraints excluded: chain A residue  361 LEU
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  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 16 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.3186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5088 r_free = 0.5088 target = 0.275437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.233470 restraints weight = 6657.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.4749 rms_B_bonded: 3.11
r_work: 0.4410 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.4410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.1331

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= 0.148
  Angle     :  0.619   9.276   8277  Z= 0.326
  Chirality :  0.041   0.209    897
  Planarity :  0.005   0.058    990
  Dihedral  : 13.929 176.293   1024
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.04 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 33.16 %
    Favored  : 61.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.31), residues: 661
  helix:  0.56 (0.36), residues: 207
  sheet: -1.24 (0.47), residues: 123
  loop : -2.99 (0.28), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.016   0.001   TYR A 239 
 PHE   0.014   0.001   PHE A 342 
 TRP   0.022   0.002   TRP A 366 
 HIS   0.005   0.001   HIS B 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 6046)
  covalent geometry    : angle       0.61942 /  0.33 ( 8277)
  hydrogen bonds       : bond        0.04542 /  3.11 (  206)
  hydrogen bonds       : angle       4.58405 /  3.07 (  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: 29
    poor density    : 70
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 GLU cc_start: 0.7764 (pm20) cc_final: 0.7465 (pm20)
REVERT: A  462 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6777 (ttp-170)
REVERT: B  202 PHE cc_start: 0.4394 (OUTLIER) cc_final: 0.4188 (t80)
REVERT: B  255 LEU cc_start: 0.7847 (mt) cc_final: 0.7642 (mt)
REVERT: B  352 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.6403 (p90)
  outliers start: 29
  outliers final: 19
  residues processed: 93
  average time/residue: 0.0976
  time to fit residues: 11.6365
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  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  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  202 PHE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 51 optimal weight:    0.0050
   chunk 48 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0980
   chunk 14 optimal weight:    0.0170
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.3632

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5123 r_free = 0.5123 target = 0.280034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4812 r_free = 0.4812 target = 0.237848 restraints weight = 6754.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.4792 rms_B_bonded: 3.59
r_work (final): 0.4792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6046  Z= 0.108
  Angle     :  0.564   6.895   8277  Z= 0.302
  Chirality :  0.039   0.193    897
  Planarity :  0.004   0.059    990
  Dihedral  : 13.857 179.041   1024
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 32.98 %
    Favored  : 61.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.31), residues: 661
  helix:  0.65 (0.37), residues: 207
  sheet: -1.16 (0.47), residues: 123
  loop : -2.94 (0.28), residues: 331

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   0.013   0.001   PHE A 388 
 TRP   0.014   0.001   TRP A 366 
 HIS   0.004   0.001   HIS B 215 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.11 ( 6046)
  covalent geometry    : angle       0.56439 /  0.30 ( 8277)
  hydrogen bonds       : bond        0.03899 /  2.65 (  206)
  hydrogen bonds       : angle       4.33511 /  2.89 (  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
  97 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  345 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7086 (mp0)
REVERT: A  462 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6639 (ttp-170)
REVERT: B  352 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5491 (p90)
  outliers start: 29
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0937
  time to fit residues: 10.6571
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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  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  328 LYS
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  345 GLU
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  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:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 36 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   overall best weight:    0.6980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5112 r_free = 0.5112 target = 0.278709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.235657 restraints weight = 6667.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.4770 rms_B_bonded: 3.43
r_work (final): 0.4770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6590
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6046  Z= 0.115
  Angle     :  0.587   9.516   8277  Z= 0.310
  Chirality :  0.040   0.264    897
  Planarity :  0.005   0.060    990
  Dihedral  : 13.830 179.420   1024
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 32.11 %
    Favored  : 63.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.31), residues: 661
  helix:  0.72 (0.37), residues: 208
  sheet: -1.04 (0.46), residues: 132
  loop : -3.04 (0.28), residues: 321

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   0.010   0.001   PHE A 282 
 TRP   0.016   0.001   TRP A 366 
 HIS   0.005   0.001   HIS B 215 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 ( 6046)
  covalent geometry    : angle       0.58680 /  0.31 ( 8277)
  hydrogen bonds       : bond        0.03928 /  2.69 (  206)
  hydrogen bonds       : angle       4.30715 /  2.88 (  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
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.5473 (mtt) cc_final: 0.5029 (ptt)
REVERT: A  341 ARG cc_start: 0.5152 (ptm-80) cc_final: 0.4780 (ptm-80)
REVERT: A  462 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6596 (ttp-170)
REVERT: B  352 HIS cc_start: 0.6052 (OUTLIER) cc_final: 0.5457 (p90)
  outliers start: 28
  outliers final: 22
  residues processed: 90
  average time/residue: 0.0955
  time to fit residues: 11.0576
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  : 0.167 
-------------------------------------------------------------------------------
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  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  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  376 LEU
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  215 HIS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 160 ASN
A 424 HIS
A 446 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5061 r_free = 0.5061 target = 0.271713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.228509 restraints weight = 6665.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.4698 rms_B_bonded: 3.32
r_work: 0.4343 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6046  Z= 0.202
  Angle     :  0.705   9.402   8277  Z= 0.364
  Chirality :  0.044   0.278    897
  Planarity :  0.005   0.064    990
  Dihedral  : 13.875 172.148   1024
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.86 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 32.46 %
    Favored  : 61.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.31), residues: 661
  helix:  0.67 (0.37), residues: 207
  sheet: -1.18 (0.46), residues: 133
  loop : -3.05 (0.28), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.019   0.002   TYR A 239 
 PHE   0.015   0.002   PHE A 342 
 TRP   0.032   0.002   TRP A 366 
 HIS   0.005   0.001   HIS B 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00467 /  0.20 ( 6046)
  covalent geometry    : angle       0.70501 /  0.36 ( 8277)
  hydrogen bonds       : bond        0.04887 /  3.30 (  206)
  hydrogen bonds       : angle       4.65065 /  3.06 (  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
  100 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 68
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A  446 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.4991 (t0)
REVERT: A  462 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6778 (ttp-170)
REVERT: B  171 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6325 (mp)
REVERT: B  402 MET cc_start: 0.7539 (mpp) cc_final: 0.7030 (mmp)
  outliers start: 32
  outliers final: 23
  residues processed: 93
  average time/residue: 0.0871
  time to fit residues: 10.4831
Evaluate side-chains
  94 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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  160 ASN
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  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  446 ASN
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  215 HIS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0980
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.6180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5094 r_free = 0.5094 target = 0.275994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.234146 restraints weight = 6621.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.4744 rms_B_bonded: 3.09
r_work: 0.4407 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6046  Z= 0.125
  Angle     :  0.626   8.714   8277  Z= 0.329
  Chirality :  0.041   0.236    897
  Planarity :  0.005   0.063    990
  Dihedral  : 13.865 177.030   1024
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 34.03 %
    Favored  : 62.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.31), residues: 661
  helix:  0.77 (0.37), residues: 208
  sheet: -1.15 (0.46), residues: 133
  loop : -3.05 (0.28), residues: 320

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   0.011   0.001   PHE A 342 
 TRP   0.019   0.002   TRP A 366 
 HIS   0.004   0.001   HIS B 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 6046)
  covalent geometry    : angle       0.62561 /  0.33 ( 8277)
  hydrogen bonds       : bond        0.04137 /  2.81 (  206)
  hydrogen bonds       : angle       4.47317 /  2.93 (  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
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.5892 (mtt) cc_final: 0.5310 (ptt)
REVERT: A  341 ARG cc_start: 0.5738 (ptm-80) cc_final: 0.5341 (ptm-80)
REVERT: A  345 GLU cc_start: 0.7702 (pm20) cc_final: 0.7463 (pm20)
REVERT: A  462 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6743 (ttp-170)
REVERT: B  402 MET cc_start: 0.7424 (mpp) cc_final: 0.6895 (mmp)
  outliers start: 20
  outliers final: 18
  residues processed: 84
  average time/residue: 0.0993
  time to fit residues: 10.5896
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
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  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  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  215 HIS
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
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:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 66 optimal weight:    8.9990
   chunk 43 optimal weight:    0.1980
   chunk 47 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5095 r_free = 0.5095 target = 0.276567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.236544 restraints weight = 6746.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.4774 rms_B_bonded: 3.31
r_work: 0.4410 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.4410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.1672

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     :  0.603   8.028   8277  Z= 0.318
  Chirality :  0.041   0.230    897
  Planarity :  0.004   0.063    990
  Dihedral  : 13.820 179.656   1022
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.53 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 34.38 %
    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 are not related in a simple way.
  whole: -2.00 (0.31), residues: 661
  helix:  0.92 (0.37), residues: 208
  sheet: -1.20 (0.46), residues: 132
  loop : -3.06 (0.28), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.017   0.001   TYR A 239 
 PHE   0.010   0.001   PHE B 251 
 TRP   0.014   0.001   TRP A 366 
 HIS   0.004   0.001   HIS B 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 ( 6046)
  covalent geometry    : angle       0.60339 /  0.32 ( 8277)
  hydrogen bonds       : bond        0.03905 /  2.64 (  206)
  hydrogen bonds       : angle       4.32407 /  2.86 (  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
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.5823 (mtt) cc_final: 0.5344 (ptt)
REVERT: A  341 ARG cc_start: 0.5632 (ptm-80) cc_final: 0.5252 (ptm-80)
REVERT: A  462 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6762 (ttp-170)
REVERT: B  402 MET cc_start: 0.7299 (mpp) cc_final: 0.6829 (mmp)
  outliers start: 19
  outliers final: 16
  residues processed: 82
  average time/residue: 0.0940
  time to fit residues: 9.7850
Evaluate side-chains
  85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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  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  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  215 HIS
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  345 THR
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 2 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0570
   chunk 20 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0970
   chunk 62 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.9498

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5092 r_free = 0.5092 target = 0.275965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.234954 restraints weight = 6788.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.4761 rms_B_bonded: 3.56
r_work (final): 0.4761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6576
moved from start:          0.1755

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= 0.128
  Angle     :  0.610   7.871   8277  Z= 0.320
  Chirality :  0.041   0.223    897
  Planarity :  0.004   0.060    990
  Dihedral  : 13.737 177.868   1020
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 34.38 %
    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 are not related in a simple way.
  whole: -2.00 (0.31), residues: 661
  helix:  0.92 (0.37), residues: 208
  sheet: -1.20 (0.45), residues: 132
  loop : -3.06 (0.28), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.017   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/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 6046)
  covalent geometry    : angle       0.61020 /  0.32 ( 8277)
  hydrogen bonds       : bond        0.03978 /  2.69 (  206)
  hydrogen bonds       : angle       4.35638 /  2.89 (  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
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  341 ARG cc_start: 0.5352 (ptm-80) cc_final: 0.5001 (ptm-80)
REVERT: A  462 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6726 (ttp-170)
  outliers start: 19
  outliers final: 18
  residues processed: 82
  average time/residue: 0.1032
  time to fit residues: 10.6226
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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  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  391 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain B residue  215 HIS
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  345 THR
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 13 optimal weight:    1.9990
   chunk 67 optimal weight:   20.0000
   chunk 7 optimal weight:    0.0050
   chunk 39 optimal weight:    0.0870
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    0.6576

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5115 r_free = 0.5115 target = 0.278243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4801 r_free = 0.4801 target = 0.237134 restraints weight = 6679.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.4773 rms_B_bonded: 3.03
r_work: 0.4426 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.4426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.1712

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= 0.121
  Angle     :  0.607   7.435   8277  Z= 0.323
  Chirality :  0.040   0.220    897
  Planarity :  0.004   0.057    990
  Dihedral  : 13.758 179.367   1020
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 34.21 %
    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 are not related in a simple way.
  whole: -2.00 (0.31), residues: 661
  helix:  0.93 (0.37), residues: 207
  sheet: -1.26 (0.45), residues: 132
  loop : -3.02 (0.28), residues: 322

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   0.010   0.001   PHE A 342 
 TRP   0.014   0.001   TRP A 366 
 HIS   0.004   0.001   HIS B 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 6046)
  covalent geometry    : angle       0.60716 /  0.32 ( 8277)
  hydrogen bonds       : bond        0.04096 /  2.75 (  206)
  hydrogen bonds       : angle       4.33148 /  2.91 (  553)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1427.37 seconds
wall clock time: 25 minutes 17.61 seconds (1517.61 seconds total)