# Date 2008-01-16 Time 00:39:39 PST -0800 (1200472779.81 s)
#phil __OFF__

Command line arguments: "../108.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16676
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 108

-------------------------------------------------------------------------------
  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, 47.8686, 88.1178, 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: 3.26, 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, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.95101
Completeness in resolution range: 0.903343
Completeness with d_max=infinity: 0.900685

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0027
                             d_min =   1.9510

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, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.95101
Completeness in resolution range: 0.903343
Completeness with d_max=infinity: 0.900685

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0031 -  4.1760 [2275/2303]  2043   232  10.2%
  bin  2:  4.1760 -  3.3265 [2193/2216]  1973   220  10.0%
  bin  3:  3.3265 -  2.9095 [2157/2182]  1950   207   9.6%
  bin  4:  2.9095 -  2.6450 [2123/2150]  1906   217  10.2%
  bin  5:  2.6450 -  2.4563 [2108/2141]  1888   220  10.4%
  bin  6:  2.4563 -  2.3121 [2131/2159]  1926   205   9.6%
  bin  7:  2.3121 -  2.1966 [2085/2121]  1881   204   9.8%
  bin  8:  2.1966 -  2.1013 [2093/2135]  1885   208   9.9%
  bin  9:  2.1013 -  2.0206 [1923/2151]  1732   191   9.9%
  bin 10:  2.0206 -  1.9510 [ 501/2127]   446    55  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_108/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: 0.14 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:
        0.96 -     1.75: 9
        1.75 -     2.54: 65
        2.54 -     3.32: 3861
        3.32 -     4.11: 9361
        4.11 -     4.90: 14975
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  0.961 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.159 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.217 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.360 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.388 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28266 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_108/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_108/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 47.8686 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5269   r_free= 0.5260   ksol= 0.00   Bsol= 0.00   scale= 0.754    |
|                                                                             |
| 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:   1.03 A                  |
| x-ray target function (ml) for work reflections: 6.317118                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6582 0.99   1479  162 0.4329 0.4431      6.6741      6.7157|
|  2:  4.6582 -  3.7159 0.99   1419  157 0.4731 0.5129      6.8759      6.9317|
|  3:  3.7159 -  3.2516 0.99   1395  158 0.5124 0.4975      6.7252      6.7422|
|  4:  3.2516 -  2.9568 0.98   1375  146 0.5257 0.5111      6.5453      6.5224|
|  5:  2.9568 -  2.7463 0.99   1387  157 0.5669 0.5710      6.3814      6.4103|
|  6:  2.7463 -  2.5852 0.99   1364  155 0.5529 0.5512      6.2909      6.2052|
|  7:  2.5852 -  2.4563 0.98   1341  161 0.5559 0.4694       6.237      6.1619|
|  8:  2.4563 -  2.3498 0.98   1383  145 0.5544 0.5639      6.1764      6.2124|
|  9:  2.3498 -  2.2597 0.99   1346  142 0.5688 0.5657      6.1299      6.1705|
| 10:  2.2597 -  2.1819 0.99   1376  146 0.5583 0.5981      6.0811      6.1078|
| 11:  2.1819 -  2.1139 0.97   1338  160 0.5640 0.5560      6.0065      6.0254|
| 12:  2.1139 -  2.0536 0.98   1314  150 0.5637 0.5590      5.9526      5.9253|
| 13:  2.0536 -  1.9997 0.66    908   95 0.5583 0.5690      5.8709      5.8285|
| 14:  1.9997 -  1.9510 0.15    205   25 0.5862 0.4873      5.9336      5.7119|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0031 -  4.6582  1479   162  0.61  41.88   0.77     0.62      97955.85|
|  2:  4.6582 -  3.7159  1419   157  0.57  46.00   0.84     0.63     157006.12|
|  3:  3.7159 -  3.2516  1395   158  0.43  57.40   0.78     0.55     165837.56|
|  4:  3.2516 -  2.9568  1375   146  0.31  66.46   0.75     0.41     139960.82|
|  5:  2.9568 -  2.7463  1387   157  0.23  73.04   0.68     0.30     106740.24|
|  6:  2.7463 -  2.5852  1364   155  0.20  74.96   0.69     0.25      89337.56|
|  7:  2.5852 -  2.4563  1341   161  0.21  74.44   0.70     0.25      78355.22|
|  8:  2.4563 -  2.3498  1383   145  0.25  71.63   0.69     0.30      66656.53|
|  9:  2.3498 -  2.2597  1346   142  0.23  72.68   0.69     0.30      64056.57|
| 10:  2.2597 -  2.1819  1376   146  0.20  75.22   0.72     0.25      56038.71|
| 11:  2.1819 -  2.1139  1338   160  0.12  80.89   0.70     0.17      56747.86|
| 12:  2.1139 -  2.0536  1314   150  0.11  81.78   0.72     0.15      51203.33|
| 13:  2.0536 -  1.9997   908    95  0.12  81.11   0.72     0.17      45472.20|
| 14:  1.9997 -  1.9510   205    25  0.21  73.97   0.74     0.23      32494.13|
|alpha:            min =        0.15 max =            0.63 mean =         0.34|
|beta:             min =    32494.13 max =       165837.56 mean =     91498.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.28|
|phase err.(work): min =        0.00 max =           90.00 mean =        68.46|
|phase err.(test): min =        0.00 max =           89.98 mean =        68.96|
|-----------------------------------------------------------------------------|

============================== 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 = 31.468589             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.515   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.228448              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.893   (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 |  0.649 -  1.074:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.074 -  1.499:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.499 -  1.924:       38 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.924 -  2.349:      230 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.349 -  2.774:      955 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.774 -  3.199:     2148 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.199 -  3.625:     3737 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.625 -  4.050:     5345 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.050 -  4.475:     7142 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.475 -  4.900:     8689 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.868 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.649 |       3.202 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    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 = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5311   r_free= 0.5283   ksol= 0.00   Bsol= 0.00   scale= 0.727    |
|                                                                             |
| 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: 6.317050                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5201   r_free= 0.5235   ksol= 0.31   Bsol= 0.00   scale= 0.952    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,10.22,9.86,0.00,0.00,0.00); trace/3= 8.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.08 A                  |
| x-ray target function (ml) for work reflections: 5.868610                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 26.504604             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.953   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.707736              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.293   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5201      final r-factor (work) = 0.4699          |
| start r-factor (free) = 0.5235      final r-factor (free) = 0.4969          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 137.5599 = 26.50 * 0.50 * 6.3153 + 1.00 * 53.8681                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.4947 = 26.50 * 0.50 * 5.8351 + 1.00 * 0.1668                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4699      final r-factor (work) = 0.4294          |
| start r-factor (free) = 0.4969      final r-factor (free) = 0.4961          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.8142 = 2.71 * 1.00 * 5.8351 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.9275 = 2.71 * 1.00 * 6.2415 + 1.00 * 0.0272                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.80  19.58    None  None   None       |
|    all(noH): 2823   0      0.00    113.80  19.58    None  None   None       |
|    Sol.    : 438    0      0.00    113.80  28.50    None  None   None       |
|    Mac.    : 2385   0      0.00    93.02   17.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.380: 1021   |   5:    56.898 -  68.278:   51        |
|      1:    11.380 -  22.759:  857   |   6:    68.278 -  79.658:   22        |
|      2:    22.759 -  34.139:  478   |   7:    79.658 -  91.037:    7        |
|      3:    34.139 -  45.519:  255   |   8:    91.037 - 102.417:    5        |
|      4:    45.519 -  56.898:  124   |   9:   102.417 - 113.797:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4294 r_free = 0.4961             target_work(ml) = 6.235         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4290 r_free = 0.4967             target_work(ml) = 6.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4290   r_free= 0.4967   ksol= 0.31   Bsol= 0.00   scale= 1.134    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,10.22,9.86,0.00,0.00,0.00); trace/3= 8.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.234698                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4279   r_free= 0.4899   ksol= 0.32   Bsol= 27.21   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.16,6.01,6.05,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.235499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.572844             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.166  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.893330              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.693  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4279      final r-factor (work) = 0.3710          |
| start r-factor (free) = 0.4899      final r-factor (free) = 0.4385          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.7488 = 15.57 * 0.50 * 6.2393 + 1.00 * 0.1668                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.3002 = 15.57 * 0.50 * 6.1875 + 1.00 * 0.1213                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3710      final r-factor (work) = 0.3557          |
| start r-factor (free) = 0.4385      final r-factor (free) = 0.4249          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5547 = 0.89 * 1.00 * 6.1875 + 1.00 * 0.0272                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4856 = 0.89 * 1.00 * 6.1252 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.01  18.00    None  None   None       |
|    all(noH): 2823   0      0.00    116.01  18.00    None  None   None       |
|    Sol.    : 438    0      0.00    116.01  29.81    None  None   None       |
|    Mac.    : 2385   0      0.00    84.48   15.83    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 -  11.601: 1086   |   5:    58.003 -  69.603:   21        |
|      1:    11.601 -  23.201:  950   |   6:    69.603 -  81.204:   12        |
|      2:    23.201 -  34.802:  474   |   7:    81.204 -  92.805:    1        |
|      3:    34.802 -  46.402:  204   |   8:    92.805 - 104.405:    2        |
|      4:    46.402 -  58.003:   72   |   9:   104.405 - 116.006:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3557 r_free = 0.4249             target_work(ml) = 6.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3555 r_free = 0.4247             target_work(ml) = 6.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3555   r_free= 0.4247   ksol= 0.32   Bsol= 27.21   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.16,6.01,6.05,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.109969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3530   r_free= 0.4209   ksol= 0.30   Bsol= 27.21   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.58,3.04,3.09,0.00,0.00,0.00); trace/3= 2.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.111035                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.642563             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.805   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.360105              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.684  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3530      final r-factor (work) = 0.2729          |
| start r-factor (free) = 0.4209      final r-factor (free) = 0.3337          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.8406 = 12.64 * 0.50 * 6.1252 + 1.00 * 0.1213                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.2168 = 12.64 * 0.50 * 6.0274 + 1.00 * 0.1159                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2729      final r-factor (work) = 0.2500          |
| start r-factor (free) = 0.3337      final r-factor (free) = 0.3084          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1844 = 0.36 * 1.00 * 6.0274 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1222 = 0.36 * 1.00 * 5.8638 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.45   16.69    None  None   None       |
|    all(noH): 2823   0      0.00    98.45   16.69    None  None   None       |
|    Sol.    : 438    0      2.52    98.45   34.25    None  None   None       |
|    Mac.    : 2385   0      0.00    79.17   13.46    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 -   9.846: 1044   |   5:    49.227 -  59.073:   51        |
|      1:     9.846 -  19.691:  987   |   6:    59.073 -  68.918:   17        |
|      2:    19.691 -  29.536:  370   |   7:    68.918 -  78.764:    6        |
|      3:    29.536 -  39.382:  205   |   8:    78.764 -  88.609:    2        |
|      4:    39.382 -  49.227:  139   |   9:    88.609 -  98.455:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2500 r_free = 0.3084             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2496 r_free = 0.3081             target_work(ml) = 5.826         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2496   r_free= 0.3081   ksol= 0.30   Bsol= 27.21   scale= 1.055   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.58,3.04,3.09,0.00,0.00,0.00); trace/3= 2.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.825634                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2473   r_free= 0.3063   ksol= 0.33   Bsol= 55.34   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,0.65,1.04,0.00,0.00,0.00); trace/3= 0.05                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.822873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.390005              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.761   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.335580              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.049  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2473      final r-factor (work) = 0.1858          |
| start r-factor (free) = 0.3063      final r-factor (free) = 0.2347          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8702 = 6.39 * 0.50 * 5.8699 + 1.00 * 0.1159                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3655 = 6.39 * 0.50 * 5.7216 + 1.00 * 0.0849                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1858      final r-factor (work) = 0.1669          |
| start r-factor (free) = 0.2347      final r-factor (free) = 0.2187          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9290 = 0.34 * 1.00 * 5.7216 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8646 = 0.34 * 1.00 * 5.5273 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.01   16.78    None  None   None       |
|    all(noH): 2823   0      0.00    90.01   16.78    None  None   None       |
|    Sol.    : 438    0      4.36    90.01   40.06    None  None   None       |
|    Mac.    : 2385   0      0.00    84.33   12.50    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 -   9.001:  966   |   5:    45.007 -  54.008:  124        |
|      1:     9.001 -  18.003: 1104   |   6:    54.008 -  63.010:   65        |
|      2:    18.003 -  27.004:  269   |   7:    63.010 -  72.011:   21        |
|      3:    27.004 -  36.005:  127   |   8:    72.011 -  81.012:    6        |
|      4:    36.005 -  45.007:  137   |   9:    81.012 -  90.014:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1669 r_free = 0.2187             target_work(ml) = 5.492         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1667 r_free = 0.2186             target_work(ml) = 5.491         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2186   ksol= 0.33   Bsol= 55.34   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,0.65,1.04,0.00,0.00,0.00); trace/3= 0.05                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.491475                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1662   r_free= 0.2184   ksol= 0.33   Bsol= 56.07   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.36,0.41,-0.00,0.00,0.00); trace/3= -0.77                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.490984                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.975972              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.777  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.322488              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.062  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1662      final r-factor (work) = 0.1387          |
| start r-factor (free) = 0.2184      final r-factor (free) = 0.1890          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0783 = 3.98 * 0.50 * 5.5299 + 1.00 * 0.0849                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8541 = 3.98 * 0.50 * 5.4197 + 1.00 * 0.0798                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1387      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.1890      final r-factor (free) = 0.1838          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7574 = 0.32 * 1.00 * 5.4197 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7302 = 0.32 * 1.00 * 5.3215 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.40   16.68    None  None   None       |
|    all(noH): 2823   0      0.00    87.40   16.68    None  None   None       |
|    Sol.    : 438    0      5.73    87.40   40.44    None  None   None       |
|    Mac.    : 2385   0      0.00    83.77   12.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.740:  920   |   5:    43.701 -  52.441:  121        |
|      1:     8.740 -  17.480: 1162   |   6:    52.441 -  61.181:   79        |
|      2:    17.480 -  26.221:  255   |   7:    61.181 -  69.921:   29        |
|      3:    26.221 -  34.961:  120   |   8:    69.921 -  78.661:   10        |
|      4:    34.961 -  43.701:  122   |   9:    78.661 -  87.402:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1331 r_free = 0.1838             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1330 r_free = 0.1838             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1838   ksol= 0.33   Bsol= 56.07   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.36,0.41,-0.00,0.00,0.00); trace/3= -0.77                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.305482                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6582 0.99   1479  162 0.1035 0.1491      5.4828      5.6942|
|  2:  4.6582 -  3.7159 0.99   1419  157 0.0945 0.1141      5.5422        5.73|
|  3:  3.7159 -  3.2516 0.99   1395  158 0.1272 0.1731      5.6235      5.9213|
|  4:  3.2516 -  2.9568 0.98   1375  146 0.1471 0.2073      5.5775      5.8186|
|  5:  2.9568 -  2.7463 0.99   1387  157 0.1651 0.1936      5.5039      5.6527|
|  6:  2.7463 -  2.5852 0.99   1364  155 0.1514 0.2316      5.3673      5.5847|
|  7:  2.5852 -  2.4563 0.98   1341  161 0.1513 0.1922      5.3089      5.4602|
|  8:  2.4563 -  2.3498 0.98   1383  145 0.1487 0.2223      5.2504      5.5006|
|  9:  2.3498 -  2.2597 0.99   1346  142 0.1388 0.1931      5.1601      5.3792|
| 10:  2.2597 -  2.1819 0.99   1376  146 0.1378 0.2117      5.1098      5.3339|
| 11:  2.1819 -  2.1139 0.97   1338  160 0.1369 0.2052       5.035      5.3599|
| 12:  2.1139 -  2.0536 0.98   1314  150 0.1384 0.1946      5.0042      5.2388|
| 13:  2.0536 -  1.9997 0.66    908   95 0.1294 0.1890      4.8842      5.0221|
| 14:  1.9997 -  1.9510 0.15    205   25 0.1148 0.2002      4.8246       5.051|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0031 -  4.6582  1479   162  0.92  11.26   0.97     0.94       9875.57|
|  2:  4.6582 -  3.7159  1419   157  0.94  10.03   1.02     1.00      11775.65|
|  3:  3.7159 -  3.2516  1395   158  0.92  13.84   1.03     1.02      13847.14|
|  4:  3.2516 -  2.9568  1375   146  0.89  17.39   1.02     1.01      13469.23|
|  5:  2.9568 -  2.7463  1387   157  0.87  19.57   1.01     0.98      12116.33|
|  6:  2.7463 -  2.5852  1364   155  0.86  20.11   0.98     0.95       9784.61|
|  7:  2.5852 -  2.4563  1341   161  0.87  19.46   1.00     0.96       8583.55|
|  8:  2.4563 -  2.3498  1383   145  0.87  19.86   1.01     0.96       7760.31|
|  9:  2.3498 -  2.2597  1346   142  0.87  19.30   1.00     0.96       6696.99|
| 10:  2.2597 -  2.1819  1376   146  0.87  19.59   1.01     0.98       6241.04|
| 11:  2.1819 -  2.1139  1338   160  0.87  19.73   1.00     0.96       5540.59|
| 12:  2.1139 -  2.0536  1314   150  0.87  19.43   1.00     1.00       5139.33|
| 13:  2.0536 -  1.9997   908    95  0.87  19.44   0.99     0.98       4233.85|
| 14:  1.9997 -  1.9510   205    25  0.91  14.73   0.97     0.92       3139.92|
|alpha:            min =        0.92 max =            1.02 mean =         0.98|
|beta:             min =     3139.92 max =        13847.14 mean =      8950.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.46|
|phase err.(test): min =        0.00 max =           89.26 mean =        16.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1838   ksol= 0.33   Bsol= 56.07   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-0.82,0.17,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.306193                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1838   ksol= 0.33   Bsol= 56.07   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-0.82,0.17,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.306193                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6582 0.99   1479  162 0.1049 0.1491      5.4791      5.6851|
|  2:  4.6582 -  3.7159 0.99   1419  157 0.0965 0.1128      5.5506      5.7327|
|  3:  3.7159 -  3.2516 0.99   1395  158 0.1279 0.1735      5.6286      5.9212|
|  4:  3.2516 -  2.9568 0.98   1375  146 0.1476 0.2074      5.5784      5.8211|
|  5:  2.9568 -  2.7463 0.99   1387  157 0.1651 0.1936      5.5045       5.654|
|  6:  2.7463 -  2.5852 0.99   1364  155 0.1514 0.2315      5.3676      5.5845|
|  7:  2.5852 -  2.4563 0.98   1341  161 0.1514 0.1927      5.3091      5.4603|
|  8:  2.4563 -  2.3498 0.98   1383  145 0.1481 0.2218      5.2492      5.5006|
|  9:  2.3498 -  2.2597 0.99   1346  142 0.1387 0.1931      5.1591      5.3795|
| 10:  2.2597 -  2.1819 0.99   1376  146 0.1375 0.2115      5.1095      5.3354|
| 11:  2.1819 -  2.1139 0.97   1338  160 0.1369 0.2050      5.0346      5.3583|
| 12:  2.1139 -  2.0536 0.98   1314  150 0.1385 0.1942      5.0043      5.2386|
| 13:  2.0536 -  1.9997 0.66    908   95 0.1295 0.1889      4.8839      5.0197|
| 14:  1.9997 -  1.9510 0.15    205   25 0.1146 0.2002      4.8258      5.0549|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0031 -  4.6582  1479   162  0.92  11.23   0.96     0.94       9733.09|
|  2:  4.6582 -  3.7159  1419   157  0.94  10.10   1.01     1.00      11775.45|
|  3:  3.7159 -  3.2516  1395   158  0.92  13.91   1.02     1.02      13989.75|
|  4:  3.2516 -  2.9568  1375   146  0.89  17.41   1.01     1.00      13464.18|
|  5:  2.9568 -  2.7463  1387   157  0.87  19.60   1.00     0.97      12146.24|
|  6:  2.7463 -  2.5852  1364   155  0.86  20.11   0.97     0.94       9807.42|
|  7:  2.5852 -  2.4563  1341   161  0.87  19.48   0.98     0.95       8601.83|
|  8:  2.4563 -  2.3498  1383   145  0.87  19.85   1.00     0.95       7761.09|
|  9:  2.3498 -  2.2597  1346   142  0.87  19.29   0.99     0.94       6696.86|
| 10:  2.2597 -  2.1819  1376   146  0.87  19.57   1.00     0.97       6243.76|
| 11:  2.1819 -  2.1139  1338   160  0.87  19.71   0.99     0.94       5533.65|
| 12:  2.1139 -  2.0536  1314   150  0.87  19.40   0.99     0.98       5130.89|
| 13:  2.0536 -  1.9997   908    95  0.87  19.42   0.98     0.96       4220.98|
| 14:  1.9997 -  1.9510   205    25  0.91  14.74   0.96     0.90       3136.57|
|alpha:            min =        0.90 max =            1.02 mean =         0.97|
|beta:             min =     3136.57 max =        13989.75 mean =      8953.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.46|
|phase err.(test): min =        0.00 max =           89.24 mean =        16.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.40   16.69    None  None   None       |
|    all(noH): 2823   0      0.00    87.40   16.69    None  None   None       |
|    Sol.    : 438    0      5.74    87.40   40.44    None  None   None       |
|    Mac.    : 2385   0      0.00    83.77   12.32    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:     0.003 -   8.743:  920   |   5:    43.704 -  52.444:  121        |
|      1:     8.743 -  17.483: 1162   |   6:    52.444 -  61.184:   79        |
|      2:    17.483 -  26.223:  255   |   7:    61.184 -  69.924:   29        |
|      3:    26.223 -  34.964:  120   |   8:    69.924 -  78.664:   10        |
|      4:    34.964 -  43.704:  122   |   9:    78.664 -  87.405:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.674 - 4.234
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 312
   mapped sites are within: 0.746 - 4.234

peak=    9.322 closest distance to " CB  VAL A 230 " =    1.407
peak=    8.184 closest distance to " O   HOH Z 203 " =    0.878
peak=    7.184 closest distance to " O   HOH Z 255 " =    1.300
peak=    6.851 closest distance to " CG1 ILE A 234 " =    1.441
peak=    6.716 closest distance to " O   HOH Z 190 " =    1.000
peak=    6.703 closest distance to " CG1 VAL A 296 " =    1.239
peak=    6.463 closest distance to " O   HOH Z 404 " =    1.824
peak=    6.416 closest distance to " O   HOH Z 169 " =    1.219
peak=    5.832 closest distance to " O   HOH Z 248 " =    1.668
peak=    5.679 closest distance to " O   HOH Z 124 " =    1.603
peak=    5.630 closest distance to " O   HOH Z 117 " =    1.522
peak=    5.421 closest distance to " O   HOH Z 210 " =    1.509
peak=    5.403 closest distance to " O   HOH Z 277 " =    1.689
peak=    5.250 closest distance to " O   HOH Z 425 " =    1.792
peak=    5.179 closest distance to " O   HOH Z 403 " =    2.136
peak=    5.035 closest distance to " CB  ARG A 275 " =    0.895
peak=    5.011 closest distance to " O   HOH Z  45 " =    1.067
peak=    4.957 closest distance to " CD2 LEU A   5 " =    1.167
peak=    4.931 closest distance to " O   HOH Z 258 " =    1.396
peak=    4.890 closest distance to " O   HOH Z 169 " =    2.319
peak=    4.882 closest distance to " O   HOH Z 142 " =    2.446
peak=    4.864 closest distance to " CG  LEU A   5 " =    1.287
peak=    4.855 closest distance to " O   HOH Z 128 " =    1.992
peak=    4.809 closest distance to " CG  PRO A 280 " =    0.954
peak=    4.722 closest distance to " O   HOH Z 394 " =    1.898
peak=    4.621 closest distance to " O   HOH Z  97 " =    1.494
peak=    4.596 closest distance to " CD2 TRP A 179 " =    1.356
peak=    4.593 closest distance to " O   HOH Z 406 " =    1.678
peak=    4.550 closest distance to " O   HOH Z  49 " =    1.633
peak=    4.549 closest distance to " NH2AARG A 145 " =    0.952
peak=    4.515 closest distance to " O   HOH Z  76 " =    1.377
peak=    4.489 closest distance to " NH2 ARG A  56 " =    2.117
peak=    4.474 closest distance to " CG  PRO A  54 " =    1.385
peak=    4.470 closest distance to " CZ  PHE A 218 " =    1.196
peak=    4.418 closest distance to " O   GLN A  11 " =    0.995
peak=    4.418 closest distance to " CD2 LEU A 228 " =    1.275
peak=    4.400 closest distance to " NH2 ARG A  56 " =    1.193
peak=    4.377 closest distance to " O   HOH Z 102 " =    1.448
peak=    4.368 closest distance to " CB  VAL A 230 " =    1.302
peak=    4.360 closest distance to " CA  TYR A  30 " =    0.980
peak=    4.344 closest distance to " O   HOH Z 431 " =    1.417
peak=    4.331 closest distance to " O   HOH Z 193 " =    2.247
peak=    4.327 closest distance to " O   HOH Z 154 " =    1.779
peak=    4.316 closest distance to " O   HOH Z 130 " =    2.674
peak=    4.300 closest distance to " O   HOH Z 359 " =    1.985
peak=    4.293 closest distance to " O  BHOH Z 338 " =    1.253
peak=    4.258 closest distance to " O   HOH Z 411 " =    3.643
peak=    4.234 closest distance to " CG AARG A 275 " =    1.312
peak=    4.218 closest distance to " CB  GLU A 152 " =    1.161
peak=    4.209 closest distance to " CB  SER A  63 " =    1.127
peak=    4.192 closest distance to " O   HOH Z  69 " =    1.178
peak=    4.186 closest distance to " NE2 GLN A  11 " =    1.164
peak=    4.185 closest distance to " CB  ASN A 148 " =    1.330
peak=    4.177 closest distance to " O   HOH Z 402 " =    1.564
peak=    4.153 closest distance to " O   HOH Z 241 " =    2.285
peak=    4.133 closest distance to " O   HOH Z 126 " =    1.637
peak=    4.117 closest distance to " OE1 GLN A  11 " =    2.019
peak=    4.096 closest distance to " O   HOH Z 368 " =    2.341
peak=    4.092 closest distance to " CB  GLN A  55 " =    0.900
peak=    4.091 closest distance to " O   HOH Z  63 " =    1.869
peak=    4.086 closest distance to " CB  SER A  26 " =    1.747
peak=    4.081 closest distance to " O   HOH Z 126 " =    1.571
peak=    4.077 closest distance to " CB  TYR A  30 " =    1.121
peak=    4.069 closest distance to " NH1AARG A 275 " =    1.139
peak=    4.057 closest distance to " O   HOH Z 236 " =    1.704
peak=    4.047 closest distance to " O   HOH Z 146 " =    1.692
peak=    4.045 closest distance to " CB  VAL A 296 " =    1.437
peak=    4.044 closest distance to " O   HOH Z 409 " =    3.721
peak=    4.036 closest distance to " O   HOH Z  85 " =    1.831
peak=    4.031 closest distance to " CB  GLN A 223 " =    1.441
peak=    4.022 closest distance to " CZ3 TRP A 266 " =    1.086
peak=    4.018 closest distance to " O   HOH Z 132 " =    2.825
peak=    4.011 closest distance to " OE1 GLN A  55 " =    1.582
peak=    4.002 closest distance to " O   HOH Z 234 " =    3.559
peak=    3.990 closest distance to " CB  GLN A 183 " =    1.280
peak=    3.983 closest distance to " CA  ALA A  51 " =    1.040
peak=    3.968 closest distance to " O   HOH Z  80 " =    2.262
peak=    3.960 closest distance to " O   HOH Z 246 " =    1.176
peak=    3.937 closest distance to " CG  PRO A 243 " =    1.072
peak=    3.935 closest distance to " O   HOH Z 146 " =    1.331
peak=    3.925 closest distance to " CD  ARG A 159 " =    0.828
peak=    3.921 closest distance to " CG2AVAL A 121 " =    2.067
peak=    3.891 closest distance to " O   HOH Z 137 " =    1.697
peak=    3.883 closest distance to " CE1 TYR A 186 " =    1.273
peak=    3.883 closest distance to " O   HOH Z   4 " =    1.788
peak=    3.862 closest distance to " O   HOH Z  68 " =    1.798
peak=    3.859 closest distance to " O   SER A  87 " =    2.247
peak=    3.852 closest distance to " CD  LYS A  76 " =    1.929
peak=    3.849 closest distance to " CG1 ILE A  20 " =    1.387
peak=    3.825 closest distance to " O   HOH Z  40 " =    2.117
peak=    3.821 closest distance to " O   HOH Z 369 " =    1.330
peak=    3.821 closest distance to " CA  ARG A  36 " =    1.077
peak=    3.809 closest distance to " O   HOH Z 328 " =    1.596
peak=    3.799 closest distance to " ND2 ASN A 249 " =    2.017
peak=    3.799 closest distance to " CB  SER A  62 " =    1.026
peak=    3.798 closest distance to " O   HOH Z 111 " =    1.582
peak=    3.796 closest distance to " CD  PRO A  54 " =    1.027
peak=    3.788 closest distance to " CD1 LEU A   5 " =    1.583
peak=    3.766 closest distance to " O   HOH Z 287 " =    1.761
peak=    3.741 closest distance to " NZ  LYS A 117 " =    2.528
peak=    3.738 closest distance to " CG2 VAL A 197 " =    1.216
peak=    3.736 closest distance to " CD  LYS A 166 " =    1.586
peak=    3.734 closest distance to " O   HOH Z 339 " =    1.541
peak=    3.733 closest distance to " CG2AVAL A  72 " =    1.744
peak=    3.728 closest distance to " O   HOH Z 213 " =    1.552
peak=    3.728 closest distance to " CB  TRP A 179 " =    1.294
peak=    3.720 closest distance to " NH2 ARG A 156 " =    1.027
peak=    3.715 closest distance to " O   HOH Z  59 " =    2.044
peak=    3.707 closest distance to " O   HOH Z 193 " =    2.104
peak=    3.705 closest distance to " OG  SER A  97 " =    2.835
peak=    3.684 closest distance to " O   HOH Z 419 " =    1.903
peak=    3.683 closest distance to " CA  ARG A 195 " =    1.136
peak=    3.678 closest distance to " O   HOH Z 214 " =    1.393
peak=    3.677 closest distance to " O   THR A 182 " =    1.560
peak=    3.675 closest distance to " O   HOH Z 251 " =    1.664
peak=    3.672 closest distance to " O   HOH Z  54 " =    1.112
peak=    3.658 closest distance to " O   HOH Z  83 " =    1.585
peak=    3.654 closest distance to " O   HOH Z 346 " =    1.541
peak=    3.647 closest distance to " CA  ASP A 162 " =    0.926
peak=    3.647 closest distance to " O   HOH Z 272 " =    1.812
peak=    3.644 closest distance to " CB  ASP A 124 " =    0.808
peak=    3.643 closest distance to " O   HOH Z 368 " =    3.335
peak=    3.641 closest distance to " CG  LEU A 228 " =    1.233
peak=    3.639 closest distance to " O   HOH Z 279 " =    1.058
peak=    3.627 closest distance to " O   HOH Z 232 " =    2.354
peak=    3.621 closest distance to " CG2 ILE A 234 " =    1.168
peak=    3.620 closest distance to " O   HOH Z 433 " =    1.526
peak=    3.614 closest distance to " O   HOH Z 134 " =    1.946
peak=    3.607 closest distance to " CE1 HIS A 108 " =    1.183
peak=    3.600 closest distance to " CG  ARG A  66 " =    1.026
peak=    3.596 closest distance to " O   ALA A 165 " =    1.345
peak=    3.594 closest distance to " O   HOH Z 142 " =    1.638
peak=    3.593 closest distance to " O   HOH Z 298 " =    2.430
peak=    3.592 closest distance to " O   HOH Z 435 " =    1.875
peak=    3.586 closest distance to " NE AARG A 145 " =    0.851
peak=    3.579 closest distance to " O   HOH Z 298 " =    4.234
peak=    3.574 closest distance to " O   HOH Z 423 " =    1.642
peak=    3.569 closest distance to " CD  GLN A 194 " =    1.500
peak=    3.566 closest distance to " CG  GLN A  58 " =    1.124
peak=    3.553 closest distance to " O   HOH Z 357 " =    2.049
peak=    3.537 closest distance to " CB  THR A 235 " =    1.225
peak=    3.535 closest distance to " O   PRO A 198 " =    1.577
peak=    3.528 closest distance to " CB  ASP A 140 " =    0.803
peak=    3.521 closest distance to " CB  ASP A 191 " =    1.167
peak=    3.521 closest distance to " O   HOH Z 212 " =    3.355
peak=    3.521 closest distance to " O   ASP A 200 " =    1.617
peak=    3.519 closest distance to " CB  SER A  62 " =    3.836
peak=    3.516 closest distance to " CE1 TYR A  30 " =    1.174
peak=    3.514 closest distance to " CB  GLN A  58 " =    1.057
peak=    3.512 closest distance to " O   HOH Z 234 " =    1.942
peak=    3.512 closest distance to " ND2BASN A 224 " =    0.902
peak=    3.507 closest distance to " NE1 TRP A  92 " =    1.425
peak=    3.505 closest distance to " CB  ALA A 248 " =    1.419
peak=    3.504 closest distance to " NE  ARG A  24 " =    1.050
peak=    3.500 closest distance to " O   HOH Z 316 " =    3.184
peak=    3.500 closest distance to " CB BVAL A  41 " =    1.170
peak=    3.497 closest distance to " CG2 THR A 221 " =    1.083
peak=    3.495 closest distance to " CD2 LEU A 297 " =    0.999
peak=    3.495 closest distance to " O   HOH Z 414 " =    2.341
peak=    3.494 closest distance to " CB  GLU A 277 " =    0.930
peak=    3.492 closest distance to " O   HOH Z 193 " =    2.042
peak=    3.491 closest distance to " CB  PRO A  54 " =    0.932
peak=    3.491 closest distance to " O   HOH Z 380 " =    1.746
peak=    3.488 closest distance to " O   GLU A   2 " =    1.723
peak=    3.482 closest distance to " O   HOH Z  67 " =    2.026
peak=    3.469 closest distance to " O   HOH Z 245 " =    1.366
peak=    3.469 closest distance to " O   HOH Z   4 " =    1.976
peak=    3.469 closest distance to " CB  GLN A  89 " =    1.375
peak=    3.467 closest distance to " CB  THR A  52 " =    0.878
peak=    3.455 closest distance to " O   HOH Z 301 " =    1.668
peak=    3.455 closest distance to " CB  ARG A  79 " =    0.851
peak=    3.453 closest distance to " O   HOH Z 189 " =    2.248
peak=    3.451 closest distance to " O   HOH Z  56 " =    1.708
peak=    3.445 closest distance to " CA  THR A  82 " =    1.644
peak=    3.443 closest distance to " CA  SER A  32 " =    1.771
peak=    3.442 closest distance to " CD1 ILE A 199 " =    1.278
peak=    3.437 closest distance to " O   HOH Z 299 " =    3.897
peak=    3.428 closest distance to " O   HOH Z 366 " =    2.524
peak=    3.426 closest distance to " O   HOH Z 107 " =    0.913
peak=    3.425 closest distance to " CB  ALA A  71 " =    1.364
peak=    3.424 closest distance to " O   HOH Z  35 " =    1.923
peak=    3.423 closest distance to " CA  ALA A 129 " =    1.154
peak=    3.418 closest distance to " O   THR A 220 " =    1.151
peak=    3.416 closest distance to " OG BSER A 212 " =    2.411
peak=    3.416 closest distance to " O  BHOH Z  74 " =    1.272
peak=    3.412 closest distance to " O   HOH Z  95 " =    1.263
peak=    3.412 closest distance to " O   HOH Z  88 " =    3.456
peak=    3.410 closest distance to " CG  ARG A 138 " =    1.392
peak=    3.409 closest distance to " CG AARG A 102 " =    1.214
peak=    3.405 closest distance to " O   HOH Z  44 " =    1.375
peak=    3.403 closest distance to " O   HOH Z 265 " =    1.946
peak=    3.401 closest distance to " O   HOH Z 199 " =    1.436
peak=    3.400 closest distance to " CD2 LEU A  83 " =    1.552
peak=    3.397 closest distance to " CA  VAL A  41 " =    0.797
peak=    3.383 closest distance to " CB  PRO A 198 " =    1.157
peak=    3.377 closest distance to " CD  LYS A 119 " =    2.041
peak=    3.376 closest distance to " O   HOH Z 188 " =    1.340
peak=    3.372 closest distance to " CZ  PHE A  38 " =    1.217
peak=    3.366 closest distance to " O   HOH Z 344 " =    1.757
peak=    3.363 closest distance to " O   HOH Z 154 " =    2.102
peak=    3.360 closest distance to " N   GLU A  44 " =    1.434
peak=    3.360 closest distance to " O   HOH Z 158 " =    1.189
peak=    3.360 closest distance to " CZ3 TRP A  92 " =    1.251
peak=    3.359 closest distance to " O   HOH Z 350 " =    1.395
peak=    3.353 closest distance to " O   HOH Z 331 " =    1.155
peak=    3.352 closest distance to " CD AARG A 190 " =    1.579
peak=    3.350 closest distance to " CG2 ILE A 120 " =    1.518
peak=    3.350 closest distance to " CZ3 TRP A  85 " =    1.087
peak=    3.349 closest distance to " CB  SER A 141 " =    1.130
peak=    3.341 closest distance to " O   HOH Z 313 " =    1.722
peak=    3.340 closest distance to " CB  MET A  40 " =    0.983
peak=    3.335 closest distance to " O   HOH Z 166 " =    1.823
peak=    3.335 closest distance to " CB  VAL A 265 " =    1.287
peak=    3.334 closest distance to " CB  ARG A 219 " =    1.130
peak=    3.334 closest distance to " CB  ASN A 142 " =    1.070
peak=    3.332 closest distance to " OD1 ASN A 301 " =    1.068
peak=    3.331 closest distance to " N   ALA A   1 " =    1.373
peak=    3.329 closest distance to " CA  SER A  12 " =    1.286
peak=    3.328 closest distance to " CG  ASN A 110 " =    1.477
peak=    3.326 closest distance to " O   HOH Z 158 " =    2.753
peak=    3.323 closest distance to " O   HOH Z 327 " =    1.701
peak=    3.323 closest distance to " O   HOH Z  46 " =    1.374
peak=    3.318 closest distance to " O   HOH Z 151 " =    1.743
peak=    3.318 closest distance to " O   HOH Z 371 " =    2.613
peak=    3.317 closest distance to " O   HOH Z  78 " =    1.660
peak=    3.310 closest distance to " CB  PRO A 243 " =    1.082
peak=    3.308 closest distance to " CG  PHE A 204 " =    0.958
peak=    3.306 closest distance to " O   HOH Z 299 " =    1.695
peak=    3.302 closest distance to " CD  ARG A 195 " =    0.819
peak=    3.300 closest distance to " CD1 LEU A  96 " =    0.975
peak=    3.293 closest distance to " O   HOH Z 137 " =    2.384
peak=    3.292 closest distance to " NH2BARG A 190 " =    1.964
peak=    3.291 closest distance to " CA  ALA A 295 " =    0.889
peak=    3.288 closest distance to " O   HOH Z  30 " =    1.300
peak=    3.281 closest distance to " NH2 ARG A  36 " =    1.928
peak=    3.277 closest distance to " OE1 GLU A   2 " =    1.550
peak=    3.275 closest distance to " NE2 GLN A  77 " =    3.208
peak=    3.274 closest distance to " CB  SER A   3 " =    1.181
peak=    3.274 closest distance to " CA  ASP A 140 " =    1.399
peak=    3.270 closest distance to " CD2 LEU A 297 " =    0.765
peak=    3.263 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.262 closest distance to " O   HOH Z 383 " =    2.041
peak=    3.260 closest distance to " O   HOH Z 345 " =    1.768
peak=    3.259 closest distance to " CD2 TYR A 186 " =    0.994
peak=    3.255 closest distance to " O   HOH Z 423 " =    1.853
peak=    3.254 closest distance to " CB  GLU A 175 " =    1.326
peak=    3.252 closest distance to " CA  ALA A 100 " =    1.051
peak=    3.251 closest distance to " CG2 THR A 220 " =    0.746
peak=    3.250 closest distance to " O   HOH Z 285 " =    1.977
peak=    3.246 closest distance to " O   HOH Z 337 " =    2.214
peak=    3.245 closest distance to " O   HOH Z  67 " =    1.327
peak=    3.237 closest distance to " O  BHOH Z 338 " =    1.928
peak=    3.233 closest distance to " CB  ASN A 285 " =    0.981
peak=    3.226 closest distance to " CA  THR A 246 " =    1.037
peak=    3.226 closest distance to " O   HOH Z 191 " =    1.109
peak=    3.222 closest distance to " OG  SER A 245 " =    1.416
peak=    3.217 closest distance to " O   HOH Z 227 " =    1.579
peak=    3.215 closest distance to " CA  LYS A 117 " =    1.229
peak=    3.212 closest distance to " CB  GLU A 128 " =    1.261
peak=    3.211 closest distance to " CA  ASN A  39 " =    1.177
peak=    3.211 closest distance to " CA  ALA A 158 " =    1.578
peak=    3.211 closest distance to " CA  ASN A 217 " =    1.139
peak=    3.209 closest distance to " O   HOH Z 438 " =    2.187
peak=    3.205 closest distance to " CE3 TRP A 274 " =    1.272
peak=    3.204 closest distance to " CB  GLU A  46 " =    1.048
peak=    3.203 closest distance to " O   HOH Z 426 " =    1.273
peak=    3.201 closest distance to " NH1BARG A 102 " =    0.995
peak=    3.201 closest distance to " CG1 VAL A 174 " =    1.578
peak=    3.198 closest distance to " CB  SER A  62 " =    1.321
peak=    3.196 closest distance to " CB  TRP A 179 " =    1.743
peak=    3.194 closest distance to " O   HOH Z 303 " =    2.294
peak=    3.194 closest distance to " O   HOH Z 417 " =    3.134
peak=    3.193 closest distance to " OD1 ASP A 231 " =    1.988
peak=    3.186 closest distance to " CB  SER A  99 " =    1.206
peak=    3.184 closest distance to " CB  THR A  31 " =    1.343
peak=    3.181 closest distance to " CG  PRO A 213 " =    1.294
peak=    3.180 closest distance to " O   HOH Z 141 " =    1.639
peak=    3.178 closest distance to " O   HOH Z 112 " =    0.956
peak=    3.177 closest distance to " O   HOH Z 255 " =    2.147
peak=    3.172 closest distance to " NH2AARG A 275 " =    3.462
peak=    3.164 closest distance to " O   HOH Z 395 " =    1.472
peak=    3.162 closest distance to " CA  TYR A 116 " =    1.466
peak=    3.161 closest distance to " CZ2 TRP A 274 " =    1.194
peak=    3.154 closest distance to " CA  ILE A 234 " =    0.879
peak=    3.147 closest distance to " O   HOH Z 427 " =    2.647
peak=    3.146 closest distance to " OG  SER A  62 " =    2.710
peak=    3.138 closest distance to " CG2 ILE A  20 " =    1.369
peak=    3.137 closest distance to " CG1 ILE A  49 " =    1.507
peak=    3.135 closest distance to " CB  ALA A   1 " =    1.264
peak=    3.120 closest distance to " NH1 ARG A  14 " =    1.021
peak=    3.119 closest distance to " CD1 LEU A 300 " =    0.898
peak=    3.118 closest distance to " O   HOH Z  39 " =    1.155
peak=    3.117 closest distance to " CB  SER A  97 " =    1.005
peak=    3.117 closest distance to " O   HOH Z 366 " =    2.291
peak=    3.111 closest distance to " CG1 ILE A 120 " =    1.030
peak=    3.110 closest distance to " CB  ARG A  79 " =    1.859
peak=    3.102 closest distance to " O   HOH Z 387 " =    2.111
peak=    3.102 closest distance to " CD  ARG A 139 " =    1.271
peak=    3.102 closest distance to " NH2 ARG A 269 " =    1.032
peak=    3.100 closest distance to " CA  GLY A 267 " =    1.526
peak=    3.098 closest distance to " CG  LYS A  76 " =    1.021
peak=    3.091 closest distance to " CB  PRO A  90 " =    1.133
peak=    3.089 closest distance to " O   HOH Z 391 " =    3.111
peak=    3.070 closest distance to " CG  ARG A 269 " =    1.826
peak=    3.060 closest distance to " O   HOH Z 350 " =    1.917
peak=    3.059 closest distance to " N   ARG A 102 " =    2.252
peak=    3.046 closest distance to " O   HOH Z 131 " =    2.419
peak=    3.043 closest distance to " CA  ALA A  21 " =    1.168
peak=    3.011 closest distance to " O   ASP A 200 " =    1.221

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.408 - 5.853
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 205
   mapped sites are within: 0.759 - 5.853

peak=   -5.652 closest distance to " CG2 VAL A 230 " =    0.759
peak=   -4.535 closest distance to " CG1 VAL A 296 " =    1.014
peak=   -4.374 closest distance to " CD2 LEU A 237 " =    2.694
peak=   -4.353 closest distance to " O   PRO A 198 " =    1.251
peak=   -4.282 closest distance to " OG BSER A 134 " =    1.465
peak=   -4.235 closest distance to " CG  GLN A  58 " =    0.891
peak=   -4.200 closest distance to " O   HOH Z 216 " =    0.951
peak=   -4.196 closest distance to " O   HOH Z 193 " =    1.046
peak=   -4.154 closest distance to " O   HOH Z 422 " =    1.270
peak=   -4.152 closest distance to " CD2 TYR A  30 " =    2.605
peak=   -4.132 closest distance to " CD1 PHE A  59 " =    2.017
peak=   -4.119 closest distance to " O   HOH Z 110 " =    1.386
peak=   -4.115 closest distance to " O   GLY A 241 " =    2.335
peak=   -4.060 closest distance to " O   HOH Z 411 " =    5.442
peak=   -4.056 closest distance to " CB  ALA A 248 " =    2.175
peak=   -4.008 closest distance to " O   HOH Z 250 " =    1.974
peak=   -3.994 closest distance to " O   HOH Z 166 " =    1.487
peak=   -3.969 closest distance to " CA  VAL A  67 " =    2.914
peak=   -3.964 closest distance to " O   HOH Z 351 " =    1.908
peak=   -3.945 closest distance to " O   HOH Z 221 " =    0.912
peak=   -3.942 closest distance to " CG  MET A  93 " =    2.448
peak=   -3.933 closest distance to " CA  ASP A 298 " =    1.030
peak=   -3.918 closest distance to " O   HOH Z 203 " =    1.324
peak=   -3.916 closest distance to " CG  PRO A 243 " =    1.654
peak=   -3.892 closest distance to " CD  ARG A  14 " =    3.261
peak=   -3.880 closest distance to " O   HOH Z 171 " =    2.391
peak=   -3.853 closest distance to " O   ASP A 107 " =    1.998
peak=   -3.839 closest distance to " CD  ARG A 156 " =    2.035
peak=   -3.817 closest distance to " CD2 TYR A 293 " =    1.896
peak=   -3.799 closest distance to " O   HOH Z  13 " =    1.933
peak=   -3.764 closest distance to " O   HOH Z 166 " =    1.318
peak=   -3.754 closest distance to " O   HOH Z 345 " =    2.962
peak=   -3.752 closest distance to " O   GLN A  11 " =    1.071
peak=   -3.751 closest distance to " O   HOH Z 214 " =    0.878
peak=   -3.748 closest distance to " OG  SER A  97 " =    2.487
peak=   -3.740 closest distance to " CH2 TRP A 179 " =    1.199
peak=   -3.730 closest distance to " CG1 VAL A 112 " =    2.426
peak=   -3.719 closest distance to " NE2 GLN A  11 " =    1.348
peak=   -3.694 closest distance to " CG2 VAL A 189 " =    1.977
peak=   -3.693 closest distance to " O   HOH Z  90 " =    3.785
peak=   -3.692 closest distance to " O   HOH Z 407 " =    2.806
peak=   -3.687 closest distance to " CZ2 TRP A  92 " =    2.833
peak=   -3.686 closest distance to " O   HOH Z 203 " =    0.993
peak=   -3.676 closest distance to " O   TRP A  92 " =    2.245
peak=   -3.674 closest distance to " OH  TYR A 172 " =    1.766
peak=   -3.642 closest distance to " O   HOH Z 423 " =    2.768
peak=   -3.642 closest distance to " O   HOH Z 246 " =    0.929
peak=   -3.631 closest distance to " CG2BVAL A  41 " =    2.590
peak=   -3.626 closest distance to " O   HOH Z 433 " =    0.940
peak=   -3.615 closest distance to " O   HOH Z 151 " =    0.804
peak=   -3.603 closest distance to " O  BHOH Z 338 " =    1.091
peak=   -3.601 closest distance to " OD2 ASP A 298 " =    0.969
peak=   -3.579 closest distance to " O   HOH Z 285 " =    1.601
peak=   -3.574 closest distance to " O   HOH Z 165 " =    1.808
peak=   -3.574 closest distance to " O   HOH Z 266 " =    1.503
peak=   -3.565 closest distance to " CA  VAL A 121 " =    1.449
peak=   -3.542 closest distance to " O   HOH Z 435 " =    1.831
peak=   -3.539 closest distance to " CB  ALA A 161 " =    2.438
peak=   -3.538 closest distance to " CG1 VAL A 296 " =    0.862
peak=   -3.537 closest distance to " O   HOH Z 269 " =    1.189
peak=   -3.530 closest distance to " CG  GLN A 103 " =    2.393
peak=   -3.522 closest distance to " CE3 TRP A 150 " =    2.380
peak=   -3.516 closest distance to " O   HOH Z   6 " =    2.063
peak=   -3.513 closest distance to " CG2 THR A 182 " =    2.336
peak=   -3.501 closest distance to " O   ASP A 200 " =    1.065
peak=   -3.500 closest distance to " CB  ALA A  43 " =    2.736
peak=   -3.497 closest distance to " O   HOH Z 179 " =    2.149
peak=   -3.495 closest distance to " O   HOH Z 190 " =    1.466
peak=   -3.495 closest distance to " CA  SER A 276 " =    1.470
peak=   -3.488 closest distance to " OXT GLY A 302 " =    2.892
peak=   -3.486 closest distance to " O   HOH Z 111 " =    1.344
peak=   -3.476 closest distance to " O   SER A 273 " =    1.080
peak=   -3.471 closest distance to " O   LYS A 289 " =    1.074
peak=   -3.453 closest distance to " SG  CYS A 260 " =    2.051
peak=   -3.449 closest distance to " CB  ASP A 286 " =    1.627
peak=   -3.443 closest distance to " O   HOH Z 377 " =    2.211
peak=   -3.431 closest distance to " C   HIS A 108 " =    1.260
peak=   -3.424 closest distance to " CE1 HIS A  81 " =    1.288
peak=   -3.424 closest distance to " CZ  TYR A 169 " =    1.725
peak=   -3.423 closest distance to " CD  GLN A 223 " =    1.422
peak=   -3.417 closest distance to " CG  ARG A 269 " =    2.236
peak=   -3.413 closest distance to " CB  ALA A 129 " =    2.435
peak=   -3.408 closest distance to " CB  PHE A 208 " =    2.249
peak=   -3.406 closest distance to " CB  ALA A  51 " =    1.871
peak=   -3.403 closest distance to " O   HOH Z 353 " =    1.223
peak=   -3.403 closest distance to " C   LYS A  76 " =    1.776
peak=   -3.398 closest distance to " O   HOH Z  56 " =    1.407
peak=   -3.397 closest distance to " OD1 ASP A 298 " =    2.080
peak=   -3.390 closest distance to " O   HOH Z 136 " =    2.292
peak=   -3.384 closest distance to " CD  ARG A 139 " =    1.080
peak=   -3.381 closest distance to " O   HOH Z 116 " =    1.288
peak=   -3.379 closest distance to " O   HOH Z 368 " =    1.930
peak=   -3.375 closest distance to " O   PRO A 163 " =    2.145
peak=   -3.372 closest distance to " N   ALA A 226 " =    2.043
peak=   -3.372 closest distance to " O   HOH Z 374 " =    1.948
peak=   -3.370 closest distance to " O   HOH Z 119 " =    1.894
peak=   -3.368 closest distance to " CG1 VAL A  78 " =    2.711
peak=   -3.365 closest distance to " OE1 GLN A 223 " =    2.673
peak=   -3.360 closest distance to " O   HOH Z  55 " =    1.360
peak=   -3.360 closest distance to " CD  GLN A 223 " =    1.179
peak=   -3.353 closest distance to " O   HOH Z 174 " =    2.055
peak=   -3.338 closest distance to " O   HOH Z 150 " =    1.918
peak=   -3.333 closest distance to " CB  ALA A  10 " =    2.173
peak=   -3.320 closest distance to " O   HOH Z  35 " =    1.409
peak=   -3.318 closest distance to " O   HOH Z 107 " =    1.074
peak=   -3.313 closest distance to " CD2 TYR A 172 " =    2.156
peak=   -3.311 closest distance to " OD1 ASP A 171 " =    1.617
peak=   -3.310 closest distance to " CG  LEU A  83 " =    2.080
peak=   -3.308 closest distance to " CD1 ILE A 109 " =    2.650
peak=   -3.303 closest distance to " O   HOH Z 340 " =    0.913
peak=   -3.299 closest distance to " O   HOH Z 214 " =    2.605
peak=   -3.297 closest distance to " O   HOH Z 131 " =    4.186
peak=   -3.296 closest distance to " O   HOH Z 164 " =    5.853
peak=   -3.296 closest distance to " NZ  LYS A 119 " =    1.306
peak=   -3.291 closest distance to " CB  TRP A  85 " =    2.644
peak=   -3.285 closest distance to " CG2 THR A  18 " =    2.888
peak=   -3.277 closest distance to " CA  PRO A 280 " =    1.075
peak=   -3.275 closest distance to " NE1 TRP A 266 " =    2.357
peak=   -3.259 closest distance to " O   GLY A 196 " =    0.961
peak=   -3.258 closest distance to " O   HOH Z 425 " =    1.208
peak=   -3.255 closest distance to " O   HOH Z  17 " =    1.470
peak=   -3.252 closest distance to " O   HOH Z 219 " =    2.650
peak=   -3.249 closest distance to " CD1 TYR A 247 " =    2.487
peak=   -3.249 closest distance to " ND2 ASN A 249 " =    1.081
peak=   -3.246 closest distance to " O   HOH Z 265 " =    1.443
peak=   -3.244 closest distance to " OD2 ASP A 191 " =    1.979
peak=   -3.235 closest distance to " NH1 ARG A 195 " =    2.495
peak=   -3.231 closest distance to " O   ARG A  56 " =    4.029
peak=   -3.226 closest distance to " O   HOH Z 259 " =    1.346
peak=   -3.226 closest distance to " O   HOH Z 437 " =    0.769
peak=   -3.224 closest distance to " O   HOH Z 124 " =    1.475
peak=   -3.223 closest distance to " CB  ALA A   9 " =    2.471
peak=   -3.220 closest distance to " O   VAL A 125 " =    2.541
peak=   -3.219 closest distance to " O   GLN A 144 " =    1.134
peak=   -3.218 closest distance to " CA  GLY A 133 " =    2.066
peak=   -3.209 closest distance to " O   HOH Z 384 " =    1.839
peak=   -3.207 closest distance to " NE2 GLN A  88 " =    1.807
peak=   -3.207 closest distance to " O   HOH Z 146 " =    1.347
peak=   -3.201 closest distance to " O   HOH Z 183 " =    1.715
peak=   -3.200 closest distance to " SD  MET A 105 " =    2.411
peak=   -3.196 closest distance to " O   HOH Z   9 " =    1.402
peak=   -3.196 closest distance to " N   ALA A 295 " =    0.938
peak=   -3.195 closest distance to " NE2 GLN A  88 " =    1.104
peak=   -3.192 closest distance to " O   GLN A  94 " =    2.401
peak=   -3.192 closest distance to " O   HOH Z 285 " =    1.472
peak=   -3.191 closest distance to " CB  SER A 245 " =    0.959
peak=   -3.191 closest distance to " CA  GLY A 203 " =    2.474
peak=   -3.188 closest distance to " C   VAL A 265 " =    0.981
peak=   -3.188 closest distance to " ND2 ASN A 209 " =    2.563
peak=   -3.187 closest distance to " O   SER A 210 " =    1.800
peak=   -3.183 closest distance to " OE2 GLU A 128 " =    2.054
peak=   -3.176 closest distance to " O   HOH Z 154 " =    1.262
peak=   -3.171 closest distance to " CG1 VAL A 268 " =    2.301
peak=   -3.170 closest distance to " O   PRO A  54 " =    1.579
peak=   -3.165 closest distance to " O   HOH Z 190 " =    0.955
peak=   -3.162 closest distance to " O   HOH Z 191 " =    5.447
peak=   -3.152 closest distance to " O   HOH Z 388 " =    2.156
peak=   -3.150 closest distance to " O   GLY A  80 " =    2.744
peak=   -3.149 closest distance to " O   SER A 146 " =    1.143
peak=   -3.148 closest distance to " O   HOH Z 387 " =    2.709
peak=   -3.144 closest distance to " CZ  ARG A 156 " =    1.749
peak=   -3.137 closest distance to " CE1 PHE A 218 " =    1.691
peak=   -3.137 closest distance to " OG1 THR A 294 " =    2.446
peak=   -3.135 closest distance to " CE1 TYR A 247 " =    2.648
peak=   -3.134 closest distance to " O   HOH Z 313 " =    2.320
peak=   -3.133 closest distance to " NE2 GLN A  77 " =    1.460
peak=   -3.130 closest distance to " CZ  ARG A 259 " =    0.937
peak=   -3.130 closest distance to " O   HOH Z 297 " =    2.603
peak=   -3.130 closest distance to " O   HOH Z 198 " =    1.736
peak=   -3.126 closest distance to " O   HOH Z 174 " =    3.722
peak=   -3.125 closest distance to " CH2 TRP A 150 " =    1.098
peak=   -3.125 closest distance to " CA  GLY A  57 " =    2.041
peak=   -3.122 closest distance to " O   HOH Z   2 " =    2.244
peak=   -3.118 closest distance to " O   ASP A 298 " =    1.714
peak=   -3.111 closest distance to " O   HOH Z  44 " =    1.438
peak=   -3.102 closest distance to " OG BSER A  99 " =    1.086
peak=   -3.099 closest distance to " O   HOH Z  52 " =    2.116
peak=   -3.097 closest distance to " CG  ASP A 298 " =    0.979
peak=   -3.096 closest distance to " CD1 PHE A  59 " =    1.920
peak=   -3.094 closest distance to " O   HOH Z  67 " =    1.589
peak=   -3.094 closest distance to " OG1 THR A 246 " =    1.700
peak=   -3.094 closest distance to " O   HOH Z 231 " =    1.187
peak=   -3.094 closest distance to " CG  ASN A 110 " =    0.932
peak=   -3.092 closest distance to " O   HOH Z  88 " =    1.992
peak=   -3.091 closest distance to " O   HOH Z 340 " =    1.751
peak=   -3.090 closest distance to " CD1 TRP A  70 " =    1.800
peak=   -3.090 closest distance to " CD1 PHE A 130 " =    2.276
peak=   -3.087 closest distance to " OG1 THR A  82 " =    1.309
peak=   -3.074 closest distance to " O   HOH Z 393 " =    1.227
peak=   -3.070 closest distance to " CG2 VAL A 202 " =    2.706
peak=   -3.067 closest distance to " CB  SER A  22 " =    1.968
peak=   -3.062 closest distance to " O   HOH Z 196 " =    2.005
peak=   -3.051 closest distance to " O   HOH Z  41 " =    1.924
peak=   -3.042 closest distance to " O   HOH Z  78 " =    1.970
peak=   -3.039 closest distance to " O   HOH Z 203 " =    1.016
peak=   -3.024 closest distance to " O   HOH Z 198 " =    2.238
peak=   -3.018 closest distance to " O   HOH Z 192 " =    2.111

================= 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    :  0.5269 0.5260   6.317118e+00   6.315560e+00
   1_bss:  0.5201 0.5235   5.868610e+00   5.862716e+00
   1_xyz:  0.4699 0.4969   6.269010e+00   6.296055e+00
   1_adp:  0.4294 0.4961   6.234727e+00   6.294203e+00
   1_occ:  0.4290 0.4967   6.234698e+00   6.295513e+00
   2_bss:  0.4279 0.4899   6.235499e+00   6.295163e+00
   2_xyz:  0.3710 0.4385   6.137920e+00   6.239327e+00
   2_adp:  0.3557 0.4249   6.110398e+00   6.218365e+00
   2_occ:  0.3555 0.4247   6.109969e+00   6.218215e+00
   3_bss:  0.3530 0.4209   6.111035e+00   6.217901e+00
   3_xyz:  0.2729 0.3337   5.898751e+00   6.056739e+00
   3_adp:  0.2500 0.3084   5.826690e+00   5.990451e+00
   3_occ:  0.2496 0.3081   5.825634e+00   5.990168e+00
   4_bss:  0.2473 0.3063   5.822873e+00   5.987101e+00
   4_xyz:  0.1858 0.2347   5.575157e+00   5.764043e+00
   4_adp:  0.1669 0.2187   5.492296e+00   5.696209e+00
   4_occ:  0.1667 0.2186   5.491475e+00   5.695480e+00
   5_bss:  0.1662 0.2184   5.490984e+00   5.694896e+00
   5_xyz:  0.1387 0.1890   5.337555e+00   5.557841e+00
   5_adp:  0.1331 0.1838   5.305501e+00   5.526113e+00
   5_occ:  0.1330 0.1838   5.305482e+00   5.526455e+00
   5_bss:  0.1334 0.1838   5.306193e+00   5.526116e+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:  0.311   0.000   6.833  10.222   9.857   0.000   0.000   0.000
   1_xyz:  0.311   0.000   6.833  10.222   9.857   0.000   0.000   0.000
   1_adp:  0.311   0.000   6.833  10.222   9.857   0.000   0.000   0.000
   1_occ:  0.311   0.000   6.833  10.222   9.857   0.000   0.000   0.000
   2_bss:  0.315  27.214   3.163   6.010   6.046   0.000   0.000   0.000
   2_xyz:  0.315  27.214   3.163   6.010   6.046   0.000   0.000   0.000
   2_adp:  0.315  27.214   3.163   6.010   6.046   0.000   0.000   0.000
   2_occ:  0.315  27.214   3.163   6.010   6.046   0.000   0.000   0.000
   3_bss:  0.296  27.214   0.576   3.035   3.088   0.000   0.000   0.000
   3_xyz:  0.296  27.214   0.576   3.035   3.088   0.000   0.000   0.000
   3_adp:  0.296  27.214   0.576   3.035   3.088   0.000   0.000   0.000
   3_occ:  0.296  27.214   0.576   3.035   3.088   0.000   0.000   0.000
   4_bss:  0.329  55.336  -1.552   0.655   1.044   0.000   0.000   0.000
   4_xyz:  0.329  55.336  -1.552   0.655   1.044   0.000   0.000   0.000
   4_adp:  0.329  55.336  -1.552   0.655   1.044   0.000   0.000   0.000
   4_occ:  0.329  55.336  -1.552   0.655   1.044   0.000   0.000   0.000
   5_bss:  0.331  56.067  -2.365  -0.355   0.412  -0.000   0.000   0.000
   5_xyz:  0.331  56.067  -2.365  -0.355   0.412  -0.000   0.000   0.000
   5_adp:  0.331  56.067  -2.365  -0.355   0.412  -0.000   0.000   0.000
   5_occ:  0.331  56.067  -2.365  -0.355   0.412  -0.000   0.000   0.000
   5_bss:  0.328  56.070  -2.544  -0.824   0.167  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  68.509 0.2830  0.3422    91496.456
   1_bss:  70.443 0.2564  0.3901    92738.961
   1_xyz:  64.500 0.3328  0.4970    79391.408
   1_adp:  62.413 0.3601  0.6255    78011.447
   1_occ:  62.510 0.3590  0.6224    78377.431
   2_bss:  61.551 0.3717  0.5787    77559.077
   2_xyz:  51.773 0.4971  0.7778    60045.323
   2_adp:  48.613 0.5373  0.8483    54966.624
   2_occ:  48.568 0.5379  0.8494    54900.713
   3_bss:  48.428 0.5396  0.7721    54845.697
   3_xyz:  36.571 0.6820  0.9433    31833.855
   3_adp:  32.653 0.7280  0.9771    26553.179
   3_occ:  32.596 0.7287  0.9775    26446.823
   4_bss:  32.320 0.7318  0.9098    26138.601
   4_xyz:  23.698 0.8244  0.9770    14775.046
   4_adp:  21.555 0.8466  0.9852    12880.815
   4_occ:  21.533 0.8469  0.9854    12875.425
   5_bss:  21.478 0.8474  0.9572    12830.312
   5_xyz:  18.104 0.8795  0.9752     9436.892
   5_adp:  17.399 0.8862  0.9758     8947.472
   5_occ:  17.407 0.8862  0.9756     8950.570
   5_bss:  17.409 0.8861  0.9657     8953.463
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3868e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3868e+01
   1_xyz:   1.830  0.014  0.111 18.620  0.007  4.106   1.6681e-01
   1_adp:   1.830  0.014  0.111 18.620  0.007  4.106   1.6681e-01
   1_occ:   1.830  0.014  0.111 18.620  0.007  4.106   1.6681e-01
   2_bss:   1.830  0.014  0.111 18.620  0.007  4.106   1.6681e-01
   2_xyz:   1.392  0.010  0.081 17.034  0.005  4.103   1.2133e-01
   2_adp:   1.392  0.010  0.081 17.034  0.005  4.103   1.2133e-01
   2_occ:   1.392  0.010  0.081 17.034  0.005  4.103   1.2133e-01
   3_bss:   1.392  0.010  0.081 17.034  0.005  4.103   1.2133e-01
   3_xyz:   1.364  0.011  0.089 16.320  0.006  4.105   1.1592e-01
   3_adp:   1.364  0.011  0.089 16.320  0.006  4.105   1.1592e-01
   3_occ:   1.364  0.011  0.089 16.320  0.006  4.105   1.1592e-01
   4_bss:   1.364  0.011  0.089 16.320  0.006  4.105   1.1592e-01
   4_xyz:   1.201  0.009  0.086 15.741  0.004  4.128   8.4886e-02
   4_adp:   1.201  0.009  0.086 15.741  0.004  4.128   8.4886e-02
   4_occ:   1.201  0.009  0.086 15.741  0.004  4.128   8.4886e-02
   5_bss:   1.201  0.009  0.086 15.741  0.004  4.128   8.4886e-02
   5_xyz:   1.183  0.010  0.089 15.489  0.004  4.118   7.9768e-02
   5_adp:   1.183  0.010  0.089 15.489  0.004  4.118   7.9768e-02
   5_occ:   1.183  0.010  0.089 15.489  0.004  4.118   7.9768e-02
   5_bss:   1.183  0.010  0.089 15.489  0.004  4.118   7.9768e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.649   6.9719e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.649   6.9719e+00
   1_xyz:  16.359  0.176  0.512 86.365  0.050  2.096   1.0920e-01
   1_adp:  16.359  0.176  0.512 86.365  0.050  2.096   1.0920e-01
   1_occ:  16.359  0.176  0.512 86.365  0.050  2.096   1.0920e-01
   2_bss:  16.359  0.176  0.512 86.365  0.050  2.096   1.0920e-01
   2_xyz:   9.011  0.074  0.326 88.845  0.036  2.093   2.1723e-01
   2_adp:   9.011  0.074  0.326 88.845  0.036  2.093   2.1723e-01
   2_occ:   9.011  0.074  0.326 88.845  0.036  2.093   2.1723e-01
   3_bss:   9.011  0.074  0.326 88.845  0.036  2.093   2.1723e-01
   3_xyz:   8.753  0.060  0.318 85.690  0.048  2.145   1.7716e-01
   3_adp:   8.753  0.060  0.318 85.690  0.048  2.145   1.7716e-01
   3_occ:   8.753  0.060  0.318 85.690  0.048  2.145   1.7716e-01
   4_bss:   8.753  0.060  0.318 85.690  0.048  2.145   1.7716e-01
   4_xyz:   7.795  0.054  0.298 81.315  0.038  2.094   6.7620e-02
   4_adp:   7.795  0.054  0.298 81.315  0.038  2.094   6.7620e-02
   4_occ:   7.795  0.054  0.298 81.315  0.038  2.094   6.7620e-02
   5_bss:   7.795  0.054  0.298 81.315  0.038  2.094   6.7620e-02
   5_xyz:   7.847  0.050  0.392 85.921  0.039  2.190   7.0497e-02
   5_adp:   7.847  0.050  0.392 85.921  0.039  2.190   7.0497e-02
   5_occ:   7.847  0.050  0.392 85.921  0.039  2.190   7.0497e-02
   5_bss:   7.847  0.050  0.392 85.921  0.039  2.190   7.0497e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp: 113.80   0.00  19.58  93.02   0.00  17.94 113.80   0.00  28.50
   1_occ: 113.80   0.00  19.58  93.02   0.00  17.94 113.80   0.00  28.50
   2_bss: 113.80   0.00  19.58  93.02   0.00  17.94 113.80   0.00  28.50
   2_xyz: 113.80   0.00  19.58  93.02   0.00  17.94 113.80   0.00  28.50
   2_adp: 116.01   0.00  18.00  84.48   0.00  15.83 116.01   0.00  29.81
   2_occ: 116.01   0.00  18.00  84.48   0.00  15.83 116.01   0.00  29.81
   3_bss: 116.01   0.00  18.00  84.48   0.00  15.83 116.01   0.00  29.81
   3_xyz: 116.01   0.00  18.00  84.48   0.00  15.83 116.01   0.00  29.81
   3_adp:  98.45   0.00  16.69  79.17   0.00  13.46  98.45   2.52  34.25
   3_occ:  98.45   0.00  16.69  79.17   0.00  13.46  98.45   2.52  34.25
   4_bss:  98.45   0.00  16.69  79.17   0.00  13.46  98.45   2.52  34.25
   4_xyz:  98.45   0.00  16.69  79.17   0.00  13.46  98.45   2.52  34.25
   4_adp:  90.01   0.00  16.78  84.33   0.00  12.50  90.01   4.36  40.06
   4_occ:  90.01   0.00  16.78  84.33   0.00  12.50  90.01   4.36  40.06
   5_bss:  90.01   0.00  16.78  84.33   0.00  12.50  90.01   4.36  40.06
   5_xyz:  90.01   0.00  16.78  84.33   0.00  12.50  90.01   4.36  40.06
   5_adp:  87.40   0.00  16.68  83.77   0.00  12.32  87.40   5.73  40.44
   5_occ:  87.40   0.00  16.68  83.77   0.00  12.32  87.40   5.73  40.44
   5_bss:  87.40   0.00  16.69  83.77   0.00  12.32  87.40   5.74  40.44
------------------------------------------------------------------------
 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:    1.308    0.028    0.417
   1_adp:    1.308    0.028    0.417
   1_occ:    1.308    0.028    0.417
   2_bss:    1.308    0.028    0.417
   2_xyz:    1.945    0.030    0.592
   2_adp:    1.945    0.030    0.592
   2_occ:    1.945    0.030    0.592
   3_bss:    1.945    0.030    0.592
   3_xyz:    1.960    0.053    0.790
   3_adp:    1.960    0.053    0.790
   3_occ:    1.960    0.053    0.790
   4_bss:    1.960    0.053    0.790
   4_xyz:    2.195    0.029    0.906
   4_adp:    2.195    0.029    0.906
   4_occ:    2.195    0.029    0.906
   5_bss:    2.195    0.029    0.906
   5_xyz:    2.264    0.046    0.959
   5_adp:    2.264    0.046    0.959
   5_occ:    2.264    0.046    0.959
   5_bss:    2.264    0.046    0.959
------------------------------------------------------------------------

CPU time actual refinement: 338.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_108/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_108/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_108/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_108/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_108/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.13 
  Macro-tasks:
    bulk solvent and scale       = 40.52  
    individual site refinement   = 144.30 
    weights calculation          = 31.94  
    collect and process          = 6.44   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 223.32 
  Micro-tasks:
    mask                            = 3.07   
    f_calc                          = 105.60 
    alpha_beta                      = 8.49   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 115.30 
    fmodel                         = 7.20   
    r_factors                      = 0.21   
    phase_errors                   = 9.84   
    foms                           = 0.18   
    TOTAL for micro-tasks          = 251.05 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.803 micro seconds
Total CPU time: 5.86 minutes
from_scatterers_fft:    614 calls, 105.30 s
gradients_fft:          558 calls, 102.68 s

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

# Date 2008-01-16 Time 00:45:31 PST -0800 (1200473131.04 s)
Start R-work = 0.5269, R-free = 0.5260 (no bulk solvent and anisotropic scale)
Final R-work = 0.1549, R-free = 0.2001 (no bulk solvent and anisotropic scale)

Start R-work = 0.5201, R-free = 0.5235
Final R-work = 0.1334, R-free = 0.1838