# Date 2008-01-16 Time 00:39:30 PST -0800 (1200472770.62 s)
#phil __OFF__

Command line arguments: "../98.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4205
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 98

-------------------------------------------------------------------------------
  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, 47.6339, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, 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, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9459 1.95104
Completeness in resolution range: 0.903427
Completeness with d_max=infinity: 0.900768

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9459
                             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, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9459 1.95104
Completeness in resolution range: 0.903427
Completeness with d_max=infinity: 0.900768

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9464 -  4.1757 [2275/2303]  2043   232  10.2%
  bin  2:  4.1757 -  3.3264 [2195/2218]  1975   220  10.0%
  bin  3:  3.3264 -  2.9094 [2155/2180]  1946   209   9.7%
  bin  4:  2.9094 -  2.6450 [2119/2137]  1905   214  10.1%
  bin  5:  2.6450 -  2.4563 [2112/2154]  1891   221  10.5%
  bin  6:  2.4563 -  2.3121 [2146/2174]  1940   206   9.6%
  bin  7:  2.3121 -  2.1967 [2077/2113]  1876   201   9.7%
  bin  8:  2.1967 -  2.1013 [2096/2138]  1884   212  10.1%
  bin  9:  2.1013 -  2.0206 [1913/2129]  1727   186   9.7%
  bin 10:  2.0206 -  1.9510 [ 501/2137]   443    58  11.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_98/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:
        0.95 -     1.74: 14
        1.74 -     2.53: 62
        2.53 -     3.32: 3846
        3.32 -     4.11: 9373
        4.11 -     4.90: 14968
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  0.955 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.122 3.040 -x+1,y-1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.195 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.216 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.392 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28258 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_98/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_98/model_refine_001.geo

CPU time processing inputs: 9.05


============================ 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 47.63395 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5231   r_free= 0.5194   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   1.02 A                  |
| x-ray target function (ml) for work reflections: 6.314142                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9464 -  4.6578 0.99   1472  162 0.4253 0.4321      6.6655      6.6973|
|  2:  4.6578 -  3.7157 0.99   1431  157 0.4658 0.5240      6.8585      6.9533|
|  3:  3.7157 -  3.2516 0.99   1396  163 0.5109 0.4867      6.7219      6.7293|
|  4:  3.2516 -  2.9568 0.99   1370  144 0.5239 0.4902      6.5412      6.5199|
|  5:  2.9568 -  2.7462 0.99   1388  157 0.5561 0.5625      6.3842      6.4143|
|  6:  2.7462 -  2.5852 0.99   1370  154 0.5520 0.5597      6.2869      6.1938|
|  7:  2.5852 -  2.4563 0.98   1333  159 0.5561 0.4627      6.2321      6.1662|
|  8:  2.4563 -  2.3498 0.98   1379  149 0.5562 0.5417      6.1791      6.1912|
|  9:  2.3498 -  2.2597 0.99   1361  138 0.5616 0.5495      6.1246      6.1766|
| 10:  2.2597 -  2.1820 0.98   1365  149 0.5556 0.6082      6.0942      6.1019|
| 11:  2.1820 -  2.1139 0.97   1334  158 0.5553 0.5462       5.996       6.023|
| 12:  2.1139 -  2.0537 0.98   1341  153 0.5647 0.5678      5.9435      5.9213|
| 13:  2.0537 -  1.9997 0.64    880   89 0.5535 0.5569      5.8786      5.8297|
| 14:  1.9997 -  1.9510 0.16    210   27 0.5835 0.5077      5.9426      5.7113|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9464 -  4.6578  1472   162  0.63  40.19   0.78     0.64      92169.60|
|  2:  4.6578 -  3.7157  1431   157  0.58  45.29   0.84     0.64     154425.34|
|  3:  3.7157 -  3.2516  1396   163  0.44  56.51   0.78     0.57     162628.99|
|  4:  3.2516 -  2.9568  1370   144  0.31  66.53   0.75     0.41     140214.95|
|  5:  2.9568 -  2.7462  1388   157  0.23  72.86   0.69     0.29     105225.41|
|  6:  2.7462 -  2.5852  1370   154  0.19  75.73   0.70     0.24      90256.88|
|  7:  2.5852 -  2.4563  1333   159  0.24  72.29   0.69     0.28      75183.18|
|  8:  2.4563 -  2.3498  1379   149  0.28  68.98   0.70     0.35      64046.19|
|  9:  2.3498 -  2.2597  1361   138  0.28  68.83   0.69     0.36      60788.83|
| 10:  2.2597 -  2.1820  1365   149  0.22  73.47   0.72     0.27      54499.07|
| 11:  2.1820 -  2.1139  1334   158  0.11  82.17   0.71     0.14      56323.29|
| 12:  2.1139 -  2.0537  1341   153  0.06  85.44   0.71     0.08      51363.79|
| 13:  2.0537 -  1.9997   880    89  0.09  83.28   0.73     0.13      45512.19|
| 14:  1.9997 -  1.9510   210    27  0.24  71.91   0.75     0.26      32159.68|
|alpha:            min =        0.08 max =            0.64 mean =         0.35|
|beta:             min =    32159.68 max =       162628.99 mean =     89731.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.29|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.89|
|phase err.(test): min =        0.00 max =           90.00 mean =        68.33|
|-----------------------------------------------------------------------------|

============================== 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 = 28.255537             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.454   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.830223              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.774   (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 |  0.813 -  1.221:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.221 -  1.630:       14 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.630 -  2.039:       53 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.039 -  2.448:      354 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.448 -  2.856:     1119 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.856 -  3.265:     2305 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.265 -  3.674:     3825 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.674 -  4.082:     5226 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.082 -  4.491:     7016 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.491 -  4.900:     8405 |
|-----------------------------------------------------------------------------|
|-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 |       53.822 |
| 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  0.813 |       3.146 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.853)------------------------------------------|
|    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 = 11.853)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5273   r_free= 0.5237   ksol= 0.00   Bsol= 0.00   scale= 0.730    |
|                                                                             |
| 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:   1.02 A                  |
| x-ray target function (ml) for work reflections: 6.314407                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5158   r_free= 0.5160   ksol= 0.31   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.12,9.21,10.81,0.00,0.00,0.00); trace/3= 9.05                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.15 A                  |
| x-ray target function (ml) for work reflections: 5.856934                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.545810             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.502   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.361031              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.782   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5158      final r-factor (work) = 0.4619          |
| start r-factor (free) = 0.5160      final r-factor (free) = 0.4897          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 128.1316 = 23.55 * 0.50 * 6.3119 + 1.00 * 53.8220                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 68.6731 = 23.55 * 0.50 * 5.8190 + 1.00 * 0.1662                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4619      final r-factor (work) = 0.4236          |
| start r-factor (free) = 0.4897      final r-factor (free) = 0.4852          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7534 = 2.36 * 1.00 * 5.8190 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.7428 = 2.36 * 1.00 * 6.2340 + 1.00 * 0.0242                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.853)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.13  17.95    None  None   None       |
|    all(noH): 2823   0      0.00    104.13  17.95    None  None   None       |
|    Sol.    : 438    0      0.00    104.13  26.16    None  None   None       |
|    Mac.    : 2385   0      0.00    86.38   16.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.413: 1009   |   5:    52.067 -  62.480:   54        |
|      1:    10.413 -  20.827:  839   |   6:    62.480 -  72.894:   21        |
|      2:    20.827 -  31.240:  512   |   7:    72.894 -  83.307:    9        |
|      3:    31.240 -  41.654:  267   |   8:    83.307 -  93.720:    3        |
|      4:    41.654 -  52.067:  107   |   9:    93.720 - 104.134:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4236 r_free = 0.4852             target_work(ml) = 6.223         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4231 r_free = 0.4852             target_work(ml) = 6.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4231   r_free= 0.4852   ksol= 0.31   Bsol= 0.00   scale= 1.125    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.12,9.21,10.81,0.00,0.00,0.00); trace/3= 9.05                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.222595                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4216   r_free= 0.4808   ksol= 0.34   Bsol= 50.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,5.31,6.82,0.00,0.00,0.00); trace/3= 5.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.224522                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.778491             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.508  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.944838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.314  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4216      final r-factor (work) = 0.3544          |
| start r-factor (free) = 0.4808      final r-factor (free) = 0.4157          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0990 = 13.78 * 0.50 * 6.2319 + 1.00 * 0.1662                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.5834 = 13.78 * 0.50 * 6.1646 + 1.00 * 0.1136                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3544      final r-factor (work) = 0.3337          |
| start r-factor (free) = 0.4157      final r-factor (free) = 0.4042          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8497 = 0.94 * 1.00 * 6.1646 + 1.00 * 0.0251                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7577 = 0.94 * 1.00 * 6.0771 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.853)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.83  17.24    None  None   None       |
|    all(noH): 2823   0      0.00    114.83  17.24    None  None   None       |
|    Sol.    : 438    0      0.00    114.83  31.15    None  None   None       |
|    Mac.    : 2385   0      0.00    88.06   14.69    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 -  11.483: 1152   |   5:    57.413 -  68.895:   37        |
|      1:    11.483 -  22.965:  924   |   6:    68.895 -  80.378:    8        |
|      2:    22.965 -  34.448:  439   |   7:    80.378 -  91.861:    3        |
|      3:    34.448 -  45.930:  192   |   8:    91.861 - 103.343:    1        |
|      4:    45.930 -  57.413:   66   |   9:   103.343 - 114.826:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3337 r_free = 0.4042             target_work(ml) = 6.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3335 r_free = 0.4044             target_work(ml) = 6.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3335   r_free= 0.4044   ksol= 0.34   Bsol= 50.00   scale= 1.084   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,5.31,6.82,0.00,0.00,0.00); trace/3= 5.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.062232                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3302   r_free= 0.4006   ksol= 0.33   Bsol= 50.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.51,2.57,3.73,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.061789                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.634541              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.773  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.385152              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.123  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3302      final r-factor (work) = 0.2619          |
| start r-factor (free) = 0.4006      final r-factor (free) = 0.3228          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3501 = 8.63 * 0.50 * 6.0771 + 1.00 * 0.1136                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9323 = 8.63 * 0.50 * 5.9851 + 1.00 * 0.0928                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2619      final r-factor (work) = 0.2450          |
| start r-factor (free) = 0.3228      final r-factor (free) = 0.3028          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3240 = 0.39 * 1.00 * 5.9851 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2839 = 0.39 * 1.00 * 5.8420 + 1.00 * 0.0338                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.853)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.93  16.60    None  None   None       |
|    all(noH): 2823   0      0.00    110.93  16.60    None  None   None       |
|    Sol.    : 438    0      2.13    110.93  35.14    None  None   None       |
|    Mac.    : 2385   0      0.00    91.25   13.19    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 -  11.093: 1299   |   5:    55.464 -  66.557:   33        |
|      1:    11.093 -  22.186:  835   |   6:    66.557 -  77.650:    9        |
|      2:    22.186 -  33.279:  345   |   7:    77.650 -  88.743:    3        |
|      3:    33.279 -  44.371:  207   |   8:    88.743 -  99.836:    2        |
|      4:    44.371 -  55.464:   89   |   9:    99.836 - 110.928:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2450 r_free = 0.3028             target_work(ml) = 5.810         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2446 r_free = 0.3025             target_work(ml) = 5.809         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2446   r_free= 0.3025   ksol= 0.33   Bsol= 50.00   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.51,2.57,3.73,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.809041                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2435   r_free= 0.3009   ksol= 0.32   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,0.66,1.93,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.809664                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.671401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.507  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.270375              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.556   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2435      final r-factor (work) = 0.1902          |
| start r-factor (free) = 0.3009      final r-factor (free) = 0.2456          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7484 = 4.67 * 0.50 * 5.8463 + 1.00 * 0.0933                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4224 = 4.67 * 0.50 * 5.7143 + 1.00 * 0.0755                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1902      final r-factor (work) = 0.1701          |
| start r-factor (free) = 0.2456      final r-factor (free) = 0.2332          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2696 = 1.27 * 1.00 * 5.7143 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0739 = 1.27 * 1.00 * 5.5566 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.853)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.29  17.60    None  None   None       |
|    all(noH): 2823   0      0.00    107.29  17.60    None  None   None       |
|    Sol.    : 438    0      3.37    107.29  45.35    None  None   None       |
|    Mac.    : 2385   0      0.00    95.56   12.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.729: 1351   |   5:    53.643 -  64.372:   85        |
|      1:    10.729 -  21.457:  823   |   6:    64.372 -  75.100:   55        |
|      2:    21.457 -  32.186:  217   |   7:    75.100 -  85.829:   31        |
|      3:    32.186 -  42.915:  141   |   8:    85.829 -  96.558:   11        |
|      4:    42.915 -  53.643:  107   |   9:    96.558 - 107.286:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1701 r_free = 0.2332             target_work(ml) = 5.530         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1700 r_free = 0.2333             target_work(ml) = 5.529         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1700   r_free= 0.2333   ksol= 0.32   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,0.66,1.93,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.529497                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1699   r_free= 0.2333   ksol= 0.33   Bsol= 63.30   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-0.06,1.19,-0.00,0.00,0.00); trace/3= -0.20                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.528671                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.090216              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.021  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.292906              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.899  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1699      final r-factor (work) = 0.1440          |
| start r-factor (free) = 0.2333      final r-factor (free) = 0.1995          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4446 = 4.09 * 0.50 * 5.5591 + 1.00 * 0.0755                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2528 = 4.09 * 0.50 * 5.4657 + 1.00 * 0.0748                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1440      final r-factor (work) = 0.1395          |
| start r-factor (free) = 0.1995      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6158 = 0.29 * 1.00 * 5.4657 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5832 = 0.29 * 1.00 * 5.3654 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.853)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    106.70  17.03    None  None   None       |
|    all(noH): 2823   0      0.75    106.70  17.03    None  None   None       |
|    Sol.    : 438    0      4.96    106.70  43.86    None  None   None       |
|    Mac.    : 2385   0      0.75    95.69   12.10    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:     0.746 -  11.342: 1497   |   5:    53.724 -  64.320:   86        |
|      1:    11.342 -  21.937:  762   |   6:    64.320 -  74.916:   43        |
|      2:    21.937 -  32.533:  162   |   7:    74.916 -  85.511:   25        |
|      3:    32.533 -  43.129:  122   |   8:    85.511 -  96.107:   10        |
|      4:    43.129 -  53.724:  115   |   9:    96.107 - 106.702:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1395 r_free = 0.1891             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1393 r_free = 0.1893             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1893   ksol= 0.33   Bsol= 63.30   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-0.06,1.19,-0.00,0.00,0.00); trace/3= -0.20                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.336536                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9464 -  4.6578 0.99   1472  162 0.1035 0.1524      5.4708      5.7054|
|  2:  4.6578 -  3.7157 0.99   1431  157 0.0975 0.1242       5.567       5.784|
|  3:  3.7157 -  3.2516 0.99   1396  163 0.1337 0.1753      5.6688      5.9241|
|  4:  3.2516 -  2.9568 0.99   1370  144 0.1566 0.2111      5.6193      5.8581|
|  5:  2.9568 -  2.7462 0.99   1388  157 0.1732 0.2037      5.5577      5.7117|
|  6:  2.7462 -  2.5852 0.99   1370  154 0.1597 0.2497      5.4068       5.638|
|  7:  2.5852 -  2.4563 0.98   1333  159 0.1583 0.1895      5.3454      5.4682|
|  8:  2.4563 -  2.3498 0.98   1379  149 0.1560 0.2328       5.275      5.5212|
|  9:  2.3498 -  2.2597 0.99   1361  138 0.1486 0.1950      5.1884      5.3987|
| 10:  2.2597 -  2.1820 0.98   1365  149 0.1417 0.2105       5.122      5.3285|
| 11:  2.1820 -  2.1139 0.97   1334  158 0.1452 0.2145      5.0692      5.4122|
| 12:  2.1139 -  2.0537 0.98   1341  153 0.1452 0.1830      5.0328      5.2208|
| 13:  2.0537 -  1.9997 0.64    880   89 0.1404 0.2081      4.9332      5.1302|
| 14:  1.9997 -  1.9510 0.16    210   27 0.1299 0.1965      4.8823      5.1209|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9464 -  4.6578  1472   162  0.92  11.22   0.96     0.94       9755.04|
|  2:  4.6578 -  3.7157  1431   157  0.94  10.35   1.02     1.00      12258.62|
|  3:  3.7157 -  3.2516  1396   163  0.91  14.83   1.04     1.03      15285.62|
|  4:  3.2516 -  2.9568  1370   144  0.88  18.04   1.02     1.01      14374.23|
|  5:  2.9568 -  2.7462  1388   157  0.85  21.36   1.01     1.00      13909.79|
|  6:  2.7462 -  2.5852  1370   154  0.86  20.69   0.99     0.93      10202.70|
|  7:  2.5852 -  2.4563  1333   159  0.86  20.28   1.00     0.96       9226.20|
|  8:  2.4563 -  2.3498  1379   149  0.86  20.55   1.02     0.98       8128.57|
|  9:  2.3498 -  2.2597  1361   138  0.87  19.64   1.01     0.95       6797.04|
| 10:  2.2597 -  2.1820  1365   149  0.87  19.68   1.02     0.99       6321.96|
| 11:  2.1820 -  2.1139  1334   158  0.86  20.31   1.01     0.98       5900.86|
| 12:  2.1139 -  2.0537  1341   153  0.87  19.99   1.01     1.00       5401.88|
| 13:  2.0537 -  1.9997   880    89  0.87  20.06   0.99     0.97       4505.44|
| 14:  1.9997 -  1.9510   210    27  0.89  16.67   0.98     0.92       3505.83|
|alpha:            min =        0.92 max =            1.03 mean =         0.98|
|beta:             min =     3505.83 max =        15285.62 mean =      9496.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.08|
|phase err.(test): min =        0.00 max =           89.74 mean =        17.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1896   ksol= 0.33   Bsol= 61.38   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.50,0.82,-0.00,0.00,0.00); trace/3= -0.57                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.338419                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1896   ksol= 0.33   Bsol= 61.38   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.50,0.82,-0.00,0.00,0.00); trace/3= -0.57                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.338419                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9464 -  4.6578 0.99   1472  162 0.1052 0.1530      5.4815      5.7077|
|  2:  4.6578 -  3.7157 0.99   1431  157 0.0983 0.1262      5.5742      5.7983|
|  3:  3.7157 -  3.2516 0.99   1396  163 0.1341 0.1758      5.6745      5.9247|
|  4:  3.2516 -  2.9568 0.99   1370  144 0.1571 0.2111      5.6196      5.8598|
|  5:  2.9568 -  2.7462 0.99   1388  157 0.1730 0.2032      5.5573      5.7107|
|  6:  2.7462 -  2.5852 0.99   1370  154 0.1596 0.2496       5.406      5.6362|
|  7:  2.5852 -  2.4563 0.98   1333  159 0.1583 0.1897      5.3451       5.468|
|  8:  2.4563 -  2.3498 0.98   1379  149 0.1557 0.2326      5.2745      5.5218|
|  9:  2.3498 -  2.2597 0.99   1361  138 0.1486 0.1952      5.1879      5.3989|
| 10:  2.2597 -  2.1820 0.98   1365  149 0.1416 0.2106      5.1222      5.3293|
| 11:  2.1820 -  2.1139 0.97   1334  158 0.1453 0.2146      5.0695      5.4112|
| 12:  2.1139 -  2.0537 0.98   1341  153 0.1453 0.1833      5.0336      5.2226|
| 13:  2.0537 -  1.9997 0.64    880   89 0.1404 0.2077      4.9335      5.1294|
| 14:  1.9997 -  1.9510 0.16    210   27 0.1299 0.1965      4.8826      5.1225|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9464 -  4.6578  1472   162  0.92  11.31   0.96     0.94       9886.88|
|  2:  4.6578 -  3.7157  1431   157  0.94  10.50   1.02     1.00      12450.94|
|  3:  3.7157 -  3.2516  1396   163  0.91  14.95   1.03     1.02      15540.23|
|  4:  3.2516 -  2.9568  1370   144  0.88  18.05   1.01     0.99      14357.07|
|  5:  2.9568 -  2.7462  1388   157  0.85  21.35   1.00     0.98      13891.26|
|  6:  2.7462 -  2.5852  1370   154  0.86  20.64   0.98     0.92      10186.07|
|  7:  2.5852 -  2.4563  1333   159  0.86  20.25   0.98     0.94       9221.41|
|  8:  2.4563 -  2.3498  1379   149  0.86  20.54   1.00     0.96       8129.07|
|  9:  2.3498 -  2.2597  1361   138  0.87  19.63   0.99     0.94       6803.32|
| 10:  2.2597 -  2.1820  1365   149  0.87  19.68   1.00     0.97       6329.90|
| 11:  2.1820 -  2.1139  1334   158  0.86  20.30   0.99     0.96       5903.09|
| 12:  2.1139 -  2.0537  1341   153  0.87  19.99   0.98     0.98       5409.61|
| 13:  2.0537 -  1.9997   880    89  0.87  20.05   0.97     0.95       4504.27|
| 14:  1.9997 -  1.9510   210    27  0.89  16.67   0.96     0.90       3501.11|
|alpha:            min =        0.90 max =            1.02 mean =         0.97|
|beta:             min =     3501.11 max =        15540.23 mean =      9540.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.99 mean =        18.10|
|phase err.(test): min =        0.00 max =           89.81 mean =        17.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.853)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    106.68  17.00    None  None   None       |
|    all(noH): 2823   0      0.72    106.68  17.00    None  None   None       |
|    Sol.    : 438    0      4.93    106.68  43.83    None  None   None       |
|    Mac.    : 2385   0      0.72    95.66   12.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.721 -  11.317: 1497   |   5:    53.699 -  64.295:   86        |
|      1:    11.317 -  21.912:  762   |   6:    64.295 -  74.890:   43        |
|      2:    21.912 -  32.508:  162   |   7:    74.890 -  85.486:   25        |
|      3:    32.508 -  43.104:  122   |   8:    85.486 -  96.082:   10        |
|      4:    43.104 -  53.699:  115   |   9:    96.082 - 106.677:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 344         
Filter by distance & map next to the model:
   mapped sites are within: 0.660 - 4.519
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 339 from: 344
   mapped sites are within: 0.702 - 4.519

peak=    9.961 closest distance to " O   HOH Z 203 " =    1.329
peak=    9.454 closest distance to " O   HOH Z 190 " =    1.873
peak=    8.553 closest distance to " CB  VAL A 230 " =    1.382
peak=    8.162 closest distance to " O   HOH Z 103 " =    1.231
peak=    7.611 closest distance to " O   HOH Z 255 " =    1.802
peak=    6.881 closest distance to " CG1 VAL A 296 " =    1.289
peak=    6.625 closest distance to " O   HOH Z 169 " =    1.583
peak=    5.893 closest distance to " O   HOH Z 248 " =    1.597
peak=    5.889 closest distance to " O   HOH Z 404 " =    1.521
peak=    5.861 closest distance to " O  BHOH Z  74 " =    1.090
peak=    5.850 closest distance to " CD2 LEU A   5 " =    1.269
peak=    5.810 closest distance to " CD1AILE A 234 " =    1.326
peak=    5.740 closest distance to " O   HOH Z 117 " =    1.547
peak=    5.264 closest distance to " O   HOH Z 124 " =    1.544
peak=    5.118 closest distance to " O   HOH Z 403 " =    2.082
peak=    5.097 closest distance to " O   HOH Z 425 " =    1.744
peak=    5.066 closest distance to " O   HOH Z 107 " =    1.145
peak=    5.063 closest distance to " O   HOH Z 210 " =    1.405
peak=    5.001 closest distance to " O   HOH Z 128 " =    1.849
peak=    4.908 closest distance to " O   HOH Z 372 " =    1.325
peak=    4.831 closest distance to " O   HOH Z 277 " =    1.501
peak=    4.732 closest distance to " CZ3 TRP A 266 " =    1.109
peak=    4.715 closest distance to " CD2 LEU A 228 " =    1.256
peak=    4.672 closest distance to " NH2AARG A 145 " =    1.060
peak=    4.662 closest distance to " O   HOH Z  97 " =    1.682
peak=    4.636 closest distance to " O   HOH Z 394 " =    1.827
peak=    4.633 closest distance to " O   HOH Z 126 " =    1.718
peak=    4.607 closest distance to " O   HOH Z 188 " =    1.422
peak=    4.600 closest distance to " CA  TYR A  30 " =    0.978
peak=    4.587 closest distance to " CB  SER A  26 " =    1.707
peak=    4.562 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.502 closest distance to " O   HOH Z  67 " =    1.459
peak=    4.495 closest distance to " O   SER A  87 " =    2.314
peak=    4.478 closest distance to " CZ  PHE A 218 " =    1.163
peak=    4.470 closest distance to " CB  VAL A 230 " =    1.373
peak=    4.463 closest distance to " O   HOH Z   4 " =    1.780
peak=    4.402 closest distance to " CD2 TRP A 179 " =    1.273
peak=    4.398 closest distance to " NH2 ARG A  56 " =    1.277
peak=    4.397 closest distance to " O   HOH Z 411 " =    3.897
peak=    4.396 closest distance to " O   HOH Z 190 " =    1.300
peak=    4.385 closest distance to " CA  ALA A 100 " =    1.025
peak=    4.369 closest distance to " CA  GLN A  58 " =    0.774
peak=    4.359 closest distance to " NH2 ARG A  56 " =    2.054
peak=    4.326 closest distance to " O   HOH Z  69 " =    1.191
peak=    4.318 closest distance to " CG  PRO A 243 " =    1.065
peak=    4.313 closest distance to " O   HOH Z 279 " =    1.022
peak=    4.307 closest distance to " O   HOH Z  49 " =    1.386
peak=    4.295 closest distance to " CG  PRO A  54 " =    1.437
peak=    4.260 closest distance to " O   HOH Z 142 " =    2.413
peak=    4.230 closest distance to " CB  GLN A  55 " =    0.943
peak=    4.226 closest distance to " O   HOH Z  65 " =    0.941
peak=    4.221 closest distance to " O   HOH Z 169 " =    2.048
peak=    4.205 closest distance to " NH2 ARG A 156 " =    1.099
peak=    4.193 closest distance to " O   HOH Z 406 " =    1.767
peak=    4.192 closest distance to " CD  PRO A  54 " =    1.004
peak=    4.185 closest distance to " NE2 GLN A  11 " =    1.181
peak=    4.181 closest distance to " O   HOH Z 331 " =    1.180
peak=    4.175 closest distance to " NH1AARG A 102 " =    1.067
peak=    4.168 closest distance to " O   HOH Z 365 " =    2.315
peak=    4.167 closest distance to " CG  LEU A   5 " =    1.282
peak=    4.156 closest distance to " O   HOH Z 431 " =    1.550
peak=    4.150 closest distance to " O   HOH Z 402 " =    1.487
peak=    4.149 closest distance to " O   HOH Z  76 " =    1.324
peak=    4.130 closest distance to " O   HOH Z 130 " =    1.164
peak=    4.114 closest distance to " O   HOH Z 214 " =    1.680
peak=    4.064 closest distance to " NE2 GLN A  77 " =    3.109
peak=    4.059 closest distance to " O   HOH Z 246 " =    1.323
peak=    4.046 closest distance to " O   HOH Z 426 " =    1.298
peak=    4.041 closest distance to " ND2 ASN A 249 " =    1.985
peak=    4.035 closest distance to " O   HOH Z 130 " =    2.316
peak=    4.033 closest distance to " O   HOH Z 375 " =    1.442
peak=    4.030 closest distance to " NE AARG A 145 " =    0.898
peak=    4.016 closest distance to " O   HOH Z 339 " =    1.461
peak=    4.011 closest distance to " O  BHOH Z 338 " =    1.236
peak=    3.993 closest distance to " O   HOH Z 191 " =    1.115
peak=    3.989 closest distance to " CB  ASN A 148 " =    1.263
peak=    3.983 closest distance to " CA  ASP A 162 " =    0.994
peak=    3.974 closest distance to " O   HOH Z 193 " =    2.395
peak=    3.971 closest distance to " CB  SER A  99 " =    1.163
peak=    3.969 closest distance to " O   HOH Z 112 " =    1.124
peak=    3.965 closest distance to " CD  LYS A  76 " =    1.765
peak=    3.959 closest distance to " CB  GLN A 223 " =    1.532
peak=    3.958 closest distance to " CB  GLN A  58 " =    1.204
peak=    3.958 closest distance to " O   HOH Z 251 " =    1.722
peak=    3.955 closest distance to " O   HOH Z  30 " =    1.447
peak=    3.950 closest distance to " O   HOH Z  67 " =    1.903
peak=    3.948 closest distance to " CD1 LEU A   5 " =    1.651
peak=    3.945 closest distance to " O   HOH Z 236 " =    1.532
peak=    3.931 closest distance to " O   HOH Z 132 " =    2.937
peak=    3.928 closest distance to " O   HOH Z 369 " =    2.089
peak=    3.919 closest distance to " CG  ARG A  56 " =    1.074
peak=    3.919 closest distance to " O   HOH Z 199 " =    1.391
peak=    3.918 closest distance to " O   HOH Z 116 " =    1.436
peak=    3.917 closest distance to " NH1AARG A 275 " =    1.156
peak=    3.907 closest distance to " CG AARG A 275 " =    1.261
peak=    3.907 closest distance to " O   HOH Z  50 " =    1.584
peak=    3.904 closest distance to " O   HOH Z 287 " =    1.679
peak=    3.904 closest distance to " CB  GLU A 152 " =    1.326
peak=    3.902 closest distance to " O   HOH Z 357 " =    2.106
peak=    3.899 closest distance to " O   HOH Z  80 " =    2.339
peak=    3.891 closest distance to " O   HOH Z  63 " =    1.856
peak=    3.862 closest distance to " CG1 ILE A 120 " =    0.933
peak=    3.846 closest distance to " OE1 GLN A  11 " =    2.048
peak=    3.837 closest distance to " O   HOH Z 110 " =    1.282
peak=    3.830 closest distance to " CA  ALA A  51 " =    1.117
peak=    3.823 closest distance to " CG1 ILE A  20 " =    1.381
peak=    3.810 closest distance to " O   HOH Z 286 " =    2.019
peak=    3.791 closest distance to " O   HOH Z 328 " =    1.581
peak=    3.786 closest distance to " O   HOH Z 188 " =    2.552
peak=    3.771 closest distance to " O   HOH Z 213 " =    1.750
peak=    3.770 closest distance to " CB  SER A  99 " =    0.893
peak=    3.763 closest distance to " O   HOH Z 102 " =    1.428
peak=    3.756 closest distance to " O   HOH Z   9 " =    1.165
peak=    3.755 closest distance to " CE3 TRP A 274 " =    1.204
peak=    3.751 closest distance to " CB  ASN A 285 " =    0.967
peak=    3.751 closest distance to " CB  SER A  62 " =    1.142
peak=    3.749 closest distance to " O   HOH Z 158 " =    1.202
peak=    3.745 closest distance to " CB  ALA A 114 " =    0.923
peak=    3.735 closest distance to " O   PRO A 198 " =    1.657
peak=    3.734 closest distance to " CB  GLU A 236 " =    1.133
peak=    3.725 closest distance to " O   HOH Z  88 " =    3.491
peak=    3.723 closest distance to " O   HOH Z 368 " =    3.189
peak=    3.716 closest distance to " O   HOH Z 423 " =    1.877
peak=    3.715 closest distance to " CG  GLN A  58 " =    1.373
peak=    3.714 closest distance to " OG ASER A 258 " =    3.037
peak=    3.708 closest distance to " O   HOH Z 232 " =    2.322
peak=    3.708 closest distance to " O   HOH Z 433 " =    1.521
peak=    3.702 closest distance to " O   HOH Z 375 " =    1.077
peak=    3.700 closest distance to " O   GLN A  11 " =    0.923
peak=    3.693 closest distance to " O   HOH Z  40 " =    1.856
peak=    3.692 closest distance to " O   HOH Z 154 " =    1.690
peak=    3.689 closest distance to " O   HOH Z 350 " =    1.524
peak=    3.678 closest distance to " CB  GLN A 183 " =    1.265
peak=    3.676 closest distance to " O   GLU A   2 " =    1.731
peak=    3.670 closest distance to " CG  ARG A 138 " =    1.484
peak=    3.668 closest distance to " CB  LEU A  83 " =    0.702
peak=    3.666 closest distance to " O   HOH Z 234 " =    3.436
peak=    3.664 closest distance to " OE1 GLN A  55 " =    1.546
peak=    3.662 closest distance to " O   HOH Z 207 " =    1.568
peak=    3.659 closest distance to " O   HOH Z 414 " =    1.912
peak=    3.655 closest distance to " O   HOH Z 209 " =    2.323
peak=    3.654 closest distance to " CG AARG A 102 " =    1.257
peak=    3.643 closest distance to " OD1 ASN A 301 " =    1.036
peak=    3.643 closest distance to " CB  SER A  63 " =    1.170
peak=    3.634 closest distance to " O   HOH Z 359 " =    1.935
peak=    3.600 closest distance to " CB  TYR A  30 " =    1.156
peak=    3.591 closest distance to " CE1 TYR A  30 " =    1.197
peak=    3.590 closest distance to " O   HOH Z 146 " =    1.525
peak=    3.589 closest distance to " O   HOH Z 298 " =    4.305
peak=    3.587 closest distance to " O   HOH Z  54 " =    0.970
peak=    3.583 closest distance to " OE1 GLU A   2 " =    1.386
peak=    3.582 closest distance to " O   HOH Z 419 " =    1.827
peak=    3.575 closest distance to " O   HOH Z 144 " =    1.647
peak=    3.572 closest distance to " CE2 PHE A  59 " =    1.024
peak=    3.570 closest distance to " CB  GLU A 277 " =    3.717
peak=    3.568 closest distance to " O   HOH Z 241 " =    1.928
peak=    3.568 closest distance to " CD  LYS A 166 " =    1.587
peak=    3.568 closest distance to " O   HOH Z  35 " =    2.093
peak=    3.559 closest distance to " CG2 VAL A 296 " =    1.053
peak=    3.557 closest distance to " O   HOH Z 132 " =    1.084
peak=    3.557 closest distance to " CB BVAL A  41 " =    1.195
peak=    3.550 closest distance to " O   HOH Z 343 " =    2.604
peak=    3.549 closest distance to " CE  MET A  93 " =    1.347
peak=    3.549 closest distance to " O   HOH Z 303 " =    2.199
peak=    3.545 closest distance to " CG2 VAL A 197 " =    1.176
peak=    3.544 closest distance to " CB  ASN A 187 " =    1.282
peak=    3.533 closest distance to " CB  SER A 146 " =    1.195
peak=    3.530 closest distance to " CE1 TYR A 186 " =    1.142
peak=    3.527 closest distance to " CB  PRO A  54 " =    0.963
peak=    3.521 closest distance to " CB  MET A  40 " =    0.953
peak=    3.521 closest distance to " NE1 TRP A  92 " =    1.585
peak=    3.520 closest distance to " O   HOH Z 132 " =    2.548
peak=    3.518 closest distance to " CB  ASN A  45 " =    1.183
peak=    3.516 closest distance to " CD  ARG A 139 " =    1.224
peak=    3.514 closest distance to " O   HOH Z   3 " =    1.889
peak=    3.510 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.507 closest distance to " O   HOH Z 151 " =    1.917
peak=    3.505 closest distance to " O   HOH Z 247 " =    1.724
peak=    3.500 closest distance to " CG2 ILE A 234 " =    1.192
peak=    3.498 closest distance to " CD  LYS A 119 " =    2.187
peak=    3.490 closest distance to " SD  MET A 185 " =    1.475
peak=    3.486 closest distance to " CB  ASN A 142 " =    1.149
peak=    3.485 closest distance to " O   HOH Z  85 " =    1.594
peak=    3.485 closest distance to " CA  ARG A  36 " =    1.062
peak=    3.478 closest distance to " CA  ARG A 195 " =    1.220
peak=    3.475 closest distance to " CB  THR A  52 " =    1.018
peak=    3.473 closest distance to " CZ  PHE A  38 " =    1.036
peak=    3.472 closest distance to " CG2 THR A  42 " =    0.824
peak=    3.461 closest distance to " O   HOH Z 371 " =    2.417
peak=    3.459 closest distance to " CB  GLU A 277 " =    0.989
peak=    3.442 closest distance to " CB  THR A 235 " =    1.296
peak=    3.435 closest distance to " CA  VAL A 112 " =    1.098
peak=    3.435 closest distance to " O   HOH Z 211 " =    0.997
peak=    3.426 closest distance to " CB  VAL A 296 " =    1.402
peak=    3.425 closest distance to " CB  ARG A 275 " =    1.219
peak=    3.424 closest distance to " O   HOH Z 154 " =    2.244
peak=    3.421 closest distance to " CB  ASP A 124 " =    0.974
peak=    3.420 closest distance to " O   HOH Z 391 " =    2.973
peak=    3.420 closest distance to " O   HOH Z 297 " =    4.519
peak=    3.420 closest distance to " O   HOH Z 346 " =    1.579
peak=    3.418 closest distance to " CB  ARG A 145 " =    0.928
peak=    3.417 closest distance to " CE  LYS A 119 " =    1.130
peak=    3.417 closest distance to " CG  LYS A 289 " =    1.498
peak=    3.410 closest distance to " CB  SER A  62 " =    3.844
peak=    3.409 closest distance to " OG  SER A  62 " =    2.670
peak=    3.408 closest distance to " CA  ILE A 234 " =    0.998
peak=    3.408 closest distance to " CG2 VAL A 257 " =    0.914
peak=    3.405 closest distance to " NE2 GLN A 103 " =    1.059
peak=    3.399 closest distance to " O   HOH Z 113 " =    2.138
peak=    3.397 closest distance to " O   HOH Z  83 " =    1.597
peak=    3.392 closest distance to " O   HOH Z 431 " =    1.967
peak=    3.388 closest distance to " O   HOH Z 272 " =    1.751
peak=    3.388 closest distance to " CD1 LEU A  96 " =    0.870
peak=    3.387 closest distance to " O   HOH Z 327 " =    1.654
peak=    3.385 closest distance to " O   HOH Z 272 " =    1.315
peak=    3.383 closest distance to " OG BSER A 212 " =    2.358
peak=    3.377 closest distance to " CD AARG A 190 " =    1.526
peak=    3.375 closest distance to " O   HOH Z 234 " =    1.850
peak=    3.371 closest distance to " ND2 ASN A 249 " =    0.887
peak=    3.370 closest distance to " O   HOH Z  46 " =    1.395
peak=    3.369 closest distance to " O   HOH Z 134 " =    1.515
peak=    3.366 closest distance to " O   HOH Z 417 " =    3.138
peak=    3.366 closest distance to " O   HOH Z 344 " =    1.636
peak=    3.365 closest distance to " CG  LEU A 228 " =    1.352
peak=    3.357 closest distance to " O   HOH Z 327 " =    3.115
peak=    3.357 closest distance to " CD  GLN A 194 " =    1.447
peak=    3.355 closest distance to " CA  GLY A  57 " =    1.229
peak=    3.353 closest distance to " OG BSER A  99 " =    3.047
peak=    3.353 closest distance to " CG  LEU A 237 " =    1.378
peak=    3.343 closest distance to " ND2BASN A 224 " =    0.816
peak=    3.342 closest distance to " OG  SER A 146 " =    0.798
peak=    3.341 closest distance to " NZ  LYS A 117 " =    2.772
peak=    3.333 closest distance to " N   SER A 164 " =    0.839
peak=    3.333 closest distance to " CD2 LEU A  83 " =    1.664
peak=    3.333 closest distance to " O   HOH Z 365 " =    2.548
peak=    3.329 closest distance to " O   HOH Z 422 " =    2.657
peak=    3.319 closest distance to " NH1AARG A 145 " =    1.285
peak=    3.318 closest distance to " O   HOH Z 337 " =    2.213
peak=    3.317 closest distance to " O   HOH Z 158 " =    2.902
peak=    3.315 closest distance to " O   ALA A 292 " =    1.415
peak=    3.314 closest distance to " CB  ASP A 191 " =    1.226
peak=    3.311 closest distance to " O   HOH Z 313 " =    1.634
peak=    3.308 closest distance to " CA  THR A 246 " =    1.041
peak=    3.308 closest distance to " OG BSER A 258 " =    2.567
peak=    3.307 closest distance to " CA  GLU A 152 " =    0.808
peak=    3.306 closest distance to " CE  LYS A  76 " =    0.853
peak=    3.305 closest distance to " CD  ARG A 195 " =    0.983
peak=    3.305 closest distance to " N   TYR A 247 " =    1.401
peak=    3.303 closest distance to " O   HOH Z 273 " =    2.812
peak=    3.301 closest distance to " CD1 ILE A 199 " =    1.157
peak=    3.299 closest distance to " NE  ARG A  56 " =    1.147
peak=    3.295 closest distance to " CB  TRP A 179 " =    1.316
peak=    3.294 closest distance to " CB  ALA A 248 " =    1.549
peak=    3.294 closest distance to " O   HOH Z 298 " =    2.201
peak=    3.280 closest distance to " CA  ALA A 129 " =    1.178
peak=    3.277 closest distance to " CA  VAL A  41 " =    0.757
peak=    3.277 closest distance to " O   HOH Z 197 " =    1.610
peak=    3.275 closest distance to " O   HOH Z 197 " =    1.206
peak=    3.272 closest distance to " O   HOH Z 366 " =    2.334
peak=    3.271 closest distance to " O   HOH Z  56 " =    1.897
peak=    3.270 closest distance to " OG  SER A 245 " =    1.456
peak=    3.269 closest distance to " CB  ALA A 295 " =    1.244
peak=    3.267 closest distance to " CG  MET A 185 " =    1.438
peak=    3.261 closest distance to " O   HOH Z 258 " =    1.730
peak=    3.259 closest distance to " CA  CYS A 260 " =    1.243
peak=    3.256 closest distance to " O   HOH Z 200 " =    3.460
peak=    3.251 closest distance to " O   HOH Z 222 " =    1.203
peak=    3.249 closest distance to " CB  GLN A  89 " =    1.398
peak=    3.249 closest distance to " CB  TRP A 179 " =    1.741
peak=    3.245 closest distance to " N   THR A  42 " =    1.562
peak=    3.244 closest distance to " CB  GLU A 175 " =    1.051
peak=    3.241 closest distance to " O   THR A 182 " =    1.531
peak=    3.238 closest distance to " CB  PRO A 280 " =    1.182
peak=    3.238 closest distance to " CG  ARG A  66 " =    0.853
peak=    3.238 closest distance to " CB  ALA A   7 " =    1.018
peak=    3.229 closest distance to " O   HOH Z 129 " =    1.413
peak=    3.228 closest distance to " CG2AVAL A  72 " =    1.547
peak=    3.228 closest distance to " CB  ASP A 140 " =    0.915
peak=    3.228 closest distance to " O   HOH Z 427 " =    2.819
peak=    3.224 closest distance to " O   ALA A 165 " =    1.271
peak=    3.219 closest distance to " CB  ASN A 110 " =    1.091
peak=    3.218 closest distance to " O   HOH Z 392 " =    1.214
peak=    3.216 closest distance to " O   HOH Z  77 " =    1.365
peak=    3.212 closest distance to " CG2 THR A  29 " =    1.457
peak=    3.210 closest distance to " NZ  LYS A 117 " =    1.150
peak=    3.209 closest distance to " O   HOH Z 111 " =    1.371
peak=    3.209 closest distance to " OD1 ASP A 231 " =    1.963
peak=    3.205 closest distance to " O   HOH Z  78 " =    1.722
peak=    3.204 closest distance to " N   GLY A 262 " =    1.188
peak=    3.203 closest distance to " O   HOH Z 143 " =    1.484
peak=    3.197 closest distance to " O   HOH Z 245 " =    1.453
peak=    3.193 closest distance to " O   ASN A 284 " =    1.734
peak=    3.192 closest distance to " O   HOH Z 235 " =    1.327
peak=    3.191 closest distance to " O   THR A 220 " =    1.143
peak=    3.187 closest distance to " CA  TYR A 116 " =    1.518
peak=    3.187 closest distance to " CD2 LEU A 297 " =    0.925
peak=    3.181 closest distance to " O   HOH Z 257 " =    1.172
peak=    3.179 closest distance to " O   HOH Z   9 " =    2.297
peak=    3.171 closest distance to " O   HOH Z   1 " =    2.998
peak=    3.169 closest distance to " O   HOH Z  95 " =    1.959
peak=    3.168 closest distance to " O   HOH Z 314 " =    1.898
peak=    3.161 closest distance to " CZ2 TRP A 150 " =    1.016
peak=    3.156 closest distance to " N   THR A  52 " =    1.323
peak=    3.156 closest distance to " CB  LEU A 300 " =    0.987
peak=    3.156 closest distance to " CB  THR A  31 " =    1.434
peak=    3.155 closest distance to " CB  PHE A 204 " =    0.967
peak=    3.152 closest distance to " NH2 ARG A  36 " =    1.852
peak=    3.150 closest distance to " O   ASP A 200 " =    1.624
peak=    3.148 closest distance to " CG  GLN A  11 " =    1.438
peak=    3.140 closest distance to " O  BHOH Z 338 " =    1.922
peak=    3.139 closest distance to " CA  THR A  82 " =    1.663
peak=    3.127 closest distance to " NE  ARG A  24 " =    1.102
peak=    3.118 closest distance to " CB  GLN A 194 " =    1.036
peak=    3.115 closest distance to " CB  ASN A 209 " =    1.067
peak=    3.115 closest distance to " CB  VAL A 265 " =    1.203
peak=    3.113 closest distance to " CB  SER A  32 " =    1.154
peak=    3.111 closest distance to " O   HOH Z 423 " =    1.906
peak=    3.111 closest distance to " CA  ALA A 295 " =    0.879
peak=    3.107 closest distance to " NH2 ARG A 269 " =    1.204
peak=    3.105 closest distance to " CA  ASP A 140 " =    1.244
peak=    3.103 closest distance to " O   HOH Z 189 " =    2.599
peak=    3.101 closest distance to " O   HOH Z 142 " =    1.582
peak=    3.101 closest distance to " CG2 THR A 221 " =    1.160
peak=    3.098 closest distance to " CB  PRO A 243 " =    1.051
peak=    3.094 closest distance to " CG  LYS A 119 " =    0.764
peak=    3.090 closest distance to " O   HOH Z  80 " =    1.687
peak=    3.087 closest distance to " O   HOH Z 163 " =    2.128
peak=    3.084 closest distance to " OD1 ASN A 285 " =    1.646
peak=    3.080 closest distance to " CB  SER A 141 " =    1.113
peak=    3.071 closest distance to " CG  GLN A  58 " =    1.289
peak=    3.066 closest distance to " CA  ASN A  39 " =    1.174
peak=    3.054 closest distance to " CA  ALA A  21 " =    1.099
peak=    3.053 closest distance to " O   HOH Z 162 " =    2.370
peak=    3.047 closest distance to " O   HOH Z  63 " =    1.838
peak=    3.047 closest distance to " CG2 THR A  31 " =    1.353
peak=    3.044 closest distance to " O   GLY A  57 " =    1.125
peak=    3.043 closest distance to " O   HOH Z 416 " =    2.713
peak=    3.042 closest distance to " O   HOH Z 263 " =    1.934
peak=    3.028 closest distance to " O   HOH Z 350 " =    2.079

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.405 - 5.691
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 207
   mapped sites are within: 0.768 - 5.691

peak=   -5.271 closest distance to " CG2 VAL A 230 " =    0.768
peak=   -4.887 closest distance to " O   HOH Z 203 " =    0.813
peak=   -4.612 closest distance to " OG BSER A 134 " =    1.480
peak=   -4.512 closest distance to " O   PRO A 198 " =    1.210
peak=   -4.393 closest distance to " CD2 TYR A 293 " =    1.838
peak=   -4.322 closest distance to " CD1 PHE A  59 " =    2.146
peak=   -4.202 closest distance to " O   HOH Z 166 " =    1.401
peak=   -4.188 closest distance to " O   HOH Z 116 " =    0.852
peak=   -4.133 closest distance to " O   GLY A 241 " =    2.353
peak=   -4.116 closest distance to " CA  GLN A  58 " =    1.065
peak=   -4.087 closest distance to " CG2BVAL A  41 " =    2.419
peak=   -4.083 closest distance to " O   HOH Z 257 " =    1.561
peak=   -4.040 closest distance to " CG1 VAL A 296 " =    1.029
peak=   -4.029 closest distance to " CG2 ILE A  49 " =    2.910
peak=   -3.919 closest distance to " CD  ARG A 139 " =    1.012
peak=   -3.911 closest distance to " O   ASP A 107 " =    2.127
peak=   -3.893 closest distance to " CD  ARG A 156 " =    2.081
peak=   -3.886 closest distance to " CE2 TYR A  30 " =    2.561
peak=   -3.860 closest distance to " O   HOH Z 423 " =    3.016
peak=   -3.856 closest distance to " CG  GLN A  58 " =    0.779
peak=   -3.851 closest distance to " CE1 PHE A 218 " =    1.434
peak=   -3.844 closest distance to " O   HOH Z  13 " =    1.945
peak=   -3.844 closest distance to " O   HOH Z 345 " =    2.967
peak=   -3.825 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.801 closest distance to " O   HOH Z 150 " =    1.882
peak=   -3.794 closest distance to " OD2 ASP A 298 " =    0.917
peak=   -3.768 closest distance to " O   GLY A  80 " =    2.674
peak=   -3.763 closest distance to " OD1 ASN A 301 " =    0.821
peak=   -3.758 closest distance to " CG  PRO A 243 " =    1.627
peak=   -3.752 closest distance to " O   HOH Z 411 " =    5.691
peak=   -3.748 closest distance to " O   HOH Z 351 " =    1.803
peak=   -3.746 closest distance to " CD  ARG A  14 " =    3.036
peak=   -3.733 closest distance to " O   HOH Z 269 " =    1.199
peak=   -3.731 closest distance to " CG2 ILE A  20 " =    2.977
peak=   -3.728 closest distance to " O   HOH Z 221 " =    0.820
peak=   -3.726 closest distance to " C   GLU A   2 " =    2.430
peak=   -3.705 closest distance to " NZ  LYS A 166 " =    1.930
peak=   -3.670 closest distance to " CE3 TRP A 150 " =    2.369
peak=   -3.650 closest distance to " CG2 VAL A 189 " =    2.034
peak=   -3.649 closest distance to " CE2 TRP A  70 " =    2.257
peak=   -3.640 closest distance to " O   HOH Z 266 " =    1.485
peak=   -3.624 closest distance to " O   HOH Z  30 " =    1.640
peak=   -3.607 closest distance to " CG1 VAL A 250 " =    2.774
peak=   -3.602 closest distance to " O  BHOH Z 338 " =    1.224
peak=   -3.599 closest distance to " CG  ARG A 269 " =    2.268
peak=   -3.595 closest distance to " O   HOH Z 119 " =    1.931
peak=   -3.595 closest distance to " O   HOH Z 103 " =    1.326
peak=   -3.594 closest distance to " O   HOH Z 216 " =    1.045
peak=   -3.584 closest distance to " O   HOH Z 422 " =    1.163
peak=   -3.546 closest distance to " O   HOH Z 278 " =    0.975
peak=   -3.543 closest distance to " CD2 TYR A 172 " =    2.259
peak=   -3.523 closest distance to " CB  ALA A 248 " =    2.186
peak=   -3.520 closest distance to " O   HOH Z 166 " =    1.688
peak=   -3.511 closest distance to " O   HOH Z 106 " =    2.046
peak=   -3.499 closest distance to " O   HOH Z 214 " =    2.555
peak=   -3.492 closest distance to " O   HOH Z 137 " =    1.499
peak=   -3.489 closest distance to " CG  PHE A  59 " =    2.004
peak=   -3.488 closest distance to " CG  GLN A 103 " =    2.332
peak=   -3.486 closest distance to " ND2BASN A 224 " =    1.998
peak=   -3.485 closest distance to " O   HOH Z  69 " =    1.177
peak=   -3.478 closest distance to " O   GLN A  11 " =    0.896
peak=   -3.475 closest distance to " CG  TRP A 266 " =    1.921
peak=   -3.474 closest distance to " O   HOH Z 297 " =    2.655
peak=   -3.474 closest distance to " CA  HIS A  86 " =    1.199
peak=   -3.464 closest distance to " CE1 TYR A 247 " =    2.631
peak=   -3.463 closest distance to " CG  MET A  93 " =    2.441
peak=   -3.456 closest distance to " CB  ASP A 286 " =    1.584
peak=   -3.455 closest distance to " O   HOH Z 136 " =    1.582
peak=   -3.453 closest distance to " NH2 ARG A 156 " =    0.977
peak=   -3.448 closest distance to " OD2 ASP A 191 " =    1.866
peak=   -3.446 closest distance to " O   HOH Z  17 " =    1.560
peak=   -3.445 closest distance to " CZ  PHE A  38 " =    2.448
peak=   -3.439 closest distance to " O   ALA A   8 " =    2.253
peak=   -3.434 closest distance to " NE2 GLN A 240 " =    1.940
peak=   -3.433 closest distance to " NH2 ARG A  79 " =    1.566
peak=   -3.432 closest distance to " NE2 GLN A  11 " =    1.395
peak=   -3.429 closest distance to " O   HOH Z 313 " =    1.095
peak=   -3.429 closest distance to " O   ASP A 253 " =    1.964
peak=   -3.426 closest distance to " O   HOH Z 275 " =    1.872
peak=   -3.425 closest distance to " C   HIS A 108 " =    1.085
peak=   -3.415 closest distance to " OG  SER A  97 " =    2.379
peak=   -3.410 closest distance to " N   ASP A 191 " =    1.515
peak=   -3.410 closest distance to " OG1 THR A  52 " =    2.491
peak=   -3.405 closest distance to " O   HOH Z 250 " =    2.066
peak=   -3.400 closest distance to " O   HOH Z  10 " =    1.635
peak=   -3.393 closest distance to " O   HOH Z 377 " =    2.136
peak=   -3.391 closest distance to " O   HOH Z 388 " =    2.230
peak=   -3.383 closest distance to " CG1 VAL A 112 " =    2.508
peak=   -3.382 closest distance to " O   HOH Z 171 " =    2.485
peak=   -3.378 closest distance to " CZ  TYR A 169 " =    1.719
peak=   -3.375 closest distance to " CD  GLN A 223 " =    1.658
peak=   -3.373 closest distance to " CA  VAL A 121 " =    1.475
peak=   -3.364 closest distance to " O   HOH Z 154 " =    1.170
peak=   -3.362 closest distance to " O   HOH Z 100 " =    0.924
peak=   -3.359 closest distance to " O   HOH Z 405 " =    2.454
peak=   -3.357 closest distance to " O   HOH Z  64 " =    2.588
peak=   -3.357 closest distance to " CD  ARG A  36 " =    1.031
peak=   -3.352 closest distance to " CB  ALA A  43 " =    2.588
peak=   -3.350 closest distance to " O   HOH Z 328 " =    1.272
peak=   -3.349 closest distance to " O   PRO A 163 " =    2.041
peak=   -3.345 closest distance to " NH2BARG A 102 " =    0.924
peak=   -3.341 closest distance to " O   HOH Z 128 " =    1.534
peak=   -3.340 closest distance to " NE1 TRP A 266 " =    2.268
peak=   -3.338 closest distance to " O   HOH Z  55 " =    1.687
peak=   -3.338 closest distance to " O   HOH Z 131 " =    4.244
peak=   -3.337 closest distance to " O   HOH Z 151 " =    0.885
peak=   -3.332 closest distance to " O   VAL A 174 " =    2.196
peak=   -3.330 closest distance to " OG  SER A  63 " =    1.240
peak=   -3.326 closest distance to " CE BMET A  47 " =    1.347
peak=   -3.318 closest distance to " SD  MET A  40 " =    1.914
peak=   -3.317 closest distance to " NE2 GLN A  88 " =    1.135
peak=   -3.314 closest distance to " CA  ALA A 114 " =    0.948
peak=   -3.314 closest distance to " CA  GLY A  57 " =    2.087
peak=   -3.308 closest distance to " O   HOH Z 183 " =    1.832
peak=   -3.300 closest distance to " O   HOH Z  90 " =    3.839
peak=   -3.297 closest distance to " CB  ALA A  10 " =    2.226
peak=   -3.293 closest distance to " O   HOH Z 340 " =    1.744
peak=   -3.283 closest distance to " CD  PRO A 243 " =    1.570
peak=   -3.283 closest distance to " O   HOH Z 165 " =    1.727
peak=   -3.275 closest distance to " CE2 TYR A 214 " =    2.198
peak=   -3.270 closest distance to " O   HOH Z 111 " =    1.348
peak=   -3.269 closest distance to " ND2 ASN A 127 " =    1.994
peak=   -3.267 closest distance to " SG  CYS A 254 " =    3.128
peak=   -3.263 closest distance to " CB  ALA A   9 " =    2.339
peak=   -3.259 closest distance to " O   HOH Z 114 " =    3.573
peak=   -3.258 closest distance to " O   HOH Z 433 " =    0.800
peak=   -3.258 closest distance to " O   HOH Z 150 " =    3.077
peak=   -3.258 closest distance to " O   HOH Z 357 " =    1.813
peak=   -3.256 closest distance to " NE2 GLN A 278 " =    1.995
peak=   -3.249 closest distance to " CZ  ARG A 156 " =    3.038
peak=   -3.249 closest distance to " C   LYS A  76 " =    1.677
peak=   -3.249 closest distance to " CD2 LEU A 237 " =    2.185
peak=   -3.248 closest distance to " CD  LYS A 289 " =    2.395
peak=   -3.246 closest distance to " CH2 TRP A 274 " =    1.059
peak=   -3.241 closest distance to " O   HOH Z 198 " =    1.643
peak=   -3.241 closest distance to " CB  GLN A  55 " =    1.264
peak=   -3.237 closest distance to " O   HOH Z 285 " =    1.383
peak=   -3.236 closest distance to " O   HOH Z 364 " =    2.609
peak=   -3.233 closest distance to " O  BHOH Z  74 " =    0.936
peak=   -3.233 closest distance to " O  BHOH Z  74 " =    0.936
peak=   -3.232 closest distance to " C   VAL A 265 " =    0.987
peak=   -3.231 closest distance to " OXT GLY A 302 " =    3.071
peak=   -3.230 closest distance to " OD2 ASP A 162 " =    1.895
peak=   -3.229 closest distance to " CA  ALA A 291 " =    2.917
peak=   -3.228 closest distance to " CD2 HIS A 207 " =    2.132
peak=   -3.228 closest distance to " O   HOH Z 384 " =    1.855
peak=   -3.222 closest distance to " CD2 LEU A   5 " =    1.144
peak=   -3.218 closest distance to " O   HOH Z 407 " =    2.582
peak=   -3.217 closest distance to " O   GLY A 203 " =    2.622
peak=   -3.211 closest distance to " CG2AVAL A  72 " =    2.639
peak=   -3.211 closest distance to " OH  TYR A 172 " =    1.781
peak=   -3.211 closest distance to " N   ALA A 226 " =    1.944
peak=   -3.210 closest distance to " O   HOH Z 312 " =    1.534
peak=   -3.208 closest distance to " CA  HIS A 207 " =    1.262
peak=   -3.207 closest distance to " CG  ARG A  56 " =    1.185
peak=   -3.205 closest distance to " CG1 VAL A  78 " =    2.340
peak=   -3.205 closest distance to " C   ASN A 285 " =    2.092
peak=   -3.203 closest distance to " SD  MET A 105 " =    2.321
peak=   -3.198 closest distance to " O   HOH Z 244 " =    1.241
peak=   -3.196 closest distance to " O   SER A 273 " =    1.037
peak=   -3.196 closest distance to " O   HOH Z 353 " =    1.416
peak=   -3.192 closest distance to " CD1 ILE A 151 " =    2.023
peak=   -3.187 closest distance to " O   HOH Z 359 " =    2.715
peak=   -3.183 closest distance to " O   HOH Z  52 " =    2.022
peak=   -3.182 closest distance to " O   HOH Z  28 " =    2.137
peak=   -3.172 closest distance to " O   HOH Z 107 " =    1.050
peak=   -3.171 closest distance to " O   HOH Z 196 " =    1.667
peak=   -3.170 closest distance to " O   HOH Z 210 " =    2.344
peak=   -3.164 closest distance to " ND2 ASN A 209 " =    2.510
peak=   -3.160 closest distance to " O   SER A 146 " =    1.165
peak=   -3.160 closest distance to " O   ASN A  45 " =    1.947
peak=   -3.159 closest distance to " CG2 THR A  18 " =    2.884
peak=   -3.157 closest distance to " CB  SER A  22 " =    1.943
peak=   -3.156 closest distance to " CH2 TRP A 150 " =    1.108
peak=   -3.154 closest distance to " NZ  LYS A 119 " =    1.150
peak=   -3.154 closest distance to " O   HOH Z 429 " =    1.505
peak=   -3.153 closest distance to " O   SER A 210 " =    2.029
peak=   -3.149 closest distance to " O   TRP A 179 " =    1.465
peak=   -3.145 closest distance to " O   HOH Z 118 " =    4.604
peak=   -3.143 closest distance to " CB  PHE A 208 " =    2.327
peak=   -3.136 closest distance to " CD1 TYR A 169 " =    2.057
peak=   -3.135 closest distance to " O   HOH Z 425 " =    1.208
peak=   -3.133 closest distance to " O   HOH Z 105 " =    1.919
peak=   -3.123 closest distance to " O   VAL A 125 " =    2.424
peak=   -3.116 closest distance to " CG1 VAL A  78 " =    2.701
peak=   -3.109 closest distance to " CB  SER A  62 " =    5.610
peak=   -3.108 closest distance to " ND2 ASN A 249 " =    2.169
peak=   -3.107 closest distance to " O   HOH Z 340 " =    1.214
peak=   -3.096 closest distance to " O   HOH Z 437 " =    1.572
peak=   -3.096 closest distance to " SG  CYS A 260 " =    1.850
peak=   -3.095 closest distance to " CD2 LEU A 167 " =    2.206
peak=   -3.090 closest distance to " O   HOH Z 203 " =    1.663
peak=   -3.085 closest distance to " CD2 LEU A 237 " =    2.383
peak=   -3.073 closest distance to " O   HOH Z 103 " =    0.962
peak=   -3.068 closest distance to " O   HOH Z 222 " =    1.369
peak=   -3.068 closest distance to " OG  SER A  22 " =    1.949
peak=   -3.054 closest distance to " O   HOH Z 404 " =    0.850
peak=   -3.052 closest distance to " O   HOH Z 150 " =    1.604
peak=   -3.047 closest distance to " OH  TYR A 172 " =    1.557
peak=   -3.031 closest distance to " OG BSER A 210 " =    1.527
peak=   -3.030 closest distance to " O   SER A 271 " =    2.084

================= 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    :  0.5231 0.5194   6.314142e+00   6.313607e+00
   1_bss:  0.5158 0.5160   5.856934e+00   5.851861e+00
   1_xyz:  0.4619 0.4897   6.261481e+00   6.292482e+00
   1_adp:  0.4236 0.4852   6.222985e+00   6.285262e+00
   1_occ:  0.4231 0.4852   6.222595e+00   6.286278e+00
   2_bss:  0.4216 0.4808   6.224522e+00   6.286916e+00
   2_xyz:  0.3544 0.4157   6.099819e+00   6.209840e+00
   2_adp:  0.3337 0.4042   6.062607e+00   6.186428e+00
   2_occ:  0.3335 0.4044   6.062232e+00   6.186498e+00
   3_bss:  0.3302 0.4006   6.061789e+00   6.185958e+00
   3_xyz:  0.2619 0.3228   5.867487e+00   6.034954e+00
   3_adp:  0.2450 0.3028   5.810237e+00   5.976992e+00
   3_occ:  0.2446 0.3025   5.809041e+00   5.976198e+00
   4_bss:  0.2435 0.3009   5.809664e+00   5.975992e+00
   4_xyz:  0.1902 0.2456   5.604341e+00   5.802853e+00
   4_adp:  0.1701 0.2332   5.529799e+00   5.753312e+00
   4_occ:  0.1700 0.2333   5.529497e+00   5.753209e+00
   5_bss:  0.1699 0.2333   5.528671e+00   5.751365e+00
   5_xyz:  0.1440 0.1995   5.376265e+00   5.607449e+00
   5_adp:  0.1395 0.1891   5.336878e+00   5.557028e+00
   5_occ:  0.1393 0.1893   5.336536e+00   5.557102e+00
   5_bss:  0.1397 0.1896   5.338419e+00   5.558554e+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:  0.310   0.000   7.118   9.211  10.807   0.000   0.000   0.000
   1_xyz:  0.310   0.000   7.118   9.211  10.807   0.000   0.000   0.000
   1_adp:  0.310   0.000   7.118   9.211  10.807   0.000   0.000   0.000
   1_occ:  0.310   0.000   7.118   9.211  10.807   0.000   0.000   0.000
   2_bss:  0.343  50.000   3.217   5.314   6.824   0.000   0.000   0.000
   2_xyz:  0.343  50.000   3.217   5.314   6.824   0.000   0.000   0.000
   2_adp:  0.343  50.000   3.217   5.314   6.824   0.000   0.000   0.000
   2_occ:  0.343  50.000   3.217   5.314   6.824   0.000   0.000   0.000
   3_bss:  0.326  50.000   0.513   2.565   3.731   0.000   0.000   0.000
   3_xyz:  0.326  50.000   0.513   2.565   3.731   0.000   0.000   0.000
   3_adp:  0.326  50.000   0.513   2.565   3.731   0.000   0.000   0.000
   3_occ:  0.326  50.000   0.513   2.565   3.731   0.000   0.000   0.000
   4_bss:  0.316  50.000  -1.089   0.660   1.929   0.000   0.000   0.000
   4_xyz:  0.316  50.000  -1.089   0.660   1.929   0.000   0.000   0.000
   4_adp:  0.316  50.000  -1.089   0.660   1.929   0.000   0.000   0.000
   4_occ:  0.316  50.000  -1.089   0.660   1.929   0.000   0.000   0.000
   5_bss:  0.331  63.297  -1.738  -0.058   1.193  -0.000   0.000   0.000
   5_xyz:  0.331  63.297  -1.738  -0.058   1.193  -0.000   0.000   0.000
   5_adp:  0.331  63.297  -1.738  -0.058   1.193  -0.000   0.000   0.000
   5_occ:  0.331  63.297  -1.738  -0.058   1.193  -0.000   0.000   0.000
   5_bss:  0.330  61.380  -2.035  -0.502   0.821  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.934 0.2902  0.3482    89741.501
   1_bss:  68.542 0.2813  0.4318    90122.035
   1_xyz:  63.544 0.3451  0.5180    77806.577
   1_adp:  58.557 0.4109  0.7173    73621.332
   1_occ:  58.707 0.4089  0.7118    73809.077
   2_bss:  58.167 0.4161  0.6427    73601.870
   2_xyz:  47.875 0.5460  0.8319    52809.578
   2_adp:  45.562 0.5748  0.8795    48504.465
   2_occ:  45.535 0.5751  0.8800    48485.252
   3_bss:  45.320 0.5777  0.8002    48264.062
   3_xyz:  34.720 0.7038  0.9426    29541.832
   3_adp:  31.421 0.7421  0.9792    25345.127
   3_occ:  31.346 0.7430  0.9799    25246.350
   4_bss:  31.272 0.7439  0.9221    25221.109
   4_xyz:  24.726 0.8140  0.9732    16056.205
   4_adp:  23.086 0.8311  0.9786    14496.557
   4_occ:  23.081 0.8312  0.9788    14499.208
   5_bss:  23.016 0.8318  0.9556    14445.972
   5_xyz:  19.309 0.8679  0.9760    10451.044
   5_adp:  18.007 0.8806  0.9791     9495.835
   5_occ:  18.009 0.8806  0.9790     9497.990
   5_bss:  18.029 0.8805  0.9656     9542.172
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3822e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3822e+01
   1_xyz:   1.824  0.015  0.110 18.645  0.007  4.106   1.6621e-01
   1_adp:   1.824  0.015  0.110 18.645  0.007  4.106   1.6621e-01
   1_occ:   1.824  0.015  0.110 18.645  0.007  4.106   1.6621e-01
   2_bss:   1.824  0.015  0.110 18.645  0.007  4.106   1.6621e-01
   2_xyz:   1.395  0.010  0.082 17.043  0.005  4.103   1.1364e-01
   2_adp:   1.395  0.010  0.082 17.043  0.005  4.103   1.1364e-01
   2_occ:   1.395  0.010  0.082 17.043  0.005  4.103   1.1364e-01
   3_bss:   1.395  0.010  0.082 17.043  0.005  4.103   1.1364e-01
   3_xyz:   1.267  0.009  0.086 16.434  0.005  4.128   9.2833e-02
   3_adp:   1.267  0.009  0.086 16.434  0.005  4.128   9.2833e-02
   3_occ:   1.267  0.009  0.086 16.434  0.005  4.128   9.2833e-02
   4_bss:   1.267  0.009  0.086 16.434  0.005  4.128   9.2833e-02
   4_xyz:   1.127  0.009  0.078 15.735  0.004  4.126   7.5496e-02
   4_adp:   1.127  0.009  0.078 15.735  0.004  4.126   7.5496e-02
   4_occ:   1.127  0.009  0.078 15.735  0.004  4.126   7.5496e-02
   5_bss:   1.127  0.009  0.078 15.735  0.004  4.126   7.5496e-02
   5_xyz:   1.128  0.009  0.084 15.527  0.004  4.126   7.4808e-02
   5_adp:   1.128  0.009  0.084 15.527  0.004  4.126   7.4808e-02
   5_occ:   1.128  0.009  0.084 15.527  0.004  4.126   7.4808e-02
   5_bss:   1.128  0.009  0.084 15.527  0.004  4.126   7.4808e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.813   6.9664e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.813   6.9664e+00
   1_xyz:  16.202  0.177  0.502 86.606  0.044  2.016   1.0872e-01
   1_adp:  16.202  0.177  0.502 86.606  0.044  2.016   1.0872e-01
   1_occ:  16.202  0.177  0.502 86.606  0.044  2.016   1.0872e-01
   2_bss:  16.202  0.177  0.502 86.606  0.044  2.016   1.0872e-01
   2_xyz:   9.750  0.097  0.289 88.151  0.040  2.111   8.4090e-02
   2_adp:   9.750  0.097  0.289 88.151  0.040  2.111   8.4090e-02
   2_occ:   9.750  0.097  0.289 88.151  0.040  2.111   8.4090e-02
   3_bss:   9.750  0.097  0.289 88.151  0.040  2.111   8.4090e-02
   3_xyz:   7.656  0.090  0.287 87.903  0.053  2.173   7.3723e-02
   3_adp:   7.656  0.090  0.287 87.903  0.053  2.173   7.3723e-02
   3_occ:   7.656  0.090  0.287 87.903  0.053  2.173   7.3723e-02
   4_bss:   7.656  0.090  0.287 87.903  0.053  2.173   7.3723e-02
   4_xyz:   7.908  0.055  0.281 81.759  0.042  2.234   5.6274e-02
   4_adp:   7.908  0.055  0.281 81.759  0.042  2.234   5.6274e-02
   4_occ:   7.908  0.055  0.281 81.759  0.042  2.234   5.6274e-02
   5_bss:   7.908  0.055  0.281 81.759  0.042  2.234   5.6274e-02
   5_xyz:   7.669  0.053  0.340 82.550  0.046  2.207   7.9049e-02
   5_adp:   7.669  0.053  0.340 82.550  0.046  2.207   7.9049e-02
   5_occ:   7.669  0.053  0.340 82.550  0.046  2.207   7.9049e-02
   5_bss:   7.669  0.053  0.340 82.550  0.046  2.207   7.9049e-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: 104.13   0.00  17.95  86.38   0.00  16.44 104.13   0.00  26.16
   1_occ: 104.13   0.00  17.95  86.38   0.00  16.44 104.13   0.00  26.16
   2_bss: 104.13   0.00  17.95  86.38   0.00  16.44 104.13   0.00  26.16
   2_xyz: 104.13   0.00  17.95  86.38   0.00  16.44 104.13   0.00  26.16
   2_adp: 114.83   0.00  17.24  88.06   0.00  14.69 114.83   0.00  31.15
   2_occ: 114.83   0.00  17.24  88.06   0.00  14.69 114.83   0.00  31.15
   3_bss: 114.83   0.00  17.24  88.06   0.00  14.69 114.83   0.00  31.15
   3_xyz: 114.83   0.00  17.24  88.06   0.00  14.69 114.83   0.00  31.15
   3_adp: 110.93   0.00  16.60  91.25   0.00  13.19 110.93   2.13  35.14
   3_occ: 110.93   0.00  16.60  91.25   0.00  13.19 110.93   2.13  35.14
   4_bss: 110.93   0.00  16.60  91.25   0.00  13.19 110.93   2.13  35.14
   4_xyz: 110.93   0.00  16.60  91.25   0.00  13.19 110.93   2.13  35.14
   4_adp: 107.29   0.00  17.60  95.56   0.00  12.51 107.29   3.37  45.35
   4_occ: 107.29   0.00  17.60  95.56   0.00  12.51 107.29   3.37  45.35
   5_bss: 107.29   0.00  17.60  95.56   0.00  12.51 107.29   3.37  45.35
   5_xyz: 107.29   0.00  17.60  95.56   0.00  12.51 107.29   3.37  45.35
   5_adp: 106.70   0.75  17.03  95.69   0.75  12.10 106.70   4.96  43.86
   5_occ: 106.70   0.75  17.03  95.69   0.75  12.10 106.70   4.96  43.86
   5_bss: 106.68   0.72  17.00  95.66   0.72  12.08 106.68   4.93  43.83
------------------------------------------------------------------------
 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:    1.318    0.019    0.417
   1_adp:    1.318    0.019    0.417
   1_occ:    1.318    0.019    0.417
   2_bss:    1.318    0.019    0.417
   2_xyz:    2.106    0.081    0.621
   2_adp:    2.106    0.081    0.621
   2_occ:    2.106    0.081    0.621
   3_bss:    2.106    0.081    0.621
   3_xyz:    1.999    0.058    0.740
   3_adp:    1.999    0.058    0.740
   3_occ:    1.999    0.058    0.740
   4_bss:    1.999    0.058    0.740
   4_xyz:    2.152    0.052    0.861
   4_adp:    2.152    0.052    0.861
   4_occ:    2.152    0.052    0.861
   5_bss:    2.152    0.052    0.861
   5_xyz:    2.138    0.047    0.902
   5_adp:    2.138    0.047    0.902
   5_occ:    2.138    0.047    0.902
   5_bss:    2.138    0.047    0.902
------------------------------------------------------------------------

CPU time actual refinement: 336.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_98/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_98/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_98/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_98/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_98/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.84 
  Macro-tasks:
    bulk solvent and scale       = 38.95  
    individual site refinement   = 141.58 
    weights calculation          = 32.50  
    collect and process          = 6.21   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 219.33 
  Micro-tasks:
    mask                            = 3.06   
    f_calc                          = 105.89 
    alpha_beta                      = 8.25   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 116.22 
    fmodel                         = 6.98   
    r_factors                      = 0.21   
    phase_errors                   = 9.76   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 251.78 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.819 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    602 calls, 105.59 s
gradients_fft:          546 calls, 104.04 s

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

# Date 2008-01-16 Time 00:45:18 PST -0800 (1200473118.72 s)
Start R-work = 0.5231, R-free = 0.5194 (no bulk solvent and anisotropic scale)
Final R-work = 0.1584, R-free = 0.2046 (no bulk solvent and anisotropic scale)

Start R-work = 0.5158, R-free = 0.5160
Final R-work = 0.1397, R-free = 0.1896