# Date 2008-01-16 Time 00:27:21 PST -0800 (1200472041.94 s)
#phil __OFF__

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

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29219
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 10

-------------------------------------------------------------------------------
  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: (68.4938, 45.7567, 88.5498, 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: 3.24, per 1000 atoms: 1.15


================================== 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: (68.4938, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8764 1.95047
Completeness in resolution range: 0.93943
Completeness with d_max=infinity: 0.936601

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8764
                             d_min =   1.9505

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: (68.4938, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8764 1.95047
Completeness in resolution range: 0.93943
Completeness with d_max=infinity: 0.936601

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8768 -  4.1741 [2190/2214]  1967   223  10.2%
  bin  2:  4.1741 -  3.3253 [2107/2127]  1900   207   9.8%
  bin  3:  3.3253 -  2.9085 [2094/2113]  1889   205   9.8%
  bin  4:  2.9085 -  2.6442 [2038/2068]  1824   214  10.5%
  bin  5:  2.6442 -  2.4556 [2053/2072]  1844   209  10.2%
  bin  6:  2.4556 -  2.3114 [2051/2076]  1852   199   9.7%
  bin  7:  2.3114 -  2.1960 [2004/2032]  1809   195   9.7%
  bin  8:  2.1960 -  2.1007 [2032/2068]  1829   203  10.0%
  bin  9:  2.1007 -  2.0200 [1930/2036]  1736   194  10.1%
  bin 10:  2.0200 -  1.9505 [1090/2046]   980   110  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_10/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: 0.13 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:
        0.91 -     1.71: 13
        1.71 -     2.51: 105
        2.51 -     3.31: 3845
        3.31 -     4.10: 9632
        4.10 -     4.90: 15309
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " NH1 ARG A  24 " - " O   GLY A  91 "  0.914 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.005 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 169 " - " O   HOH Z  43 "  1.005 3.040 -x+1,y-1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.059 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  94 " - " NH1BARG A 145 "  1.311 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28899 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_10/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_10/model_refine_001.geo

CPU time processing inputs: 11.25


============================ 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 = 68.49375 45.75675 88.54975 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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5341   r_free= 0.5375   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:   1.09 A                  |
| x-ray target function (ml) for work reflections: 6.321547                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8768 -  4.6559 0.99   1424  155 0.4603 0.4676      6.6996      6.7157|
|  2:  4.6559 -  3.7145 0.99   1367  156 0.4935 0.5316      6.8922      6.9368|
|  3:  3.7145 -  3.2505 0.99   1341  150 0.5263 0.4974      6.7577      6.7721|
|  4:  3.2505 -  2.9559 0.99   1332  145 0.5448 0.5336      6.5829      6.5469|
|  5:  2.9559 -  2.7454 0.99   1328  150 0.5639 0.5601      6.3966      6.4622|
|  6:  2.7454 -  2.5844 0.99   1336  145 0.5619 0.5395      6.3126       6.212|
|  7:  2.5844 -  2.4556 0.99   1296  157 0.5618 0.5374      6.2569      6.1654|
|  8:  2.4556 -  2.3491 0.98   1330  140 0.5681 0.5510       6.186      6.2047|
|  9:  2.3491 -  2.2590 0.98   1284  141 0.5419 0.5845      6.1251      6.2172|
| 10:  2.2590 -  2.1813 1.00   1331  144 0.5497 0.5823      6.1085      6.1163|
| 11:  2.1813 -  2.1133 0.98   1266  146 0.5472 0.5585      6.0276      6.0317|
| 12:  2.1133 -  2.0531 0.98   1306  136 0.5515 0.5322      5.9653      6.0088|
| 13:  2.0531 -  1.9991 0.86   1123  127 0.5515 0.5623      5.9113      5.8269|
| 14:  1.9991 -  1.9505 0.44    566   67 0.5591 0.5530      5.8952      5.8145|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8768 -  4.6559  1424   155  0.59  43.41   0.75     0.65     107933.39|
|  2:  4.6559 -  3.7145  1367   156  0.52  50.31   0.82     0.59     180435.15|
|  3:  3.7145 -  3.2505  1341   150  0.35  63.39   0.79     0.47     190598.51|
|  4:  3.2505 -  2.9559  1332   145  0.22  73.73   0.74     0.30     166446.91|
|  5:  2.9559 -  2.7454  1328   150  0.17  77.20   0.69     0.23     113934.42|
|  6:  2.7454 -  2.5844  1336   145  0.16  77.97   0.69     0.20      93414.01|
|  7:  2.5844 -  2.4556  1296   157  0.15  78.45   0.73     0.19      79529.77|
|  8:  2.4556 -  2.3491  1330   140  0.15  78.86   0.71     0.18      71037.22|
|  9:  2.3491 -  2.2590  1284   141  0.12  80.75   0.72     0.16      67204.55|
| 10:  2.2590 -  2.1813  1331   144  0.13  80.15   0.73     0.16      58413.60|
| 11:  2.1813 -  2.1133  1266   146  0.09  83.04   0.74     0.13      59707.73|
| 12:  2.1133 -  2.0531  1306   136  0.12  81.22   0.74     0.16      51568.66|
| 13:  2.0531 -  1.9991  1123   127  0.16  78.18   0.73     0.22      44365.47|
| 14:  1.9991 -  1.9505   566    67  0.31  66.96   0.72     0.35      32220.54|
|alpha:            min =        0.13 max =            0.65 mean =         0.29|
|beta:             min =    32220.54 max =       190598.51 mean =     97920.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.23|
|phase err.(work): min =        0.00 max =           90.00 mean =        72.28|
|phase err.(test): min =        0.00 max =           89.98 mean =        72.59|
|-----------------------------------------------------------------------------|

============================== 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 = 43.401245             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.999   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.648058              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.451   (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 |  1.124 -  1.502:       11 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.502 -  1.879:       37 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.879 -  2.257:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.257 -  2.635:      668 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.635 -  3.012:     1457 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.012 -  3.390:     2654 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.390 -  3.767:     4010 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.767 -  4.145:     5218 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.145 -  4.522:     6744 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.522 -  4.900:     8053 |
|-----------------------------------------------------------------------------|
|-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 |       52.833 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  1.124 |       3.832 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    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 = 11.374)------------------------------------------|
|    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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5377   r_free= 0.5390   ksol= 0.00   Bsol= 0.00   scale= 0.729    |
|                                                                             |
| 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:   1.07 A                  |
| x-ray target function (ml) for work reflections: 6.321551                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5276   r_free= 0.5304   ksol= 0.37   Bsol= 20.00   scale= 0.911   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.12,6.48,8.92,0.00,0.00,0.00); trace/3= 6.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.06 A                  |
| x-ray target function (ml) for work reflections: 6.319539                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 32.475883             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 88.157   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.161758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.445   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5276      final r-factor (work) = 0.4869          |
| start r-factor (free) = 0.5304      final r-factor (free) = 0.5207          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 155.4167 = 32.48 * 0.50 * 6.3175 + 1.00 * 52.8332                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 102.3732 = 32.48 * 0.50 * 6.2936 + 1.00 * 0.1781                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4869      final r-factor (work) = 0.4534          |
| start r-factor (free) = 0.5207      final r-factor (free) = 0.5121          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.9132 = 3.16 * 1.00 * 6.2936 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.8484 = 3.16 * 1.00 * 6.2695 + 1.00 * 0.0257                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.94   18.71    None  None   None       |
|    all(noH): 2823   0      0.00    91.94   18.71    None  None   None       |
|    Sol.    : 438    0      0.00    91.94   22.16    None  None   None       |
|    Mac.    : 2385   0      0.00    70.68   18.08    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 -   9.194:  751   |   5:    45.969 -  55.163:   70        |
|      1:     9.194 -  18.388:  805   |   6:    55.163 -  64.357:   34        |
|      2:    18.388 -  27.582:  603   |   7:    64.357 -  73.551:    8        |
|      3:    27.582 -  36.775:  370   |   8:    73.551 -  82.745:    0        |
|      4:    36.775 -  45.969:  180   |   9:    82.745 -  91.938:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4534 r_free = 0.5121             target_work(ml) = 6.266         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4530 r_free = 0.5132             target_work(ml) = 6.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4530   r_free= 0.5132   ksol= 0.37   Bsol= 20.00   scale= 1.082   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.12,6.48,8.92,0.00,0.00,0.00); trace/3= 6.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.99 A                  |
| x-ray target function (ml) for work reflections: 6.265096                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4533   r_free= 0.5128   ksol= 0.37   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.94,3.95,6.22,0.00,0.00,0.00); trace/3= 4.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.00 A                  |
| x-ray target function (ml) for work reflections: 6.266388                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 22.851337             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.020  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.380905              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.622  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4533      final r-factor (work) = 0.4192          |
| start r-factor (free) = 0.5128      final r-factor (free) = 0.4975          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.7994 = 22.85 * 0.50 * 6.2685 + 1.00 * 0.1781                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.4173 = 22.85 * 0.50 * 6.2402 + 1.00 * 0.1189                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4192      final r-factor (work) = 0.4142          |
| start r-factor (free) = 0.4975      final r-factor (free) = 0.4959          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6436 = 1.38 * 1.00 * 6.2402 + 1.00 * 0.0265                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5993 = 1.38 * 1.00 * 6.2167 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.88   18.64    None  None   None       |
|    all(noH): 2823   0      0.00    92.88   18.64    None  None   None       |
|    Sol.    : 438    0      0.00    89.82   21.40    None  None   None       |
|    Mac.    : 2385   0      0.00    92.88   18.13    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 -   9.288:  657   |   5:    46.439 -  55.727:   39        |
|      1:     9.288 -  18.576:  910   |   6:    55.727 -  65.015:   18        |
|      2:    18.576 -  27.863:  705   |   7:    65.015 -  74.303:    5        |
|      3:    27.863 -  37.151:  349   |   8:    74.303 -  83.590:    0        |
|      4:    37.151 -  46.439:  136   |   9:    83.590 -  92.878:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4142 r_free = 0.4959             target_work(ml) = 6.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4141 r_free = 0.4961             target_work(ml) = 6.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4141   r_free= 0.4961   ksol= 0.37   Bsol= 50.00   scale= 1.067   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.94,3.95,6.22,0.00,0.00,0.00); trace/3= 4.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.215600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4147   r_free= 0.4961   ksol= 0.35   Bsol= 50.00   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,2.63,4.89,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.217709                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.393299             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.876  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.400003              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.533  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4147      final r-factor (work) = 0.3904          |
| start r-factor (free) = 0.4961      final r-factor (free) = 0.4668          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.8611 = 14.39 * 0.50 * 6.2171 + 1.00 * 0.1189                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.7164 = 14.39 * 0.50 * 6.2010 + 1.00 * 0.0903                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3904      final r-factor (work) = 0.3654          |
| start r-factor (free) = 0.4668      final r-factor (free) = 0.4727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 39.7010 = 6.40 * 1.00 * 6.2010 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 39.4383 = 6.40 * 1.00 * 6.1546 + 1.00 * 0.0491                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.14  22.84    None  None   None       |
|    all(noH): 2823   0      0.00    113.14  22.84    None  None   None       |
|    Sol.    : 438    0      0.00    113.14  28.14    None  None   None       |
|    Mac.    : 2385   0      0.00    111.69  21.87    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 -  11.314: 1057   |   5:    56.572 -  67.886:  123        |
|      1:    11.314 -  22.629:  614   |   6:    67.886 -  79.200:   58        |
|      2:    22.629 -  33.943:  433   |   7:    79.200 -  90.515:   33        |
|      3:    33.943 -  45.257:  276   |   8:    90.515 - 101.829:   14        |
|      4:    45.257 -  56.572:  212   |   9:   101.829 - 113.143:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3654 r_free = 0.4727             target_work(ml) = 6.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3652 r_free = 0.4727             target_work(ml) = 6.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3652   r_free= 0.4727   ksol= 0.35   Bsol= 50.00   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,2.63,4.89,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.163506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3652   r_free= 0.4729   ksol= 0.36   Bsol= 69.55   scale= 1.094   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,4.39,6.38,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.164339                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.222655             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.356  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.270190              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.268  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3652      final r-factor (work) = 0.3450          |
| start r-factor (free) = 0.4729      final r-factor (free) = 0.4534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.7337 = 12.22 * 0.50 * 6.1596 + 1.00 * 0.0904                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6581 = 12.22 * 0.50 * 6.1488 + 1.00 * 0.0807                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3450      final r-factor (work) = 0.3478          |
| start r-factor (free) = 0.4534      final r-factor (free) = 0.4343          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8604 = 1.27 * 1.00 * 6.1488 + 1.00 * 0.0503                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8086 = 1.27 * 1.00 * 6.1296 + 1.00 * 0.0227                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.17  17.39    None  None   None       |
|    all(noH): 2823   0      0.00    103.17  17.39    None  None   None       |
|    Sol.    : 438    0      0.00    103.17  24.71    None  None   None       |
|    Mac.    : 2385   0      0.00    93.22   16.05    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 -  10.317: 1047   |   5:    51.583 -  61.900:   40        |
|      1:    10.317 -  20.633:  854   |   6:    61.900 -  72.216:   13        |
|      2:    20.633 -  30.950:  512   |   7:    72.216 -  82.533:    7        |
|      3:    30.950 -  41.266:  218   |   8:    82.533 -  92.849:    6        |
|      4:    41.266 -  51.583:  123   |   9:    92.849 - 103.166:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3478 r_free = 0.4343             target_work(ml) = 6.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3478 r_free = 0.4342             target_work(ml) = 6.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3478   r_free= 0.4342   ksol= 0.36   Bsol= 69.55   scale= 1.077   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,4.39,6.38,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.109586                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3477   r_free= 0.4337   ksol= 0.35   Bsol= 69.55   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,3.45,5.30,0.00,0.00,0.00); trace/3= 3.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.108881                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.870698             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.828  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.928368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.267   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3477      final r-factor (work) = 0.3004          |
| start r-factor (free) = 0.4337      final r-factor (free) = 0.3895          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.7114 = 15.87 * 0.50 * 6.1284 + 1.00 * 0.0807                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.2450 = 15.87 * 0.50 * 6.0651 + 1.00 * 0.1164                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3004      final r-factor (work) = 0.2737          |
| start r-factor (free) = 0.3895      final r-factor (free) = 0.3659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7147 = 1.93 * 1.00 * 6.0651 + 1.00 * 0.0190                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5193 = 1.93 * 1.00 * 5.9621 + 1.00 * 0.0222                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.14  17.20    None  None   None       |
|    all(noH): 2823   0      0.00    100.14  17.20    None  None   None       |
|    Sol.    : 438    0      0.00    99.95   33.87    None  None   None       |
|    Mac.    : 2385   0      0.00    100.14  14.13    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 -  10.014: 1184   |   5:    50.072 -  60.086:   61        |
|      1:    10.014 -  20.029:  732   |   6:    60.086 -  70.101:   40        |
|      2:    20.029 -  30.043:  414   |   7:    70.101 -  80.115:   13        |
|      3:    30.043 -  40.058:  233   |   8:    80.115 -  90.130:    7        |
|      4:    40.058 -  50.072:  132   |   9:    90.130 - 100.144:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2737 r_free = 0.3659             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2733 r_free = 0.3655             target_work(ml) = 5.933         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2733   r_free= 0.3655   ksol= 0.35   Bsol= 69.55   scale= 1.071   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,3.45,5.30,0.00,0.00,0.00); trace/3= 3.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.933387                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8768 -  4.6559 0.99   1424  155 0.1339 0.2418      5.8458      6.1527|
|  2:  4.6559 -  3.7145 0.99   1367  156 0.1664 0.3004      6.1424       6.557|
|  3:  3.7145 -  3.2505 0.99   1341  150 0.2710 0.3578      6.3235      6.5295|
|  4:  3.2505 -  2.9559 0.99   1332  145 0.3051 0.4039       6.233      6.3932|
|  5:  2.9559 -  2.7454 0.99   1328  150 0.3202 0.3508      6.0814       6.214|
|  6:  2.7454 -  2.5844 0.99   1336  145 0.3025 0.4109      5.9676      6.0681|
|  7:  2.5844 -  2.4556 0.99   1296  157 0.2983 0.3917      5.9426       6.067|
|  8:  2.4556 -  2.3491 0.98   1330  140 0.3281 0.4088      5.9327      6.0747|
|  9:  2.3491 -  2.2590 0.98   1284  141 0.3244 0.3954      5.8406      6.0122|
| 10:  2.2590 -  2.1813 1.00   1331  144 0.3208 0.4162      5.7939      5.9493|
| 11:  2.1813 -  2.1133 0.98   1266  146 0.3192 0.4302      5.7379      5.9295|
| 12:  2.1133 -  2.0531 0.98   1306  136 0.3376 0.4123      5.7195       5.889|
| 13:  2.0531 -  1.9991 0.86   1123  127 0.3336 0.3772      5.6615      5.6655|
| 14:  1.9991 -  1.9505 0.44    566   67 0.2954 0.4475      5.5811      5.6994|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8768 -  4.6559  1424   155  0.84  21.14   0.99     0.95      27652.79|
|  2:  4.6559 -  3.7145  1367   156  0.82  23.65   1.10     1.05      49078.72|
|  3:  3.7145 -  3.2505  1341   150  0.70  35.39   1.12     1.04      73569.07|
|  4:  3.2505 -  2.9559  1332   145  0.65  39.26   1.07     0.94      63042.87|
|  5:  2.9559 -  2.7454  1328   150  0.60  43.41   1.08     0.91      49855.91|
|  6:  2.7454 -  2.5844  1336   145  0.61  42.83   1.02     0.80      38079.45|
|  7:  2.5844 -  2.4556  1296   157  0.59  44.54   1.07     0.82      38140.27|
|  8:  2.4556 -  2.3491  1330   140  0.58  45.80   1.10     0.90      38407.29|
|  9:  2.3491 -  2.2590  1284   141  0.62  42.59   1.06     0.83      28324.38|
| 10:  2.2590 -  2.1813  1331   144  0.61  43.48   1.11     0.92      27160.59|
| 11:  2.1813 -  2.1133  1266   146  0.60  43.87   1.14     0.94      25837.50|
| 12:  2.1133 -  2.0531  1306   136  0.56  47.36   1.15     0.92      26284.99|
| 13:  2.0531 -  1.9991  1123   127  0.57  46.79   1.12     0.86      21906.95|
| 14:  1.9991 -  1.9505   566    67  0.63  42.09   1.09     0.85      17908.01|
|alpha:            min =        0.80 max =            1.05 mean =         0.91|
|beta:             min =    17908.01 max =        73569.07 mean =     38626.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.99 mean =        39.82|
|phase err.(test): min =        0.00 max =           89.16 mean =        38.67|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2732   r_free= 0.3637   ksol= 0.32   Bsol= 65.55   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-0.47,1.63,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.931331                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2732   r_free= 0.3637   ksol= 0.32   Bsol= 65.55   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-0.47,1.63,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.931331                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8768 -  4.6559 0.99   1424  155 0.1381 0.2307      5.8311      6.1294|
|  2:  4.6559 -  3.7145 0.99   1367  156 0.1671 0.3014       6.133      6.5694|
|  3:  3.7145 -  3.2505 0.99   1341  150 0.2705 0.3562      6.3236       6.527|
|  4:  3.2505 -  2.9559 0.99   1332  145 0.3053 0.4042      6.2329      6.3947|
|  5:  2.9559 -  2.7454 0.99   1328  150 0.3201 0.3507      6.0812      6.2136|
|  6:  2.7454 -  2.5844 0.99   1336  145 0.3026 0.4100      5.9664      6.0676|
|  7:  2.5844 -  2.4556 0.99   1296  157 0.2983 0.3921      5.9422      6.0674|
|  8:  2.4556 -  2.3491 0.98   1330  140 0.3282 0.4092      5.9331      6.0756|
|  9:  2.3491 -  2.2590 0.98   1284  141 0.3245 0.3953      5.8407      6.0116|
| 10:  2.2590 -  2.1813 1.00   1331  144 0.3207 0.4165      5.7938      5.9496|
| 11:  2.1813 -  2.1133 0.98   1266  146 0.3191 0.4309      5.7378      5.9302|
| 12:  2.1133 -  2.0531 0.98   1306  136 0.3375 0.4121      5.7192      5.8888|
| 13:  2.0531 -  1.9991 0.86   1123  127 0.3334 0.3772      5.6614      5.6657|
| 14:  1.9991 -  1.9505 0.44    566   67 0.2955 0.4478       5.581         5.7|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8768 -  4.6559  1424   155  0.84  20.58   0.98     0.95      25862.68|
|  2:  4.6559 -  3.7145  1367   156  0.83  23.17   1.08     1.04      47167.69|
|  3:  3.7145 -  3.2505  1341   150  0.70  35.36   1.09     1.01      73694.20|
|  4:  3.2505 -  2.9559  1332   145  0.65  39.14   1.03     0.91      62877.14|
|  5:  2.9559 -  2.7454  1328   150  0.60  43.35   1.03     0.87      49820.64|
|  6:  2.7454 -  2.5844  1336   145  0.61  42.75   0.98     0.76      38032.28|
|  7:  2.5844 -  2.4556  1296   157  0.59  44.50   1.01     0.78      38139.12|
|  8:  2.4556 -  2.3491  1330   140  0.58  45.80   1.04     0.85      38478.89|
|  9:  2.3491 -  2.2590  1284   141  0.62  42.60   0.99     0.78      28385.42|
| 10:  2.2590 -  2.1813  1331   144  0.61  43.45   1.03     0.86      27184.90|
| 11:  2.1813 -  2.1133  1266   146  0.60  43.83   1.05     0.87      25856.46|
| 12:  2.1133 -  2.0531  1306   136  0.56  47.30   1.06     0.86      26273.38|
| 13:  2.0531 -  1.9991  1123   127  0.57  46.76   1.03     0.79      21931.98|
| 14:  1.9991 -  1.9505   566    67  0.63  42.08   1.00     0.78      17930.93|
|alpha:            min =        0.76 max =            1.04 mean =         0.87|
|beta:             min =    17930.93 max =        73694.20 mean =     38339.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.65|
|phase err.(work): min =        0.00 max =           90.00 mean =        39.70|
|phase err.(test): min =        0.00 max =           89.87 mean =        38.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.44    102.58  19.63    None  None   None       |
|    all(noH): 2823   0      2.44    102.58  19.63    None  None   None       |
|    Sol.    : 438    0      2.44    102.39  36.31    None  None   None       |
|    Mac.    : 2385   0      2.44    102.58  16.57    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:     2.438 -  12.453: 1184   |   5:    52.510 -  62.524:   61        |
|      1:    12.453 -  22.467:  732   |   6:    62.524 -  72.539:   40        |
|      2:    22.467 -  32.481:  414   |   7:    72.539 -  82.553:   13        |
|      3:    32.481 -  42.496:  233   |   8:    82.553 -  92.568:    7        |
|      4:    42.496 -  52.510:  132   |   9:    92.568 - 102.582:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.374 - 5.257
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 316
   mapped sites are within: 0.739 - 5.257

peak=    6.258 closest distance to " C   THR A  82 " =    1.212
peak=    5.306 closest distance to " O   TYR A 116 " =    1.020
peak=    5.197 closest distance to " N   PHE A  59 " =    1.134
peak=    5.125 closest distance to " CD2 LEU A   5 " =    1.853
peak=    5.086 closest distance to " O   GLU A  46 " =    1.417
peak=    5.028 closest distance to " O   ILE A  49 " =    0.890
peak=    5.010 closest distance to " C   ASP A  65 " =    1.283
peak=    5.005 closest distance to " C   GLN A  11 " =    1.244
peak=    4.968 closest distance to " C   SER A  62 " =    0.963
peak=    4.928 closest distance to " OD1 ASN A 110 " =    0.853
peak=    4.833 closest distance to " O   LYS A 117 " =    1.256
peak=    4.813 closest distance to " O   ASN A  45 " =    1.163
peak=    4.806 closest distance to " N   PHE A  61 " =    1.166
peak=    4.730 closest distance to " N   VAL A  67 " =    0.944
peak=    4.706 closest distance to " OD1 ASP A  65 " =    1.412
peak=    4.664 closest distance to " C   PHE A  61 " =    1.274
peak=    4.661 closest distance to " C   HIS A 115 " =    1.155
peak=    4.645 closest distance to " CB  LEU A   5 " =    1.490
peak=    4.613 closest distance to " N   ASP A  65 " =    1.106
peak=    4.570 closest distance to " OE1 GLU A  46 " =    1.304
peak=    4.546 closest distance to " CG  ASP A  27 " =    1.568
peak=    4.494 closest distance to " O   HOH Z 105 " =    1.871
peak=    4.474 closest distance to " O   ALA A  10 " =    0.982
peak=    4.455 closest distance to " CE  MET A  93 " =    2.417
peak=    4.440 closest distance to " C   LEU A  25 " =    1.195
peak=    4.436 closest distance to " CB  ASP A  27 " =    1.289
peak=    4.435 closest distance to " O   HOH Z 110 " =    1.315
peak=    4.428 closest distance to " CG2 VAL A 232 " =    1.943
peak=    4.427 closest distance to " O   ASN A  69 " =    1.168
peak=    4.402 closest distance to " O  BHOH Z  74 " =    1.965
peak=    4.401 closest distance to " O   HOH Z 103 " =    2.067
peak=    4.397 closest distance to " O   SER A  63 " =    1.040
peak=    4.393 closest distance to " O   HOH Z 203 " =    1.672
peak=    4.381 closest distance to " CD1 LEU A  96 " =    1.453
peak=    4.357 closest distance to " N   ASP A  27 " =    1.020
peak=    4.353 closest distance to " O   PHE A  59 " =    1.158
peak=    4.351 closest distance to " CA  VAL A 230 " =    1.424
peak=    4.341 closest distance to " CB  VAL A 230 " =    1.201
peak=    4.339 closest distance to " C   ILE A 263 " =    1.401
peak=    4.335 closest distance to " O   MET A  47 " =    1.055
peak=    4.334 closest distance to " OD2 ASP A  65 " =    0.981
peak=    4.317 closest distance to " CB  ALA A 114 " =    1.286
peak=    4.290 closest distance to " CB  GLN A  88 " =    1.254
peak=    4.265 closest distance to " O   ASN A 110 " =    1.054
peak=    4.243 closest distance to " O   VAL A 174 " =    1.138
peak=    4.242 closest distance to " C   CYS A 260 " =    0.899
peak=    4.125 closest distance to " CB  ASP A 270 " =    0.918
peak=    4.121 closest distance to " CB  MET A  93 " =    1.322
peak=    4.113 closest distance to " OD1 ASP A  50 " =    1.743
peak=    4.102 closest distance to " CE BLYS A 290 " =    1.746
peak=    4.094 closest distance to " O   LYS A  48 " =    1.062
peak=    4.086 closest distance to " CA  ASP A 200 " =    0.813
peak=    4.081 closest distance to " NH2 ARG A 138 " =    2.460
peak=    4.080 closest distance to " N   GLU A  37 " =    1.145
peak=    4.074 closest distance to " O   HOH Z 181 " =    1.860
peak=    4.071 closest distance to " CG1 VAL A 112 " =    1.204
peak=    4.060 closest distance to " OE2 GLU A  53 " =    1.009
peak=    4.043 closest distance to " CA  ARG A  36 " =    1.288
peak=    4.035 closest distance to " O   ARG A 275 " =    1.086
peak=    4.012 closest distance to " NE2 GLN A 122 " =    2.284
peak=    4.000 closest distance to " O   HOH Z 169 " =    1.302
peak=    3.997 closest distance to " CA  ARG A  24 " =    1.062
peak=    3.993 closest distance to " CB  ARG A  79 " =    1.236
peak=    3.978 closest distance to " N   GLU A  53 " =    0.947
peak=    3.967 closest distance to " CE1 TYR A  15 " =    1.321
peak=    3.960 closest distance to " NH2 ARG A  79 " =    1.335
peak=    3.945 closest distance to " O   GLY A  35 " =    0.881
peak=    3.927 closest distance to " NH2 ARG A 269 " =    1.196
peak=    3.926 closest distance to " CG2 THR A  29 " =    1.064
peak=    3.925 closest distance to " OH  TYR A  30 " =    1.665
peak=    3.918 closest distance to " O   HOH Z 262 " =    1.792
peak=    3.916 closest distance to " C   VAL A  72 " =    1.362
peak=    3.909 closest distance to " O   SER A 164 " =    1.614
peak=    3.907 closest distance to " CB  ALA A   8 " =    2.254
peak=    3.904 closest distance to " OG  SER A  63 " =    2.419
peak=    3.896 closest distance to " N   ASN A  69 " =    1.178
peak=    3.889 closest distance to " O   HOH Z 131 " =    1.757
peak=    3.876 closest distance to " CD1 TYR A 293 " =    0.863
peak=    3.874 closest distance to " CB  ARG A 139 " =    1.428
peak=    3.873 closest distance to " N   GLU A  46 " =    1.271
peak=    3.870 closest distance to " NH1 ARG A 138 " =    1.347
peak=    3.857 closest distance to " O   HOH Z 331 " =    1.512
peak=    3.856 closest distance to " CA  ALA A 100 " =    1.167
peak=    3.850 closest distance to " O   VAL A 112 " =    0.927
peak=    3.838 closest distance to " CA  VAL A 121 " =    1.007
peak=    3.833 closest distance to " O   HOH Z 368 " =    2.353
peak=    3.832 closest distance to " CG  ASP A 253 " =    1.420
peak=    3.824 closest distance to " O   HOH Z   4 " =    1.745
peak=    3.819 closest distance to " N   THR A 220 " =    0.818
peak=    3.812 closest distance to " O   HOH Z 428 " =    1.818
peak=    3.808 closest distance to " N   ALA A 158 " =    0.920
peak=    3.803 closest distance to " O   ARG A  66 " =    2.007
peak=    3.802 closest distance to " NE2 GLN A  73 " =    1.645
peak=    3.801 closest distance to " O   HOH Z 216 " =    2.569
peak=    3.799 closest distance to " O   HOH Z 161 " =    2.200
peak=    3.795 closest distance to " O   HOH Z 172 " =    2.736
peak=    3.794 closest distance to " C   TRP A 274 " =    1.297
peak=    3.791 closest distance to " O   ASN A  39 " =    1.138
peak=    3.783 closest distance to " OG ASER A  99 " =    2.276
peak=    3.782 closest distance to " O   ASP A 124 " =    0.904
peak=    3.782 closest distance to " NE1 TRP A 266 " =    1.007
peak=    3.775 closest distance to " O   HOH Z 402 " =    2.205
peak=    3.770 closest distance to " CE  MET A 113 " =    2.248
peak=    3.756 closest distance to " CA  ALA A 100 " =    1.056
peak=    3.751 closest distance to " CB  MET A  47 " =    0.967
peak=    3.749 closest distance to " N   ALA A  43 " =    1.059
peak=    3.748 closest distance to " N   TYR A  15 " =    1.270
peak=    3.745 closest distance to " CD  PRO A  54 " =    0.828
peak=    3.743 closest distance to " CB  LYS A 117 " =    1.902
peak=    3.738 closest distance to " CB  ILE A 120 " =    1.163
peak=    3.736 closest distance to " CD2 TRP A  70 " =    1.281
peak=    3.735 closest distance to " CD2 PHE A 204 " =    0.853
peak=    3.733 closest distance to " CG  ASP A  50 " =    1.675
peak=    3.729 closest distance to " CB  ASN A 148 " =    1.562
peak=    3.719 closest distance to " OG1 THR A 264 " =    1.165
peak=    3.719 closest distance to " N   MET A 113 " =    1.524
peak=    3.718 closest distance to " O   THR A  29 " =    1.131
peak=    3.709 closest distance to " O   HOH Z 130 " =    1.604
peak=    3.709 closest distance to " O   ASP A 149 " =    1.896
peak=    3.703 closest distance to " O   HOH Z 180 " =    3.611
peak=    3.668 closest distance to " O   HOH Z   8 " =    1.879
peak=    3.664 closest distance to " O   VAL A  67 " =    1.156
peak=    3.660 closest distance to " C   GLN A  73 " =    1.359
peak=    3.660 closest distance to " O   HOH Z 219 " =    2.209
peak=    3.656 closest distance to " O   HOH Z 317 " =    2.431
peak=    3.654 closest distance to " O   HOH Z 320 " =    1.491
peak=    3.649 closest distance to " CZ3 TRP A  70 " =    1.866
peak=    3.647 closest distance to " O   HOH Z 101 " =    1.394
peak=    3.645 closest distance to " O   LYS A  76 " =    0.954
peak=    3.642 closest distance to " OG  SER A 271 " =    1.073
peak=    3.642 closest distance to " O   HOH Z 167 " =    1.062
peak=    3.642 closest distance to " N   ASN A 142 " =    1.416
peak=    3.640 closest distance to " O   HOH Z 210 " =    1.426
peak=    3.639 closest distance to " N   ARG A  24 " =    1.016
peak=    3.636 closest distance to " O   HOH Z 211 " =    1.091
peak=    3.632 closest distance to " O   HOH Z 336 " =    2.021
peak=    3.618 closest distance to " NE2 GLN A 205 " =    1.416
peak=    3.617 closest distance to " CE2 TYR A  30 " =    1.521
peak=    3.606 closest distance to " CG2BVAL A  41 " =    1.037
peak=    3.602 closest distance to " CD2 PHE A 218 " =    1.399
peak=    3.600 closest distance to " CG AARG A 102 " =    1.284
peak=    3.591 closest distance to " C   ALA A 248 " =    0.965
peak=    3.560 closest distance to " CB  ARG A  36 " =    1.154
peak=    3.560 closest distance to " CG1 ILE A 106 " =    1.227
peak=    3.555 closest distance to " O   HOH Z 212 " =    4.127
peak=    3.553 closest distance to " CB  GLN A  77 " =    1.028
peak=    3.543 closest distance to " CB  SER A  62 " =    4.011
peak=    3.542 closest distance to " OG  SER A 276 " =    1.117
peak=    3.542 closest distance to " CD1 PHE A 283 " =    1.982
peak=    3.536 closest distance to " N   THR A  29 " =    1.066
peak=    3.535 closest distance to " O   SER A 146 " =    1.212
peak=    3.534 closest distance to " O   HOH Z  68 " =    2.432
peak=    3.532 closest distance to " CA  VAL A 202 " =    1.223
peak=    3.531 closest distance to " CB  ALA A  21 " =    1.113
peak=    3.528 closest distance to " N   THR A 235 " =    0.739
peak=    3.522 closest distance to " O   HOH Z 430 " =    4.314
peak=    3.522 closest distance to " CB  THR A 246 " =    1.608
peak=    3.518 closest distance to " CB  TRP A 123 " =    0.782
peak=    3.514 closest distance to " OG ASER A 164 " =    0.772
peak=    3.509 closest distance to " CB  MET A  40 " =    1.789
peak=    3.508 closest distance to " CG  MET A 105 " =    1.128
peak=    3.506 closest distance to " CE3 TRP A  92 " =    1.335
peak=    3.505 closest distance to " CD1 TYR A 169 " =    1.725
peak=    3.499 closest distance to " CG1 VAL A 296 " =    0.934
peak=    3.482 closest distance to " O   THR A 220 " =    1.319
peak=    3.475 closest distance to " O   ASP A 272 " =    1.049
peak=    3.474 closest distance to " O   HOH Z 379 " =    2.712
peak=    3.467 closest distance to " O   HOH Z 429 " =    1.233
peak=    3.466 closest distance to " CG  ARG A 138 " =    0.819
peak=    3.465 closest distance to " CZ  PHE A  61 " =    1.209
peak=    3.464 closest distance to " O   HOH Z 412 " =    2.204
peak=    3.462 closest distance to " NZ BLYS A 290 " =    1.305
peak=    3.460 closest distance to " CB  LEU A 101 " =    1.451
peak=    3.457 closest distance to " O   HOH Z 374 " =    1.835
peak=    3.456 closest distance to " NH2AARG A 102 " =    1.206
peak=    3.456 closest distance to " O   HOH Z 215 " =    2.890
peak=    3.450 closest distance to " O   ASN A 252 " =    1.876
peak=    3.449 closest distance to " O   HOH Z  99 " =    2.893
peak=    3.447 closest distance to " O   ARG A  24 " =    1.302
peak=    3.443 closest distance to " O   HOH Z 362 " =    3.487
peak=    3.439 closest distance to " CD2 LEU A  25 " =    1.765
peak=    3.437 closest distance to " O   HOH Z  15 " =    1.307
peak=    3.429 closest distance to " O   HOH Z 139 " =    1.559
peak=    3.422 closest distance to " O   HOH Z 342 " =    1.248
peak=    3.416 closest distance to " CB  LYS A  76 " =    1.217
peak=    3.407 closest distance to " OD1 ASP A  27 " =    1.495
peak=    3.404 closest distance to " CB  GLU A  37 " =    1.039
peak=    3.403 closest distance to " CE2 TYR A 172 " =    1.061
peak=    3.400 closest distance to " CD2 TYR A 116 " =    1.531
peak=    3.399 closest distance to " CZ  TYR A 293 " =    0.970
peak=    3.397 closest distance to " NE  ARG A  56 " =    1.265
peak=    3.393 closest distance to " CB  THR A 178 " =    1.567
peak=    3.391 closest distance to " O   HOH Z  57 " =    1.636
peak=    3.389 closest distance to " NH2 ARG A 159 " =    1.171
peak=    3.387 closest distance to " N   GLY A  13 " =    1.177
peak=    3.382 closest distance to " O   HOH Z  84 " =    1.187
peak=    3.382 closest distance to " O   HOH Z 188 " =    2.364
peak=    3.381 closest distance to " O   HOH Z 127 " =    1.014
peak=    3.379 closest distance to " O   HOH Z 353 " =    1.805
peak=    3.371 closest distance to " O   SER A  97 " =    1.281
peak=    3.359 closest distance to " O   HOH Z 197 " =    1.845
peak=    3.359 closest distance to " O   HOH Z 330 " =    2.019
peak=    3.358 closest distance to " N   ASN A 217 " =    1.094
peak=    3.357 closest distance to " CA  THR A 246 " =    1.266
peak=    3.356 closest distance to " CB  ASN A  39 " =    1.510
peak=    3.354 closest distance to " NH1 ARG A  66 " =    3.310
peak=    3.351 closest distance to " CA  ASN A  39 " =    1.218
peak=    3.349 closest distance to " C   PHE A 208 " =    1.024
peak=    3.348 closest distance to " O   LEU A  96 " =    1.076
peak=    3.348 closest distance to " O   HOH Z 254 " =    2.098
peak=    3.345 closest distance to " CD2 HIS A  86 " =    1.004
peak=    3.339 closest distance to " CE1 PHE A 218 " =    1.382
peak=    3.337 closest distance to " CB  SER A 210 " =    1.198
peak=    3.336 closest distance to " O   HOH Z 349 " =    1.770
peak=    3.320 closest distance to " O   HOH Z 102 " =    2.217
peak=    3.319 closest distance to " CZ  ARG A 195 " =    1.317
peak=    3.318 closest distance to " O   HOH Z  89 " =    1.947
peak=    3.318 closest distance to " CB  ALA A   9 " =    1.699
peak=    3.314 closest distance to " CZ  PHE A 192 " =    1.158
peak=    3.312 closest distance to " N   SER A   3 " =    0.908
peak=    3.309 closest distance to " CA  GLN A  11 " =    1.856
peak=    3.309 closest distance to " N   LYS A  76 " =    1.182
peak=    3.309 closest distance to " O   HOH Z  12 " =    1.411
peak=    3.308 closest distance to " O   ALA A  84 " =    1.237
peak=    3.297 closest distance to " N   LEU A  25 " =    0.954
peak=    3.294 closest distance to " OG  SER A 146 " =    1.234
peak=    3.293 closest distance to " O   VAL A  41 " =    0.850
peak=    3.286 closest distance to " O   HOH Z 298 " =    1.992
peak=    3.284 closest distance to " C   ARG A  56 " =    1.381
peak=    3.282 closest distance to " CE1 PHE A 208 " =    1.120
peak=    3.280 closest distance to " CA  PHE A 283 " =    1.243
peak=    3.278 closest distance to " O   HOH Z 390 " =    2.343
peak=    3.277 closest distance to " O   HOH Z 125 " =    2.479
peak=    3.274 closest distance to " CB  SER A 271 " =    1.462
peak=    3.270 closest distance to " CE1 HIS A  81 " =    1.592
peak=    3.264 closest distance to " O   VAL A 230 " =    1.969
peak=    3.256 closest distance to " O   HOH Z 327 " =    1.338
peak=    3.255 closest distance to " O   HOH Z 230 " =    1.417
peak=    3.254 closest distance to " O   HOH Z 392 " =    2.716
peak=    3.252 closest distance to " O   HOH Z 190 " =    1.057
peak=    3.252 closest distance to " O   HOH Z 197 " =    2.850
peak=    3.252 closest distance to " O   HOH Z  70 " =    1.273
peak=    3.250 closest distance to " O   HOH Z 206 " =    1.776
peak=    3.248 closest distance to " CA  ARG A 195 " =    0.985
peak=    3.244 closest distance to " O   GLY A 118 " =    1.085
peak=    3.243 closest distance to " O   HOH Z 416 " =    1.592
peak=    3.241 closest distance to " C   LEU A 297 " =    1.480
peak=    3.236 closest distance to " ND2 ASN A  45 " =    2.055
peak=    3.235 closest distance to " CG2 VAL A 112 " =    1.125
peak=    3.232 closest distance to " CD2 LEU A 228 " =    1.858
peak=    3.231 closest distance to " SD  MET A 185 " =    1.822
peak=    3.229 closest distance to " OG  SER A 245 " =    3.205
peak=    3.229 closest distance to " O   SER A 245 " =    0.982
peak=    3.223 closest distance to " O   HOH Z 307 " =    1.760
peak=    3.218 closest distance to " O   HOH Z 284 " =    2.326
peak=    3.218 closest distance to " N   VAL A  72 " =    1.643
peak=    3.215 closest distance to " C   SER A  22 " =    0.952
peak=    3.211 closest distance to " C   SER A  99 " =    0.939
peak=    3.210 closest distance to " O   GLN A  55 " =    1.054
peak=    3.208 closest distance to " O   HOH Z  43 " =    2.871
peak=    3.199 closest distance to " O   HOH Z 359 " =    1.595
peak=    3.199 closest distance to " CD  GLU A  37 " =    1.155
peak=    3.198 closest distance to " CG2 VAL A  67 " =    1.733
peak=    3.198 closest distance to " O   ALA A 129 " =    1.905
peak=    3.196 closest distance to " NE2 GLN A  11 " =    1.699
peak=    3.196 closest distance to " O   HOH Z 153 " =    2.840
peak=    3.189 closest distance to " CG1 VAL A 265 " =    1.262
peak=    3.188 closest distance to " O   HOH Z 116 " =    4.422
peak=    3.185 closest distance to " OD1 ASP A 140 " =    1.264
peak=    3.185 closest distance to " O   ARG A  36 " =    0.749
peak=    3.184 closest distance to " CB  ASP A 298 " =    1.054
peak=    3.183 closest distance to " N   VAL A 202 " =    1.027
peak=    3.181 closest distance to " O   ASP A  27 " =    0.981
peak=    3.177 closest distance to " O   HOH Z 420 " =    3.123
peak=    3.175 closest distance to " CA  ARG A  36 " =    1.007
peak=    3.175 closest distance to " O   HOH Z 271 " =    2.163
peak=    3.174 closest distance to " O   HOH Z 275 " =    1.119
peak=    3.171 closest distance to " ND2 ASN A  60 " =    2.747
peak=    3.168 closest distance to " O   HOH Z 287 " =    1.985
peak=    3.167 closest distance to " O   HOH Z  37 " =    2.040
peak=    3.165 closest distance to " CE2 TYR A  15 " =    0.862
peak=    3.164 closest distance to " CB  GLN A 122 " =    0.954
peak=    3.162 closest distance to " CD1 ILE A 106 " =    2.057
peak=    3.161 closest distance to " CG2 VAL A 268 " =    1.016
peak=    3.153 closest distance to " O   HOH Z 177 " =    2.135
peak=    3.151 closest distance to " CG  GLN A 205 " =    1.898
peak=    3.146 closest distance to " C   GLY A  98 " =    1.100
peak=    3.142 closest distance to " CA  GLY A 229 " =    2.039
peak=    3.141 closest distance to " O   HOH Z 202 " =    2.416
peak=    3.141 closest distance to " O   HOH Z 352 " =    1.703
peak=    3.133 closest distance to " N   HIS A  86 " =    0.942
peak=    3.129 closest distance to " O   HOH Z  66 " =    1.618
peak=    3.128 closest distance to " O   HOH Z 350 " =    2.842
peak=    3.128 closest distance to " CG  GLU A   2 " =    1.873
peak=    3.120 closest distance to " O   HOH Z 219 " =    5.257
peak=    3.118 closest distance to " O   GLY A 302 " =    2.054
peak=    3.114 closest distance to " N   TRP A 150 " =    1.246
peak=    3.109 closest distance to " OG  SER A  62 " =    2.261
peak=    3.103 closest distance to " SD AMET A  47 " =    1.763
peak=    3.102 closest distance to " O   HOH Z 419 " =    2.036
peak=    3.101 closest distance to " CE2 TYR A 116 " =    2.332
peak=    3.099 closest distance to " CG1 VAL A  67 " =    1.756
peak=    3.082 closest distance to " CA  GLY A 136 " =    0.851
peak=    3.080 closest distance to " O   HOH Z 117 " =    1.977
peak=    3.071 closest distance to " CB  ASN A 173 " =    1.051
peak=    3.071 closest distance to " CB  VAL A  72 " =    1.515
peak=    3.070 closest distance to " CA  GLY A  57 " =    1.108
peak=    3.067 closest distance to " O   HOH Z  19 " =    1.955
peak=    3.064 closest distance to " O   VAL A 250 " =    0.935
peak=    3.054 closest distance to " O   ILE A 109 " =    2.314
peak=    3.031 closest distance to " O   HOH Z  44 " =    2.176

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 226         
Filter by distance & map next to the model:
   mapped sites are within: 0.271 - 5.359
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 224 from: 226
   mapped sites are within: 0.841 - 5.359

peak=   -4.871 closest distance to " O   TYR A 116 " =    1.819
peak=   -4.704 closest distance to " CG  GLU A 277 " =    2.959
peak=   -4.697 closest distance to " O   ASN A  69 " =    1.023
peak=   -4.534 closest distance to " N   HIS A 115 " =    1.801
peak=   -4.516 closest distance to " N   ARG A  24 " =    1.211
peak=   -4.387 closest distance to " C   LEU A 297 " =    0.858
peak=   -4.319 closest distance to " N   GLU A  53 " =    0.936
peak=   -4.205 closest distance to " CB  GLN A 122 " =    0.878
peak=   -4.191 closest distance to " C   ALA A  21 " =    1.259
peak=   -4.176 closest distance to " CG1BVAL A 121 " =    1.038
peak=   -4.167 closest distance to " C   SER A  62 " =    1.168
peak=   -4.166 closest distance to " O   THR A  82 " =    1.392
peak=   -4.131 closest distance to " CG  ASP A  50 " =    0.920
peak=   -4.130 closest distance to " O   ILE A 106 " =    0.889
peak=   -4.028 closest distance to " C   ASN A  69 " =    1.261
peak=   -3.988 closest distance to " O   HOH Z 375 " =    2.313
peak=   -3.969 closest distance to " O   HOH Z 376 " =    1.168
peak=   -3.963 closest distance to " CG  GLU A 236 " =    1.417
peak=   -3.954 closest distance to " C   ASP A 124 " =    1.223
peak=   -3.947 closest distance to " O   ASP A 124 " =    1.578
peak=   -3.947 closest distance to " C   MET A 113 " =    1.982
peak=   -3.933 closest distance to " O   HOH Z 430 " =    3.753
peak=   -3.929 closest distance to " O   HOH Z  48 " =    2.410
peak=   -3.924 closest distance to " O   HOH Z 426 " =    1.704
peak=   -3.914 closest distance to " N   ALA A 180 " =    1.653
peak=   -3.893 closest distance to " CB  GLN A  89 " =    2.101
peak=   -3.892 closest distance to " N   ALA A   1 " =    2.149
peak=   -3.849 closest distance to " O   HOH Z 277 " =    1.968
peak=   -3.845 closest distance to " N   VAL A  67 " =    1.387
peak=   -3.842 closest distance to " O   ARG A 159 " =    1.682
peak=   -3.834 closest distance to " N   ARG A 145 " =    1.133
peak=   -3.828 closest distance to " O   HOH Z 359 " =    1.330
peak=   -3.827 closest distance to " CG AARG A 275 " =    1.086
peak=   -3.813 closest distance to " C   ARG A  66 " =    0.965
peak=   -3.809 closest distance to " O   HOH Z 362 " =    4.153
peak=   -3.804 closest distance to " C   ILE A 234 " =    1.323
peak=   -3.801 closest distance to " O   HOH Z 400 " =    1.786
peak=   -3.773 closest distance to " CG  MET A  93 " =    1.172
peak=   -3.769 closest distance to " N   GLN A  77 " =    1.267
peak=   -3.758 closest distance to " OE1 GLN A 194 " =    1.446
peak=   -3.736 closest distance to " OD1 ASN A 110 " =    1.126
peak=   -3.735 closest distance to " C   VAL A  67 " =    1.305
peak=   -3.734 closest distance to " CE  LYS A 117 " =    0.980
peak=   -3.730 closest distance to " O   HOH Z 123 " =    1.181
peak=   -3.722 closest distance to " CD  ARG A  66 " =    1.186
peak=   -3.719 closest distance to " O   HOH Z 183 " =    1.381
peak=   -3.719 closest distance to " CG2 THR A  42 " =    1.374
peak=   -3.697 closest distance to " CD1 ILE A  20 " =    2.916
peak=   -3.683 closest distance to " N   ALA A 242 " =    1.271
peak=   -3.665 closest distance to " CB  GLN A 205 " =    2.014
peak=   -3.651 closest distance to " C   GLY A 111 " =    0.937
peak=   -3.642 closest distance to " O   HOH Z 415 " =    1.860
peak=   -3.640 closest distance to " CB  VAL A 230 " =    0.913
peak=   -3.638 closest distance to " OE2 GLU A 152 " =    1.474
peak=   -3.637 closest distance to " OD1 ASP A  65 " =    1.213
peak=   -3.615 closest distance to " O   HOH Z  98 " =    3.425
peak=   -3.613 closest distance to " O   HOH Z   1 " =    3.022
peak=   -3.601 closest distance to " O   GLN A  77 " =    1.504
peak=   -3.599 closest distance to " O   HOH Z 192 " =    1.335
peak=   -3.583 closest distance to " O   HOH Z 386 " =    1.290
peak=   -3.578 closest distance to " O   HOH Z 239 " =    0.859
peak=   -3.575 closest distance to " CA  THR A  29 " =    1.051
peak=   -3.568 closest distance to " O   ALA A 114 " =    0.970
peak=   -3.556 closest distance to " N   TYR A  15 " =    1.645
peak=   -3.539 closest distance to " O   GLY A 147 " =    1.722
peak=   -3.534 closest distance to " CB  ASN A 301 " =    1.909
peak=   -3.533 closest distance to " CB  LEU A  83 " =    1.454
peak=   -3.531 closest distance to " O   HOH Z 260 " =    1.561
peak=   -3.529 closest distance to " O   HOH Z 167 " =    1.802
peak=   -3.528 closest distance to " OE2 GLU A 128 " =    1.477
peak=   -3.515 closest distance to " SD  MET A  93 " =    1.600
peak=   -3.515 closest distance to " CE2 PHE A 204 " =    1.917
peak=   -3.514 closest distance to " O   HOH Z 397 " =    1.456
peak=   -3.512 closest distance to " O   PRO A 163 " =    1.469
peak=   -3.512 closest distance to " C   GLY A  98 " =    1.107
peak=   -3.512 closest distance to " C   LEU A 143 " =    1.036
peak=   -3.509 closest distance to " O   HOH Z 281 " =    1.888
peak=   -3.508 closest distance to " O   SER A  22 " =    1.648
peak=   -3.507 closest distance to " CD2 LEU A 297 " =    1.243
peak=   -3.503 closest distance to " C   ASN A  45 " =    1.186
peak=   -3.502 closest distance to " CG  ARG A  56 " =    1.599
peak=   -3.496 closest distance to " O   HOH Z 336 " =    4.291
peak=   -3.494 closest distance to " NH1 ARG A  56 " =    2.308
peak=   -3.491 closest distance to " O   HOH Z  52 " =    1.072
peak=   -3.489 closest distance to " O   HOH Z 166 " =    1.553
peak=   -3.478 closest distance to " CD1 ILE A  33 " =    2.001
peak=   -3.476 closest distance to " O   HOH Z 413 " =    1.848
peak=   -3.473 closest distance to " CA  ASP A 149 " =    1.532
peak=   -3.473 closest distance to " O   ALA A  10 " =    0.903
peak=   -3.471 closest distance to " CB  ASN A 285 " =    1.301
peak=   -3.470 closest distance to " C   PHE A  38 " =    1.652
peak=   -3.454 closest distance to " O   HOH Z 308 " =    1.470
peak=   -3.453 closest distance to " O   HOH Z  32 " =    1.869
peak=   -3.453 closest distance to " O   PHE A  59 " =    1.067
peak=   -3.450 closest distance to " O   SER A 276 " =    1.249
peak=   -3.442 closest distance to " CG  ARG A 219 " =    2.293
peak=   -3.441 closest distance to " CB  ALA A  71 " =    1.388
peak=   -3.435 closest distance to " O   LEU A  25 " =    0.958
peak=   -3.435 closest distance to " CD  GLN A 223 " =    1.230
peak=   -3.434 closest distance to " N   SER A  63 " =    1.513
peak=   -3.434 closest distance to " O   HOH Z 115 " =    4.471
peak=   -3.429 closest distance to " OD1BASN A 224 " =    2.588
peak=   -3.421 closest distance to " O   SER A 276 " =    1.758
peak=   -3.418 closest distance to " N   PHE A  16 " =    0.880
peak=   -3.417 closest distance to " CD2 HIS A 115 " =    1.302
peak=   -3.417 closest distance to " NE1 TRP A 266 " =    0.989
peak=   -3.415 closest distance to " O   HOH Z  79 " =    1.153
peak=   -3.415 closest distance to " O   HOH Z 203 " =    1.233
peak=   -3.414 closest distance to " CB  ASP A 149 " =    2.330
peak=   -3.413 closest distance to " CA  SER A 164 " =    1.167
peak=   -3.410 closest distance to " CZ  PHE A  59 " =    0.935
peak=   -3.408 closest distance to " O   HOH Z 166 " =    3.782
peak=   -3.402 closest distance to " O   HOH Z  97 " =    1.568
peak=   -3.402 closest distance to " O   ALA A  34 " =    1.305
peak=   -3.401 closest distance to " CE2 TYR A 116 " =    1.182
peak=   -3.398 closest distance to " C   ARG A  36 " =    1.178
peak=   -3.395 closest distance to " CB  ARG A 159 " =    1.186
peak=   -3.391 closest distance to " CE2 TRP A 150 " =    1.482
peak=   -3.388 closest distance to " O   GLY A 196 " =    1.080
peak=   -3.383 closest distance to " CG2 THR A   4 " =    1.355
peak=   -3.382 closest distance to " CG  PHE A 283 " =    2.451
peak=   -3.381 closest distance to " OG1 THR A 157 " =    1.814
peak=   -3.378 closest distance to " NH1 ARG A  66 " =    1.639
peak=   -3.375 closest distance to " OG BSER A 258 " =    1.610
peak=   -3.359 closest distance to " CG2 VAL A 153 " =    1.512
peak=   -3.357 closest distance to " O   ASN A 142 " =    1.767
peak=   -3.345 closest distance to " O   ALA A  21 " =    1.351
peak=   -3.342 closest distance to " O   VAL A 125 " =    2.776
peak=   -3.341 closest distance to " O   HOH Z 385 " =    3.351
peak=   -3.340 closest distance to " O   HOH Z 215 " =    2.075
peak=   -3.339 closest distance to " O   HOH Z 215 " =    2.103
peak=   -3.336 closest distance to " CD2 PHE A 130 " =    2.312
peak=   -3.335 closest distance to " SD  MET A 105 " =    2.116
peak=   -3.330 closest distance to " O   HOH Z 118 " =    3.404
peak=   -3.329 closest distance to " CA  ARG A  36 " =    1.166
peak=   -3.323 closest distance to " CD  ARG A 159 " =    1.152
peak=   -3.319 closest distance to " O   HOH Z 244 " =    1.587
peak=   -3.319 closest distance to " OG1 THR A  18 " =    1.447
peak=   -3.314 closest distance to " C   LEU A   5 " =    1.196
peak=   -3.313 closest distance to " O   HOH Z 238 " =    3.760
peak=   -3.307 closest distance to " CG2 THR A  31 " =    0.841
peak=   -3.305 closest distance to " O   ALA A  10 " =    0.968
peak=   -3.303 closest distance to " CB  SER A 271 " =    1.005
peak=   -3.301 closest distance to " O   HOH Z 181 " =    1.091
peak=   -3.297 closest distance to " OE1 GLN A 223 " =    1.759
peak=   -3.294 closest distance to " O  BHOH Z  74 " =    2.187
peak=   -3.292 closest distance to " O   HOH Z 304 " =    1.134
peak=   -3.291 closest distance to " CA  PRO A 280 " =    1.074
peak=   -3.287 closest distance to " CA  GLY A 267 " =    1.715
peak=   -3.284 closest distance to " N   ILE A 199 " =    1.211
peak=   -3.284 closest distance to " C   PRO A 198 " =    2.175
peak=   -3.280 closest distance to " O   HOH Z 135 " =    2.312
peak=   -3.280 closest distance to " O   HOH Z 298 " =    2.008
peak=   -3.280 closest distance to " O   HOH Z 345 " =    1.931
peak=   -3.279 closest distance to " O   ASN A 110 " =    1.215
peak=   -3.274 closest distance to " O   HOH Z 279 " =    3.225
peak=   -3.273 closest distance to " N   PHE A  59 " =    2.821
peak=   -3.272 closest distance to " OG BSER A 134 " =    4.081
peak=   -3.270 closest distance to " C   PRO A  54 " =    1.018
peak=   -3.269 closest distance to " CE1 PHE A  16 " =    2.055
peak=   -3.268 closest distance to " O   HOH Z 111 " =    2.503
peak=   -3.268 closest distance to " CB  THR A 246 " =    1.107
peak=   -3.263 closest distance to " OD1 ASN A 110 " =    1.697
peak=   -3.262 closest distance to " OD2 ASP A  65 " =    1.156
peak=   -3.257 closest distance to " O   HOH Z 100 " =    0.901
peak=   -3.253 closest distance to " CD1 ILE A 106 " =    1.728
peak=   -3.246 closest distance to " O   HOH Z 127 " =    1.857
peak=   -3.246 closest distance to " CG1 VAL A 153 " =    2.657
peak=   -3.236 closest distance to " O   HOH Z 172 " =    4.203
peak=   -3.235 closest distance to " CB  PHE A 208 " =    1.250
peak=   -3.227 closest distance to " CA  VAL A 296 " =    0.986
peak=   -3.226 closest distance to " NE2 HIS A 207 " =    1.371
peak=   -3.223 closest distance to " O   ASP A 171 " =    1.220
peak=   -3.221 closest distance to " OD2 ASP A 286 " =    1.357
peak=   -3.217 closest distance to " N   CYS A 201 " =    2.045
peak=   -3.212 closest distance to " OE1 GLU A  44 " =    1.750
peak=   -3.208 closest distance to " CB  TYR A  30 " =    1.361
peak=   -3.207 closest distance to " O   HOH Z 159 " =    1.109
peak=   -3.207 closest distance to " OD1 ASN A 249 " =    1.891
peak=   -3.204 closest distance to " CD2 LEU A 237 " =    2.332
peak=   -3.199 closest distance to " O   HOH Z 285 " =    4.005
peak=   -3.197 closest distance to " N   GLY A 203 " =    1.799
peak=   -3.196 closest distance to " CA  VAL A 257 " =    1.645
peak=   -3.195 closest distance to " OD1 ASN A  60 " =    2.012
peak=   -3.194 closest distance to " CB  PHE A 225 " =    1.365
peak=   -3.193 closest distance to " O   HOH Z  25 " =    2.243
peak=   -3.193 closest distance to " O   HOH Z 297 " =    3.883
peak=   -3.192 closest distance to " C   TYR A 172 " =    1.547
peak=   -3.192 closest distance to " CB  ARG A 259 " =    0.943
peak=   -3.189 closest distance to " O   HOH Z 158 " =    1.869
peak=   -3.188 closest distance to " O   HOH Z 353 " =    2.981
peak=   -3.187 closest distance to " O   HOH Z 113 " =    1.368
peak=   -3.186 closest distance to " O   HOH Z 134 " =    3.374
peak=   -3.183 closest distance to " CB  TYR A 247 " =    0.940
peak=   -3.180 closest distance to " CB  ASP A 149 " =    1.718
peak=   -3.179 closest distance to " CD2 LEU A  25 " =    1.218
peak=   -3.177 closest distance to " CD  GLN A 122 " =    1.207
peak=   -3.177 closest distance to " O   HOH Z 210 " =    1.707
peak=   -3.176 closest distance to " CA  ARG A  56 " =    1.833
peak=   -3.176 closest distance to " O   HOH Z  73 " =    2.870
peak=   -3.170 closest distance to " O   HOH Z 154 " =    1.783
peak=   -3.169 closest distance to " CE1 HIS A 115 " =    1.010
peak=   -3.166 closest distance to " CG  ARG A  36 " =    1.327
peak=   -3.163 closest distance to " O   HOH Z 173 " =    2.561
peak=   -3.160 closest distance to " CE3 TRP A  70 " =    1.951
peak=   -3.160 closest distance to " OG  SER A  62 " =    4.357
peak=   -3.148 closest distance to " OD1 ASP A 191 " =    1.495
peak=   -3.148 closest distance to " CG  GLN A  73 " =    1.672
peak=   -3.141 closest distance to " CB  PHE A 204 " =    1.772
peak=   -3.138 closest distance to " O   SER A  63 " =    0.959
peak=   -3.137 closest distance to " CB  ASP A 162 " =    1.379
peak=   -3.133 closest distance to " N   SER A  99 " =    2.035
peak=   -3.126 closest distance to " CB  ALA A 227 " =    2.390
peak=   -3.125 closest distance to " O   GLU A 152 " =    1.466
peak=   -3.114 closest distance to " O   GLN A 205 " =    1.840
peak=   -3.097 closest distance to " CB  SER A  62 " =    5.359
peak=   -3.092 closest distance to " CZ2 TRP A 179 " =    2.587
peak=   -3.089 closest distance to " N   ASN A  74 " =    1.022
peak=   -3.088 closest distance to " C   ASP A 162 " =    1.234
peak=   -3.080 closest distance to " O   HOH Z 147 " =    1.845
peak=   -3.062 closest distance to " O   HOH Z 212 " =    0.901
peak=   -3.039 closest distance to " O   HOH Z 276 " =    1.490
peak=   -3.027 closest distance to " O   MET A 105 " =    0.933
peak=   -3.017 closest distance to " CB  ALA A  21 " =    1.230

================= 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    :  0.5341 0.5375   6.321547e+00   6.319383e+00
   1_bss:  0.5276 0.5304   6.319539e+00   6.316396e+00
   1_xyz:  0.4869 0.5207   6.287233e+00   6.308480e+00
   1_adp:  0.4534 0.5121   6.265914e+00   6.305596e+00
   1_occ:  0.4530 0.5132   6.265096e+00   6.305871e+00
   2_bss:  0.4533 0.5128   6.266388e+00   6.306254e+00
   2_xyz:  0.4192 0.4975   6.217066e+00   6.290801e+00
   2_adp:  0.4142 0.4959   6.215292e+00   6.291247e+00
   2_occ:  0.4141 0.4961   6.215600e+00   6.291349e+00
   3_bss:  0.4147 0.4961   6.217709e+00   6.290790e+00
   3_xyz:  0.3904 0.4668   6.173917e+00   6.264160e+00
   3_adp:  0.3654 0.4727   6.163377e+00   6.268560e+00
   3_occ:  0.3652 0.4727   6.163506e+00   6.268618e+00
   4_bss:  0.3652 0.4729   6.164339e+00   6.268751e+00
   4_xyz:  0.3450 0.4534   6.123375e+00   6.250264e+00
   4_adp:  0.3478 0.4343   6.109900e+00   6.229198e+00
   4_occ:  0.3478 0.4342   6.109586e+00   6.229184e+00
   5_bss:  0.3477 0.4337   6.108881e+00   6.229229e+00
   5_xyz:  0.3004 0.3895   5.992930e+00   6.153367e+00
   5_adp:  0.2737 0.3659   5.934362e+00   6.111232e+00
   5_occ:  0.2733 0.3655   5.933387e+00   6.110442e+00
   5_bss:  0.2732 0.3637   5.931331e+00   6.109579e+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:  0.370  20.000   5.122   6.483   8.923   0.000   0.000   0.000
   1_xyz:  0.370  20.000   5.122   6.483   8.923   0.000   0.000   0.000
   1_adp:  0.370  20.000   5.122   6.483   8.923   0.000   0.000   0.000
   1_occ:  0.370  20.000   5.122   6.483   8.923   0.000   0.000   0.000
   2_bss:  0.367  50.000   2.940   3.954   6.223   0.000   0.000   0.000
   2_xyz:  0.367  50.000   2.940   3.954   6.223   0.000   0.000   0.000
   2_adp:  0.367  50.000   2.940   3.954   6.223   0.000   0.000   0.000
   2_occ:  0.367  50.000   2.940   3.954   6.223   0.000   0.000   0.000
   3_bss:  0.349  50.001   1.981   2.635   4.895   0.000   0.000   0.000
   3_xyz:  0.349  50.001   1.981   2.635   4.895   0.000   0.000   0.000
   3_adp:  0.349  50.001   1.981   2.635   4.895   0.000   0.000   0.000
   3_occ:  0.349  50.001   1.981   2.635   4.895   0.000   0.000   0.000
   4_bss:  0.365  69.546   3.776   4.387   6.381   0.000   0.000   0.000
   4_xyz:  0.365  69.546   3.776   4.387   6.381   0.000   0.000   0.000
   4_adp:  0.365  69.546   3.776   4.387   6.381   0.000   0.000   0.000
   4_occ:  0.365  69.546   3.776   4.387   6.381   0.000   0.000   0.000
   5_bss:  0.354  69.546   2.654   3.451   5.304   0.000   0.000   0.000
   5_xyz:  0.354  69.546   2.654   3.451   5.304   0.000   0.000   0.000
   5_adp:  0.354  69.546   2.654   3.451   5.304   0.000   0.000   0.000
   5_occ:  0.354  69.546   2.654   3.451   5.304   0.000   0.000   0.000
   5_bss:  0.323  65.555  -1.155  -0.470   1.625  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  72.312 0.2331  0.2863    97933.790
   1_bss:  71.773 0.2397  0.3544    97573.843
   1_xyz:  68.252 0.2852  0.4155    90878.731
   1_adp:  68.267 0.2848  0.4706    90783.265
   1_occ:  68.198 0.2857  0.4706    90703.442
   2_bss:  67.976 0.2886  0.4411    90230.218
   2_xyz:  63.556 0.3452  0.5309    80060.072
   2_adp:  63.072 0.3517  0.5589    80570.293
   2_occ:  63.186 0.3502  0.5563    80703.793
   3_bss:  63.220 0.3498  0.5345    80737.946
   3_xyz:  58.502 0.4101  0.6272    71303.761
   3_adp:  59.263 0.4003  0.5849    73011.859
   3_occ:  59.285 0.4000  0.5844    73024.731
   4_bss:  59.317 0.3995  0.6158    73031.579
   4_xyz:  55.392 0.4501  0.6997    66415.331
   4_adp:  51.710 0.4974  0.7604    60621.890
   4_occ:  51.687 0.4976  0.7605    60582.877
   5_bss:  51.588 0.4988  0.7347    60348.873
   5_xyz:  43.004 0.6054  0.8832    43852.978
   5_adp:  39.777 0.6447  0.9126    38751.109
   5_occ:  39.704 0.6456  0.9134    38629.066
   5_bss:  39.583 0.6468  0.8713    38341.401
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2833e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2833e+01
   1_xyz:   1.872  0.015  0.111 18.573  0.007  4.099   1.7814e-01
   1_adp:   1.872  0.015  0.111 18.573  0.007  4.099   1.7814e-01
   1_occ:   1.872  0.015  0.111 18.573  0.007  4.099   1.7814e-01
   2_bss:   1.872  0.015  0.111 18.573  0.007  4.099   1.7814e-01
   2_xyz:   1.301  0.009  0.079 17.338  0.006  4.097   1.1889e-01
   2_adp:   1.301  0.009  0.079 17.338  0.006  4.097   1.1889e-01
   2_occ:   1.301  0.009  0.079 17.338  0.006  4.097   1.1889e-01
   3_bss:   1.301  0.009  0.079 17.338  0.006  4.097   1.1889e-01
   3_xyz:   1.167  0.008  0.076 16.523  0.004  4.111   9.0323e-02
   3_adp:   1.167  0.008  0.076 16.523  0.004  4.111   9.0323e-02
   3_occ:   1.167  0.008  0.076 16.523  0.004  4.111   9.0323e-02
   4_bss:   1.167  0.008  0.076 16.523  0.004  4.111   9.0323e-02
   4_xyz:   1.063  0.006  0.072 16.381  0.005  4.107   8.0677e-02
   4_adp:   1.063  0.006  0.072 16.381  0.005  4.107   8.0677e-02
   4_occ:   1.063  0.006  0.072 16.381  0.005  4.107   8.0677e-02
   5_bss:   1.063  0.006  0.072 16.381  0.005  4.107   8.0677e-02
   5_xyz:   1.339  0.011  0.094 17.076  0.006  4.103   1.1636e-01
   5_adp:   1.339  0.011  0.094 17.076  0.006  4.103   1.1636e-01
   5_occ:   1.339  0.011  0.094 17.076  0.006  4.103   1.1636e-01
   5_bss:   1.339  0.011  0.094 17.076  0.006  4.103   1.1636e-01
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.124   6.8337e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.124   6.8337e+00
   1_xyz:  15.285  0.196  0.462 85.993  0.044  2.025   1.0773e-01
   1_adp:  15.285  0.196  0.462 85.993  0.044  2.025   1.0773e-01
   1_occ:  15.285  0.196  0.462 85.993  0.044  2.025   1.0773e-01
   2_bss:  15.285  0.196  0.462 85.993  0.044  2.025   1.0773e-01
   2_xyz:   7.922  0.080  0.256 79.133  0.056  2.015   6.2918e-02
   2_adp:   7.922  0.080  0.256 79.133  0.056  2.015   6.2918e-02
   2_occ:   7.922  0.080  0.256 79.133  0.056  2.015   6.2918e-02
   3_bss:   7.922  0.080  0.256 79.133  0.056  2.015   6.2918e-02
   3_xyz:   7.246  0.079  0.259 70.762  0.032  2.169   6.0721e-02
   3_adp:   7.246  0.079  0.259 70.762  0.032  2.169   6.0721e-02
   3_occ:   7.246  0.079  0.259 70.762  0.032  2.169   6.0721e-02
   4_bss:   7.246  0.079  0.259 70.762  0.032  2.169   6.0721e-02
   4_xyz:   6.489  0.030  0.271 77.063  0.048  2.204   4.5061e-02
   4_adp:   6.489  0.030  0.271 77.063  0.048  2.204   4.5061e-02
   4_occ:   6.489  0.030  0.271 77.063  0.048  2.204   4.5061e-02
   5_bss:   6.489  0.030  0.271 77.063  0.048  2.204   4.5061e-02
   5_xyz:   7.887  0.068  0.325 82.078  0.042  2.030   1.0004e-01
   5_adp:   7.887  0.068  0.325 82.078  0.042  2.030   1.0004e-01
   5_occ:   7.887  0.068  0.325 82.078  0.042  2.030   1.0004e-01
   5_bss:   7.887  0.068  0.325 82.078  0.042  2.030   1.0004e-01
------------------------------------------------------------------------
           |-----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:  91.94   0.00  18.71  70.68   0.00  18.08  91.94   0.00  22.16
   1_occ:  91.94   0.00  18.71  70.68   0.00  18.08  91.94   0.00  22.16
   2_bss:  91.94   0.00  18.71  70.68   0.00  18.08  91.94   0.00  22.16
   2_xyz:  91.94   0.00  18.71  70.68   0.00  18.08  91.94   0.00  22.16
   2_adp:  92.88   0.00  18.64  92.88   0.00  18.13  89.82   0.00  21.40
   2_occ:  92.88   0.00  18.64  92.88   0.00  18.13  89.82   0.00  21.40
   3_bss:  92.88   0.00  18.64  92.88   0.00  18.13  89.82   0.00  21.40
   3_xyz:  92.88   0.00  18.64  92.88   0.00  18.13  89.82   0.00  21.40
   3_adp: 113.14   0.00  22.84 111.69   0.00  21.87 113.14   0.00  28.14
   3_occ: 113.14   0.00  22.84 111.69   0.00  21.87 113.14   0.00  28.14
   4_bss: 113.14   0.00  22.84 111.69   0.00  21.87 113.14   0.00  28.14
   4_xyz: 113.14   0.00  22.84 111.69   0.00  21.87 113.14   0.00  28.14
   4_adp: 103.17   0.00  17.39  93.22   0.00  16.05 103.17   0.00  24.71
   4_occ: 103.17   0.00  17.39  93.22   0.00  16.05 103.17   0.00  24.71
   5_bss: 103.17   0.00  17.39  93.22   0.00  16.05 103.17   0.00  24.71
   5_xyz: 103.17   0.00  17.39  93.22   0.00  16.05 103.17   0.00  24.71
   5_adp: 100.14   0.00  17.20 100.14   0.00  14.13  99.95   0.00  33.87
   5_occ: 100.14   0.00  17.20 100.14   0.00  14.13  99.95   0.00  33.87
   5_bss: 102.58   2.44  19.63 102.58   2.44  16.57 102.39   2.44  36.31
------------------------------------------------------------------------
 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:    1.336    0.028    0.423
   1_adp:    1.336    0.028    0.423
   1_occ:    1.336    0.028    0.423
   2_bss:    1.336    0.028    0.423
   2_xyz:    1.864    0.035    0.570
   2_adp:    1.864    0.035    0.570
   2_occ:    1.864    0.035    0.570
   3_bss:    1.864    0.035    0.570
   3_xyz:    1.647    0.032    0.654
   3_adp:    1.647    0.032    0.654
   3_occ:    1.647    0.032    0.654
   4_bss:    1.647    0.032    0.654
   4_xyz:    1.808    0.047    0.735
   4_adp:    1.808    0.047    0.735
   4_occ:    1.808    0.047    0.735
   5_bss:    1.808    0.047    0.735
   5_xyz:    2.215    0.078    0.906
   5_adp:    2.215    0.078    0.906
   5_occ:    2.215    0.078    0.906
   5_bss:    2.215    0.078    0.906
------------------------------------------------------------------------

CPU time actual refinement: 349.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_10/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_10/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_10/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_10/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_10/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.85 
  Macro-tasks:
    bulk solvent and scale       = 42.45  
    individual site refinement   = 178.17 
    weights calculation          = 32.24  
    collect and process          = 5.83   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 258.81 
  Micro-tasks:
    mask                            = 2.98   
    f_calc                          = 108.26 
    alpha_beta                      = 8.16   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 124.78 
    fmodel                         = 6.54   
    r_factors                      = 0.14   
    phase_errors                   = 8.13   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 260.35 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.882 micro seconds
Total CPU time: 6.08 minutes
from_scatterers_fft:    560 calls, 107.90 s
gradients_fft:          504 calls, 111.28 s

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

# Date 2008-01-16 Time 00:33:28 PST -0800 (1200472408.73 s)
Start R-work = 0.5341, R-free = 0.5375 (no bulk solvent and anisotropic scale)
Final R-work = 0.2852, R-free = 0.3758 (no bulk solvent and anisotropic scale)

Start R-work = 0.5276, R-free = 0.5304
Final R-work = 0.2732, R-free = 0.3637