# Date 2008-01-16 Time 02:38:11 PST -0800 (1200479891.22 s)
#phil __OFF__

Command line arguments: "../913.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32510
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 913

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.1647, 84.2302, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95138
Completeness in resolution range: 0.9258
Completeness with d_max=infinity: 0.923052

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95138
Completeness in resolution range: 0.9258
Completeness with d_max=infinity: 0.923052

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1767 [2219/2248]  1999   220   9.9%
  bin  2:  4.1767 -  3.3271 [2129/2152]  1916   213  10.0%
  bin  3:  3.3271 -  2.9100 [2096/2121]  1881   215  10.3%
  bin  4:  2.9100 -  2.6455 [2099/2115]  1896   203   9.7%
  bin  5:  2.6455 -  2.4568 [2053/2092]  1846   207  10.1%
  bin  6:  2.4568 -  2.3125 [2080/2113]  1876   204   9.8%
  bin  7:  2.3125 -  2.1970 [2039/2075]  1827   212  10.4%
  bin  8:  2.1970 -  2.1017 [2022/2064]  1823   199   9.8%
  bin  9:  2.1017 -  2.0210 [2059/2097]  1856   203   9.9%
  bin 10:  2.0210 -  1.9514 [ 793/2082]   710    83  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_913/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:
        1.49 -     2.18: 20
        2.18 -     2.86: 1150
        2.86 -     3.54: 4448
        3.54 -     4.22: 9282
        4.22 -     4.90: 13576
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.494 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.511 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.810 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  17 " - " O   HOH Z 333 "  1.877 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28471 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_913/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_913/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.16465 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4713   r_free= 0.4730   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.274563                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6590 0.99   1439  162 0.3894 0.3822      6.5855      6.5758|
|  2:  4.6590 -  3.7166 0.99   1384  149 0.3842 0.3942      6.7634      6.8281|
|  3:  3.7166 -  3.2522 0.99   1364  155 0.4355 0.4127      6.6584      6.6714|
|  4:  3.2522 -  2.9574 0.99   1349  149 0.4492 0.4678      6.4966      6.4996|
|  5:  2.9574 -  2.7468 0.98   1332  147 0.5012 0.5107      6.3584      6.3573|
|  6:  2.7468 -  2.5857 0.99   1344  151 0.4926 0.5270      6.2605      6.2234|
|  7:  2.5857 -  2.4568 0.99   1326  145 0.5101 0.4478      6.2428      6.1401|
|  8:  2.4568 -  2.3503 0.99   1329  148 0.5297 0.5390      6.1552      6.1989|
|  9:  2.3503 -  2.2601 0.99   1314  151 0.5179 0.5008      6.1233      6.1068|
| 10:  2.2601 -  2.1823 0.98   1331  146 0.5248 0.5208      6.0822      6.0937|
| 11:  2.1823 -  2.1143 0.98   1313  138 0.5138 0.5445      6.0196      6.0329|
| 12:  2.1143 -  2.0540 1.00   1315  150 0.5376 0.5590      5.9475      5.9858|
| 13:  2.0540 -  2.0001 0.87   1163  138 0.5255 0.5038      5.8693      5.8337|
| 14:  2.0001 -  1.9514 0.24    327   30 0.5462 0.5976      5.8216      5.8229|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6590  1439   162  0.71  33.66   0.80     0.73      68294.54|
|  2:  4.6590 -  3.7166  1384   149  0.70  35.25   0.88     0.78     104277.63|
|  3:  3.7166 -  3.2522  1364   155  0.58  45.24   0.84     0.71     117917.28|
|  4:  3.2522 -  2.9574  1349   149  0.48  53.62   0.81     0.59     107829.88|
|  5:  2.9574 -  2.7468  1332   147  0.39  60.49   0.74     0.49      88306.80|
|  6:  2.7468 -  2.5857  1344   151  0.40  60.03   0.75     0.47      70655.27|
|  7:  2.5857 -  2.4568  1326   145  0.41  59.25   0.75     0.46      60744.82|
|  8:  2.4568 -  2.3503  1329   148  0.38  61.11   0.72     0.46      56515.98|
|  9:  2.3503 -  2.2601  1314   151  0.36  63.15   0.75     0.43      53205.85|
| 10:  2.2601 -  2.1823  1331   146  0.32  65.87   0.75     0.40      52018.31|
| 11:  2.1823 -  2.1143  1313   138  0.29  68.62   0.78     0.36      48151.29|
| 12:  2.1143 -  2.0540  1315   150  0.24  72.34   0.74     0.32      47025.54|
| 13:  2.0540 -  2.0001  1163   138  0.23  72.91   0.73     0.30      40499.30|
| 14:  2.0001 -  1.9514   327    30  0.24  71.77   0.70     0.30      33214.87|
|alpha:            min =        0.30 max =            0.78 mean =         0.50|
|beta:             min =    33214.87 max =       117917.28 mean =     70295.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.65|
|phase err.(test): min =        0.00 max =           89.99 mean =        57.92|
|-----------------------------------------------------------------------------|

============================== 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 = 14.244168             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.472   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.258943              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.455   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      714 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1507 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2657 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3963 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5034 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6656 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7765 |
|-----------------------------------------------------------------------------|
|-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 |       53.476 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.982 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    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 = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4777   r_free= 0.4790   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.276921                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4633   r_free= 0.4613   ksol= 0.34   Bsol= 10.61   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,7.87,9.58,0.00,0.00,0.00); trace/3= 8.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.273851                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.332330             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.792   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.142349              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.889   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4633      final r-factor (work) = 0.3875          |
| start r-factor (free) = 0.4613      final r-factor (free) = 0.4219          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.0212 = 11.33 * 0.50 * 6.2732 + 1.00 * 53.4760                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.2011 = 11.33 * 0.50 * 6.1883 + 1.00 * 0.1373                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3875      final r-factor (work) = 0.3444          |
| start r-factor (free) = 0.4219      final r-factor (free) = 0.4048          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0835 = 1.14 * 1.00 * 6.1883 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9947 = 1.14 * 1.00 * 6.1101 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.71   12.86    None  None   None       |
|    all(noH): 2823   0      0.00    76.71   12.86    None  None   None       |
|    Sol.    : 438    0      0.00    69.32   26.12    None  None   None       |
|    Mac.    : 2385   0      0.00    76.71   10.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.671: 1183   |   5:    38.355 -  46.026:   60        |
|      1:     7.671 -  15.342:  765   |   6:    46.026 -  53.697:   35        |
|      2:    15.342 -  23.013:  408   |   7:    53.697 -  61.368:   16        |
|      3:    23.013 -  30.684:  224   |   8:    61.368 -  69.039:    4        |
|      4:    30.684 -  38.355:  123   |   9:    69.039 -  76.710:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3444 r_free = 0.4048             target_work(ml) = 6.092         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3440 r_free = 0.4052             target_work(ml) = 6.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3440   r_free= 0.4052   ksol= 0.34   Bsol= 10.61   scale= 1.097   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,7.87,9.58,0.00,0.00,0.00); trace/3= 8.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.091882                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3411   r_free= 0.3998   ksol= 0.34   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,4.16,6.33,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.091853                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.413788              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.122   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.602322              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.149  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3411      final r-factor (work) = 0.2569          |
| start r-factor (free) = 0.3998      final r-factor (free) = 0.3220          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8277 = 8.41 * 0.50 * 6.1067 + 1.00 * 0.1373                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2587 = 8.41 * 0.50 * 5.9844 + 1.00 * 0.0830                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2569      final r-factor (work) = 0.2351          |
| start r-factor (free) = 0.3220      final r-factor (free) = 0.2979          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6196 = 0.60 * 1.00 * 5.9844 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5472 = 0.60 * 1.00 * 5.8304 + 1.00 * 0.0354                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.24   13.33    None  None   None       |
|    all(noH): 2823   0      0.00    76.24   13.33    None  None   None       |
|    Sol.    : 438    0      1.42    70.25   31.84    None  None   None       |
|    Mac.    : 2385   0      0.00    76.24   9.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.624: 1221   |   5:    38.122 -  45.746:  105        |
|      1:     7.624 -  15.249:  783   |   6:    45.746 -  53.371:   61        |
|      2:    15.249 -  22.873:  313   |   7:    53.371 -  60.995:   14        |
|      3:    22.873 -  30.498:  177   |   8:    60.995 -  68.619:    6        |
|      4:    30.498 -  38.122:  139   |   9:    68.619 -  76.244:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2351 r_free = 0.2979             target_work(ml) = 5.796         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2350 r_free = 0.2976             target_work(ml) = 5.795         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2350   r_free= 0.2976   ksol= 0.34   Bsol= 50.00   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,4.16,6.33,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.795195                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2328   r_free= 0.2943   ksol= 0.34   Bsol= 46.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,2.49,3.56,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.792660                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.587179              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.596  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.597296              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.465   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2328      final r-factor (work) = 0.1780          |
| start r-factor (free) = 0.2943      final r-factor (free) = 0.2335          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5477 = 3.59 * 0.50 * 5.8345 + 1.00 * 0.0830                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2685 = 3.59 * 0.50 * 5.6902 + 1.00 * 0.0626                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1780      final r-factor (work) = 0.1593          |
| start r-factor (free) = 0.2335      final r-factor (free) = 0.2158          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1048 = 1.60 * 1.00 * 5.6902 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8061 = 1.60 * 1.00 * 5.5039 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.98   14.38    None  None   None       |
|    all(noH): 2823   0      0.00    94.98   14.38    None  None   None       |
|    Sol.    : 438    0      2.24    83.93   40.12    None  None   None       |
|    Mac.    : 2385   0      0.00    94.98   9.65     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.498: 1582   |   5:    47.489 -  56.987:   83        |
|      1:     9.498 -  18.996:  648   |   6:    56.987 -  66.485:   64        |
|      2:    18.996 -  28.494:  167   |   7:    66.485 -  75.983:   26        |
|      3:    28.494 -  37.992:  113   |   8:    75.983 -  85.481:   13        |
|      4:    37.992 -  47.489:  125   |   9:    85.481 -  94.979:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1593 r_free = 0.2158             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1592 r_free = 0.2157             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1592   r_free= 0.2157   ksol= 0.34   Bsol= 46.23   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,2.49,3.56,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.464729                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1588   r_free= 0.2149   ksol= 0.32   Bsol= 40.94   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.59,1.89,2.26,0.00,0.00,0.00); trace/3= 1.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.461944                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.723945              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.149  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.434859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.989  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1588      final r-factor (work) = 0.1347          |
| start r-factor (free) = 0.2149      final r-factor (free) = 0.1850          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5632 = 2.72 * 0.50 * 5.5072 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4098 = 2.72 * 0.50 * 5.3964 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1347      final r-factor (work) = 0.1298          |
| start r-factor (free) = 0.1850      final r-factor (free) = 0.1771          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3613 = 0.43 * 1.00 * 5.3964 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3152 = 0.43 * 1.00 * 5.2970 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.89   13.93    None  None   None       |
|    all(noH): 2823   0      0.00    98.89   13.93    None  None   None       |
|    Sol.    : 438    0      2.81    84.66   38.85    None  None   None       |
|    Mac.    : 2385   0      0.00    98.89   9.35     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.889: 1683   |   5:    49.445 -  59.334:   79        |
|      1:     9.889 -  19.778:  603   |   6:    59.334 -  69.223:   42        |
|      2:    19.778 -  29.667:  155   |   7:    69.223 -  79.112:   17        |
|      3:    29.667 -  39.556:  115   |   8:    79.112 -  89.001:    9        |
|      4:    39.556 -  49.445:  118   |   9:    89.001 -  98.890:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1298 r_free = 0.1771             target_work(ml) = 5.272         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1296 r_free = 0.1770             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1770   ksol= 0.32   Bsol= 40.94   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.59,1.89,2.26,0.00,0.00,0.00); trace/3= 1.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.270562                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1777   ksol= 0.32   Bsol= 42.25   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,1.71,1.91,0.00,0.00,0.00); trace/3= 1.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273256                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.305778              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.878  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.610364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.215  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1299      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1777      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1676 = 2.31 * 0.50 * 5.2976 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1087 = 2.31 * 0.50 * 5.2438 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1659      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2123 = 0.61 * 1.00 * 5.2438 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1884 = 0.61 * 1.00 * 5.2031 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.01  13.71    None  None   None       |
|    all(noH): 2823   0      0.00    104.01  13.71    None  None   None       |
|    Sol.    : 438    0      2.28    85.90   38.17    None  None   None       |
|    Mac.    : 2385   0      0.00    104.01  9.22     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 -  10.401: 1770   |   5:    52.004 -  62.405:   63        |
|      1:    10.401 -  20.802:  551   |   6:    62.405 -  72.806:   35        |
|      2:    20.802 -  31.203:  148   |   7:    72.806 -  83.207:    9        |
|      3:    31.203 -  41.604:  127   |   8:    83.207 -  93.608:    6        |
|      4:    41.604 -  52.004:  112   |   9:    93.608 - 104.009:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1182 r_free = 0.1653             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1653             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1653   ksol= 0.32   Bsol= 42.25   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,1.71,1.91,0.00,0.00,0.00); trace/3= 1.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.201014                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6590 0.99   1439  162 0.0988 0.1294      5.3844      5.5514|
|  2:  4.6590 -  3.7166 0.99   1384  149 0.0908 0.1147      5.4666      5.6867|
|  3:  3.7166 -  3.2522 0.99   1364  155 0.1105 0.1708      5.5081      5.8934|
|  4:  3.2522 -  2.9574 0.99   1349  149 0.1333 0.1511      5.4998      5.6039|
|  5:  2.9574 -  2.7468 0.98   1332  147 0.1388 0.1807       5.365      5.5401|
|  6:  2.7468 -  2.5857 0.99   1344  151 0.1330 0.2088      5.2814      5.5577|
|  7:  2.5857 -  2.4568 0.99   1326  145 0.1327 0.1769      5.2379      5.4391|
|  8:  2.4568 -  2.3503 0.99   1329  148 0.1233 0.1767      5.1123      5.3419|
|  9:  2.3503 -  2.2601 0.99   1314  151 0.1209 0.1977      5.0542      5.3342|
| 10:  2.2601 -  2.1823 0.98   1331  146 0.1202 0.1741      5.0231      5.2477|
| 11:  2.1823 -  2.1143 0.98   1313  138 0.1208 0.1967      4.9728      5.3358|
| 12:  2.1143 -  2.0540 1.00   1315  150 0.1197 0.1749      4.9225      5.1155|
| 13:  2.0540 -  2.0001 0.87   1163  138 0.1202 0.1882      4.8126      5.0696|
| 14:  2.0001 -  1.9514 0.24    327   30 0.1165 0.1682       4.701      4.9794|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6590  1439   162  0.94   9.05   0.98     0.96       7267.81|
|  2:  4.6590 -  3.7166  1384   149  0.95   8.28   1.01     1.00       9148.54|
|  3:  3.7166 -  3.2522  1364   155  0.93  12.00   1.03     1.03      11173.75|
|  4:  3.2522 -  2.9574  1349   149  0.91  14.79   1.01     0.99      11048.25|
|  5:  2.9574 -  2.7468  1332   147  0.89  17.29   0.99     0.96       9135.63|
|  6:  2.7468 -  2.5857  1344   151  0.89  17.60   0.99     0.96       8276.31|
|  7:  2.5857 -  2.4568  1326   145  0.89  17.13   0.99     0.95       7344.48|
|  8:  2.4568 -  2.3503  1329   148  0.89  17.17   0.99     0.95       6057.26|
|  9:  2.3503 -  2.2601  1314   151  0.89  16.98   1.01     0.98       5444.72|
| 10:  2.2601 -  2.1823  1331   146  0.90  16.38   1.00     0.97       5079.65|
| 11:  2.1823 -  2.1143  1313   138  0.89  17.05   0.99     0.96       4720.54|
| 12:  2.1143 -  2.0540  1315   150  0.90  17.11   1.00     1.00       4453.88|
| 13:  2.0540 -  2.0001  1163   138  0.89  17.12   1.00     0.98       3561.18|
| 14:  2.0001 -  1.9514   327    30  0.89  17.28   0.99     0.97       2849.34|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2849.34 max =        11173.75 mean =      7112.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.18|
|phase err.(test): min =        0.00 max =           88.96 mean =        14.66|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1653   ksol= 0.32   Bsol= 42.73   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.22,0.01,0.21,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200999                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1653   ksol= 0.32   Bsol= 42.73   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.22,0.01,0.21,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200999                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6590 0.99   1439  162 0.0987 0.1293      5.3839      5.5505|
|  2:  4.6590 -  3.7166 0.99   1384  149 0.0907 0.1146      5.4657      5.6856|
|  3:  3.7166 -  3.2522 0.99   1364  155 0.1105 0.1708      5.5076      5.8932|
|  4:  3.2522 -  2.9574 0.99   1349  149 0.1333 0.1512      5.4998      5.6039|
|  5:  2.9574 -  2.7468 0.98   1332  147 0.1388 0.1808      5.3652      5.5404|
|  6:  2.7468 -  2.5857 0.99   1344  151 0.1331 0.2088      5.2816      5.5578|
|  7:  2.5857 -  2.4568 0.99   1326  145 0.1327 0.1768      5.2381      5.4392|
|  8:  2.4568 -  2.3503 0.99   1329  148 0.1233 0.1769      5.1125      5.3425|
|  9:  2.3503 -  2.2601 0.99   1314  151 0.1209 0.1976      5.0544      5.3341|
| 10:  2.2601 -  2.1823 0.98   1331  146 0.1202 0.1741      5.0233      5.2479|
| 11:  2.1823 -  2.1143 0.98   1313  138 0.1208 0.1967      4.9729      5.3358|
| 12:  2.1143 -  2.0540 1.00   1315  150 0.1197 0.1750      4.9226      5.1156|
| 13:  2.0540 -  2.0001 0.87   1163  138 0.1202 0.1883      4.8128      5.0699|
| 14:  2.0001 -  1.9514 0.24    327   30 0.1165 0.1683      4.7012      4.9795|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6590  1439   162  0.94   9.04   0.98     0.96       7253.43|
|  2:  4.6590 -  3.7166  1384   149  0.95   8.28   1.01     1.00       9132.11|
|  3:  3.7166 -  3.2522  1364   155  0.93  11.98   1.03     1.03      11157.26|
|  4:  3.2522 -  2.9574  1349   149  0.91  14.79   1.01     0.99      11045.18|
|  5:  2.9574 -  2.7468  1332   147  0.89  17.29   0.99     0.96       9137.07|
|  6:  2.7468 -  2.5857  1344   151  0.89  17.60   0.99     0.96       8279.68|
|  7:  2.5857 -  2.4568  1326   145  0.89  17.13   0.99     0.95       7348.00|
|  8:  2.4568 -  2.3503  1329   148  0.89  17.17   0.99     0.95       6059.95|
|  9:  2.3503 -  2.2601  1314   151  0.89  16.98   1.01     0.98       5447.23|
| 10:  2.2601 -  2.1823  1331   146  0.90  16.38   1.00     0.97       5081.16|
| 11:  2.1823 -  2.1143  1313   138  0.89  17.05   0.99     0.96       4722.25|
| 12:  2.1143 -  2.0540  1315   150  0.90  17.11   1.00     1.00       4455.05|
| 13:  2.0540 -  2.0001  1163   138  0.89  17.12   1.00     0.98       3562.93|
| 14:  2.0001 -  1.9514   327    30  0.89  17.28   0.99     0.97       2851.05|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2851.05 max =        11157.26 mean =      7109.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        15.18|
|phase err.(test): min =        0.00 max =           89.17 mean =        14.67|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.782)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    105.71  15.41    None  None   None       |
|    all(noH): 2823   0      1.70    105.71  15.41    None  None   None       |
|    Sol.    : 438    0      3.99    87.60   39.87    None  None   None       |
|    Mac.    : 2385   0      1.70    105.71  10.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.701 -  12.102: 1770   |   5:    53.705 -  64.106:   63        |
|      1:    12.102 -  22.503:  551   |   6:    64.106 -  74.507:   35        |
|      2:    22.503 -  32.904:  148   |   7:    74.507 -  84.908:    9        |
|      3:    32.904 -  43.305:  127   |   8:    84.908 -  95.309:    6        |
|      4:    43.305 -  53.705:  112   |   9:    95.309 - 105.710:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.457 - 5.818
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 346
   mapped sites are within: 0.743 - 5.818

peak=   10.206 closest distance to " CB  VAL A 230 " =    1.455
peak=    9.578 closest distance to " CG2 VAL A 296 " =    1.384
peak=    6.858 closest distance to " O   HOH Z  37 " =    1.455
peak=    6.789 closest distance to " CG  ARG A 138 " =    1.078
peak=    6.428 closest distance to " NH2 ARG A  56 " =    2.261
peak=    6.409 closest distance to " O   HOH Z 120 " =    1.196
peak=    6.158 closest distance to " CG  LEU A   5 " =    1.303
peak=    6.026 closest distance to " O   HOH Z 278 " =    1.403
peak=    5.933 closest distance to " O   HOH Z 279 " =    1.231
peak=    5.853 closest distance to " O   HOH Z 277 " =    1.201
peak=    5.520 closest distance to " CD2 LEU A   5 " =    1.204
peak=    5.464 closest distance to " O   HOH Z 132 " =    1.599
peak=    5.393 closest distance to " CB  GLN A 223 " =    1.399
peak=    5.260 closest distance to " O   HOH Z 247 " =    1.373
peak=    5.162 closest distance to " O   HOH Z 124 " =    1.464
peak=    5.058 closest distance to " O   HOH Z  48 " =    1.891
peak=    4.951 closest distance to " CG  PRO A  54 " =    1.221
peak=    4.947 closest distance to " CD1AILE A 234 " =    1.033
peak=    4.912 closest distance to " NH2BARG A 102 " =    0.974
peak=    4.862 closest distance to " CB  SER A  63 " =    1.326
peak=    4.859 closest distance to " NE2 GLN A  11 " =    1.134
peak=    4.844 closest distance to " CG  PRO A 198 " =    1.332
peak=    4.781 closest distance to " O   HOH Z 142 " =    1.759
peak=    4.769 closest distance to " CB  GLN A 183 " =    1.320
peak=    4.759 closest distance to " CG  PRO A 213 " =    1.247
peak=    4.747 closest distance to " O   HOH Z 202 " =    1.363
peak=    4.658 closest distance to " CG  LEU A 228 " =    1.259
peak=    4.633 closest distance to " O   HOH Z  97 " =    2.007
peak=    4.502 closest distance to " CB  VAL A 230 " =    1.234
peak=    4.484 closest distance to " CB  PRO A  54 " =    0.830
peak=    4.461 closest distance to " CD2 LEU A 228 " =    1.197
peak=    4.453 closest distance to " O   HOH Z 411 " =    3.715
peak=    4.418 closest distance to " NH1 ARG A 138 " =    1.058
peak=    4.400 closest distance to " O   HOH Z 427 " =    3.067
peak=    4.363 closest distance to " CB  TYR A 169 " =    0.951
peak=    4.357 closest distance to " CB  SER A   3 " =    1.406
peak=    4.334 closest distance to " CB  ASN A 148 " =    1.333
peak=    4.310 closest distance to " O   HOH Z 371 " =    3.260
peak=    4.293 closest distance to " O   HOH Z 128 " =    2.003
peak=    4.285 closest distance to " O   HOH Z 263 " =    1.436
peak=    4.269 closest distance to " O   HOH Z 193 " =    1.763
peak=    4.234 closest distance to " O   HOH Z 295 " =    1.601
peak=    4.234 closest distance to " CB  GLU A 152 " =    1.109
peak=    4.218 closest distance to " O   HOH Z  59 " =    2.327
peak=    4.217 closest distance to " CB  ARG A 275 " =    0.864
peak=    4.215 closest distance to " O   HOH Z 260 " =    1.277
peak=    4.214 closest distance to " O   HOH Z 316 " =    2.388
peak=    4.213 closest distance to " O   HOH Z 126 " =    1.867
peak=    4.209 closest distance to " O   HOH Z 276 " =    1.378
peak=    4.207 closest distance to " CA  ALA A  21 " =    1.240
peak=    4.156 closest distance to " O   HOH Z 389 " =    1.834
peak=    4.153 closest distance to " O   HOH Z 272 " =    1.905
peak=    4.151 closest distance to " CG1BVAL A  72 " =    1.604
peak=    4.138 closest distance to " O   HOH Z 134 " =    1.538
peak=    4.128 closest distance to " O   HOH Z 334 " =    3.050
peak=    4.112 closest distance to " O   PRO A 198 " =    1.499
peak=    4.109 closest distance to " O   HOH Z 136 " =    1.330
peak=    4.104 closest distance to " O   SER A  87 " =    2.276
peak=    4.100 closest distance to " O   HOH Z 192 " =    1.233
peak=    4.093 closest distance to " O   HOH Z 199 " =    1.030
peak=    4.092 closest distance to " O   HOH Z 303 " =    2.119
peak=    4.079 closest distance to " O   HOH Z  78 " =    1.944
peak=    4.077 closest distance to " O   HOH Z 108 " =    1.485
peak=    4.062 closest distance to " CA  VAL A  41 " =    0.896
peak=    4.031 closest distance to " CG2 THR A 221 " =    1.007
peak=    4.026 closest distance to " O   HOH Z  88 " =    3.201
peak=    4.017 closest distance to " O   HOH Z 126 " =    1.605
peak=    4.015 closest distance to " CB  VAL A 265 " =    1.214
peak=    4.008 closest distance to " O   HOH Z 368 " =    2.049
peak=    4.007 closest distance to " CB  LEU A 228 " =    1.298
peak=    4.003 closest distance to " CB  VAL A 202 " =    1.637
peak=    4.000 closest distance to " OD2 ASP A 286 " =    2.786
peak=    3.999 closest distance to " O   HOH Z 344 " =    2.711
peak=    3.991 closest distance to " O   HOH Z  15 " =    2.007
peak=    3.983 closest distance to " O   HOH Z 180 " =    2.138
peak=    3.972 closest distance to " O   HOH Z  92 " =    0.916
peak=    3.958 closest distance to " NH1 ARG A  14 " =    1.088
peak=    3.942 closest distance to " OD1 ASN A  69 " =    2.664
peak=    3.937 closest distance to " O   HOH Z 232 " =    2.173
peak=    3.920 closest distance to " CB  GLU A 128 " =    1.156
peak=    3.918 closest distance to " CD  ARG A 269 " =    0.916
peak=    3.917 closest distance to " O   HOH Z 236 " =    1.664
peak=    3.913 closest distance to " CB  TRP A 179 " =    1.289
peak=    3.911 closest distance to " OE1 GLN A  58 " =    5.818
peak=    3.907 closest distance to " CD  ARG A 138 " =    1.206
peak=    3.877 closest distance to " O   HOH Z  80 " =    1.837
peak=    3.876 closest distance to " O   HOH Z  20 " =    1.927
peak=    3.875 closest distance to " O   HOH Z 298 " =    1.955
peak=    3.861 closest distance to " O   HOH Z  93 " =    2.552
peak=    3.859 closest distance to " O   HOH Z 426 " =    1.381
peak=    3.857 closest distance to " O   HOH Z 203 " =    1.566
peak=    3.849 closest distance to " CD  LYS A 119 " =    1.402
peak=    3.844 closest distance to " O   HOH Z  63 " =    1.341
peak=    3.835 closest distance to " O   HOH Z 369 " =    2.062
peak=    3.832 closest distance to " O   HOH Z 346 " =    1.469
peak=    3.814 closest distance to " O   HOH Z 214 " =    2.208
peak=    3.798 closest distance to " O   MET A 105 " =    1.745
peak=    3.798 closest distance to " O   HOH Z 326 " =    1.427
peak=    3.796 closest distance to " CA  LEU A 282 " =    1.017
peak=    3.787 closest distance to " CA  ASP A 191 " =    0.848
peak=    3.786 closest distance to " O   HOH Z  54 " =    1.563
peak=    3.785 closest distance to " O   HOH Z  11 " =    1.203
peak=    3.785 closest distance to " CA  TYR A  30 " =    0.997
peak=    3.777 closest distance to " CB  GLU A 277 " =    3.588
peak=    3.767 closest distance to " O   HOH Z 423 " =    1.838
peak=    3.766 closest distance to " O   HOH Z  68 " =    1.798
peak=    3.766 closest distance to " O   HOH Z 189 " =    2.298
peak=    3.762 closest distance to " O   ASP A 132 " =    3.768
peak=    3.761 closest distance to " CD1 ILE A  33 " =    1.628
peak=    3.756 closest distance to " CD1 LEU A 300 " =    1.112
peak=    3.742 closest distance to " O   HOH Z 236 " =    1.810
peak=    3.741 closest distance to " O   HOH Z 209 " =    2.372
peak=    3.737 closest distance to " O   HOH Z  55 " =    2.413
peak=    3.735 closest distance to " O   HOH Z 217 " =    1.556
peak=    3.723 closest distance to " O   HOH Z 133 " =    1.664
peak=    3.714 closest distance to " CG1 VAL A 153 " =    1.015
peak=    3.700 closest distance to " O   HOH Z 215 " =    1.585
peak=    3.679 closest distance to " O   HOH Z 116 " =    1.706
peak=    3.679 closest distance to " CB  SER A 273 " =    0.867
peak=    3.673 closest distance to " CA  THR A 221 " =    0.915
peak=    3.671 closest distance to " CG  GLN A  88 " =    1.062
peak=    3.671 closest distance to " O   HOH Z  61 " =    1.559
peak=    3.671 closest distance to " O   HOH Z  49 " =    2.452
peak=    3.670 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.668 closest distance to " CA  VAL A 126 " =    1.152
peak=    3.668 closest distance to " NH1 ARG A  56 " =    1.026
peak=    3.667 closest distance to " CG2 VAL A 174 " =    1.338
peak=    3.663 closest distance to " CG  PRO A 243 " =    1.215
peak=    3.662 closest distance to " O   HOH Z 193 " =    2.019
peak=    3.661 closest distance to " O   HOH Z 291 " =    1.580
peak=    3.652 closest distance to " O   HOH Z 126 " =    2.177
peak=    3.652 closest distance to " CA  ALA A 295 " =    1.095
peak=    3.652 closest distance to " O   HOH Z 261 " =    1.780
peak=    3.645 closest distance to " O   HOH Z 345 " =    3.297
peak=    3.639 closest distance to " NZ  LYS A 117 " =    3.317
peak=    3.639 closest distance to " O   HOH Z 280 " =    1.532
peak=    3.637 closest distance to " O   HOH Z  30 " =    1.411
peak=    3.633 closest distance to " CA  LEU A 101 " =    1.634
peak=    3.631 closest distance to " O   HOH Z 118 " =    1.635
peak=    3.629 closest distance to " OE1 GLU A   2 " =    2.100
peak=    3.626 closest distance to " CG  ARG A  66 " =    2.716
peak=    3.624 closest distance to " O   HOH Z 112 " =    1.432
peak=    3.624 closest distance to " CG  PRO A 280 " =    0.743
peak=    3.616 closest distance to " O   HOH Z  58 " =    1.419
peak=    3.609 closest distance to " O   HOH Z 403 " =    1.727
peak=    3.608 closest distance to " OD1 ASN A 217 " =    1.672
peak=    3.607 closest distance to " O   HOH Z 374 " =    2.960
peak=    3.598 closest distance to " CB  ALA A 291 " =    1.360
peak=    3.598 closest distance to " CB  ARG A 139 " =    0.896
peak=    3.597 closest distance to " O   HOH Z   3 " =    1.509
peak=    3.595 closest distance to " CG1 ILE A  33 " =    1.339
peak=    3.592 closest distance to " OG  SER A  22 " =    2.878
peak=    3.582 closest distance to " O   HOH Z 394 " =    1.690
peak=    3.581 closest distance to " CD BLYS A 290 " =    1.046
peak=    3.577 closest distance to " O   HOH Z  71 " =    1.281
peak=    3.577 closest distance to " O   HOH Z  44 " =    2.387
peak=    3.562 closest distance to " CG  MET A 188 " =    1.345
peak=    3.561 closest distance to " O   HOH Z   4 " =    1.657
peak=    3.560 closest distance to " OE1 GLN A  11 " =    1.701
peak=    3.556 closest distance to " O   HOH Z 331 " =    1.306
peak=    3.555 closest distance to " CA  ASN A  74 " =    1.294
peak=    3.555 closest distance to " CD2 LEU A 255 " =    1.307
peak=    3.550 closest distance to " O   TRP A 274 " =    1.855
peak=    3.544 closest distance to " O   HOH Z 108 " =    1.890
peak=    3.544 closest distance to " O   HOH Z 227 " =    1.745
peak=    3.537 closest distance to " O   ALA A 158 " =    1.292
peak=    3.534 closest distance to " O   HOH Z 163 " =    1.419
peak=    3.530 closest distance to " CB  TRP A 266 " =    0.980
peak=    3.525 closest distance to " O   HOH Z 155 " =    1.674
peak=    3.521 closest distance to " O   HOH Z  48 " =    2.054
peak=    3.521 closest distance to " CB  TYR A  30 " =    1.457
peak=    3.509 closest distance to " C   SER A  32 " =    1.124
peak=    3.502 closest distance to " CG BARG A 102 " =    1.838
peak=    3.502 closest distance to " O   HOH Z 407 " =    2.479
peak=    3.499 closest distance to " O   HOH Z 374 " =    1.071
peak=    3.499 closest distance to " O   HOH Z 193 " =    1.467
peak=    3.490 closest distance to " O   HOH Z  21 " =    1.841
peak=    3.488 closest distance to " O   HOH Z  40 " =    1.438
peak=    3.485 closest distance to " CB  SER A  62 " =    1.276
peak=    3.479 closest distance to " CA  ASP A 140 " =    1.233
peak=    3.479 closest distance to " O   HOH Z 366 " =    2.983
peak=    3.470 closest distance to " O   HOH Z 332 " =    1.552
peak=    3.469 closest distance to " CA  LYS A 117 " =    1.253
peak=    3.468 closest distance to " CB  ALA A 161 " =    0.938
peak=    3.466 closest distance to " O   HOH Z 221 " =    1.470
peak=    3.462 closest distance to " O   HOH Z 171 " =    2.564
peak=    3.459 closest distance to " C   ALA A 299 " =    0.962
peak=    3.455 closest distance to " O   HOH Z 425 " =    1.400
peak=    3.451 closest distance to " O   HOH Z 355 " =    1.834
peak=    3.450 closest distance to " CD2 HIS A  81 " =    1.135
peak=    3.446 closest distance to " CG2 VAL A 257 " =    0.786
peak=    3.445 closest distance to " CG AARG A 275 " =    1.056
peak=    3.445 closest distance to " CG  LEU A 167 " =    1.161
peak=    3.438 closest distance to " O   HOH Z 271 " =    1.919
peak=    3.437 closest distance to " O   HOH Z 419 " =    1.580
peak=    3.432 closest distance to " N   ASN A  39 " =    1.227
peak=    3.432 closest distance to " NH2BARG A 145 " =    2.202
peak=    3.432 closest distance to " O   HOH Z 407 " =    3.649
peak=    3.422 closest distance to " CA  ALA A 158 " =    1.057
peak=    3.417 closest distance to " O   HOH Z  19 " =    2.286
peak=    3.411 closest distance to " N   ALA A 256 " =    0.874
peak=    3.399 closest distance to " CB  SER A 216 " =    0.754
peak=    3.397 closest distance to " O   HOH Z 284 " =    1.359
peak=    3.393 closest distance to " CB  PRO A 198 " =    1.017
peak=    3.391 closest distance to " CB  LEU A 255 " =    0.797
peak=    3.387 closest distance to " O   HOH Z 344 " =    1.305
peak=    3.384 closest distance to " NE2 GLN A  58 " =    4.086
peak=    3.382 closest distance to " CB  LEU A 143 " =    1.142
peak=    3.379 closest distance to " CA  GLY A 211 " =    1.185
peak=    3.377 closest distance to " CA  ALA A  51 " =    0.988
peak=    3.375 closest distance to " CG  GLN A  58 " =    2.658
peak=    3.374 closest distance to " NZ  LYS A  76 " =    1.371
peak=    3.367 closest distance to " CA  ALA A 160 " =    0.790
peak=    3.364 closest distance to " O   HOH Z 426 " =    3.054
peak=    3.361 closest distance to " O   HOH Z 422 " =    2.620
peak=    3.359 closest distance to " O   HOH Z 273 " =    2.690
peak=    3.357 closest distance to " OG BSER A 164 " =    2.184
peak=    3.356 closest distance to " O   HOH Z 283 " =    1.912
peak=    3.355 closest distance to " O   SER A  26 " =    1.670
peak=    3.355 closest distance to " O   HOH Z  13 " =    1.249
peak=    3.351 closest distance to " O   HOH Z 152 " =    1.579
peak=    3.342 closest distance to " O   THR A  31 " =    1.498
peak=    3.341 closest distance to " CA  ARG A  36 " =    1.082
peak=    3.339 closest distance to " CB  ALA A   9 " =    1.546
peak=    3.334 closest distance to " O   HOH Z 133 " =    2.108
peak=    3.330 closest distance to " O   HOH Z 423 " =    3.224
peak=    3.327 closest distance to " CD2 TYR A 186 " =    0.989
peak=    3.321 closest distance to " O   HOH Z 114 " =    1.410
peak=    3.318 closest distance to " O   HOH Z 329 " =    3.488
peak=    3.318 closest distance to " O   HOH Z 279 " =    2.238
peak=    3.315 closest distance to " O   GLN A 278 " =    1.240
peak=    3.310 closest distance to " O   HOH Z 313 " =    1.866
peak=    3.308 closest distance to " CZ2 TRP A 274 " =    1.819
peak=    3.308 closest distance to " CA  MET A  40 " =    1.028
peak=    3.303 closest distance to " CA  GLN A 194 " =    1.182
peak=    3.298 closest distance to " O   HOH Z 250 " =    1.317
peak=    3.296 closest distance to " CA  ASN A 215 " =    1.225
peak=    3.295 closest distance to " O   HOH Z 132 " =    3.358
peak=    3.293 closest distance to " O   HOH Z 359 " =    3.703
peak=    3.282 closest distance to " O   HOH Z 207 " =    2.248
peak=    3.281 closest distance to " O   HOH Z 185 " =    1.655
peak=    3.281 closest distance to " CA  SER A  87 " =    0.896
peak=    3.280 closest distance to " CA  ALA A 248 " =    1.161
peak=    3.280 closest distance to " O   HOH Z 215 " =    1.434
peak=    3.276 closest distance to " CB  LYS A 193 " =    1.131
peak=    3.275 closest distance to " CB  ALA A 100 " =    1.312
peak=    3.274 closest distance to " OD1 ASP A 231 " =    1.814
peak=    3.273 closest distance to " O   HOH Z 374 " =    2.450
peak=    3.270 closest distance to " CD2 LEU A 282 " =    1.883
peak=    3.269 closest distance to " CA  TYR A 186 " =    1.416
peak=    3.269 closest distance to " CA  THR A 264 " =    0.792
peak=    3.259 closest distance to " CB  ALA A 256 " =    1.102
peak=    3.249 closest distance to " O   HOH Z 411 " =    1.774
peak=    3.246 closest distance to " CE1 TYR A 186 " =    1.206
peak=    3.246 closest distance to " O   HOH Z  97 " =    0.910
peak=    3.245 closest distance to " CZ  PHE A 192 " =    1.122
peak=    3.245 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.244 closest distance to " CB  SER A  26 " =    1.625
peak=    3.239 closest distance to " O   HOH Z 175 " =    3.494
peak=    3.237 closest distance to " CB  GLU A 236 " =    1.253
peak=    3.237 closest distance to " O   HOH Z  68 " =    2.505
peak=    3.235 closest distance to " CD1 ILE A 199 " =    0.946
peak=    3.235 closest distance to " ND1 HIS A  81 " =    1.613
peak=    3.234 closest distance to " O   HOH Z 127 " =    1.236
peak=    3.234 closest distance to " NH2 ARG A 156 " =    1.062
peak=    3.232 closest distance to " O   ALA A   1 " =    1.410
peak=    3.232 closest distance to " CB  LEU A 237 " =    0.953
peak=    3.231 closest distance to " O   HOH Z 270 " =    1.745
peak=    3.227 closest distance to " O   ASN A 217 " =    1.324
peak=    3.220 closest distance to " O   HOH Z  37 " =    2.825
peak=    3.220 closest distance to " NH1AARG A 145 " =    0.945
peak=    3.214 closest distance to " O   HOH Z 184 " =    1.354
peak=    3.211 closest distance to " CB  THR A  82 " =    1.328
peak=    3.210 closest distance to " O   ALA A  10 " =    1.620
peak=    3.210 closest distance to " CB  ARG A  79 " =    1.393
peak=    3.210 closest distance to " CA  ALA A 154 " =    1.327
peak=    3.209 closest distance to " O   HOH Z 425 " =    2.181
peak=    3.209 closest distance to " O   HOH Z 128 " =    2.031
peak=    3.208 closest distance to " O   HOH Z 281 " =    4.303
peak=    3.207 closest distance to " O   HOH Z  49 " =    1.853
peak=    3.199 closest distance to " O   HOH Z 156 " =    2.787
peak=    3.195 closest distance to " CG2 VAL A 268 " =    0.936
peak=    3.193 closest distance to " O   HOH Z 149 " =    2.009
peak=    3.192 closest distance to " O   HOH Z 158 " =    2.948
peak=    3.191 closest distance to " O   HOH Z 290 " =    1.130
peak=    3.189 closest distance to " CD  LYS A 166 " =    1.404
peak=    3.184 closest distance to " O   HOH Z 420 " =    2.132
peak=    3.183 closest distance to " CE  MET A  93 " =    1.496
peak=    3.181 closest distance to " CA  TYR A 116 " =    1.631
peak=    3.180 closest distance to " CG2 ILE A 120 " =    1.425
peak=    3.178 closest distance to " CB  SER A 141 " =    1.044
peak=    3.171 closest distance to " O   HOH Z  10 " =    1.922
peak=    3.167 closest distance to " CG2 THR A 294 " =    1.666
peak=    3.166 closest distance to " CZ2 TRP A 179 " =    1.645
peak=    3.161 closest distance to " CE1 PHE A 208 " =    1.074
peak=    3.160 closest distance to " OG1 THR A 294 " =    2.340
peak=    3.156 closest distance to " O   HOH Z 406 " =    1.667
peak=    3.150 closest distance to " O   HOH Z 197 " =    2.059
peak=    3.148 closest distance to " NE  ARG A 156 " =    1.005
peak=    3.144 closest distance to " NH2 ARG A  79 " =    1.240
peak=    3.141 closest distance to " OG  SER A 206 " =    1.249
peak=    3.139 closest distance to " O   HOH Z 155 " =    2.688
peak=    3.136 closest distance to " O   HOH Z 434 " =    3.129
peak=    3.136 closest distance to " CG  MET A  93 " =    1.060
peak=    3.135 closest distance to " O   THR A 220 " =    1.391
peak=    3.134 closest distance to " CB  ALA A  71 " =    1.297
peak=    3.132 closest distance to " CB  MET A  47 " =    1.332
peak=    3.130 closest distance to " CG2AVAL A 121 " =    2.310
peak=    3.129 closest distance to " O   HOH Z 383 " =    2.159
peak=    3.128 closest distance to " O   HOH Z 214 " =    1.014
peak=    3.128 closest distance to " O   HOH Z 388 " =    1.816
peak=    3.127 closest distance to " CB BVAL A  41 " =    1.257
peak=    3.127 closest distance to " ND2 ASN A  45 " =    3.292
peak=    3.123 closest distance to " CB  PHE A  61 " =    1.374
peak=    3.123 closest distance to " CB  THR A  31 " =    1.609
peak=    3.122 closest distance to " O   HOH Z 406 " =    3.119
peak=    3.117 closest distance to " CA  ALA A 233 " =    1.911
peak=    3.117 closest distance to " CB  ASN A 142 " =    1.054
peak=    3.116 closest distance to " O   HOH Z   9 " =    1.609
peak=    3.115 closest distance to " NH1 ARG A 269 " =    0.849
peak=    3.108 closest distance to " OD2 ASP A 298 " =    4.080
peak=    3.107 closest distance to " ND2 ASN A 187 " =    1.711
peak=    3.104 closest distance to " O   HOH Z 166 " =    1.483
peak=    3.104 closest distance to " CD  ARG A 159 " =    0.782
peak=    3.103 closest distance to " CB  GLN A  89 " =    1.053
peak=    3.097 closest distance to " CG  GLN A  11 " =    1.500
peak=    3.092 closest distance to " CG1BVAL A 121 " =    1.135
peak=    3.090 closest distance to " OG  SER A  97 " =    3.543
peak=    3.089 closest distance to " CH2 TRP A 274 " =    2.259
peak=    3.086 closest distance to " O   HOH Z 110 " =    1.648
peak=    3.082 closest distance to " O   HOH Z 365 " =    5.678
peak=    3.074 closest distance to " CB  ASN A  39 " =    0.796
peak=    3.065 closest distance to " CB  LYS A 117 " =    1.151
peak=    3.062 closest distance to " OG  SER A  97 " =    2.511
peak=    3.053 closest distance to " O   HOH Z 211 " =    2.141
peak=    3.041 closest distance to " O   HOH Z 272 " =    2.483
peak=    3.034 closest distance to " NH2BARG A 190 " =    1.785
peak=    3.032 closest distance to " O   HOH Z 334 " =    1.434
peak=    3.032 closest distance to " CD  ARG A 219 " =    0.985
peak=    3.031 closest distance to " O   HOH Z 327 " =    2.021
peak=    3.030 closest distance to " CG2 THR A 220 " =    1.058

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.740 - 5.276
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 196
   mapped sites are within: 0.740 - 5.276

peak=   -5.065 closest distance to " CG2 VAL A 230 " =    0.867
peak=   -4.634 closest distance to " CG  ARG A 138 " =    0.949
peak=   -4.576 closest distance to " OG ASER A 134 " =    1.189
peak=   -4.451 closest distance to " O   HOH Z 198 " =    2.419
peak=   -4.309 closest distance to " O   ILE A 109 " =    2.681
peak=   -4.205 closest distance to " O   HOH Z  92 " =    1.294
peak=   -4.198 closest distance to " CD  ARG A 156 " =    2.004
peak=   -4.157 closest distance to " O   HOH Z  13 " =    1.182
peak=   -4.076 closest distance to " O   HOH Z 266 " =    4.298
peak=   -4.072 closest distance to " O   HOH Z 290 " =    1.104
peak=   -4.038 closest distance to " O   HOH Z 274 " =    2.608
peak=   -4.034 closest distance to " O   HOH Z  19 " =    2.102
peak=   -3.982 closest distance to " O   HOH Z 231 " =    1.647
peak=   -3.971 closest distance to " OG1 THR A   4 " =    1.766
peak=   -3.963 closest distance to " C   ASN A 187 " =    1.787
peak=   -3.954 closest distance to " NH2 ARG A  66 " =    1.563
peak=   -3.954 closest distance to " CD  GLN A  88 " =    2.265
peak=   -3.938 closest distance to " O   HOH Z  11 " =    1.705
peak=   -3.923 closest distance to " CD  ARG A 138 " =    1.462
peak=   -3.911 closest distance to " O   HOH Z 377 " =    1.871
peak=   -3.903 closest distance to " O   HOH Z 266 " =    4.583
peak=   -3.897 closest distance to " NH2AARG A 275 " =    5.276
peak=   -3.888 closest distance to " CA  SER A 164 " =    2.034
peak=   -3.881 closest distance to " O   HOH Z 166 " =    1.780
peak=   -3.872 closest distance to " O   HOH Z  43 " =    1.611
peak=   -3.867 closest distance to " CB  TYR A  15 " =    2.187
peak=   -3.867 closest distance to " C   ALA A 158 " =    1.186
peak=   -3.849 closest distance to " CD  ARG A 139 " =    1.679
peak=   -3.843 closest distance to " CD  ARG A  14 " =    3.283
peak=   -3.817 closest distance to " CG  ASP A 231 " =    0.813
peak=   -3.801 closest distance to " O   HOH Z 388 " =    1.852
peak=   -3.798 closest distance to " CD2 LEU A 237 " =    2.646
peak=   -3.755 closest distance to " N   SER A 276 " =    1.316
peak=   -3.746 closest distance to " O   HOH Z  98 " =    1.669
peak=   -3.742 closest distance to " CG  ASN A  45 " =    1.682
peak=   -3.741 closest distance to " CB  SER A 134 " =    1.744
peak=   -3.729 closest distance to " CE2 TYR A  30 " =    2.805
peak=   -3.723 closest distance to " O   HOH Z  52 " =    1.728
peak=   -3.706 closest distance to " CG  GLN A 223 " =    2.288
peak=   -3.683 closest distance to " NH1 ARG A  56 " =    2.501
peak=   -3.678 closest distance to " O   HOH Z 166 " =    1.557
peak=   -3.677 closest distance to " O   HOH Z 151 " =    1.398
peak=   -3.677 closest distance to " N   GLY A 133 " =    1.813
peak=   -3.670 closest distance to " CD1 LEU A 228 " =    2.372
peak=   -3.670 closest distance to " OE2 GLU A   2 " =    1.760
peak=   -3.661 closest distance to " CD1 LEU A 101 " =    2.580
peak=   -3.652 closest distance to " O   HOH Z 103 " =    1.845
peak=   -3.650 closest distance to " NH2 ARG A  79 " =    1.903
peak=   -3.649 closest distance to " O   HOH Z 407 " =    3.142
peak=   -3.642 closest distance to " O   HOH Z  17 " =    1.307
peak=   -3.632 closest distance to " N   GLN A  58 " =    1.736
peak=   -3.628 closest distance to " CG  MET A 105 " =    0.913
peak=   -3.616 closest distance to " O   HOH Z 292 " =    4.415
peak=   -3.607 closest distance to " CB  ALA A 248 " =    1.894
peak=   -3.601 closest distance to " CD2 LEU A 167 " =    1.783
peak=   -3.592 closest distance to " CA  TYR A  68 " =    2.771
peak=   -3.588 closest distance to " O   HOH Z  97 " =    2.096
peak=   -3.587 closest distance to " CD2 LEU A 300 " =    2.899
peak=   -3.586 closest distance to " OG1 THR A  82 " =    1.643
peak=   -3.580 closest distance to " O   GLY A 196 " =    1.060
peak=   -3.579 closest distance to " O   HOH Z 165 " =    2.101
peak=   -3.571 closest distance to " N   ALA A 226 " =    2.054
peak=   -3.565 closest distance to " O   ASN A 187 " =    1.430
peak=   -3.565 closest distance to " O   HOH Z  97 " =    1.508
peak=   -3.561 closest distance to " CG  GLU A 277 " =    1.181
peak=   -3.560 closest distance to " O   ALA A 161 " =    1.365
peak=   -3.547 closest distance to " C   HIS A 108 " =    1.102
peak=   -3.531 closest distance to " CD  LYS A 289 " =    2.524
peak=   -3.531 closest distance to " CD1 PHE A  59 " =    1.793
peak=   -3.528 closest distance to " O   HOH Z 221 " =    1.273
peak=   -3.526 closest distance to " CG  LYS A 193 " =    2.329
peak=   -3.513 closest distance to " CZ  TYR A 169 " =    1.866
peak=   -3.512 closest distance to " O   HOH Z 308 " =    1.733
peak=   -3.509 closest distance to " CG  ASP A  50 " =    2.199
peak=   -3.489 closest distance to " CE3 TRP A 150 " =    2.217
peak=   -3.488 closest distance to " O   HOH Z  71 " =    1.005
peak=   -3.477 closest distance to " O   HOH Z 423 " =    2.209
peak=   -3.475 closest distance to " N   GLN A 122 " =    1.628
peak=   -3.472 closest distance to " CB  ALA A  43 " =    2.376
peak=   -3.463 closest distance to " O   HOH Z 275 " =    1.457
peak=   -3.458 closest distance to " O   HOH Z  63 " =    0.740
peak=   -3.450 closest distance to " O   HOH Z 149 " =    1.842
peak=   -3.446 closest distance to " OG BSER A 134 " =    1.194
peak=   -3.443 closest distance to " O   HOH Z  97 " =    0.813
peak=   -3.442 closest distance to " ND2 ASN A  60 " =    1.430
peak=   -3.439 closest distance to " CA  ASP A 298 " =    1.056
peak=   -3.437 closest distance to " CB  ALA A 227 " =    2.381
peak=   -3.425 closest distance to " C   ASN A 285 " =    2.461
peak=   -3.424 closest distance to " O   HOH Z 388 " =    1.873
peak=   -3.417 closest distance to " CD  GLN A  88 " =    1.020
peak=   -3.414 closest distance to " O   HOH Z 234 " =    4.234
peak=   -3.413 closest distance to " CB  PRO A 243 " =    2.749
peak=   -3.406 closest distance to " OG  SER A  87 " =    1.292
peak=   -3.406 closest distance to " CG  GLU A 152 " =    2.515
peak=   -3.405 closest distance to " CB  ALA A  51 " =    1.797
peak=   -3.402 closest distance to " OG  SER A 206 " =    1.810
peak=   -3.398 closest distance to " CB  ASP A 124 " =    2.161
peak=   -3.397 closest distance to " OD1 ASN A 249 " =    1.155
peak=   -3.396 closest distance to " O   HOH Z  15 " =    1.629
peak=   -3.393 closest distance to " O   HOH Z 147 " =    2.078
peak=   -3.392 closest distance to " O   VAL A  67 " =    2.520
peak=   -3.387 closest distance to " O   PRO A 198 " =    1.328
peak=   -3.382 closest distance to " N   THR A 157 " =    1.538
peak=   -3.381 closest distance to " CG  GLU A  53 " =    1.465
peak=   -3.379 closest distance to " CD2 TYR A 293 " =    2.167
peak=   -3.375 closest distance to " O   HOH Z  60 " =    2.155
peak=   -3.372 closest distance to " O   HOH Z 184 " =    1.285
peak=   -3.363 closest distance to " O   HOH Z  93 " =    1.528
peak=   -3.356 closest distance to " OD2 ASP A 171 " =    1.919
peak=   -3.353 closest distance to " O   HOH Z 241 " =    1.371
peak=   -3.351 closest distance to " O   HOH Z 295 " =    1.312
peak=   -3.348 closest distance to " O   HOH Z  70 " =    1.360
peak=   -3.345 closest distance to " ND2 ASN A  45 " =    1.009
peak=   -3.337 closest distance to " O   HOH Z 113 " =    2.005
peak=   -3.337 closest distance to " O   ALA A 158 " =    0.996
peak=   -3.332 closest distance to " O   SER A 271 " =    2.137
peak=   -3.329 closest distance to " CB  CYS A 254 " =    2.371
peak=   -3.329 closest distance to " O   ASP A 270 " =    1.851
peak=   -3.328 closest distance to " CG2 VAL A 112 " =    2.574
peak=   -3.326 closest distance to " CG  TRP A 266 " =    1.637
peak=   -3.322 closest distance to " O   HOH Z 377 " =    1.230
peak=   -3.317 closest distance to " O   HOH Z 435 " =    2.738
peak=   -3.313 closest distance to " CE  MET A 105 " =    2.098
peak=   -3.309 closest distance to " O   HOH Z  10 " =    1.517
peak=   -3.307 closest distance to " CB  SER A 245 " =    2.374
peak=   -3.306 closest distance to " CA  ASN A 127 " =    1.026
peak=   -3.304 closest distance to " O   GLU A  44 " =    1.571
peak=   -3.300 closest distance to " O   GLY A  80 " =    2.543
peak=   -3.297 closest distance to " O   HOH Z 128 " =    2.463
peak=   -3.297 closest distance to " O   LEU A 228 " =    2.383
peak=   -3.297 closest distance to " CD1 TYR A  30 " =    2.247
peak=   -3.296 closest distance to " CB  PRO A 163 " =    2.695
peak=   -3.294 closest distance to " O   HOH Z 341 " =    1.225
peak=   -3.289 closest distance to " O   HOH Z 426 " =    2.279
peak=   -3.288 closest distance to " CA  ASN A 142 " =    1.286
peak=   -3.287 closest distance to " O   HOH Z 189 " =    2.049
peak=   -3.287 closest distance to " O   ASN A 301 " =    1.653
peak=   -3.286 closest distance to " CZ  TYR A 172 " =    1.667
peak=   -3.284 closest distance to " OD1 ASP A 200 " =    1.253
peak=   -3.282 closest distance to " CG  LEU A 228 " =    1.023
peak=   -3.276 closest distance to " O   HOH Z 243 " =    1.605
peak=   -3.269 closest distance to " O   HOH Z 365 " =    1.583
peak=   -3.262 closest distance to " O   ALA A 256 " =    1.501
peak=   -3.261 closest distance to " O   HOH Z 221 " =    1.338
peak=   -3.258 closest distance to " OG1 THR A 178 " =    1.164
peak=   -3.253 closest distance to " CE3 TRP A  70 " =    1.731
peak=   -3.253 closest distance to " CE  MET A  93 " =    1.278
peak=   -3.252 closest distance to " CD1 LEU A   5 " =    2.483
peak=   -3.250 closest distance to " OXT GLY A 302 " =    3.283
peak=   -3.249 closest distance to " O   GLY A 211 " =    1.366
peak=   -3.245 closest distance to " O   HOH Z  37 " =    1.510
peak=   -3.237 closest distance to " CE BMET A  47 " =    1.697
peak=   -3.224 closest distance to " O   HOH Z 292 " =    2.878
peak=   -3.224 closest distance to " O   MET A  40 " =    2.781
peak=   -3.221 closest distance to " CB  ALA A 291 " =    2.481
peak=   -3.217 closest distance to " O   PRO A 198 " =    1.320
peak=   -3.207 closest distance to " O   ALA A   8 " =    1.939
peak=   -3.199 closest distance to " CG  PRO A 163 " =    2.554
peak=   -3.199 closest distance to " N   ALA A   9 " =    1.492
peak=   -3.199 closest distance to " CH2 TRP A 179 " =    1.262
peak=   -3.197 closest distance to " NH2 ARG A 159 " =    2.374
peak=   -3.196 closest distance to " O   SER A 135 " =    1.486
peak=   -3.192 closest distance to " CD1 TRP A 179 " =    1.116
peak=   -3.191 closest distance to " CG  PHE A  59 " =    2.197
peak=   -3.188 closest distance to " CB  ASN A  39 " =    2.174
peak=   -3.188 closest distance to " C   LEU A 143 " =    1.270
peak=   -3.187 closest distance to " CA  VAL A 232 " =    2.431
peak=   -3.187 closest distance to " O   HOH Z 351 " =    1.325
peak=   -3.186 closest distance to " CD1 ILE A 263 " =    2.444
peak=   -3.186 closest distance to " CG1 VAL A 296 " =    1.367
peak=   -3.185 closest distance to " O   HOH Z 310 " =    1.652
peak=   -3.182 closest distance to " CB  GLN A  55 " =    1.575
peak=   -3.177 closest distance to " N   ALA A 248 " =    1.672
peak=   -3.175 closest distance to " N   HIS A 115 " =    2.007
peak=   -3.174 closest distance to " O   HOH Z 411 " =    3.600
peak=   -3.170 closest distance to " NH2 ARG A 156 " =    1.184
peak=   -3.162 closest distance to " OH  TYR A 214 " =    1.219
peak=   -3.145 closest distance to " O   HOH Z 252 " =    4.245
peak=   -3.145 closest distance to " O   HOH Z   9 " =    2.011
peak=   -3.132 closest distance to " O   HOH Z 396 " =    1.570
peak=   -3.132 closest distance to " O   HOH Z 317 " =    2.372
peak=   -3.132 closest distance to " O   HOH Z 389 " =    1.585
peak=   -3.128 closest distance to " O   ALA A 160 " =    1.261
peak=   -3.120 closest distance to " CG2 VAL A 296 " =    1.774
peak=   -3.119 closest distance to " CG  PHE A 283 " =    2.726
peak=   -3.116 closest distance to " C   GLN A 240 " =    2.150
peak=   -3.115 closest distance to " O   HOH Z 430 " =    1.812
peak=   -3.102 closest distance to " OE1 GLN A  73 " =    2.388
peak=   -3.090 closest distance to " O   HOH Z 256 " =    1.132
peak=   -3.083 closest distance to " O   HOH Z  40 " =    3.324
peak=   -3.068 closest distance to " O   HOH Z 352 " =    0.996
peak=   -3.048 closest distance to " O   HOH Z 399 " =    2.183
peak=   -3.046 closest distance to " CG1 VAL A 112 " =    2.662
peak=   -3.035 closest distance to " CB  TRP A  85 " =    2.380
peak=   -3.021 closest distance to " N   ALA A  43 " =    2.511

================= 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    :  0.4713 0.4730   6.274563e+00   6.273161e+00
   1_bss:  0.4633 0.4613   6.273851e+00   6.265870e+00
   1_xyz:  0.3875 0.4219   6.164513e+00   6.211058e+00
   1_adp:  0.3444 0.4048   6.092251e+00   6.185916e+00
   1_occ:  0.3440 0.4052   6.091882e+00   6.185987e+00
   2_bss:  0.3411 0.3998   6.091853e+00   6.183799e+00
   2_xyz:  0.2569 0.3220   5.868319e+00   6.027455e+00
   2_adp:  0.2351 0.2979   5.796152e+00   5.973509e+00
   2_occ:  0.2350 0.2976   5.795195e+00   5.973465e+00
   3_bss:  0.2328 0.2943   5.792660e+00   5.969235e+00
   3_xyz:  0.1780 0.2335   5.552493e+00   5.760598e+00
   3_adp:  0.1593 0.2158   5.465214e+00   5.690935e+00
   3_occ:  0.1592 0.2157   5.464729e+00   5.690539e+00
   4_bss:  0.1588 0.2149   5.461944e+00   5.687477e+00
   4_xyz:  0.1347 0.1850   5.310677e+00   5.543441e+00
   4_adp:  0.1298 0.1771   5.271533e+00   5.498782e+00
   4_occ:  0.1296 0.1770   5.270562e+00   5.498103e+00
   5_bss:  0.1299 0.1777   5.273256e+00   5.500663e+00
   5_xyz:  0.1204 0.1659   5.210234e+00   5.441364e+00
   5_adp:  0.1182 0.1653   5.201259e+00   5.437492e+00
   5_occ:  0.1182 0.1653   5.201014e+00   5.437598e+00
   5_bss:  0.1182 0.1653   5.200999e+00   5.437533e+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:  0.337  10.609   7.388   7.872   9.577   0.000   0.000   0.000
   1_xyz:  0.337  10.609   7.388   7.872   9.577   0.000   0.000   0.000
   1_adp:  0.337  10.609   7.388   7.872   9.577   0.000   0.000   0.000
   1_occ:  0.337  10.609   7.388   7.872   9.577   0.000   0.000   0.000
   2_bss:  0.337  50.000   3.724   4.156   6.327   0.000   0.000   0.000
   2_xyz:  0.337  50.000   3.724   4.156   6.327   0.000   0.000   0.000
   2_adp:  0.337  50.000   3.724   4.156   6.327   0.000   0.000   0.000
   2_occ:  0.337  50.000   3.724   4.156   6.327   0.000   0.000   0.000
   3_bss:  0.337  46.225   2.126   2.486   3.565   0.000   0.000   0.000
   3_xyz:  0.337  46.225   2.126   2.486   3.565   0.000   0.000   0.000
   3_adp:  0.337  46.225   2.126   2.486   3.565   0.000   0.000   0.000
   3_occ:  0.337  46.225   2.126   2.486   3.565   0.000   0.000   0.000
   4_bss:  0.317  40.938   1.590   1.889   2.263   0.000   0.000   0.000
   4_xyz:  0.317  40.938   1.590   1.889   2.263   0.000   0.000   0.000
   4_adp:  0.317  40.938   1.590   1.889   2.263   0.000   0.000   0.000
   4_occ:  0.317  40.938   1.590   1.889   2.263   0.000   0.000   0.000
   5_bss:  0.318  42.254   1.477   1.714   1.912   0.000   0.000   0.000
   5_xyz:  0.318  42.254   1.477   1.714   1.912   0.000   0.000   0.000
   5_adp:  0.318  42.254   1.477   1.714   1.912   0.000   0.000   0.000
   5_occ:  0.318  42.254   1.477   1.714   1.912   0.000   0.000   0.000
   5_bss:  0.316  42.729  -0.224   0.013   0.211   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.681 0.4233  0.5006    70294.178
   1_bss:  58.459 0.4103  0.6061    67540.917
   1_xyz:  50.195 0.5148  0.7529    52779.648
   1_adp:  46.668 0.5597  0.8621    47998.453
   1_occ:  46.692 0.5594  0.8619    48116.974
   2_bss:  46.286 0.5644  0.7726    47645.052
   2_xyz:  34.464 0.7065  0.9468    28849.906
   2_adp:  31.190 0.7443  0.9911    24637.854
   2_occ:  31.175 0.7445  0.9906    24591.601
   3_bss:  30.936 0.7468  0.9234    24251.486
   3_xyz:  23.131 0.8305  0.9842    14271.048
   3_adp:  21.056 0.8516  0.9910    12249.595
   3_occ:  21.040 0.8517  0.9908    12231.942
   4_bss:  20.923 0.8527  0.9627    12112.435
   4_xyz:  17.632 0.8834  0.9798     8925.045
   4_adp:  16.476 0.8942  0.9828     8142.600
   4_occ:  16.449 0.8945  0.9828     8129.886
   5_bss:  16.514 0.8941  0.9748     8225.100
   5_xyz:  15.275 0.9045  0.9789     7184.487
   5_adp:  15.127 0.9060  0.9765     7109.600
   5_occ:  15.125 0.9060  0.9763     7112.286
   5_bss:  15.125 0.9060  0.9763     7109.807
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3476e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3476e+01
   1_xyz:   1.661  0.013  0.106 18.164  0.007  4.109   1.3728e-01
   1_adp:   1.661  0.013  0.106 18.164  0.007  4.109   1.3728e-01
   1_occ:   1.661  0.013  0.106 18.164  0.007  4.109   1.3728e-01
   2_bss:   1.661  0.013  0.106 18.164  0.007  4.109   1.3728e-01
   2_xyz:   1.152  0.009  0.081 16.255  0.005  4.114   8.3048e-02
   2_adp:   1.152  0.009  0.081 16.255  0.005  4.114   8.3048e-02
   2_occ:   1.152  0.009  0.081 16.255  0.005  4.114   8.3048e-02
   3_bss:   1.152  0.009  0.081 16.255  0.005  4.114   8.3048e-02
   3_xyz:   1.041  0.006  0.074 15.340  0.004  4.112   6.2575e-02
   3_adp:   1.041  0.006  0.074 15.340  0.004  4.112   6.2575e-02
   3_occ:   1.041  0.006  0.074 15.340  0.004  4.112   6.2575e-02
   4_bss:   1.041  0.006  0.074 15.340  0.004  4.112   6.2575e-02
   4_xyz:   1.000  0.006  0.076 15.364  0.003  4.115   6.0112e-02
   4_adp:   1.000  0.006  0.076 15.364  0.003  4.115   6.0112e-02
   4_occ:   1.000  0.006  0.076 15.364  0.003  4.115   6.0112e-02
   5_bss:   1.000  0.006  0.076 15.364  0.003  4.115   6.0112e-02
   5_xyz:   1.038  0.007  0.077 15.460  0.003  4.118   6.3181e-02
   5_adp:   1.038  0.007  0.077 15.460  0.003  4.118   6.3181e-02
   5_occ:   1.038  0.007  0.077 15.460  0.003  4.118   6.3181e-02
   5_bss:   1.038  0.007  0.077 15.460  0.003  4.118   6.3181e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9313e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9313e+00
   1_xyz:  14.222  0.165  0.448 84.945  0.054  2.197   9.5800e-02
   1_adp:  14.222  0.165  0.448 84.945  0.054  2.197   9.5800e-02
   1_occ:  14.222  0.165  0.448 84.945  0.054  2.197   9.5800e-02
   2_bss:  14.222  0.165  0.448 84.945  0.054  2.197   9.5800e-02
   2_xyz:   7.290  0.066  0.258 81.457  0.032  2.200   6.1635e-02
   2_adp:   7.290  0.066  0.258 81.457  0.032  2.200   6.1635e-02
   2_occ:   7.290  0.066  0.258 81.457  0.032  2.200   6.1635e-02
   3_bss:   7.290  0.066  0.258 81.457  0.032  2.200   6.1635e-02
   3_xyz:   7.511  0.047  0.339 88.453  0.049  2.316   4.1654e-02
   3_adp:   7.511  0.047  0.339 88.453  0.049  2.316   4.1654e-02
   3_occ:   7.511  0.047  0.339 88.453  0.049  2.316   4.1654e-02
   4_bss:   7.511  0.047  0.339 88.453  0.049  2.316   4.1654e-02
   4_xyz:   7.434  0.044  0.388 79.841  0.029  2.352   4.0725e-02
   4_adp:   7.434  0.044  0.388 79.841  0.029  2.352   4.0725e-02
   4_occ:   7.434  0.044  0.388 79.841  0.029  2.352   4.0725e-02
   5_bss:   7.434  0.044  0.388 79.841  0.029  2.352   4.0725e-02
   5_xyz:   8.014  0.054  0.441 83.551  0.029  2.356   6.1052e-02
   5_adp:   8.014  0.054  0.441 83.551  0.029  2.356   6.1052e-02
   5_occ:   8.014  0.054  0.441 83.551  0.029  2.356   6.1052e-02
   5_bss:   8.014  0.054  0.441 83.551  0.029  2.356   6.1052e-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:  76.71   0.00  12.86  76.71   0.00  10.42  69.32   0.00  26.12
   1_occ:  76.71   0.00  12.86  76.71   0.00  10.42  69.32   0.00  26.12
   2_bss:  76.71   0.00  12.86  76.71   0.00  10.42  69.32   0.00  26.12
   2_xyz:  76.71   0.00  12.86  76.71   0.00  10.42  69.32   0.00  26.12
   2_adp:  76.24   0.00  13.33  76.24   0.00   9.93  70.25   1.42  31.84
   2_occ:  76.24   0.00  13.33  76.24   0.00   9.93  70.25   1.42  31.84
   3_bss:  76.24   0.00  13.33  76.24   0.00   9.93  70.25   1.42  31.84
   3_xyz:  76.24   0.00  13.33  76.24   0.00   9.93  70.25   1.42  31.84
   3_adp:  94.98   0.00  14.38  94.98   0.00   9.65  83.93   2.24  40.12
   3_occ:  94.98   0.00  14.38  94.98   0.00   9.65  83.93   2.24  40.12
   4_bss:  94.98   0.00  14.38  94.98   0.00   9.65  83.93   2.24  40.12
   4_xyz:  94.98   0.00  14.38  94.98   0.00   9.65  83.93   2.24  40.12
   4_adp:  98.89   0.00  13.93  98.89   0.00   9.35  84.66   2.81  38.85
   4_occ:  98.89   0.00  13.93  98.89   0.00   9.35  84.66   2.81  38.85
   5_bss:  98.89   0.00  13.93  98.89   0.00   9.35  84.66   2.81  38.85
   5_xyz:  98.89   0.00  13.93  98.89   0.00   9.35  84.66   2.81  38.85
   5_adp: 104.01   0.00  13.71 104.01   0.00   9.22  85.90   2.28  38.17
   5_occ: 104.01   0.00  13.71 104.01   0.00   9.22  85.90   2.28  38.17
   5_bss: 105.71   1.70  15.41 105.71   1.70  10.92  87.60   3.99  39.87
------------------------------------------------------------------------
 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:    1.224    0.029    0.408
   1_adp:    1.224    0.029    0.408
   1_occ:    1.224    0.029    0.408
   2_bss:    1.224    0.029    0.408
   2_xyz:    1.728    0.038    0.580
   2_adp:    1.728    0.038    0.580
   2_occ:    1.728    0.038    0.580
   3_bss:    1.728    0.038    0.580
   3_xyz:    1.711    0.042    0.651
   3_adp:    1.711    0.042    0.651
   3_occ:    1.711    0.042    0.651
   4_bss:    1.711    0.042    0.651
   4_xyz:    1.710    0.018    0.698
   4_adp:    1.710    0.018    0.698
   4_occ:    1.710    0.018    0.698
   5_bss:    1.710    0.018    0.698
   5_xyz:    1.733    0.033    0.716
   5_adp:    1.733    0.033    0.716
   5_occ:    1.733    0.033    0.716
   5_bss:    1.733    0.033    0.716
------------------------------------------------------------------------

CPU time actual refinement: 354.63


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_913/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_913/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_913/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_913/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_913/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.47 
  Macro-tasks:
    bulk solvent and scale       = 42.33  
    individual site refinement   = 148.11 
    weights calculation          = 32.78  
    collect and process          = 6.47   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 229.80 
  Micro-tasks:
    mask                            = 2.52   
    f_calc                          = 112.46 
    alpha_beta                      = 8.11   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 122.10 
    fmodel                         = 7.39   
    r_factors                      = 0.23   
    phase_errors                   = 10.56  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 264.81 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.001 micro seconds
Total CPU time: 6.14 minutes
from_scatterers_fft:    634 calls, 112.05 s
gradients_fft:          578 calls, 109.24 s

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

# Date 2008-01-16 Time 02:44:18 PST -0800 (1200480258.90 s)
Start R-work = 0.4713, R-free = 0.4730 (no bulk solvent and anisotropic scale)
Final R-work = 0.1346, R-free = 0.1828 (no bulk solvent and anisotropic scale)

Start R-work = 0.4633, R-free = 0.4613
Final R-work = 0.1182, R-free = 0.1653