# Date 2008-01-16 Time 02:10:47 PST -0800 (1200478247.19 s)
#phil __OFF__

Command line arguments: "../732.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3534
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 732

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 45.7567, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.23, per 1000 atoms: 1.14


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.7567, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.95362
Completeness in resolution range: 0.934099
Completeness with d_max=infinity: 0.931435

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   1.9536

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.7567, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.95362
Completeness in resolution range: 0.934099
Completeness with d_max=infinity: 0.931435

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.1818 [2202/2229]  1981   221  10.0%
  bin  2:  4.1818 -  3.3310 [2121/2141]  1909   212  10.0%
  bin  3:  3.3310 -  2.9134 [2089/2108]  1882   207   9.9%
  bin  4:  2.9134 -  2.6486 [2065/2095]  1854   211  10.2%
  bin  5:  2.6486 -  2.4596 [2064/2083]  1867   197   9.5%
  bin  6:  2.4596 -  2.3152 [2060/2085]  1847   213  10.3%
  bin  7:  2.3152 -  2.1996 [2032/2060]  1824   208  10.2%
  bin  8:  2.1996 -  2.1041 [2019/2055]  1818   201  10.0%
  bin  9:  2.1041 -  2.0233 [2024/2066]  1828   196   9.7%
  bin 10:  2.0233 -  1.9536 [ 913/2049]   820    93  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_732/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 29
        2.32 -     2.97: 1787
        2.97 -     3.61: 4610
        3.61 -     4.26: 9242
        4.26 -     4.90: 12827
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.718 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.740 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28490 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_732/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_732/model_refine_001.geo

CPU time processing inputs: 8.66


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 45.75675 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4910   r_free= 0.4864   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.297701                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6649 0.99   1426  158 0.4276 0.4192      6.6399      6.6814|
|  2:  4.6649 -  3.7210 0.99   1383  155 0.4226 0.3770      6.8451      6.7725|
|  3:  3.7210 -  3.2561 0.99   1347  144 0.4500 0.4292      6.6916      6.6654|
|  4:  3.2561 -  2.9608 0.99   1346  156 0.4798 0.4733      6.5496      6.5161|
|  5:  2.9608 -  2.7500 0.99   1333  150 0.5260 0.5254      6.3745      6.3861|
|  6:  2.7500 -  2.5887 0.99   1333  148 0.5197 0.5472       6.279      6.2253|
|  7:  2.5887 -  2.4596 0.99   1325  137 0.5181 0.5112      6.2443      6.1671|
|  8:  2.4596 -  2.3530 0.98   1302  154 0.5331 0.5096      6.1768      6.1947|
|  9:  2.3530 -  2.2627 0.98   1303  143 0.5327 0.5591      6.1263      6.1929|
| 10:  2.2627 -  2.1849 1.00   1329  152 0.5301 0.5069      6.0965      6.0764|
| 11:  2.1849 -  2.1167 0.98   1310  137 0.5039 0.5147      6.0288      6.0306|
| 12:  2.1167 -  2.0564 0.98   1289  147 0.5201 0.5795      5.9424      5.9821|
| 13:  2.0564 -  2.0024 0.96   1253  136 0.5591 0.5472      5.8896       5.804|
| 14:  2.0024 -  1.9536 0.27    351   42 0.5481 0.4616      5.8662      5.8481|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.6649  1426   158  0.63  40.63   0.78     0.68      94955.72|
|  2:  4.6649 -  3.7210  1383   155  0.68  36.74   0.85     0.77     117906.05|
|  3:  3.7210 -  3.2561  1347   144  0.57  45.96   0.85     0.72     121313.54|
|  4:  3.2561 -  2.9608  1346   156  0.48  53.41   0.78     0.58     108477.68|
|  5:  2.9608 -  2.7500  1333   150  0.36  63.12   0.73     0.45      91404.89|
|  6:  2.7500 -  2.5887  1333   148  0.33  65.53   0.71     0.39      78493.22|
|  7:  2.5887 -  2.4596  1325   137  0.29  68.32   0.75     0.34      71987.44|
|  8:  2.4596 -  2.3530  1302   154  0.28  69.33   0.72     0.33      64933.16|
|  9:  2.3530 -  2.2627  1303   143  0.28  69.10   0.73     0.34      59680.63|
| 10:  2.2627 -  2.1849  1329   152  0.31  67.12   0.75     0.38      51662.56|
| 11:  2.1849 -  2.1167  1310   137  0.29  68.46   0.78     0.36      50301.42|
| 12:  2.1167 -  2.0564  1289   147  0.25  71.54   0.76     0.33      47078.32|
| 13:  2.0564 -  2.0024  1253   136  0.24  72.40   0.70     0.32      41005.33|
| 14:  2.0024 -  1.9536   351    42  0.35  64.33   0.73     0.39      29902.91|
|alpha:            min =        0.32 max =            0.77 mean =         0.46|
|beta:             min =    29902.91 max =       121313.54 mean =     76526.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.65|
|phase err.(test): min =        0.00 max =           89.94 mean =        60.93|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.917527             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.748   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.612186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.138   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      709 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1516 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2658 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3954 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5144 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6570 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7771 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.441 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.317 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4955   r_free= 0.4865   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.298979                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4819   r_free= 0.4735   ksol= 0.36   Bsol= 0.93   scale= 0.981    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.00,9.98,8.07,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.292899                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.457350             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.967   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.604000              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.235   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4819      final r-factor (work) = 0.4141          |
| start r-factor (free) = 0.4735      final r-factor (free) = 0.4399          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 105.2213 = 16.46 * 0.50 * 6.2927 + 1.00 * 53.4407                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.4522 = 16.46 * 0.50 * 6.2349 + 1.00 * 0.1471                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4141      final r-factor (work) = 0.3766          |
| start r-factor (free) = 0.4399      final r-factor (free) = 0.4396          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0152 = 1.60 * 1.00 * 6.2349 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9358 = 1.60 * 1.00 * 6.1827 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.85   14.24    None  None   None       |
|    all(noH): 2823   0      0.00    80.85   14.24    None  None   None       |
|    Sol.    : 438    0      0.00    76.35   22.15    None  None   None       |
|    Mac.    : 2385   0      0.00    80.85   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.085: 1016   |   5:    40.423 -  48.508:   71        |
|      1:     8.085 -  16.169:  853   |   6:    48.508 -  56.593:   22        |
|      2:    16.169 -  24.254:  477   |   7:    56.593 -  64.677:   19        |
|      3:    24.254 -  32.339:  236   |   8:    64.677 -  72.762:    2        |
|      4:    32.339 -  40.423:  125   |   9:    72.762 -  80.847:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3766 r_free = 0.4396             target_work(ml) = 6.177         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3764 r_free = 0.4392             target_work(ml) = 6.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3764   r_free= 0.4392   ksol= 0.36   Bsol= 0.93   scale= 1.100    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.00,9.98,8.07,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.177107                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3737   r_free= 0.4341   ksol= 0.37   Bsol= 46.23   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,5.91,4.56,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.177227                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.960102              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.165  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.814688              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.935  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3737      final r-factor (work) = 0.3296          |
| start r-factor (free) = 0.4341      final r-factor (free) = 0.4094          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9210 = 9.96 * 0.50 * 6.1794 + 1.00 * 0.1471                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.5875 = 9.96 * 0.50 * 6.1244 + 1.00 * 0.0878                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3296      final r-factor (work) = 0.3171          |
| start r-factor (free) = 0.4094      final r-factor (free) = 0.3979          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0082 = 0.81 * 1.00 * 6.1244 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9780 = 0.81 * 1.00 * 6.0710 + 1.00 * 0.0320                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.50   14.23    None  None   None       |
|    all(noH): 2823   0      0.00    77.50   14.23    None  None   None       |
|    Sol.    : 438    0      0.00    74.58   24.56    None  None   None       |
|    Mac.    : 2385   0      0.00    77.50   12.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.750:  977   |   5:    38.748 -  46.497:   68        |
|      1:     7.750 -  15.499:  830   |   6:    46.497 -  54.247:   26        |
|      2:    15.499 -  23.249:  508   |   7:    54.247 -  61.997:   12        |
|      3:    23.249 -  30.998:  270   |   8:    61.997 -  69.746:    7        |
|      4:    30.998 -  38.748:  123   |   9:    69.746 -  77.496:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3171 r_free = 0.3979             target_work(ml) = 6.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3170 r_free = 0.3977             target_work(ml) = 6.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3170   r_free= 0.3977   ksol= 0.37   Bsol= 46.23   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,5.91,4.56,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.056575                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3174   r_free= 0.3959   ksol= 0.36   Bsol= 67.36   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,3.62,3.48,0.00,0.00,0.00); trace/3= 3.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.057998                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.575621             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.877  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.622188              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.272   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3174      final r-factor (work) = 0.2549          |
| start r-factor (free) = 0.3959      final r-factor (free) = 0.3274          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.2600 = 12.58 * 0.50 * 6.0708 + 1.00 * 0.0878                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6905 = 12.58 * 0.50 * 5.9763 + 1.00 * 0.1128                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2549      final r-factor (work) = 0.2250          |
| start r-factor (free) = 0.3274      final r-factor (free) = 0.3047          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7171 = 1.62 * 1.00 * 5.9763 + 1.00 * 0.0225                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4545 = 1.62 * 1.00 * 5.8168 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.94   15.43    None  None   None       |
|    all(noH): 2823   0      0.00    93.94   15.43    None  None   None       |
|    Sol.    : 438    0      0.00    93.94   37.26    None  None   None       |
|    Mac.    : 2385   0      0.00    76.05   11.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.394: 1331   |   5:    46.972 -  56.366:   88        |
|      1:     9.394 -  18.789:  706   |   6:    56.366 -  65.760:   53        |
|      2:    18.789 -  28.183:  312   |   7:    65.760 -  75.155:   16        |
|      3:    28.183 -  37.577:  160   |   8:    75.155 -  84.549:    5        |
|      4:    37.577 -  46.972:  150   |   9:    84.549 -  93.943:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2250 r_free = 0.3047             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2248 r_free = 0.3049             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2248   r_free= 0.3049   ksol= 0.36   Bsol= 67.36   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,3.62,3.48,0.00,0.00,0.00); trace/3= 3.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.775473                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2236   r_free= 0.3041   ksol= 0.34   Bsol= 63.23   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,1.88,2.78,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.772219                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.353719              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.354  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.191478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.505  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2236      final r-factor (work) = 0.1842          |
| start r-factor (free) = 0.3041      final r-factor (free) = 0.2512          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7736 = 4.35 * 0.50 * 5.8161 + 1.00 * 0.1128                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4672 = 4.35 * 0.50 * 5.6980 + 1.00 * 0.0633                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1842      final r-factor (work) = 0.1677          |
| start r-factor (free) = 0.2512      final r-factor (free) = 0.2311          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8076 = 1.19 * 1.00 * 5.6980 + 1.00 * 0.0185                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6377 = 1.19 * 1.00 * 5.5550 + 1.00 * 0.0190                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.15   15.37    None  None   None       |
|    all(noH): 2823   0      0.00    98.15   15.37    None  None   None       |
|    Sol.    : 438    0      1.57    98.15   42.41    None  None   None       |
|    Mac.    : 2385   0      0.00    89.37   10.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.815: 1538   |   5:    49.076 -  58.891:  101        |
|      1:     9.815 -  19.630:  644   |   6:    58.891 -  68.706:   69        |
|      2:    19.630 -  29.446:  190   |   7:    68.706 -  78.521:   23        |
|      3:    29.446 -  39.261:  130   |   8:    78.521 -  88.336:    7        |
|      4:    39.261 -  49.076:  117   |   9:    88.336 -  98.152:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1677 r_free = 0.2311             target_work(ml) = 5.510         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1673 r_free = 0.2308             target_work(ml) = 5.509         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1673   r_free= 0.2308   ksol= 0.34   Bsol= 63.23   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,1.88,2.78,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.508553                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1675   r_free= 0.2307   ksol= 0.32   Bsol= 52.88   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.39,1.11,2.62,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.506893                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.059080              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.873  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.516312              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.466   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1675      final r-factor (work) = 0.1424          |
| start r-factor (free) = 0.2307      final r-factor (free) = 0.2016          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5592 = 3.06 * 0.50 * 5.5546 + 1.00 * 0.0631                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3867 = 3.06 * 0.50 * 5.4429 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1424      final r-factor (work) = 0.1368          |
| start r-factor (free) = 0.2016      final r-factor (free) = 0.1923          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8297 = 0.52 * 1.00 * 5.4429 + 1.00 * 0.0195                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8054 = 0.52 * 1.00 * 5.3590 + 1.00 * 0.0385                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.69   14.91    None  None   None       |
|    all(noH): 2823   0      0.00    97.69   14.91    None  None   None       |
|    Sol.    : 438    0      2.78    97.69   42.00    None  None   None       |
|    Mac.    : 2385   0      0.00    92.77   9.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.769: 1626   |   5:    48.844 -  58.613:   95        |
|      1:     9.769 -  19.538:  600   |   6:    58.613 -  68.382:   75        |
|      2:    19.538 -  29.307:  166   |   7:    68.382 -  78.151:   21        |
|      3:    29.307 -  39.075:  120   |   8:    78.151 -  87.919:    8        |
|      4:    39.075 -  48.844:  107   |   9:    87.919 -  97.688:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1368 r_free = 0.1923             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1366 r_free = 0.1921             target_work(ml) = 5.332         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1366   r_free= 0.1921   ksol= 0.32   Bsol= 52.88   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.39,1.11,2.62,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331614                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6649 0.99   1426  158 0.1008 0.1429      5.4226      5.6558|
|  2:  4.6649 -  3.7210 0.99   1383  155 0.0952 0.1280      5.5468      5.7889|
|  3:  3.7210 -  3.2561 0.99   1347  144 0.1277 0.1805       5.633      5.9606|
|  4:  3.2561 -  2.9608 0.99   1346  156 0.1557 0.2026      5.6599      5.8053|
|  5:  2.9608 -  2.7500 0.99   1333  150 0.1655 0.2217      5.5256      5.7812|
|  6:  2.7500 -  2.5887 0.99   1333  148 0.1494 0.2275      5.3795      5.6092|
|  7:  2.5887 -  2.4596 0.99   1325  137 0.1536 0.1999      5.3369       5.493|
|  8:  2.4596 -  2.3530 0.98   1302  154 0.1512 0.2161      5.2827      5.5566|
|  9:  2.3530 -  2.2627 0.98   1303  143 0.1551 0.2317      5.2478       5.516|
| 10:  2.2627 -  2.1849 1.00   1329  152 0.1393 0.2114       5.152      5.3824|
| 11:  2.1849 -  2.1167 0.98   1310  137 0.1416 0.2218      5.1409      5.4975|
| 12:  2.1167 -  2.0564 0.98   1289  147 0.1479 0.2168       5.085      5.3169|
| 13:  2.0564 -  2.0024 0.96   1253  136 0.1449 0.1972      4.9687      5.1566|
| 14:  2.0024 -  1.9536 0.27    351   42 0.1299 0.1960      4.8454      5.1002|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.6649  1426   158  0.93  10.40   0.97     0.95       8655.96|
|  2:  4.6649 -  3.7210  1383   155  0.94   9.71   1.03     1.02      11636.79|
|  3:  3.7210 -  3.2561  1347   144  0.91  14.75   1.05     1.05      14743.13|
|  4:  3.2561 -  2.9608  1346   156  0.88  18.48   1.02     1.00      16191.55|
|  5:  2.9608 -  2.7500  1333   150  0.86  20.09   1.01     0.98      12606.68|
|  6:  2.7500 -  2.5887  1333   148  0.86  20.78   0.99     0.95      10328.72|
|  7:  2.5887 -  2.4596  1325   137  0.87  19.37   1.00     0.96       9007.68|
|  8:  2.4596 -  2.3530  1302   154  0.86  20.93   1.01     0.98       8625.71|
|  9:  2.3530 -  2.2627  1303   143  0.86  20.77   1.00     0.94       7862.88|
| 10:  2.2627 -  2.1849  1329   152  0.86  20.70   1.01     0.96       6993.50|
| 11:  2.1849 -  2.1167  1310   137  0.86  20.97   1.01     0.95       6831.69|
| 12:  2.1167 -  2.0564  1289   147  0.86  21.24   1.01     1.00       6272.78|
| 13:  2.0564 -  2.0024  1253   136  0.86  21.22   1.01     0.97       4923.39|
| 14:  2.0024 -  1.9536   351    42  0.90  17.07   1.00     0.97       3531.74|
|alpha:            min =        0.94 max =            1.05 mean =         0.98|
|beta:             min =     3531.74 max =        16191.55 mean =      9518.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.29|
|phase err.(test): min =        0.00 max =           89.83 mean =        17.51|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1917   ksol= 0.31   Bsol= 49.56   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.70,0.98,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.330153                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1917   ksol= 0.31   Bsol= 49.56   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.70,0.98,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.330153                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6649 0.99   1426  158 0.1022 0.1389      5.4088      5.6235|
|  2:  4.6649 -  3.7210 0.99   1383  155 0.0955 0.1275      5.5425      5.7919|
|  3:  3.7210 -  3.2561 0.99   1347  144 0.1280 0.1808      5.6321      5.9609|
|  4:  3.2561 -  2.9608 0.99   1346  156 0.1561 0.2031      5.6607       5.808|
|  5:  2.9608 -  2.7500 0.99   1333  150 0.1659 0.2209      5.5262      5.7789|
|  6:  2.7500 -  2.5887 0.99   1333  148 0.1492 0.2277      5.3789      5.6084|
|  7:  2.5887 -  2.4596 0.99   1325  137 0.1540 0.1996      5.3374      5.4924|
|  8:  2.4596 -  2.3530 0.98   1302  154 0.1511 0.2162      5.2827      5.5578|
|  9:  2.3530 -  2.2627 0.98   1303  143 0.1549 0.2311      5.2474      5.5135|
| 10:  2.2627 -  2.1849 1.00   1329  152 0.1393 0.2119      5.1522      5.3849|
| 11:  2.1849 -  2.1167 0.98   1310  137 0.1415 0.2216      5.1409      5.4991|
| 12:  2.1167 -  2.0564 0.98   1289  147 0.1479 0.2168      5.0854      5.3167|
| 13:  2.0564 -  2.0024 0.96   1253  136 0.1449 0.1966      4.9684      5.1553|
| 14:  2.0024 -  1.9536 0.27    351   42 0.1299 0.1954      4.8439      5.0984|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.6649  1426   158  0.93  10.01   0.97     0.95       8048.22|
|  2:  4.6649 -  3.7210  1383   155  0.94   9.46   1.03     1.02      11225.84|
|  3:  3.7210 -  3.2561  1347   144  0.91  14.63   1.05     1.05      14632.16|
|  4:  3.2561 -  2.9608  1346   156  0.88  18.49   1.02     1.00      16188.47|
|  5:  2.9608 -  2.7500  1333   150  0.86  20.06   1.01     0.98      12589.05|
|  6:  2.7500 -  2.5887  1333   148  0.86  20.76   0.99     0.94      10314.96|
|  7:  2.5887 -  2.4596  1325   137  0.87  19.35   1.00     0.96       9003.22|
|  8:  2.4596 -  2.3530  1302   154  0.86  20.95   1.00     0.97       8632.99|
|  9:  2.3530 -  2.2627  1303   143  0.86  20.77   0.99     0.93       7858.79|
| 10:  2.2627 -  2.1849  1329   152  0.86  20.72   1.01     0.96       7006.89|
| 11:  2.1849 -  2.1167  1310   137  0.86  20.99   1.00     0.94       6846.65|
| 12:  2.1167 -  2.0564  1289   147  0.86  21.26   1.01     1.00       6282.62|
| 13:  2.0564 -  2.0024  1253   136  0.86  21.21   1.00     0.96       4919.62|
| 14:  2.0024 -  1.9536   351    42  0.90  17.01   0.99     0.96       3518.49|
|alpha:            min =        0.93 max =            1.05 mean =         0.97|
|beta:             min =     3518.49 max =        16188.47 mean =      9428.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.88 mean =        18.23|
|phase err.(test): min =        0.00 max =           89.95 mean =        17.44|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    99.29   16.52    None  None   None       |
|    all(noH): 2823   0      1.60    99.29   16.52    None  None   None       |
|    Sol.    : 438    0      4.38    99.29   43.61    None  None   None       |
|    Mac.    : 2385   0      1.60    94.38   11.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.604 -  11.373: 1626   |   5:    50.448 -  60.217:   95        |
|      1:    11.373 -  21.142:  600   |   6:    60.217 -  69.986:   75        |
|      2:    21.142 -  30.910:  166   |   7:    69.986 -  79.755:   21        |
|      3:    30.910 -  40.679:  120   |   8:    79.755 -  89.523:    8        |
|      4:    40.679 -  50.448:  107   |   9:    89.523 -  99.292:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.479 - 5.738
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 339 from: 343
   mapped sites are within: 0.731 - 5.738

peak=    8.102 closest distance to " CB  VAL A 230 " =    1.506
peak=    7.576 closest distance to " O   HOH Z 268 " =    1.201
peak=    7.567 closest distance to " O   HOH Z 130 " =    2.195
peak=    6.646 closest distance to " CD2 LEU A   5 " =    1.459
peak=    6.474 closest distance to " CG  ARG A 138 " =    1.245
peak=    6.051 closest distance to " O   HOH Z 415 " =    1.553
peak=    5.970 closest distance to " O   HOH Z 387 " =    1.573
peak=    5.729 closest distance to " O   HOH Z 350 " =    1.571
peak=    5.689 closest distance to " CD1AILE A 234 " =    1.106
peak=    5.627 closest distance to " O   HOH Z  46 " =    1.201
peak=    5.626 closest distance to " O   HOH Z 105 " =    1.259
peak=    5.558 closest distance to " O   HOH Z  65 " =    1.801
peak=    5.515 closest distance to " O   HOH Z 375 " =    1.391
peak=    5.447 closest distance to " NE2 GLN A  11 " =    1.212
peak=    5.434 closest distance to " O   HOH Z 424 " =    1.707
peak=    5.347 closest distance to " O   HOH Z   9 " =    1.957
peak=    5.322 closest distance to " NH1 ARG A 138 " =    1.015
peak=    5.273 closest distance to " O   PRO A 198 " =    1.331
peak=    5.199 closest distance to " O   HOH Z 403 " =    1.507
peak=    5.175 closest distance to " O   HOH Z 111 " =    2.008
peak=    5.149 closest distance to " O   HOH Z 139 " =    1.927
peak=    5.138 closest distance to " CB  VAL A 296 " =    1.211
peak=    5.016 closest distance to " O   HOH Z 417 " =    1.929
peak=    5.014 closest distance to " CB  PRO A  54 " =    1.151
peak=    4.986 closest distance to " O   HOH Z 124 " =    1.735
peak=    4.954 closest distance to " O   HOH Z   7 " =    2.012
peak=    4.944 closest distance to " O   HOH Z  63 " =    1.809
peak=    4.916 closest distance to " O   HOH Z  24 " =    2.044
peak=    4.844 closest distance to " CB  VAL A 230 " =    1.237
peak=    4.823 closest distance to " O   HOH Z 410 " =    1.585
peak=    4.772 closest distance to " O   HOH Z 127 " =    1.228
peak=    4.770 closest distance to " O   HOH Z 222 " =    1.546
peak=    4.731 closest distance to " CG1 VAL A 296 " =    1.245
peak=    4.698 closest distance to " CG  PRO A  54 " =    1.369
peak=    4.681 closest distance to " O   HOH Z  27 " =    1.074
peak=    4.676 closest distance to " O   HOH Z 427 " =    2.230
peak=    4.635 closest distance to " O   HOH Z  59 " =    1.610
peak=    4.627 closest distance to " O   HOH Z 214 " =    1.409
peak=    4.618 closest distance to " O   HOH Z 255 " =    0.916
peak=    4.616 closest distance to " OD1 ASP A  50 " =    0.745
peak=    4.601 closest distance to " NZ BLYS A 290 " =    1.028
peak=    4.576 closest distance to " O   HOH Z 225 " =    1.764
peak=    4.531 closest distance to " O   HOH Z 418 " =    1.310
peak=    4.520 closest distance to " O   HOH Z 142 " =    1.915
peak=    4.519 closest distance to " O   HOH Z 427 " =    1.221
peak=    4.488 closest distance to " CE  MET A  93 " =    1.513
peak=    4.483 closest distance to " O   HOH Z 232 " =    2.137
peak=    4.478 closest distance to " O   HOH Z 358 " =    1.513
peak=    4.435 closest distance to " O   HOH Z 209 " =    2.450
peak=    4.417 closest distance to " O   HOH Z 126 " =    1.992
peak=    4.393 closest distance to " CB  SER A 216 " =    1.057
peak=    4.388 closest distance to " OG ASER A 258 " =    3.097
peak=    4.376 closest distance to " O   HOH Z 390 " =    1.139
peak=    4.371 closest distance to " O   HOH Z 400 " =    0.773
peak=    4.352 closest distance to " OE1 GLU A   2 " =    1.851
peak=    4.306 closest distance to " O   HOH Z 360 " =    1.171
peak=    4.304 closest distance to " CB  SER A   3 " =    1.496
peak=    4.295 closest distance to " O   HOH Z 361 " =    1.812
peak=    4.285 closest distance to " CG  LEU A   5 " =    1.196
peak=    4.281 closest distance to " CB  ASP A 124 " =    1.004
peak=    4.248 closest distance to " O   HOH Z 239 " =    1.508
peak=    4.237 closest distance to " NH2AARG A 145 " =    2.313
peak=    4.233 closest distance to " O   HOH Z 133 " =    1.805
peak=    4.232 closest distance to " O   HOH Z 257 " =    2.364
peak=    4.214 closest distance to " CA  ILE A 234 " =    1.134
peak=    4.187 closest distance to " CG  LEU A 228 " =    1.151
peak=    4.187 closest distance to " O   HOH Z 416 " =    1.325
peak=    4.181 closest distance to " O   HOH Z 112 " =    1.136
peak=    4.169 closest distance to " CG  LEU A 167 " =    1.394
peak=    4.144 closest distance to " O   HOH Z  78 " =    1.807
peak=    4.126 closest distance to " O   HOH Z 369 " =    2.165
peak=    4.125 closest distance to " CB  ARG A 275 " =    1.133
peak=    4.124 closest distance to " CD2 LEU A 228 " =    1.358
peak=    4.102 closest distance to " O   HOH Z 293 " =    1.416
peak=    4.067 closest distance to " CG2 ILE A 234 " =    1.090
peak=    4.064 closest distance to " O   HOH Z 287 " =    1.703
peak=    4.058 closest distance to " CB  LYS A 290 " =    0.981
peak=    4.057 closest distance to " CG  PRO A 280 " =    0.918
peak=    4.056 closest distance to " O   HOH Z 233 " =    1.449
peak=    4.051 closest distance to " OG  SER A 276 " =    0.959
peak=    4.035 closest distance to " CB  SER A  63 " =    1.324
peak=    4.030 closest distance to " O   HOH Z 236 " =    2.010
peak=    4.015 closest distance to " O   HOH Z 303 " =    2.168
peak=    4.015 closest distance to " CD  ARG A 138 " =    0.920
peak=    4.014 closest distance to " O   HOH Z 419 " =    2.237
peak=    4.004 closest distance to " O   HOH Z 414 " =    1.765
peak=    4.004 closest distance to " CG  PRO A 198 " =    1.362
peak=    3.972 closest distance to " CB  ALA A 114 " =    1.182
peak=    3.967 closest distance to " NH2AARG A 145 " =    1.085
peak=    3.967 closest distance to " O   HOH Z 423 " =    1.859
peak=    3.958 closest distance to " O   ASN A 285 " =    0.844
peak=    3.953 closest distance to " CG  PRO A 243 " =    1.094
peak=    3.926 closest distance to " CE3 TRP A 274 " =    1.401
peak=    3.925 closest distance to " O   HOH Z 132 " =    1.158
peak=    3.922 closest distance to " O   HOH Z 359 " =    1.286
peak=    3.921 closest distance to " CA  LEU A 222 " =    1.125
peak=    3.920 closest distance to " O   HOH Z 357 " =    1.276
peak=    3.886 closest distance to " CB  GLN A 223 " =    1.437
peak=    3.876 closest distance to " CG2 THR A 178 " =    1.327
peak=    3.868 closest distance to " O   HOH Z  43 " =    1.300
peak=    3.864 closest distance to " O   HOH Z  57 " =    1.239
peak=    3.860 closest distance to " CD  ARG A  66 " =    2.421
peak=    3.850 closest distance to " CG2 ILE A 120 " =    0.921
peak=    3.833 closest distance to " CG2 THR A 221 " =    1.204
peak=    3.830 closest distance to " O   HOH Z 380 " =    2.072
peak=    3.826 closest distance to " CA  ASN A 127 " =    1.180
peak=    3.819 closest distance to " N   GLN A 278 " =    1.039
peak=    3.812 closest distance to " O   HOH Z 371 " =    2.918
peak=    3.809 closest distance to " NE2 GLN A  58 " =    5.738
peak=    3.795 closest distance to " O   HOH Z 212 " =    1.658
peak=    3.795 closest distance to " O   HOH Z  52 " =    1.005
peak=    3.781 closest distance to " O   HOH Z  66 " =    1.145
peak=    3.780 closest distance to " O   THR A 220 " =    1.774
peak=    3.780 closest distance to " O   HOH Z 146 " =    1.611
peak=    3.771 closest distance to " CG1BVAL A 121 " =    2.298
peak=    3.758 closest distance to " O   HOH Z 384 " =    1.637
peak=    3.753 closest distance to " CB  ASN A  39 " =    0.893
peak=    3.750 closest distance to " O   HOH Z 411 " =    3.288
peak=    3.744 closest distance to " O   HOH Z 392 " =    1.641
peak=    3.743 closest distance to " O   HOH Z  77 " =    1.213
peak=    3.737 closest distance to " O   HOH Z 153 " =    3.473
peak=    3.728 closest distance to " N   TYR A  15 " =    0.983
peak=    3.724 closest distance to " O   HOH Z 371 " =    2.187
peak=    3.715 closest distance to " CB  VAL A 202 " =    1.643
peak=    3.715 closest distance to " N   GLY A 136 " =    1.190
peak=    3.713 closest distance to " O   HOH Z 426 " =    1.110
peak=    3.710 closest distance to " CB  ASN A 148 " =    1.408
peak=    3.708 closest distance to " CG1AVAL A 121 " =    0.791
peak=    3.704 closest distance to " OD1 ASP A 200 " =    1.487
peak=    3.704 closest distance to " N   VAL A 296 " =    1.774
peak=    3.702 closest distance to " NE AARG A 275 " =    1.639
peak=    3.701 closest distance to " CB  GLU A 128 " =    1.026
peak=    3.698 closest distance to " CA  ALA A 295 " =    0.936
peak=    3.695 closest distance to " NZ  LYS A 117 " =    1.243
peak=    3.688 closest distance to " CB  TRP A 266 " =    0.917
peak=    3.683 closest distance to " O   HOH Z 342 " =    1.022
peak=    3.681 closest distance to " O   HOH Z 389 " =    1.647
peak=    3.679 closest distance to " O   HOH Z  47 " =    1.773
peak=    3.677 closest distance to " C   VAL A 153 " =    1.147
peak=    3.676 closest distance to " O   HOH Z  30 " =    1.284
peak=    3.673 closest distance to " O   HOH Z  88 " =    3.410
peak=    3.666 closest distance to " O   HOH Z 363 " =    1.040
peak=    3.651 closest distance to " O   HOH Z  26 " =    1.725
peak=    3.645 closest distance to " CB  ARG A 138 " =    0.937
peak=    3.642 closest distance to " NH2 ARG A 269 " =    0.993
peak=    3.641 closest distance to " O   GLY A 302 " =    2.430
peak=    3.636 closest distance to " O   HOH Z  68 " =    2.045
peak=    3.636 closest distance to " O   HOH Z 114 " =    2.107
peak=    3.633 closest distance to " ND2BASN A 224 " =    0.956
peak=    3.630 closest distance to " CB  GLN A 183 " =    1.164
peak=    3.624 closest distance to " O   HOH Z 238 " =    1.321
peak=    3.623 closest distance to " O   HOH Z 193 " =    1.833
peak=    3.623 closest distance to " O   HOH Z 374 " =    0.993
peak=    3.620 closest distance to " O   HOH Z 298 " =    2.091
peak=    3.611 closest distance to " O   HOH Z 158 " =    2.544
peak=    3.603 closest distance to " O   HOH Z   1 " =    1.902
peak=    3.597 closest distance to " CG2 THR A 279 " =    0.982
peak=    3.594 closest distance to " O   HOH Z 405 " =    1.915
peak=    3.592 closest distance to " O   HOH Z 353 " =    1.928
peak=    3.586 closest distance to " CG  PRO A 213 " =    1.336
peak=    3.586 closest distance to " CG1 VAL A 296 " =    1.523
peak=    3.579 closest distance to " CG2 VAL A 296 " =    0.973
peak=    3.579 closest distance to " O   HOH Z  61 " =    1.812
peak=    3.577 closest distance to " O   HOH Z  58 " =    2.019
peak=    3.574 closest distance to " O   HOH Z 378 " =    1.152
peak=    3.571 closest distance to " O   HOH Z 119 " =    1.474
peak=    3.570 closest distance to " O   HOH Z  39 " =    1.483
peak=    3.568 closest distance to " O   HOH Z 211 " =    1.366
peak=    3.567 closest distance to " OE1 GLU A   2 " =    1.988
peak=    3.565 closest distance to " O   HOH Z 425 " =    1.988
peak=    3.560 closest distance to " N   CYS A 260 " =    1.154
peak=    3.557 closest distance to " O   HOH Z 217 " =    3.051
peak=    3.551 closest distance to " O   VAL A  72 " =    0.814
peak=    3.546 closest distance to " O   HOH Z 368 " =    3.119
peak=    3.546 closest distance to " O   HOH Z 353 " =    2.086
peak=    3.541 closest distance to " CG  ARG A 159 " =    0.852
peak=    3.537 closest distance to " ND2 ASN A  60 " =    3.142
peak=    3.530 closest distance to " O   HOH Z 133 " =    2.641
peak=    3.528 closest distance to " O   HOH Z 123 " =    1.109
peak=    3.528 closest distance to " O   HOH Z 356 " =    1.895
peak=    3.528 closest distance to " CA  ALA A  21 " =    0.988
peak=    3.525 closest distance to " O   HOH Z 193 " =    1.546
peak=    3.515 closest distance to " O   HOH Z 245 " =    1.283
peak=    3.512 closest distance to " CD1 ILE A  33 " =    1.831
peak=    3.504 closest distance to " O   HOH Z 248 " =    2.054
peak=    3.497 closest distance to " O   HOH Z 239 " =    1.677
peak=    3.496 closest distance to " CG BARG A 102 " =    1.991
peak=    3.494 closest distance to " CB  SER A 273 " =    1.000
peak=    3.492 closest distance to " CZ3 TRP A 266 " =    1.228
peak=    3.491 closest distance to " OD2 ASP A  50 " =    1.092
peak=    3.491 closest distance to " CD2 LEU A 167 " =    1.198
peak=    3.487 closest distance to " OE1 GLN A  77 " =    1.205
peak=    3.484 closest distance to " O   HOH Z  51 " =    1.572
peak=    3.471 closest distance to " O   HOH Z 103 " =    0.887
peak=    3.468 closest distance to " N   ARG A 156 " =    1.378
peak=    3.462 closest distance to " CD1 LEU A 228 " =    1.679
peak=    3.458 closest distance to " CG1 ILE A  33 " =    1.363
peak=    3.456 closest distance to " CB  GLU A 277 " =    0.981
peak=    3.455 closest distance to " CD  ARG A 269 " =    0.913
peak=    3.452 closest distance to " O   HOH Z   6 " =    1.991
peak=    3.452 closest distance to " C   ASN A 209 " =    1.880
peak=    3.450 closest distance to " O   HOH Z 172 " =    1.872
peak=    3.447 closest distance to " O   ALA A  71 " =    1.333
peak=    3.444 closest distance to " CB  LEU A 300 " =    0.905
peak=    3.441 closest distance to " O   HOH Z 423 " =    1.545
peak=    3.439 closest distance to " OG BSER A 258 " =    0.945
peak=    3.439 closest distance to " CB  PHE A 225 " =    1.518
peak=    3.436 closest distance to " O   HOH Z 357 " =    2.236
peak=    3.435 closest distance to " CB  TRP A 179 " =    1.448
peak=    3.435 closest distance to " N   GLN A  73 " =    1.027
peak=    3.432 closest distance to " O   HOH Z 422 " =    2.723
peak=    3.428 closest distance to " O   HOH Z 365 " =    3.060
peak=    3.420 closest distance to " OE2 GLU A  53 " =    1.901
peak=    3.418 closest distance to " O   HOH Z 167 " =    1.718
peak=    3.415 closest distance to " CD  LYS A 166 " =    1.463
peak=    3.409 closest distance to " OE1 GLN A 240 " =    1.788
peak=    3.408 closest distance to " O   HOH Z 381 " =    0.966
peak=    3.407 closest distance to " CG  GLN A 278 " =    3.967
peak=    3.403 closest distance to " O   HOH Z  20 " =    1.698
peak=    3.403 closest distance to " CE3 TRP A 150 " =    1.127
peak=    3.399 closest distance to " CA  ALA A  51 " =    1.175
peak=    3.398 closest distance to " O  BHOH Z  74 " =    1.313
peak=    3.398 closest distance to " O   HOH Z 148 " =    1.716
peak=    3.398 closest distance to " CA  ALA A 158 " =    1.134
peak=    3.397 closest distance to " O   HOH Z  49 " =    3.058
peak=    3.396 closest distance to " OE2 GLU A   2 " =    2.101
peak=    3.395 closest distance to " CA  LEU A 282 " =    1.065
peak=    3.393 closest distance to " CB  SER A  62 " =    1.125
peak=    3.390 closest distance to " O   HOH Z   7 " =    3.161
peak=    3.389 closest distance to " O   HOH Z 217 " =    1.453
peak=    3.386 closest distance to " CD BLYS A 290 " =    1.036
peak=    3.385 closest distance to " O   HOH Z 389 " =    1.295
peak=    3.382 closest distance to " O   HOH Z 180 " =    2.126
peak=    3.381 closest distance to " CB  GLU A 277 " =    3.631
peak=    3.374 closest distance to " OD2 ASP A 286 " =    2.452
peak=    3.368 closest distance to " CB  ASN A 187 " =    1.007
peak=    3.368 closest distance to " O   HOH Z  92 " =    1.159
peak=    3.360 closest distance to " O   HOH Z 368 " =    0.865
peak=    3.357 closest distance to " CB  ALA A  43 " =    0.910
peak=    3.354 closest distance to " N   GLU A   2 " =    1.328
peak=    3.354 closest distance to " O   HOH Z  55 " =    2.177
peak=    3.352 closest distance to " CE3 TRP A  85 " =    1.120
peak=    3.352 closest distance to " CB  THR A  31 " =    1.702
peak=    3.352 closest distance to " CA  ARG A  36 " =    1.043
peak=    3.343 closest distance to " O   HOH Z  91 " =    2.497
peak=    3.341 closest distance to " NH2BARG A 145 " =    1.888
peak=    3.339 closest distance to " CA  ARG A 159 " =    1.203
peak=    3.337 closest distance to " CB  ASN A 215 " =    1.578
peak=    3.337 closest distance to " CG  LYS A  76 " =    1.620
peak=    3.329 closest distance to " CE  LYS A  48 " =    1.099
peak=    3.327 closest distance to " N   PHE A 130 " =    1.203
peak=    3.326 closest distance to " CB  TRP A 150 " =    1.163
peak=    3.319 closest distance to " O   HOH Z 368 " =    1.733
peak=    3.307 closest distance to " O   HOH Z 125 " =    1.792
peak=    3.301 closest distance to " O   HOH Z 158 " =    1.044
peak=    3.299 closest distance to " O   GLN A  73 " =    0.968
peak=    3.287 closest distance to " O   HOH Z 244 " =    1.559
peak=    3.287 closest distance to " O   HOH Z 158 " =    2.904
peak=    3.282 closest distance to " O   HOH Z 279 " =    2.427
peak=    3.277 closest distance to " CB  ASN A 285 " =    0.978
peak=    3.272 closest distance to " O   HOH Z 431 " =    0.933
peak=    3.265 closest distance to " O   ILE A  20 " =    1.935
peak=    3.263 closest distance to " O   HOH Z  11 " =    1.092
peak=    3.262 closest distance to " O   HOH Z  97 " =    1.575
peak=    3.257 closest distance to " CG  GLN A  11 " =    2.187
peak=    3.254 closest distance to " O   HOH Z 128 " =    2.221
peak=    3.253 closest distance to " CB  ALA A 114 " =    1.756
peak=    3.251 closest distance to " CB  ALA A  10 " =    1.041
peak=    3.251 closest distance to " C   ASN A 301 " =    0.937
peak=    3.249 closest distance to " O   HOH Z 294 " =    1.597
peak=    3.241 closest distance to " O   HOH Z 328 " =    1.522
peak=    3.240 closest distance to " O   HOH Z 106 " =    4.021
peak=    3.238 closest distance to " O   HOH Z 184 " =    1.676
peak=    3.237 closest distance to " N   LYS A 290 " =    1.274
peak=    3.235 closest distance to " CA  PHE A 283 " =    1.321
peak=    3.235 closest distance to " O   HOH Z  88 " =    3.886
peak=    3.225 closest distance to " O   HOH Z 352 " =    1.420
peak=    3.221 closest distance to " O   HOH Z 214 " =    1.747
peak=    3.219 closest distance to " CG  GLU A   2 " =    0.998
peak=    3.218 closest distance to " CB  SER A 276 " =    1.111
peak=    3.216 closest distance to " CA  ARG A 195 " =    1.318
peak=    3.212 closest distance to " CB  ASP A 140 " =    1.023
peak=    3.209 closest distance to " CB  LEU A 228 " =    1.420
peak=    3.207 closest distance to " O   HOH Z 379 " =    1.337
peak=    3.203 closest distance to " O   HOH Z 406 " =    1.729
peak=    3.201 closest distance to " O   HOH Z 196 " =    1.257
peak=    3.200 closest distance to " O   HOH Z  22 " =    2.521
peak=    3.195 closest distance to " O   HOH Z 353 " =    1.753
peak=    3.193 closest distance to " CG  GLN A 205 " =    1.074
peak=    3.193 closest distance to " O   HOH Z 334 " =    2.008
peak=    3.192 closest distance to " CG  LYS A 119 " =    1.140
peak=    3.191 closest distance to " O   ASN A 301 " =    2.003
peak=    3.191 closest distance to " CA  ALA A 160 " =    0.998
peak=    3.189 closest distance to " O   HOH Z 272 " =    1.840
peak=    3.189 closest distance to " O   HOH Z 422 " =    0.833
peak=    3.184 closest distance to " NE2 GLN A  73 " =    1.463
peak=    3.178 closest distance to " O   HOH Z 128 " =    1.812
peak=    3.174 closest distance to " CB  ASP A  50 " =    1.261
peak=    3.171 closest distance to " CA  TYR A  30 " =    1.032
peak=    3.170 closest distance to " O   HOH Z  94 " =    1.698
peak=    3.169 closest distance to " O   HOH Z 362 " =    1.562
peak=    3.167 closest distance to " NH1AARG A 275 " =    1.013
peak=    3.166 closest distance to " O   HOH Z 364 " =    1.252
peak=    3.164 closest distance to " NE2 GLN A  58 " =    4.038
peak=    3.163 closest distance to " CB  ASN A 142 " =    0.983
peak=    3.161 closest distance to " O   HOH Z  76 " =    1.140
peak=    3.159 closest distance to " O   ALA A 165 " =    1.398
peak=    3.159 closest distance to " O   HOH Z 392 " =    1.900
peak=    3.156 closest distance to " O   HOH Z  44 " =    2.499
peak=    3.154 closest distance to " O   HOH Z 326 " =    1.840
peak=    3.152 closest distance to " CE  LYS A 119 " =    1.049
peak=    3.151 closest distance to " CA  ASN A 215 " =    1.058
peak=    3.146 closest distance to " N   ASN A 285 " =    0.740
peak=    3.141 closest distance to " OG BSER A  12 " =    0.731
peak=    3.139 closest distance to " O   HOH Z 110 " =    1.669
peak=    3.133 closest distance to " O   HOH Z 323 " =    1.696
peak=    3.128 closest distance to " NH1 ARG A  56 " =    1.216
peak=    3.125 closest distance to " OD1 ASN A 217 " =    1.687
peak=    3.122 closest distance to " O   HOH Z  95 " =    1.283
peak=    3.118 closest distance to " ND2 ASN A 249 " =    0.774
peak=    3.118 closest distance to " O   HOH Z  88 " =    2.049
peak=    3.113 closest distance to " O   HOH Z 434 " =    1.559
peak=    3.112 closest distance to " O   HOH Z 247 " =    1.248
peak=    3.110 closest distance to " O   HOH Z 215 " =    3.029
peak=    3.109 closest distance to " OG ASER A 212 " =    1.546
peak=    3.108 closest distance to " CB  ARG A  79 " =    1.170
peak=    3.105 closest distance to " O   HOH Z 106 " =    2.694
peak=    3.105 closest distance to " O   HOH Z 344 " =    1.099
peak=    3.097 closest distance to " CG2 VAL A 202 " =    1.410
peak=    3.097 closest distance to " CZ  PHE A 192 " =    0.851
peak=    3.096 closest distance to " CB  VAL A 265 " =    1.441
peak=    3.077 closest distance to " CD2 PHE A 204 " =    0.933
peak=    3.059 closest distance to " CA  ALA A 299 " =    0.927
peak=    3.057 closest distance to " CG  GLN A  58 " =    1.243
peak=    3.053 closest distance to " O   GLY A 302 " =    1.775
peak=    3.050 closest distance to " O   HOH Z 215 " =    2.046
peak=    3.038 closest distance to " O   HOH Z 112 " =    0.845
peak=    3.025 closest distance to " O   HOH Z 380 " =    1.618
peak=    3.007 closest distance to " O   HOH Z 438 " =    2.482

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.621 - 5.405
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 202
   mapped sites are within: 0.786 - 5.405

peak=   -4.701 closest distance to " CG2 VAL A 230 " =    0.825
peak=   -4.589 closest distance to " CD  ARG A 138 " =    1.246
peak=   -4.530 closest distance to " OE1 GLU A 277 " =    2.451
peak=   -4.523 closest distance to " OG BSER A 134 " =    1.626
peak=   -4.512 closest distance to " CG  MET A 105 " =    0.935
peak=   -4.484 closest distance to " O   PRO A 198 " =    1.185
peak=   -4.451 closest distance to " CD  ARG A  14 " =    3.121
peak=   -4.277 closest distance to " O   HOH Z 385 " =    0.942
peak=   -4.269 closest distance to " O   HOH Z 163 " =    1.604
peak=   -4.253 closest distance to " O   SER A 135 " =    1.591
peak=   -4.178 closest distance to " OG1 THR A 157 " =    1.703
peak=   -4.159 closest distance to " OG  SER A  97 " =    2.255
peak=   -4.097 closest distance to " CB  ASP A  27 " =    2.498
peak=   -3.979 closest distance to " O   HOH Z 415 " =    0.908
peak=   -3.969 closest distance to " O   ASP A 191 " =    1.764
peak=   -3.895 closest distance to " CD  LYS A 166 " =    2.564
peak=   -3.861 closest distance to " O   HOH Z 286 " =    1.585
peak=   -3.859 closest distance to " O   HOH Z  39 " =    0.997
peak=   -3.835 closest distance to " CG2AVAL A  41 " =    2.777
peak=   -3.829 closest distance to " O   HOH Z 313 " =    0.992
peak=   -3.799 closest distance to " O   HOH Z  95 " =    1.406
peak=   -3.795 closest distance to " O   ALA A  51 " =    1.235
peak=   -3.791 closest distance to " CB  VAL A 230 " =    0.952
peak=   -3.785 closest distance to " CB  PHE A 130 " =    1.166
peak=   -3.776 closest distance to " O   HOH Z 300 " =    1.035
peak=   -3.768 closest distance to " CA  GLY A 133 " =    2.095
peak=   -3.751 closest distance to " CD  LYS A 289 " =    2.205
peak=   -3.736 closest distance to " O   HOH Z 131 " =    3.652
peak=   -3.730 closest distance to " O   HOH Z 102 " =    1.683
peak=   -3.719 closest distance to " O   HOH Z 389 " =    2.351
peak=   -3.710 closest distance to " O   HOH Z  24 " =    1.211
peak=   -3.709 closest distance to " O   HOH Z 186 " =    1.411
peak=   -3.696 closest distance to " N   LEU A 282 " =    2.363
peak=   -3.682 closest distance to " N   PRO A 163 " =    1.299
peak=   -3.678 closest distance to " OG ASER A 134 " =    1.096
peak=   -3.647 closest distance to " CB  ASN A  39 " =    2.269
peak=   -3.641 closest distance to " CA  GLY A 203 " =    2.456
peak=   -3.639 closest distance to " O   GLN A  11 " =    1.515
peak=   -3.627 closest distance to " OG  SER A  63 " =    1.447
peak=   -3.619 closest distance to " O   HOH Z  28 " =    1.138
peak=   -3.613 closest distance to " O   HOH Z 129 " =    4.652
peak=   -3.610 closest distance to " CD2 LEU A   5 " =    0.986
peak=   -3.595 closest distance to " C   PHE A 155 " =    0.792
peak=   -3.591 closest distance to " O   ALA A  10 " =    1.601
peak=   -3.582 closest distance to " O   HOH Z 136 " =    3.078
peak=   -3.581 closest distance to " O   HOH Z 300 " =    2.333
peak=   -3.569 closest distance to " O   HOH Z 435 " =    2.358
peak=   -3.568 closest distance to " NH2AARG A 275 " =    5.405
peak=   -3.565 closest distance to " CD1 TRP A 179 " =    1.230
peak=   -3.564 closest distance to " N   VAL A  72 " =    1.981
peak=   -3.563 closest distance to " CD2 TYR A 116 " =    2.182
peak=   -3.561 closest distance to " CG  PRO A 163 " =    2.568
peak=   -3.558 closest distance to " CD2 TYR A 293 " =    1.728
peak=   -3.550 closest distance to " O   THR A 178 " =    0.981
peak=   -3.549 closest distance to " O   HOH Z 271 " =    0.914
peak=   -3.536 closest distance to " O   HOH Z 275 " =    1.819
peak=   -3.530 closest distance to " CG  TRP A 266 " =    1.800
peak=   -3.518 closest distance to " CG1 VAL A 296 " =    1.042
peak=   -3.494 closest distance to " O   HOH Z 111 " =    1.825
peak=   -3.485 closest distance to " CG  GLU A 277 " =    1.278
peak=   -3.484 closest distance to " OD2 ASP A 272 " =    1.432
peak=   -3.481 closest distance to " CD1 LEU A 222 " =    2.403
peak=   -3.476 closest distance to " CB  ALA A   9 " =    2.460
peak=   -3.474 closest distance to " CA  HIS A  86 " =    2.155
peak=   -3.467 closest distance to " CB  PRO A 243 " =    2.566
peak=   -3.466 closest distance to " O   HOH Z 431 " =    1.178
peak=   -3.443 closest distance to " OG  SER A 245 " =    1.337
peak=   -3.434 closest distance to " CG  PHE A  59 " =    1.794
peak=   -3.433 closest distance to " O   HOH Z  77 " =    1.844
peak=   -3.422 closest distance to " OD2 ASP A  50 " =    1.430
peak=   -3.420 closest distance to " CA  ASN A 127 " =    1.223
peak=   -3.418 closest distance to " O   HOH Z 274 " =    3.227
peak=   -3.417 closest distance to " O   HOH Z 198 " =    2.201
peak=   -3.416 closest distance to " CG BLYS A 290 " =    0.959
peak=   -3.411 closest distance to " O   PRO A 163 " =    1.901
peak=   -3.411 closest distance to " NH2 ARG A  79 " =    2.076
peak=   -3.409 closest distance to " O   HOH Z 353 " =    1.099
peak=   -3.406 closest distance to " OG  SER A  87 " =    1.430
peak=   -3.406 closest distance to " OG  SER A  26 " =    0.937
peak=   -3.405 closest distance to " O   HOH Z 126 " =    1.602
peak=   -3.403 closest distance to " CD1 LEU A 297 " =    2.340
peak=   -3.394 closest distance to " CE2 TYR A  30 " =    2.527
peak=   -3.394 closest distance to " O   HOH Z 298 " =    2.574
peak=   -3.394 closest distance to " N   ASP A 270 " =    1.396
peak=   -3.392 closest distance to " O   ARG A 145 " =    1.398
peak=   -3.381 closest distance to " O   SER A  22 " =    2.636
peak=   -3.377 closest distance to " CA  GLY A  35 " =    1.893
peak=   -3.376 closest distance to " O   HOH Z 275 " =    1.688
peak=   -3.371 closest distance to " O   HOH Z  76 " =    1.231
peak=   -3.369 closest distance to " CD1 TRP A  85 " =    1.044
peak=   -3.363 closest distance to " O   GLY A  80 " =    2.482
peak=   -3.362 closest distance to " O   HOH Z 350 " =    2.034
peak=   -3.357 closest distance to " O   HOH Z 132 " =    4.616
peak=   -3.357 closest distance to " O   HOH Z 216 " =    1.608
peak=   -3.356 closest distance to " CG  ARG A 138 " =    1.075
peak=   -3.354 closest distance to " NE2 GLN A  11 " =    1.389
peak=   -3.351 closest distance to " O   HOH Z 185 " =    2.107
peak=   -3.349 closest distance to " CG  ASP A  50 " =    0.983
peak=   -3.346 closest distance to " O   HOH Z 352 " =    1.651
peak=   -3.345 closest distance to " N   SER A 276 " =    1.143
peak=   -3.336 closest distance to " C   VAL A  72 " =    0.912
peak=   -3.332 closest distance to " OH  TYR A 214 " =    1.112
peak=   -3.330 closest distance to " CB  SER A 276 " =    1.740
peak=   -3.327 closest distance to " O   ASN A 301 " =    1.351
peak=   -3.321 closest distance to " OE1 GLN A  58 " =    2.880
peak=   -3.320 closest distance to " O   ALA A  84 " =    1.674
peak=   -3.308 closest distance to " CD1 ILE A 239 " =    2.388
peak=   -3.306 closest distance to " O   ILE A 106 " =    2.068
peak=   -3.303 closest distance to " CB  TYR A  68 " =    1.135
peak=   -3.302 closest distance to " CG  MET A  40 " =    2.246
peak=   -3.301 closest distance to " O   VAL A 125 " =    2.239
peak=   -3.300 closest distance to " NE2 GLN A  55 " =    1.215
peak=   -3.300 closest distance to " C   GLU A 236 " =    1.028
peak=   -3.293 closest distance to " O   HOH Z 132 " =    1.017
peak=   -3.289 closest distance to " O   TRP A 179 " =    1.741
peak=   -3.287 closest distance to " O   HOH Z 207 " =    2.074
peak=   -3.285 closest distance to " O   HOH Z 111 " =    1.138
peak=   -3.279 closest distance to " O   HOH Z 409 " =    1.913
peak=   -3.278 closest distance to " ND2 ASN A 252 " =    2.181
peak=   -3.277 closest distance to " CB  ALA A 114 " =    2.415
peak=   -3.268 closest distance to " O   HOH Z 328 " =    0.844
peak=   -3.267 closest distance to " OE2 GLU A 152 " =    2.337
peak=   -3.266 closest distance to " NE2 GLN A 223 " =    1.564
peak=   -3.266 closest distance to " CG2 ILE A 120 " =    1.418
peak=   -3.262 closest distance to " O   THR A  82 " =    1.231
peak=   -3.262 closest distance to " O   GLY A 203 " =    2.433
peak=   -3.254 closest distance to " O   THR A 220 " =    1.551
peak=   -3.253 closest distance to " CD2 LEU A 228 " =    1.127
peak=   -3.252 closest distance to " CG  PRO A 213 " =    2.218
peak=   -3.247 closest distance to " O   TRP A  70 " =    1.557
peak=   -3.247 closest distance to " O   HOH Z 413 " =    4.360
peak=   -3.247 closest distance to " O   HOH Z 337 " =    1.447
peak=   -3.247 closest distance to " O   HOH Z 376 " =    2.356
peak=   -3.246 closest distance to " CD2 LEU A 237 " =    2.466
peak=   -3.236 closest distance to " O   HOH Z 420 " =    3.114
peak=   -3.233 closest distance to " CB  ALA A   7 " =    1.923
peak=   -3.233 closest distance to " CG  ARG A 219 " =    2.377
peak=   -3.226 closest distance to " O   HOH Z 428 " =    1.508
peak=   -3.226 closest distance to " CA  GLY A  98 " =    1.869
peak=   -3.223 closest distance to " O   HOH Z 177 " =    2.430
peak=   -3.223 closest distance to " O   HOH Z  11 " =    1.947
peak=   -3.223 closest distance to " O   HOH Z 358 " =    1.598
peak=   -3.220 closest distance to " O   HOH Z 201 " =    1.751
peak=   -3.216 closest distance to " O   HOH Z 189 " =    3.242
peak=   -3.215 closest distance to " O   ALA A   1 " =    1.258
peak=   -3.215 closest distance to " NH2BARG A 102 " =    1.311
peak=   -3.212 closest distance to " O   ARG A  56 " =    2.146
peak=   -3.209 closest distance to " CD  GLN A  77 " =    1.205
peak=   -3.202 closest distance to " N   ALA A  43 " =    2.653
peak=   -3.201 closest distance to " CZ2 TRP A 274 " =    0.896
peak=   -3.200 closest distance to " CE3 TRP A 150 " =    2.416
peak=   -3.199 closest distance to " N   ALA A   1 " =    1.092
peak=   -3.192 closest distance to " CB  SER A  62 " =    5.299
peak=   -3.191 closest distance to " C   ALA A 299 " =    1.287
peak=   -3.187 closest distance to " OG  SER A  87 " =    1.582
peak=   -3.186 closest distance to " O   HOH Z 266 " =    4.873
peak=   -3.186 closest distance to " O   HOH Z 200 " =    3.613
peak=   -3.185 closest distance to " O   ILE A  49 " =    1.604
peak=   -3.185 closest distance to " O   HOH Z 369 " =    1.715
peak=   -3.180 closest distance to " O   HOH Z 231 " =    1.922
peak=   -3.179 closest distance to " O   HOH Z  54 " =    1.517
peak=   -3.178 closest distance to " O   HOH Z 268 " =    0.786
peak=   -3.175 closest distance to " CD1 ILE A  33 " =    2.258
peak=   -3.166 closest distance to " O   HOH Z 268 " =    0.963
peak=   -3.161 closest distance to " CB  ALA A 291 " =    1.992
peak=   -3.160 closest distance to " O   HOH Z 364 " =    1.030
peak=   -3.156 closest distance to " N   GLN A  58 " =    1.177
peak=   -3.152 closest distance to " C   ILE A 239 " =    1.962
peak=   -3.150 closest distance to " CG  GLN A  88 " =    0.846
peak=   -3.149 closest distance to " CD1 PHE A  59 " =    2.112
peak=   -3.147 closest distance to " CD1 TRP A 274 " =    1.122
peak=   -3.146 closest distance to " O   SER A 141 " =    1.713
peak=   -3.144 closest distance to " O   HOH Z 100 " =    1.658
peak=   -3.135 closest distance to " NE1 TRP A 177 " =    1.777
peak=   -3.135 closest distance to " O   HOH Z 235 " =    1.034
peak=   -3.133 closest distance to " O   HOH Z 140 " =    1.512
peak=   -3.129 closest distance to " O   HOH Z 108 " =    2.249
peak=   -3.126 closest distance to " O   HOH Z 387 " =    1.338
peak=   -3.122 closest distance to " CD  ARG A 139 " =    1.711
peak=   -3.121 closest distance to " O   HOH Z  52 " =    1.003
peak=   -3.117 closest distance to " C   VAL A 265 " =    0.909
peak=   -3.113 closest distance to " OE1 GLN A 223 " =    2.334
peak=   -3.113 closest distance to " O   HOH Z  60 " =    1.871
peak=   -3.094 closest distance to " OG  SER A 206 " =    1.958
peak=   -3.090 closest distance to " CA  GLY A  57 " =    2.137
peak=   -3.085 closest distance to " OD1 ASN A 249 " =    1.587
peak=   -3.082 closest distance to " O   HOH Z 298 " =    0.857
peak=   -3.081 closest distance to " C   ARG A  79 " =    2.588
peak=   -3.080 closest distance to " CB  GLN A  55 " =    1.254
peak=   -3.079 closest distance to " O   HOH Z 429 " =    1.464
peak=   -3.078 closest distance to " CB  TYR A 172 " =    2.139
peak=   -3.078 closest distance to " O   HOH Z 128 " =    2.402
peak=   -3.068 closest distance to " O   HOH Z 135 " =    1.638
peak=   -3.063 closest distance to " CB  ALA A 100 " =    2.005
peak=   -3.050 closest distance to " O   HOH Z  52 " =    2.032
peak=   -3.046 closest distance to " CB  ASN A  45 " =    2.092
peak=   -3.043 closest distance to " CZ  ARG A  66 " =    2.189
peak=   -3.043 closest distance to " CA  LEU A 143 " =    0.908
peak=   -3.035 closest distance to " O   HOH Z 414 " =    1.889

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.4910 0.4864   6.297701e+00   6.283601e+00
   1_bss:  0.4819 0.4735   6.292899e+00   6.276804e+00
   1_xyz:  0.4141 0.4399   6.219691e+00   6.250759e+00
   1_adp:  0.3766 0.4396   6.177263e+00   6.248635e+00
   1_occ:  0.3764 0.4392   6.177107e+00   6.249189e+00
   2_bss:  0.3737 0.4341   6.177227e+00   6.247726e+00
   2_xyz:  0.3296 0.4094   6.079478e+00   6.199102e+00
   2_adp:  0.3171 0.3979   6.056832e+00   6.183044e+00
   2_occ:  0.3170 0.3977   6.056575e+00   6.183112e+00
   3_bss:  0.3174 0.3959   6.057998e+00   6.182550e+00
   3_xyz:  0.2549 0.3274   5.867616e+00   6.034763e+00
   3_adp:  0.2250 0.3047   5.775827e+00   5.978084e+00
   3_occ:  0.2248 0.3049   5.775473e+00   5.978243e+00
   4_bss:  0.2236 0.3041   5.772219e+00   5.975127e+00
   4_xyz:  0.1842 0.2512   5.592063e+00   5.813988e+00
   4_adp:  0.1677 0.2311   5.510000e+00   5.737576e+00
   4_occ:  0.1673 0.2308   5.508553e+00   5.736005e+00
   5_bss:  0.1675 0.2307   5.506893e+00   5.734461e+00
   5_xyz:  0.1424 0.2016   5.372191e+00   5.619581e+00
   5_adp:  0.1368 0.1923   5.332639e+00   5.574212e+00
   5_occ:  0.1366 0.1921   5.331614e+00   5.573053e+00
   5_bss:  0.1370 0.1917   5.330153e+00   5.570712e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.357   0.925   6.995   9.978   8.070   0.000   0.000   0.000
   1_xyz:  0.357   0.925   6.995   9.978   8.070   0.000   0.000   0.000
   1_adp:  0.357   0.925   6.995   9.978   8.070   0.000   0.000   0.000
   1_occ:  0.357   0.925   6.995   9.978   8.070   0.000   0.000   0.000
   2_bss:  0.371  46.228   3.788   5.908   4.560   0.000   0.000   0.000
   2_xyz:  0.371  46.228   3.788   5.908   4.560   0.000   0.000   0.000
   2_adp:  0.371  46.228   3.788   5.908   4.560   0.000   0.000   0.000
   2_occ:  0.371  46.228   3.788   5.908   4.560   0.000   0.000   0.000
   3_bss:  0.365  67.357   2.708   3.625   3.482   0.000   0.000   0.000
   3_xyz:  0.365  67.357   2.708   3.625   3.482   0.000   0.000   0.000
   3_adp:  0.365  67.357   2.708   3.625   3.482   0.000   0.000   0.000
   3_occ:  0.365  67.357   2.708   3.625   3.482   0.000   0.000   0.000
   4_bss:  0.342  63.225   1.742   1.884   2.779   0.000   0.000   0.000
   4_xyz:  0.342  63.225   1.742   1.884   2.779   0.000   0.000   0.000
   4_adp:  0.342  63.225   1.742   1.884   2.779   0.000   0.000   0.000
   4_occ:  0.342  63.225   1.742   1.884   2.779   0.000   0.000   0.000
   5_bss:  0.324  52.884   1.391   1.112   2.616   0.000   0.000   0.000
   5_xyz:  0.324  52.884   1.391   1.112   2.616   0.000   0.000   0.000
   5_adp:  0.324  52.884   1.391   1.112   2.616   0.000   0.000   0.000
   5_occ:  0.324  52.884   1.391   1.112   2.616   0.000   0.000   0.000
   5_bss:  0.315  49.557  -0.279  -0.698   0.976   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.679 0.3851  0.4631    76525.644
   1_bss:  59.739 0.3966  0.6051    74387.078
   1_xyz:  54.285 0.4658  0.6967    64055.357
   1_adp:  53.831 0.4711  0.7554    63362.657
   1_occ:  53.939 0.4698  0.7525    63654.838
   2_bss:  53.350 0.4774  0.6824    62855.098
   2_xyz:  47.440 0.5505  0.7822    50739.905
   2_adp:  44.924 0.5823  0.8340    47522.459
   2_occ:  44.953 0.5819  0.8331    47504.077
   3_bss:  44.742 0.5845  0.7940    47225.508
   3_xyz:  34.736 0.7036  0.9332    29918.436
   3_adp:  31.256 0.7436  0.9601    25320.008
   3_occ:  31.261 0.7436  0.9597    25305.098
   4_bss:  31.125 0.7449  0.9230    25047.124
   4_xyz:  25.171 0.8085  0.9702    16374.218
   4_adp:  22.548 0.8361  0.9772    13731.607
   4_occ:  22.489 0.8367  0.9768    13639.554
   5_bss:  22.420 0.8372  0.9617    13534.494
   5_xyz:  19.471 0.8661  0.9769    10412.468
   5_adp:  18.233 0.8783  0.9769     9560.316
   5_occ:  18.209 0.8785  0.9766     9519.515
   5_bss:  18.148 0.8789  0.9729     9429.260
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3441e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3441e+01
   1_xyz:   1.703  0.013  0.106 18.408  0.007  4.105   1.4714e-01
   1_adp:   1.703  0.013  0.106 18.408  0.007  4.105   1.4714e-01
   1_occ:   1.703  0.013  0.106 18.408  0.007  4.105   1.4714e-01
   2_bss:   1.703  0.013  0.106 18.408  0.007  4.105   1.4714e-01
   2_xyz:   1.156  0.008  0.078 16.422  0.005  4.105   8.7816e-02
   2_adp:   1.156  0.008  0.078 16.422  0.005  4.105   8.7816e-02
   2_occ:   1.156  0.008  0.078 16.422  0.005  4.105   8.7816e-02
   3_bss:   1.156  0.008  0.078 16.422  0.005  4.105   8.7816e-02
   3_xyz:   1.369  0.010  0.097 16.948  0.005  4.104   1.1281e-01
   3_adp:   1.369  0.010  0.097 16.948  0.005  4.104   1.1281e-01
   3_occ:   1.369  0.010  0.097 16.948  0.005  4.104   1.1281e-01
   4_bss:   1.369  0.010  0.097 16.948  0.005  4.104   1.1281e-01
   4_xyz:   0.998  0.007  0.072 15.601  0.004  4.115   6.3335e-02
   4_adp:   0.998  0.007  0.072 15.601  0.004  4.115   6.3335e-02
   4_occ:   0.998  0.007  0.072 15.601  0.004  4.115   6.3335e-02
   5_bss:   0.998  0.007  0.072 15.601  0.004  4.115   6.3335e-02
   5_xyz:   0.997  0.007  0.073 15.429  0.003  4.116   6.1636e-02
   5_adp:   0.997  0.007  0.073 15.429  0.003  4.116   6.1636e-02
   5_occ:   0.997  0.007  0.073 15.429  0.003  4.116   6.1636e-02
   5_bss:   0.997  0.007  0.073 15.429  0.003  4.116   6.1636e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9243e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9243e+00
   1_xyz:  13.058  0.192  0.407 85.734  0.034  2.131   1.0036e-01
   1_adp:  13.058  0.192  0.407 85.734  0.034  2.131   1.0036e-01
   1_occ:  13.058  0.192  0.407 85.734  0.034  2.131   1.0036e-01
   2_bss:  13.058  0.192  0.407 85.734  0.034  2.131   1.0036e-01
   2_xyz:   7.499  0.095  0.326 77.687  0.051  1.925   7.3451e-02
   2_adp:   7.499  0.095  0.326 77.687  0.051  1.925   7.3451e-02
   2_occ:   7.499  0.095  0.326 77.687  0.051  1.925   7.3451e-02
   3_bss:   7.499  0.095  0.326 77.687  0.051  1.925   7.3451e-02
   3_xyz:   7.474  0.061  0.338 85.973  0.034  1.999   9.9369e-02
   3_adp:   7.474  0.061  0.338 85.973  0.034  1.999   9.9369e-02
   3_occ:   7.474  0.061  0.338 85.973  0.034  1.999   9.9369e-02
   4_bss:   7.474  0.061  0.338 85.973  0.034  1.999   9.9369e-02
   4_xyz:   6.684  0.055  0.241 83.636  0.023  2.335   5.1869e-02
   4_adp:   6.684  0.055  0.241 83.636  0.023  2.335   5.1869e-02
   4_occ:   6.684  0.055  0.241 83.636  0.023  2.335   5.1869e-02
   5_bss:   6.684  0.055  0.241 83.636  0.023  2.335   5.1869e-02
   5_xyz:   7.096  0.048  0.291 81.029  0.028  2.322   4.4837e-02
   5_adp:   7.096  0.048  0.291 81.029  0.028  2.322   4.4837e-02
   5_occ:   7.096  0.048  0.291 81.029  0.028  2.322   4.4837e-02
   5_bss:   7.096  0.048  0.291 81.029  0.028  2.322   4.4837e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  80.85   0.00  14.24  80.85   0.00  12.79  76.35   0.00  22.15
   1_occ:  80.85   0.00  14.24  80.85   0.00  12.79  76.35   0.00  22.15
   2_bss:  80.85   0.00  14.24  80.85   0.00  12.79  76.35   0.00  22.15
   2_xyz:  80.85   0.00  14.24  80.85   0.00  12.79  76.35   0.00  22.15
   2_adp:  77.50   0.00  14.23  77.50   0.00  12.34  74.58   0.00  24.56
   2_occ:  77.50   0.00  14.23  77.50   0.00  12.34  74.58   0.00  24.56
   3_bss:  77.50   0.00  14.23  77.50   0.00  12.34  74.58   0.00  24.56
   3_xyz:  77.50   0.00  14.23  77.50   0.00  12.34  74.58   0.00  24.56
   3_adp:  93.94   0.00  15.43  76.05   0.00  11.42  93.94   0.00  37.26
   3_occ:  93.94   0.00  15.43  76.05   0.00  11.42  93.94   0.00  37.26
   4_bss:  93.94   0.00  15.43  76.05   0.00  11.42  93.94   0.00  37.26
   4_xyz:  93.94   0.00  15.43  76.05   0.00  11.42  93.94   0.00  37.26
   4_adp:  98.15   0.00  15.37  89.37   0.00  10.40  98.15   1.57  42.41
   4_occ:  98.15   0.00  15.37  89.37   0.00  10.40  98.15   1.57  42.41
   5_bss:  98.15   0.00  15.37  89.37   0.00  10.40  98.15   1.57  42.41
   5_xyz:  98.15   0.00  15.37  89.37   0.00  10.40  98.15   1.57  42.41
   5_adp:  97.69   0.00  14.91  92.77   0.00   9.94  97.69   2.78  42.00
   5_occ:  97.69   0.00  14.91  92.77   0.00   9.94  97.69   2.78  42.00
   5_bss:  99.29   1.60  16.52  94.38   1.60  11.54  99.29   4.38  43.61
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.272    0.016    0.412
   1_adp:    1.272    0.016    0.412
   1_occ:    1.272    0.016    0.412
   2_bss:    1.272    0.016    0.412
   2_xyz:    1.558    0.041    0.553
   2_adp:    1.558    0.041    0.553
   2_occ:    1.558    0.041    0.553
   3_bss:    1.558    0.041    0.553
   3_xyz:    1.726    0.020    0.733
   3_adp:    1.726    0.020    0.733
   3_occ:    1.726    0.020    0.733
   4_bss:    1.726    0.020    0.733
   4_xyz:    2.005    0.050    0.807
   4_adp:    2.005    0.050    0.807
   4_occ:    2.005    0.050    0.807
   5_bss:    2.005    0.050    0.807
   5_xyz:    2.054    0.061    0.853
   5_adp:    2.054    0.061    0.853
   5_occ:    2.054    0.061    0.853
   5_bss:    2.054    0.061    0.853
------------------------------------------------------------------------

CPU time actual refinement: 365.21


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_732/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_732/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_732/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_732/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_732/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 365.07 
  Macro-tasks:
    bulk solvent and scale       = 43.64  
    individual site refinement   = 159.70 
    weights calculation          = 32.18  
    collect and process          = 6.29   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 241.90 
  Micro-tasks:
    mask                            = 2.87   
    f_calc                          = 118.71 
    alpha_beta                      = 8.37   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 124.68 
    fmodel                         = 7.45   
    r_factors                      = 0.18   
    phase_errors                   = 10.61  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 274.32 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.057 micro seconds
Total CPU time: 6.30 minutes
from_scatterers_fft:    655 calls, 118.37 s
gradients_fft:          600 calls, 113.02 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 02:17:05 PST -0800 (1200478625.74 s)
Start R-work = 0.4910, R-free = 0.4864 (no bulk solvent and anisotropic scale)
Final R-work = 0.1519, R-free = 0.2060 (no bulk solvent and anisotropic scale)

Start R-work = 0.4819, R-free = 0.4735
Final R-work = 0.1370, R-free = 0.1917