# Date 2008-01-16 Time 01:09:36 PST -0800 (1200474576.14 s)
#phil __OFF__

Command line arguments: "../303.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 = 19455
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 303

-------------------------------------------------------------------------------
  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: (69.1963, 46.93, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.9707
Completeness in resolution range: 0.9537
Completeness with d_max=infinity: 0.950738

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8486
                             d_min =   1.9707

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: (69.1963, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.9707
Completeness in resolution range: 0.9537
Completeness with d_max=infinity: 0.950738

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8490 -  4.2164 [2167/2194]  1948   219  10.1%
  bin  2:  4.2164 -  3.3594 [2063/2079]  1860   203   9.8%
  bin  3:  3.3594 -  2.9385 [2052/2071]  1846   206  10.0%
  bin  4:  2.9385 -  2.6715 [2022/2052]  1822   200   9.9%
  bin  5:  2.6715 -  2.4810 [2007/2026]  1802   205  10.2%
  bin  6:  2.4810 -  2.3353 [2015/2051]  1814   201  10.0%
  bin  7:  2.3353 -  2.2188 [1988/2021]  1794   194   9.8%
  bin  8:  2.2188 -  2.1225 [1985/2020]  1781   204  10.3%
  bin  9:  2.1225 -  2.0410 [1980/2007]  1786   194   9.8%
  bin 10:  2.0410 -  1.9707 [1310/2019]  1177   133  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_303/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 22
        2.41 -     3.03: 2153
        3.03 -     3.66: 4672
        3.66 -     4.28: 9124
        4.28 -     4.90: 12490
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.790 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.801 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.928 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.969 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28456 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_303/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_303/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 69.19625 46.93 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4316   r_free= 0.4212   ksol= 0.00   Bsol= 0.00   scale= 0.827    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.225025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1402  155 0.3562 0.3452      6.5115         6.5|
|  2:  4.7025 -  3.7523 0.99   1350  154 0.3219 0.3339      6.6156      6.6615|
|  3:  3.7523 -  3.2839 0.99   1317  145 0.3745 0.3557      6.5438       6.546|
|  4:  3.2839 -  2.9863 0.99   1309  137 0.4144 0.4011      6.4405      6.4013|
|  5:  2.9863 -  2.7737 0.99   1310  152 0.4495 0.4616      6.3078      6.3409|
|  6:  2.7737 -  2.6111 0.99   1302  144 0.4559 0.5198      6.2324      6.2008|
|  7:  2.6111 -  2.4810 0.99   1288  146 0.4654 0.4608      6.1988      6.1346|
|  8:  2.4810 -  2.3734 0.98   1302  141 0.4786 0.4460      6.1453      6.1337|
|  9:  2.3734 -  2.2824 0.98   1283  145 0.4945 0.4645      6.0828      6.1081|
| 10:  2.2824 -  2.2039 0.98   1270  138 0.4951 0.4472      6.1094      6.0004|
| 11:  2.2039 -  2.1352 1.00   1285  145 0.5022 0.4485      6.0298       6.008|
| 12:  2.1352 -  2.0743 0.97   1273  137 0.4974 0.4621      5.9522      5.9637|
| 13:  2.0743 -  2.0199 0.98   1259  143 0.4957 0.4713      5.8707      5.7992|
| 14:  2.0199 -  1.9707 0.53    680   77 0.4998 0.4671      5.8758      5.7511|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1402   155  0.72  32.35   0.82     0.74      62800.16|
|  2:  4.7025 -  3.7523  1350   154  0.77  29.40   0.92     0.81      76442.93|
|  3:  3.7523 -  3.2839  1317   145  0.70  35.11   0.89     0.79      77890.76|
|  4:  3.2839 -  2.9863  1309   137  0.64  40.57   0.83     0.71      69553.57|
|  5:  2.9863 -  2.7737  1310   152  0.53  49.35   0.77     0.61      64643.58|
|  6:  2.7737 -  2.6111  1302   144  0.49  53.09   0.75     0.55      60331.09|
|  7:  2.6111 -  2.4810  1288   146  0.47  54.71   0.78     0.53      56614.90|
|  8:  2.4810 -  2.3734  1302   141  0.49  53.21   0.76     0.56      47876.02|
|  9:  2.3734 -  2.2824  1283   145  0.51  51.55   0.75     0.60      41650.75|
| 10:  2.2824 -  2.2039  1270   138  0.54  48.95   0.76     0.62      35397.18|
| 11:  2.2039 -  2.1352  1285   145  0.52  50.62   0.77     0.62      34237.15|
| 12:  2.1352 -  2.0743  1273   137  0.49  53.18   0.80     0.60      32980.91|
| 13:  2.0743 -  2.0199  1259   143  0.47  54.85   0.76     0.56      29448.06|
| 14:  2.0199 -  1.9707   680    77  0.50  51.93   0.75     0.52      22708.72|
|alpha:            min =        0.52 max =            0.81 mean =         0.64|
|beta:             min =    22708.72 max =        77890.76 mean =     52197.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           90.00 mean =        46.70|
|phase err.(test): min =        0.00 max =           89.88 mean =        46.99|
|-----------------------------------------------------------------------------|

============================== 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 = 7.194870              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.093   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.599111              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.540   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      695 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1522 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2640 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3967 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5082 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6615 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7772 |
|-----------------------------------------------------------------------------|
|-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 |       53.477 |
| 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 |       1.978 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.741)------------------------------------------|
|    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 = 11.741)------------------------------------------|
|    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: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4406   r_free= 0.4258   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.230504                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4235   r_free= 0.4099   ksol= 0.36   Bsol= 20.00   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.10,8.03,8.68,0.00,0.00,0.00); trace/3= 8.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.216080                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.890464              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.757   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.596946              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.646   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4235      final r-factor (work) = 0.3138          |
| start r-factor (free) = 0.4099      final r-factor (free) = 0.3306          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 74.9730 = 6.89 * 0.50 * 6.2393 + 1.00 * 53.4772                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0123 = 6.89 * 0.50 * 6.0653 + 1.00 * 0.1161                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3138      final r-factor (work) = 0.2474          |
| start r-factor (free) = 0.3306      final r-factor (free) = 0.2801          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6353 = 0.60 * 1.00 * 6.0653 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5140 = 0.60 * 1.00 * 5.8672 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 37     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.741)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.61   10.67    None  None   None       |
|    all(noH): 2823   0      0.00    57.61   10.67    None  None   None       |
|    Sol.    : 438    0      0.00    55.02   27.20    None  None   None       |
|    Mac.    : 2385   0      0.00    57.61   7.63     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 -   5.761: 1240   |   5:    28.805 -  34.567:  103        |
|      1:     5.761 -  11.522:  725   |   6:    34.567 -  40.328:   69        |
|      2:    11.522 -  17.283:  317   |   7:    40.328 -  46.089:   55        |
|      3:    17.283 -  23.044:  147   |   8:    46.089 -  51.850:   23        |
|      4:    23.044 -  28.805:  137   |   9:    51.850 -  57.611:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2474 r_free = 0.2801             target_work(ml) = 5.798         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2469 r_free = 0.2802             target_work(ml) = 5.797         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2469   r_free= 0.2802   ksol= 0.36   Bsol= 20.00   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.10,8.03,8.68,0.00,0.00,0.00); trace/3= 8.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.796606                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2414   r_free= 0.2741   ksol= 0.33   Bsol= 37.40   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.36,4.08,5.32,0.00,0.00,0.00); trace/3= 4.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.795254                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.799307              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.917   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.310950              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.638  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2414      final r-factor (work) = 0.1600          |
| start r-factor (free) = 0.2741      final r-factor (free) = 0.1963          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2921 = 3.80 * 0.50 * 5.8834 + 1.00 * 0.1157                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7245 = 3.80 * 0.50 * 5.6118 + 1.00 * 0.0641                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1600      final r-factor (work) = 0.1449          |
| start r-factor (free) = 0.1963      final r-factor (free) = 0.1836          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7832 = 0.31 * 1.00 * 5.6118 + 1.00 * 0.0382                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8352 = 0.31 * 1.00 * 5.3759 + 1.00 * 0.1636                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.741)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.85   10.99    None  None   None       |
|    all(noH): 2823   0      0.00    67.85   10.99    None  None   None       |
|    Sol.    : 438    0      0.20    56.79   30.98    None  None   None       |
|    Mac.    : 2385   0      0.00    67.85   7.32     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.785: 1501   |   5:    33.923 -  40.707:  135        |
|      1:     6.785 -  13.569:  646   |   6:    40.707 -  47.492:   73        |
|      2:    13.569 -  20.354:  207   |   7:    47.492 -  54.276:   33        |
|      3:    20.354 -  27.138:  105   |   8:    54.276 -  61.061:    7        |
|      4:    27.138 -  33.923:  114   |   9:    61.061 -  67.845:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1449 r_free = 0.1836             target_work(ml) = 5.342         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1448 r_free = 0.1835             target_work(ml) = 5.342         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1448   r_free= 0.1835   ksol= 0.33   Bsol= 37.40   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.36,4.08,5.32,0.00,0.00,0.00); trace/3= 4.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.341662                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1440   r_free= 0.1831   ksol= 0.32   Bsol= 37.40   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,3.41,4.54,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.340276                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.572326              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.574  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.242879              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.311   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1440      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1831      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2949 = 1.57 * 0.50 * 5.3819 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2031 = 1.57 * 0.50 * 5.2774 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1255      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.1575 = 3.24 * 1.00 * 5.2774 + 1.00 * 0.0436                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.8937 = 3.24 * 1.00 * 5.2042 + 1.00 * 0.0171                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.741)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.65   11.98    None  None   None       |
|    all(noH): 2823   0      0.00    80.65   11.98    None  None   None       |
|    Sol.    : 438    0      0.45    74.32   35.84    None  None   None       |
|    Mac.    : 2385   0      0.00    80.65   7.60     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.065: 1714   |   5:    40.323 -  48.388:   95        |
|      1:     8.065 -  16.129:  513   |   6:    48.388 -  56.452:   77        |
|      2:    16.129 -  24.194:  163   |   7:    56.452 -  64.517:   36        |
|      3:    24.194 -  32.258:   95   |   8:    64.517 -  72.581:   15        |
|      4:    32.258 -  40.323:  109   |   9:    72.581 -  80.646:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1626             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1625             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1625   ksol= 0.32   Bsol= 37.40   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,3.41,4.54,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199558                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1625   ksol= 0.32   Bsol= 44.10   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,3.41,4.54,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199116                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.064719              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.274  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.440556              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.866  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4264 = 2.06 * 0.50 * 5.2037 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3990 = 2.06 * 0.50 * 5.1703 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2933 = 0.44 * 1.00 * 5.1703 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2864 = 0.44 * 1.00 * 5.1537 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.741)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.13   11.56    None  None   None       |
|    all(noH): 2823   0      0.00    84.13   11.56    None  None   None       |
|    Sol.    : 438    0      0.44    74.12   34.14    None  None   None       |
|    Mac.    : 2385   0      0.00    84.13   7.42     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 -   8.413: 1771   |   5:    42.064 -  50.477:   96        |
|      1:     8.413 -  16.826:  502   |   6:    50.477 -  58.890:   48        |
|      2:    16.826 -  25.239:  143   |   7:    58.890 -  67.303:   22        |
|      3:    25.239 -  33.651:  124   |   8:    67.303 -  75.715:    9        |
|      4:    33.651 -  42.064:  105   |   9:    75.715 -  84.128:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1126 r_free = 0.1552             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1552             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1552   ksol= 0.32   Bsol= 44.10   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,3.41,4.54,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1558   ksol= 0.33   Bsol= 43.88   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,3.41,4.54,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.148193                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.485920              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.881  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.302037              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.534  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1558      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4663 = 2.49 * 0.50 * 5.1530 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4490 = 2.49 * 0.50 * 5.1365 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5749 = 0.30 * 1.00 * 5.1365 + 1.00 * 0.0234                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5614 = 0.30 * 1.00 * 5.1332 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.741)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.93   11.20    None  None   None       |
|    all(noH): 2823   0      0.00    83.93   11.20    None  None   None       |
|    Sol.    : 438    0      0.87    72.65   32.71    None  None   None       |
|    Mac.    : 2385   0      0.00    83.93   7.25     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.393: 1798   |   5:    41.965 -  50.358:   90        |
|      1:     8.393 -  16.786:  491   |   6:    50.358 -  58.751:   38        |
|      2:    16.786 -  25.179:  145   |   7:    58.751 -  67.144:   18        |
|      3:    25.179 -  33.572:  127   |   8:    67.144 -  75.538:    6        |
|      4:    33.572 -  41.965:  107   |   9:    75.538 -  83.931:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1546             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1546             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1546   ksol= 0.33   Bsol= 43.88   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,3.41,4.54,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.129975                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1402  155 0.1001 0.1324      5.3935       5.543|
|  2:  4.7025 -  3.7523 0.99   1350  154 0.0859 0.1099      5.4373      5.6061|
|  3:  3.7523 -  3.2839 0.99   1317  145 0.1045 0.1505      5.4561      5.8318|
|  4:  3.2839 -  2.9863 0.99   1309  137 0.1166 0.1546      5.4208      5.5918|
|  5:  2.9863 -  2.7737 0.99   1310  152 0.1281 0.1595       5.301      5.4933|
|  6:  2.7737 -  2.6111 0.99   1302  144 0.1207 0.2023      5.1904      5.4854|
|  7:  2.6111 -  2.4810 0.99   1288  146 0.1218 0.1578      5.1486      5.3229|
|  8:  2.4810 -  2.3734 0.98   1302  141 0.1109 0.1622       5.038      5.2942|
|  9:  2.3734 -  2.2824 0.98   1283  145 0.1181 0.1893      5.0121      5.3208|
| 10:  2.2824 -  2.2039 0.98   1270  138 0.1116 0.1461      4.9375      5.0937|
| 11:  2.2039 -  2.1352 1.00   1285  145 0.1111 0.1726      4.9185      5.2642|
| 12:  2.1352 -  2.0743 0.97   1273  137 0.1109 0.1614      4.8565      5.1626|
| 13:  2.0743 -  2.0199 0.98   1259  143 0.1102 0.1704      4.7621      4.9857|
| 14:  2.0199 -  1.9707 0.53    680   77 0.1015 0.1685      4.6549      4.9312|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1402   155  0.94   9.26   0.98     0.96       7259.58|
|  2:  4.7025 -  3.7523  1350   154  0.95   7.87   1.02     1.00       8903.65|
|  3:  3.7523 -  3.2839  1317   145  0.94  11.00   1.03     1.02       9999.95|
|  4:  3.2839 -  2.9863  1309   137  0.92  13.01   1.01     1.00       9847.36|
|  5:  2.9863 -  2.7737  1310   152  0.90  15.44   1.00     0.96       7887.54|
|  6:  2.7737 -  2.6111  1302   144  0.90  16.03   0.98     0.96       6777.01|
|  7:  2.6111 -  2.4810  1288   146  0.91  14.92   0.98     0.94       5779.28|
|  8:  2.4810 -  2.3734  1302   141  0.92  14.30   1.00     0.98       4982.03|
|  9:  2.3734 -  2.2824  1283   145  0.91  15.16   1.01     0.99       4757.10|
| 10:  2.2824 -  2.2039  1270   138  0.90  15.57   1.01     0.97       4215.42|
| 11:  2.2039 -  2.1352  1285   145  0.91  15.62   1.00     0.97       4206.11|
| 12:  2.1352 -  2.0743  1273   137  0.91  14.99   1.02     1.01       3745.07|
| 13:  2.0743 -  2.0199  1259   143  0.91  15.51   1.01     1.00       3150.90|
| 14:  2.0199 -  1.9707   680    77  0.92  13.86   0.99     0.95       2414.93|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2414.93 max =         9999.95 mean =      6158.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.69|
|phase err.(test): min =        0.00 max =           88.37 mean =        13.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1545   ksol= 0.33   Bsol= 45.67   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-0.17,1.02,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.129998                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1545   ksol= 0.33   Bsol= 45.67   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-0.17,1.02,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.129998                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1402  155 0.1001 0.1321      5.3932      5.5419|
|  2:  4.7025 -  3.7523 0.99   1350  154 0.0856 0.1095      5.4353      5.6035|
|  3:  3.7523 -  3.2839 0.99   1317  145 0.1044 0.1503      5.4545      5.8304|
|  4:  3.2839 -  2.9863 0.99   1309  137 0.1166 0.1546      5.4209      5.5921|
|  5:  2.9863 -  2.7737 0.99   1310  152 0.1282 0.1598      5.3021      5.4946|
|  6:  2.7737 -  2.6111 0.99   1302  144 0.1209 0.2024      5.1913      5.4859|
|  7:  2.6111 -  2.4810 0.99   1288  146 0.1219 0.1578      5.1492      5.3233|
|  8:  2.4810 -  2.3734 0.98   1302  141 0.1109 0.1621      5.0378      5.2936|
|  9:  2.3734 -  2.2824 0.98   1283  145 0.1182 0.1892      5.0123      5.3206|
| 10:  2.2824 -  2.2039 0.98   1270  138 0.1116 0.1460      4.9379      5.0939|
| 11:  2.2039 -  2.1352 1.00   1285  145 0.1112 0.1731      4.9193      5.2652|
| 12:  2.1352 -  2.0743 0.97   1273  137 0.1109 0.1619      4.8571      5.1645|
| 13:  2.0743 -  2.0199 0.98   1259  143 0.1103 0.1703      4.7624      4.9846|
| 14:  2.0199 -  1.9707 0.53    680   77 0.1015 0.1690      4.6546      4.9326|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1402   155  0.94   9.24   0.98     0.96       7250.12|
|  2:  4.7025 -  3.7523  1350   154  0.95   7.85   1.02     1.00       8872.18|
|  3:  3.7523 -  3.2839  1317   145  0.94  10.97   1.03     1.02       9958.25|
|  4:  3.2839 -  2.9863  1309   137  0.92  13.01   1.01     1.00       9848.34|
|  5:  2.9863 -  2.7737  1310   152  0.90  15.46   1.00     0.96       7899.00|
|  6:  2.7737 -  2.6111  1302   144  0.90  16.05   0.98     0.96       6790.55|
|  7:  2.6111 -  2.4810  1288   146  0.91  14.93   0.98     0.94       5781.98|
|  8:  2.4810 -  2.3734  1302   141  0.92  14.29   1.00     0.98       4979.81|
|  9:  2.3734 -  2.2824  1283   145  0.91  15.16   1.01     0.98       4754.41|
| 10:  2.2824 -  2.2039  1270   138  0.90  15.59   1.01     0.97       4222.86|
| 11:  2.2039 -  2.1352  1285   145  0.90  15.65   1.00     0.97       4215.35|
| 12:  2.1352 -  2.0743  1273   137  0.91  15.01   1.02     1.01       3751.91|
| 13:  2.0743 -  2.0199  1259   143  0.91  15.52   1.01     0.99       3154.52|
| 14:  2.0199 -  1.9707   680    77  0.92  13.87   0.98     0.95       2419.27|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2419.27 max =         9958.25 mean =      6156.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.70|
|phase err.(test): min =        0.00 max =           88.42 mean =        13.22|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.741)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.58    87.51   14.78    None  None   None       |
|    all(noH): 2823   0      3.58    87.51   14.78    None  None   None       |
|    Sol.    : 438    0      4.45    76.23   36.29    None  None   None       |
|    Mac.    : 2385   0      3.58    87.51   10.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.579 -  11.972: 1798   |   5:    45.544 -  53.937:   90        |
|      1:    11.972 -  20.365:  491   |   6:    53.937 -  62.331:   38        |
|      2:    20.365 -  28.758:  145   |   7:    62.331 -  70.724:   18        |
|      3:    28.758 -  37.151:  127   |   8:    70.724 -  79.117:    6        |
|      4:    37.151 -  45.544:  107   |   9:    79.117 -  87.510:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.232 - 4.122
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 294
   mapped sites are within: 0.701 - 4.122

peak=   11.670 closest distance to " CB  VAL A 230 " =    1.480
peak=    8.614 closest distance to " CG2 VAL A 296 " =    1.260
peak=    6.809 closest distance to " CG  LEU A   5 " =    1.241
peak=    5.737 closest distance to " O   HOH Z 142 " =    1.800
peak=    5.594 closest distance to " NH2 ARG A  56 " =    2.161
peak=    5.505 closest distance to " CG  PRO A  54 " =    1.292
peak=    5.504 closest distance to " NE2 GLN A  11 " =    1.133
peak=    5.394 closest distance to " CG  LEU A 228 " =    1.194
peak=    5.210 closest distance to " CB  ARG A 275 " =    0.953
peak=    5.161 closest distance to " CD2 LEU A   5 " =    1.140
peak=    5.014 closest distance to " O   HOH Z 209 " =    2.279
peak=    4.974 closest distance to " CB  GLN A 183 " =    1.268
peak=    4.913 closest distance to " CB  GLN A 223 " =    1.488
peak=    4.904 closest distance to " O   HOH Z 232 " =    2.374
peak=    4.704 closest distance to " O   HOH Z 402 " =    1.472
peak=    4.635 closest distance to " CB  PRO A  54 " =    0.964
peak=    4.634 closest distance to " O   HOH Z 346 " =    1.605
peak=    4.627 closest distance to " O   HOH Z 193 " =    1.741
peak=    4.613 closest distance to " O   HOH Z 272 " =    1.882
peak=    4.545 closest distance to " CB  SER A  63 " =    1.216
peak=    4.544 closest distance to " CB  GLU A 152 " =    1.117
peak=    4.522 closest distance to " ND2 ASN A 187 " =    1.545
peak=    4.520 closest distance to " CB  ARG A  79 " =    1.407
peak=    4.519 closest distance to " CB  VAL A 296 " =    1.046
peak=    4.499 closest distance to " O   HOH Z 126 " =    1.946
peak=    4.481 closest distance to " O   HOH Z 423 " =    1.863
peak=    4.433 closest distance to " O   SER A  87 " =    2.173
peak=    4.430 closest distance to " O   HOH Z 427 " =    2.951
peak=    4.419 closest distance to " CG  PRO A 213 " =    1.231
peak=    4.407 closest distance to " O   HOH Z 369 " =    2.220
peak=    4.379 closest distance to " O   HOH Z  61 " =    1.635
peak=    4.352 closest distance to " CB  ASN A 148 " =    1.417
peak=    4.350 closest distance to " CB  VAL A 230 " =    1.171
peak=    4.308 closest distance to " O   HOH Z  85 " =    1.376
peak=    4.305 closest distance to " O   HOH Z 126 " =    2.053
peak=    4.287 closest distance to " C   PRO A 198 " =    1.468
peak=    4.284 closest distance to " O   HOH Z 236 " =    1.993
peak=    4.268 closest distance to " CG  PRO A 243 " =    1.111
peak=    4.255 closest distance to " O   HOH Z 189 " =    2.884
peak=    4.197 closest distance to " O   HOH Z 234 " =    3.589
peak=    4.181 closest distance to " O   HOH Z 316 " =    3.071
peak=    4.159 closest distance to " O   HOH Z 248 " =    1.567
peak=    4.127 closest distance to " O   HOH Z 250 " =    1.366
peak=    4.115 closest distance to " CZ  PHE A 218 " =    1.127
peak=    4.106 closest distance to " CB  ASN A  39 " =    0.867
peak=    4.091 closest distance to " O   HOH Z 368 " =    2.115
peak=    4.063 closest distance to " O   HOH Z  59 " =    1.994
peak=    4.060 closest distance to " CB  TRP A 266 " =    0.995
peak=    4.058 closest distance to " CD2 TRP A 179 " =    1.391
peak=    4.054 closest distance to " CB  VAL A 265 " =    1.284
peak=    4.051 closest distance to " O   HOH Z 298 " =    1.725
peak=    4.013 closest distance to " N   ASN A  39 " =    1.221
peak=    4.008 closest distance to " O   HOH Z  78 " =    1.657
peak=    3.997 closest distance to " O   HOH Z 403 " =    1.711
peak=    3.981 closest distance to " O   HOH Z 313 " =    1.880
peak=    3.968 closest distance to " O   HOH Z 265 " =    2.297
peak=    3.959 closest distance to " CB  ASN A 187 " =    1.298
peak=    3.953 closest distance to " O   HOH Z  43 " =    2.055
peak=    3.943 closest distance to " CB  ALA A   9 " =    1.613
peak=    3.929 closest distance to " O   HOH Z 407 " =    2.435
peak=    3.927 closest distance to " O   HOH Z  15 " =    2.127
peak=    3.923 closest distance to " O   HOH Z 158 " =    3.144
peak=    3.896 closest distance to " CD2 LEU A 228 " =    1.271
peak=    3.886 closest distance to " O   HOH Z 303 " =    2.084
peak=    3.884 closest distance to " O   HOH Z  97 " =    2.007
peak=    3.869 closest distance to " CB  SER A   3 " =    1.210
peak=    3.837 closest distance to " O   HOH Z 280 " =    2.965
peak=    3.833 closest distance to " O   HOH Z 411 " =    3.755
peak=    3.832 closest distance to " CA  ASN A 215 " =    1.012
peak=    3.831 closest distance to " CG  PRO A 198 " =    1.197
peak=    3.824 closest distance to " CG2 ILE A  20 " =    1.465
peak=    3.816 closest distance to " OD1 ASN A  69 " =    2.531
peak=    3.811 closest distance to " CG1BVAL A  72 " =    1.592
peak=    3.794 closest distance to " CB  SER A  26 " =    1.728
peak=    3.783 closest distance to " CB  ARG A 139 " =    0.959
peak=    3.781 closest distance to " O   HOH Z 128 " =    2.046
peak=    3.779 closest distance to " O   HOH Z 128 " =    2.140
peak=    3.776 closest distance to " CB  TRP A 179 " =    1.369
peak=    3.775 closest distance to " CB  GLU A 277 " =    3.528
peak=    3.774 closest distance to " CA  TYR A  30 " =    0.904
peak=    3.763 closest distance to " CB  ARG A 190 " =    1.679
peak=    3.758 closest distance to " O   HOH Z 261 " =    1.842
peak=    3.757 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.756 closest distance to " CB  ASN A 142 " =    1.079
peak=    3.754 closest distance to " O   HOH Z 273 " =    2.826
peak=    3.746 closest distance to " O   HOH Z 203 " =    1.547
peak=    3.744 closest distance to " CB  THR A  31 " =    1.476
peak=    3.738 closest distance to " CG  LEU A 167 " =    1.207
peak=    3.735 closest distance to " O   HOH Z  97 " =    2.415
peak=    3.734 closest distance to " O   HOH Z  40 " =    1.456
peak=    3.717 closest distance to " CG  MET A 185 " =    1.144
peak=    3.712 closest distance to " NH1BARG A 190 " =    2.141
peak=    3.708 closest distance to " O   HOH Z 371 " =    2.991
peak=    3.699 closest distance to " CB  VAL A 202 " =    1.526
peak=    3.697 closest distance to " OG BSER A 164 " =    2.183
peak=    3.693 closest distance to " CB  GLN A  88 " =    1.134
peak=    3.688 closest distance to " O   HOH Z 145 " =    2.268
peak=    3.664 closest distance to " O   HOH Z 214 " =    2.269
peak=    3.652 closest distance to " CB  GLU A  46 " =    1.040
peak=    3.647 closest distance to " CG  ARG A  66 " =    2.804
peak=    3.631 closest distance to " CB  ASP A 140 " =    1.019
peak=    3.629 closest distance to " O   HOH Z 366 " =    2.832
peak=    3.625 closest distance to " O   HOH Z  68 " =    2.251
peak=    3.623 closest distance to " CB  GLU A 128 " =    0.986
peak=    3.613 closest distance to " CB  ASN A 148 " =    1.922
peak=    3.609 closest distance to " O   HOH Z  44 " =    1.672
peak=    3.597 closest distance to " O   HOH Z  54 " =    1.589
peak=    3.593 closest distance to " CA  PHE A 283 " =    1.113
peak=    3.592 closest distance to " CA  ALA A  21 " =    1.122
peak=    3.590 closest distance to " O   HOH Z 261 " =    1.955
peak=    3.584 closest distance to " CG2 VAL A 257 " =    0.862
peak=    3.573 closest distance to " O   HOH Z  80 " =    1.679
peak=    3.569 closest distance to " O   HOH Z 180 " =    2.100
peak=    3.567 closest distance to " O   HOH Z 193 " =    1.866
peak=    3.566 closest distance to " O   HOH Z 392 " =    2.970
peak=    3.557 closest distance to " CA  ALA A  51 " =    0.943
peak=    3.557 closest distance to " O   TRP A 274 " =    1.847
peak=    3.550 closest distance to " O  BHOH Z 338 " =    2.428
peak=    3.546 closest distance to " O   HOH Z 124 " =    1.327
peak=    3.543 closest distance to " CB  ASN A 110 " =    1.079
peak=    3.540 closest distance to " CB  ALA A 248 " =    1.354
peak=    3.540 closest distance to " O   HOH Z 251 " =    1.454
peak=    3.533 closest distance to " O   HOH Z 299 " =    4.122
peak=    3.532 closest distance to " O   HOH Z   9 " =    1.997
peak=    3.530 closest distance to " O   HOH Z  21 " =    1.784
peak=    3.525 closest distance to " CB AVAL A  41 " =    1.111
peak=    3.521 closest distance to " CG1 ILE A  49 " =    1.487
peak=    3.519 closest distance to " CD  ARG A 269 " =    0.977
peak=    3.516 closest distance to " O   HOH Z 380 " =    1.994
peak=    3.512 closest distance to " N   PHE A 130 " =    1.257
peak=    3.510 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.502 closest distance to " CA  ASP A 162 " =    0.998
peak=    3.500 closest distance to " NZ  LYS A  48 " =    1.231
peak=    3.493 closest distance to " CA  LYS A 117 " =    1.247
peak=    3.493 closest distance to " OE1 GLU A   2 " =    2.157
peak=    3.491 closest distance to " O   HOH Z 147 " =    1.782
peak=    3.489 closest distance to " NZ  LYS A 117 " =    2.857
peak=    3.484 closest distance to " O   HOH Z 148 " =    3.360
peak=    3.472 closest distance to " O   HOH Z 353 " =    2.548
peak=    3.471 closest distance to " O   HOH Z 258 " =    2.337
peak=    3.463 closest distance to " O   HOH Z 126 " =    1.520
peak=    3.457 closest distance to " O   HOH Z 357 " =    1.859
peak=    3.455 closest distance to " NE2 GLN A  77 " =    3.218
peak=    3.450 closest distance to " O   HOH Z 337 " =    3.469
peak=    3.449 closest distance to " O   LYS A 290 " =    2.383
peak=    3.444 closest distance to " O   HOH Z 345 " =    3.139
peak=    3.444 closest distance to " O   HOH Z 327 " =    1.479
peak=    3.443 closest distance to " O   HOH Z  19 " =    2.127
peak=    3.434 closest distance to " O   HOH Z 286 " =    2.347
peak=    3.434 closest distance to " CB  ALA A 291 " =    1.245
peak=    3.433 closest distance to " O   HOH Z 164 " =    2.007
peak=    3.427 closest distance to " OE2 GLU A  53 " =    2.007
peak=    3.426 closest distance to " CG AARG A 275 " =    1.220
peak=    3.424 closest distance to " O   HOH Z 417 " =    3.388
peak=    3.421 closest distance to " N   ARG A 156 " =    1.338
peak=    3.419 closest distance to " CG2 ILE A 120 " =    1.221
peak=    3.417 closest distance to " O   ASN A  74 " =    1.523
peak=    3.413 closest distance to " O   HOH Z 141 " =    1.609
peak=    3.412 closest distance to " O   HOH Z 344 " =    2.835
peak=    3.405 closest distance to " O   HOH Z 435 " =    1.935
peak=    3.405 closest distance to " CB  ARG A 219 " =    1.143
peak=    3.397 closest distance to " CA  ARG A  36 " =    1.024
peak=    3.395 closest distance to " CD  ARG A 159 " =    0.701
peak=    3.393 closest distance to " CB  GLN A 278 " =    0.911
peak=    3.387 closest distance to " O   HOH Z 422 " =    2.559
peak=    3.384 closest distance to " N   ASP A 162 " =    1.207
peak=    3.381 closest distance to " O   HOH Z 329 " =    3.965
peak=    3.381 closest distance to " CB  TRP A 150 " =    1.400
peak=    3.380 closest distance to " CG1 ILE A  33 " =    1.308
peak=    3.375 closest distance to " CB  SER A 273 " =    0.864
peak=    3.370 closest distance to " CG  LYS A  76 " =    0.924
peak=    3.366 closest distance to " O   HOH Z 389 " =    1.799
peak=    3.364 closest distance to " CB  LYS A 290 " =    1.004
peak=    3.363 closest distance to " CE1 TYR A 186 " =    1.311
peak=    3.361 closest distance to " CG BARG A 102 " =    1.709
peak=    3.361 closest distance to " O   HOH Z 233 " =    1.910
peak=    3.357 closest distance to " CB  ALA A 114 " =    1.287
peak=    3.355 closest distance to " CA  VAL A  41 " =    0.759
peak=    3.348 closest distance to " O   HOH Z  94 " =    2.096
peak=    3.347 closest distance to " CA  ALA A 291 " =    0.823
peak=    3.341 closest distance to " CG2 THR A 294 " =    1.638
peak=    3.341 closest distance to " O   HOH Z  88 " =    2.604
peak=    3.340 closest distance to " O   HOH Z  88 " =    2.744
peak=    3.339 closest distance to " NH1AARG A 145 " =    1.156
peak=    3.329 closest distance to " CD2 LEU A 297 " =    1.002
peak=    3.328 closest distance to " CB  HIS A 108 " =    0.828
peak=    3.324 closest distance to " OD2 ASP A 286 " =    2.723
peak=    3.320 closest distance to " O   ASP A 124 " =    1.216
peak=    3.316 closest distance to " O   HOH Z  10 " =    1.785
peak=    3.316 closest distance to " N   ARG A 190 " =    0.981
peak=    3.312 closest distance to " O   HOH Z 425 " =    1.320
peak=    3.309 closest distance to " O   HOH Z 188 " =    2.345
peak=    3.308 closest distance to " CA  ASN A 176 " =    1.047
peak=    3.308 closest distance to " O   HOH Z 102 " =    1.263
peak=    3.304 closest distance to " CB  GLN A 205 " =    1.184
peak=    3.299 closest distance to " O   HOH Z 172 " =    3.771
peak=    3.299 closest distance to " CD1 ILE A  33 " =    1.644
peak=    3.297 closest distance to " CA  ALA A 158 " =    1.288
peak=    3.294 closest distance to " CG1 VAL A 296 " =    1.164
peak=    3.293 closest distance to " CA  SER A 146 " =    1.800
peak=    3.291 closest distance to " CA  ASN A 127 " =    1.056
peak=    3.287 closest distance to " NH1 ARG A  66 " =    1.528
peak=    3.280 closest distance to " CG  GLN A  88 " =    1.061
peak=    3.279 closest distance to " O   GLY A  91 " =    1.511
peak=    3.278 closest distance to " O   HOH Z 368 " =    3.605
peak=    3.277 closest distance to " O   ARG A  56 " =    2.843
peak=    3.273 closest distance to " OG  SER A 276 " =    1.264
peak=    3.268 closest distance to " N   SER A 135 " =    1.312
peak=    3.265 closest distance to " O   HOH Z 245 " =    1.424
peak=    3.265 closest distance to " CD BLYS A 290 " =    1.209
peak=    3.251 closest distance to " O   LEU A 228 " =    1.791
peak=    3.251 closest distance to " CA  ILE A 106 " =    0.744
peak=    3.250 closest distance to " CA  ALA A 233 " =    1.216
peak=    3.250 closest distance to " NH2BARG A 145 " =    2.042
peak=    3.250 closest distance to " CG  LYS A  76 " =    1.746
peak=    3.242 closest distance to " O   HOH Z 118 " =    1.511
peak=    3.241 closest distance to " O   HOH Z 227 " =    1.527
peak=    3.238 closest distance to " O   HOH Z 404 " =    2.311
peak=    3.236 closest distance to " CB  ASN A 215 " =    1.180
peak=    3.235 closest distance to " OG ASER A  99 " =    1.483
peak=    3.230 closest distance to " O   HOH Z 227 " =    2.144
peak=    3.229 closest distance to " CD1 ILE A 106 " =    1.164
peak=    3.228 closest distance to " CA  ASN A 217 " =    1.274
peak=    3.221 closest distance to " ND2 ASN A 110 " =    1.585
peak=    3.219 closest distance to " O   HOH Z   3 " =    1.773
peak=    3.219 closest distance to " O   HOH Z 294 " =    1.525
peak=    3.218 closest distance to " CE1 HIS A 108 " =    1.141
peak=    3.218 closest distance to " O   HOH Z 128 " =    2.014
peak=    3.216 closest distance to " O   HOH Z   1 " =    1.910
peak=    3.216 closest distance to " CA  PHE A  59 " =    0.946
peak=    3.214 closest distance to " O   HOH Z 426 " =    1.657
peak=    3.212 closest distance to " CB  PRO A  90 " =    1.117
peak=    3.210 closest distance to " CG2 VAL A 202 " =    1.129
peak=    3.210 closest distance to " CG  MET A 185 " =    1.019
peak=    3.209 closest distance to " CB  THR A 157 " =    1.199
peak=    3.209 closest distance to " O   HOH Z 263 " =    1.683
peak=    3.205 closest distance to " CG  GLN A  77 " =    2.249
peak=    3.203 closest distance to " NH2BARG A 190 " =    1.691
peak=    3.202 closest distance to " O   HOH Z 419 " =    1.588
peak=    3.202 closest distance to " CG1 VAL A 153 " =    0.923
peak=    3.199 closest distance to " CA  THR A 264 " =    0.823
peak=    3.198 closest distance to " CG2 THR A  18 " =    1.608
peak=    3.193 closest distance to " CG1 ILE A 120 " =    1.167
peak=    3.185 closest distance to " O   HOH Z 425 " =    2.060
peak=    3.181 closest distance to " CG  LYS A 119 " =    1.070
peak=    3.177 closest distance to " CD  LYS A 119 " =    1.863
peak=    3.175 closest distance to " O   HOH Z 421 " =    1.616
peak=    3.174 closest distance to " O   HOH Z 290 " =    1.138
peak=    3.171 closest distance to " CB  SER A  62 " =    1.358
peak=    3.170 closest distance to " ND2 ASN A 249 " =    0.942
peak=    3.166 closest distance to " OG  SER A  62 " =    2.764
peak=    3.163 closest distance to " O   HOH Z 301 " =    1.782
peak=    3.163 closest distance to " O   HOH Z 285 " =    2.741
peak=    3.159 closest distance to " O   MET A 105 " =    1.910
peak=    3.158 closest distance to " CA  ARG A 195 " =    1.194
peak=    3.157 closest distance to " CA  ASP A 140 " =    1.237
peak=    3.154 closest distance to " CA  ASP A 191 " =    1.138
peak=    3.154 closest distance to " CB  ALA A 242 " =    0.909
peak=    3.151 closest distance to " CB  THR A 279 " =    1.639
peak=    3.150 closest distance to " O   HOH Z 251 " =    1.683
peak=    3.146 closest distance to " O   HOH Z 183 " =    1.730
peak=    3.145 closest distance to " O   ASN A 284 " =    1.774
peak=    3.144 closest distance to " NE2 HIS A 207 " =    1.263
peak=    3.139 closest distance to " CB  TYR A 247 " =    0.954
peak=    3.138 closest distance to " CA  LYS A 290 " =    1.204
peak=    3.129 closest distance to " CD2 TYR A 186 " =    1.035
peak=    3.127 closest distance to " O   HOH Z 112 " =    1.664
peak=    3.123 closest distance to " CG2 THR A 221 " =    1.311
peak=    3.123 closest distance to " N   ASN A 127 " =    1.237
peak=    3.123 closest distance to " O   SER A 164 " =    1.259
peak=    3.122 closest distance to " CB  ILE A 120 " =    1.320
peak=    3.121 closest distance to " CB  ASP A 124 " =    0.705
peak=    3.117 closest distance to " CZ2 TRP A 274 " =    1.504
peak=    3.117 closest distance to " CA  SER A  87 " =    1.047
peak=    3.113 closest distance to " CA  ALA A 129 " =    1.615
peak=    3.110 closest distance to " CB  ILE A  20 " =    1.502
peak=    3.104 closest distance to " CA  LEU A 282 " =    1.118
peak=    3.098 closest distance to " O   HOH Z 419 " =    1.790
peak=    3.091 closest distance to " CD1 LEU A 261 " =    1.162
peak=    3.091 closest distance to " O   HOH Z  19 " =    2.331
peak=    3.088 closest distance to " CZ3 TRP A  85 " =    0.937
peak=    3.088 closest distance to " O   HOH Z  83 " =    1.557
peak=    3.084 closest distance to " CA  GLY A 267 " =    0.889
peak=    3.076 closest distance to " O   HOH Z 359 " =    3.829
peak=    3.072 closest distance to " O   HOH Z 213 " =    2.228
peak=    3.049 closest distance to " O   HOH Z  40 " =    2.528
peak=    3.047 closest distance to " CG  LEU A 281 " =    1.039
peak=    3.046 closest distance to " O   HOH Z 406 " =    1.591

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.505 - 5.508
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 185 from: 188
   mapped sites are within: 0.799 - 5.508

peak=   -5.006 closest distance to " SG  CYS A 254 " =    3.269
peak=   -4.486 closest distance to " CD  ARG A 156 " =    2.038
peak=   -4.359 closest distance to " CG  GLN A  58 " =    1.110
peak=   -4.343 closest distance to " C   HIS A 108 " =    1.235
peak=   -4.338 closest distance to " O   HOH Z 266 " =    5.219
peak=   -4.335 closest distance to " CG  GLN A 223 " =    2.023
peak=   -4.330 closest distance to " OG BSER A 134 " =    1.136
peak=   -4.262 closest distance to " O   VAL A  67 " =    2.599
peak=   -4.172 closest distance to " CB  PRO A 243 " =    2.667
peak=   -4.168 closest distance to " O   HOH Z 290 " =    1.097
peak=   -4.111 closest distance to " OXT GLY A 302 " =    2.758
peak=   -4.089 closest distance to " CG2 ILE A  20 " =    2.907
peak=   -4.064 closest distance to " O   PRO A 163 " =    2.032
peak=   -4.052 closest distance to " O   HOH Z 351 " =    1.473
peak=   -4.049 closest distance to " CB  PHE A 192 " =    1.997
peak=   -4.004 closest distance to " CG2 VAL A 296 " =    1.457
peak=   -3.989 closest distance to " CD1 LEU A 255 " =    2.739
peak=   -3.986 closest distance to " ND2 ASN A 187 " =    1.495
peak=   -3.912 closest distance to " O   HOH Z 211 " =    1.621
peak=   -3.907 closest distance to " CB  ALA A  43 " =    2.270
peak=   -3.907 closest distance to " CB  ALA A 161 " =    2.468
peak=   -3.882 closest distance to " N   GLN A  58 " =    1.818
peak=   -3.874 closest distance to " O   PRO A 198 " =    1.174
peak=   -3.872 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -3.869 closest distance to " O   HOH Z 394 " =    1.480
peak=   -3.869 closest distance to " CE  MET A 105 " =    2.197
peak=   -3.863 closest distance to " ND2 ASN A  45 " =    1.178
peak=   -3.862 closest distance to " O   HOH Z 114 " =    3.116
peak=   -3.848 closest distance to " O   HOH Z 231 " =    2.149
peak=   -3.825 closest distance to " CB  PRO A 163 " =    2.514
peak=   -3.823 closest distance to " CB  ALA A 248 " =    2.355
peak=   -3.796 closest distance to " O   HOH Z 166 " =    1.971
peak=   -3.793 closest distance to " O   HOH Z 429 " =    1.962
peak=   -3.779 closest distance to " CD1 LEU A 101 " =    2.290
peak=   -3.758 closest distance to " CG2 VAL A 296 " =    0.862
peak=   -3.752 closest distance to " CD1 ILE A 263 " =    2.729
peak=   -3.731 closest distance to " CG2 THR A 178 " =    2.221
peak=   -3.722 closest distance to " O   HOH Z  11 " =    1.895
peak=   -3.685 closest distance to " NE2 GLN A  88 " =    1.883
peak=   -3.683 closest distance to " O   SER A 210 " =    1.971
peak=   -3.660 closest distance to " CG  ASP A 231 " =    0.799
peak=   -3.650 closest distance to " CG  TRP A 266 " =    1.912
peak=   -3.650 closest distance to " CZ3 TRP A 179 " =    1.279
peak=   -3.649 closest distance to " O   HOH Z 103 " =    1.884
peak=   -3.625 closest distance to " N   ALA A 248 " =    1.658
peak=   -3.623 closest distance to " OD2 ASP A 171 " =    2.270
peak=   -3.617 closest distance to " N   ALA A 226 " =    1.976
peak=   -3.609 closest distance to " CG1 VAL A 230 " =    1.872
peak=   -3.608 closest distance to " CD1 PHE A  59 " =    1.967
peak=   -3.601 closest distance to " O   HOH Z 196 " =    2.091
peak=   -3.600 closest distance to " O   GLY A 196 " =    1.128
peak=   -3.591 closest distance to " O   HOH Z 185 " =    2.427
peak=   -3.575 closest distance to " NE2 GLN A  88 " =    1.068
peak=   -3.555 closest distance to " CB  ASP A 132 " =    2.291
peak=   -3.551 closest distance to " CG1 VAL A 112 " =    2.696
peak=   -3.535 closest distance to " O   HOH Z  60 " =    2.038
peak=   -3.526 closest distance to " O   HOH Z 389 " =    2.015
peak=   -3.525 closest distance to " O   HOH Z  13 " =    1.756
peak=   -3.524 closest distance to " CD  LYS A 289 " =    2.463
peak=   -3.523 closest distance to " OG  SER A  97 " =    2.305
peak=   -3.516 closest distance to " C   ILE A 239 " =    1.989
peak=   -3.511 closest distance to " CA  ASP A 298 " =    1.105
peak=   -3.502 closest distance to " O   PHE A 218 " =    1.670
peak=   -3.495 closest distance to " O   MET A  40 " =    2.783
peak=   -3.476 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.475 closest distance to " CB  ASP A 132 " =    2.401
peak=   -3.468 closest distance to " N   HIS A 115 " =    2.111
peak=   -3.464 closest distance to " CZ  PHE A  59 " =    1.505
peak=   -3.457 closest distance to " O   HOH Z  63 " =    1.405
peak=   -3.454 closest distance to " N   THR A  52 " =    1.677
peak=   -3.452 closest distance to " OG  SER A   3 " =    1.496
peak=   -3.449 closest distance to " O   ALA A  51 " =    1.305
peak=   -3.434 closest distance to " CD  ARG A 139 " =    1.628
peak=   -3.422 closest distance to " O   HOH Z 407 " =    2.904
peak=   -3.419 closest distance to " C   GLN A 205 " =    1.920
peak=   -3.415 closest distance to " CB  ALA A 291 " =    2.289
peak=   -3.414 closest distance to " O   HOH Z 165 " =    1.975
peak=   -3.411 closest distance to " CA  GLY A 133 " =    1.876
peak=   -3.407 closest distance to " O   HOH Z 166 " =    1.553
peak=   -3.404 closest distance to " CG2 ILE A 263 " =    2.279
peak=   -3.401 closest distance to " NH2AARG A 275 " =    5.000
peak=   -3.394 closest distance to " O   ALA A 161 " =    1.738
peak=   -3.394 closest distance to " CD2 LEU A 300 " =    2.548
peak=   -3.392 closest distance to " O   HOH Z 421 " =    3.200
peak=   -3.391 closest distance to " OD1 ASN A 301 " =    2.020
peak=   -3.390 closest distance to " O   HOH Z 359 " =    3.187
peak=   -3.386 closest distance to " N   THR A 157 " =    1.556
peak=   -3.385 closest distance to " CG2 VAL A 202 " =    2.632
peak=   -3.380 closest distance to " NE2 GLN A 278 " =    1.895
peak=   -3.379 closest distance to " O   HOH Z 102 " =    1.651
peak=   -3.372 closest distance to " NH2 ARG A  79 " =    1.979
peak=   -3.370 closest distance to " CG  LEU A   5 " =    0.878
peak=   -3.365 closest distance to " C   ASP A 231 " =    2.435
peak=   -3.365 closest distance to " O   GLN A 240 " =    2.133
peak=   -3.357 closest distance to " O   HOH Z 313 " =    1.708
peak=   -3.355 closest distance to " O   HOH Z 191 " =    5.508
peak=   -3.348 closest distance to " CB  ASN A  39 " =    2.238
peak=   -3.339 closest distance to " C   MET A 188 " =    1.438
peak=   -3.339 closest distance to " NH2 ARG A  79 " =    1.656
peak=   -3.335 closest distance to " CA  GLY A 241 " =    2.363
peak=   -3.326 closest distance to " CB  ASN A  69 " =    1.158
peak=   -3.322 closest distance to " O   HOH Z 243 " =    1.868
peak=   -3.319 closest distance to " O   PRO A 198 " =    1.278
peak=   -3.310 closest distance to " O   ALA A   8 " =    1.859
peak=   -3.309 closest distance to " CD2 TYR A 293 " =    2.073
peak=   -3.304 closest distance to " OG BSER A 134 " =    1.804
peak=   -3.301 closest distance to " OD2 ASP A  50 " =    2.188
peak=   -3.300 closest distance to " CE BMET A  47 " =    1.397
peak=   -3.297 closest distance to " O   SER A  22 " =    2.350
peak=   -3.291 closest distance to " CG  PHE A 283 " =    2.629
peak=   -3.284 closest distance to " CG1 VAL A 197 " =    2.214
peak=   -3.284 closest distance to " CE2 PHE A 218 " =    2.606
peak=   -3.283 closest distance to " O   HOH Z 423 " =    2.177
peak=   -3.280 closest distance to " NE2 GLN A 194 " =    1.805
peak=   -3.280 closest distance to " OXT GLY A 302 " =    3.536
peak=   -3.280 closest distance to " OD1 ASN A 148 " =    1.490
peak=   -3.277 closest distance to " O   HOH Z 139 " =    3.203
peak=   -3.275 closest distance to " ND2 ASN A  39 " =    1.131
peak=   -3.272 closest distance to " CB  ALA A 291 " =    2.164
peak=   -3.268 closest distance to " CG  GLU A  53 " =    1.607
peak=   -3.265 closest distance to " OD1 ASN A  39 " =    2.196
peak=   -3.263 closest distance to " O   HOH Z 193 " =    1.949
peak=   -3.255 closest distance to " O   ASN A  45 " =    1.921
peak=   -3.255 closest distance to " O   SER A  95 " =    1.533
peak=   -3.254 closest distance to " CD1 ILE A 239 " =    2.387
peak=   -3.250 closest distance to " CG1 VAL A  78 " =    2.818
peak=   -3.249 closest distance to " O   HOH Z 295 " =    1.421
peak=   -3.245 closest distance to " CG1 VAL A 112 " =    2.884
peak=   -3.242 closest distance to " O   SER A 271 " =    2.162
peak=   -3.240 closest distance to " O   ASN A 301 " =    1.590
peak=   -3.239 closest distance to " O   HOH Z 369 " =    2.187
peak=   -3.238 closest distance to " CA  GLY A 241 " =    3.082
peak=   -3.238 closest distance to " O   HOH Z 193 " =    1.654
peak=   -3.238 closest distance to " CG  LEU A 228 " =    0.929
peak=   -3.238 closest distance to " O   ARG A  24 " =    1.905
peak=   -3.233 closest distance to " OG  SER A 206 " =    1.548
peak=   -3.232 closest distance to " CE1 TYR A 247 " =    2.588
peak=   -3.232 closest distance to " CE3 TRP A 150 " =    2.062
peak=   -3.230 closest distance to " O   LEU A 167 " =    1.586
peak=   -3.218 closest distance to " O   ILE A 106 " =    1.958
peak=   -3.215 closest distance to " O   HOH Z 426 " =    1.675
peak=   -3.215 closest distance to " O   VAL A 189 " =    2.586
peak=   -3.211 closest distance to " CA  GLY A  98 " =    1.832
peak=   -3.208 closest distance to " O   HOH Z  47 " =    1.643
peak=   -3.207 closest distance to " O   HOH Z 372 " =    2.336
peak=   -3.204 closest distance to " O   HOH Z  38 " =    1.786
peak=   -3.204 closest distance to " O   HOH Z 174 " =    4.198
peak=   -3.201 closest distance to " N   ALA A  43 " =    2.662
peak=   -3.199 closest distance to " O   HOH Z 139 " =    5.028
peak=   -3.194 closest distance to " O   HOH Z 431 " =    1.949
peak=   -3.192 closest distance to " O   HOH Z 131 " =    4.068
peak=   -3.192 closest distance to " O   HOH Z 427 " =    1.496
peak=   -3.187 closest distance to " NE2 GLN A 103 " =    1.718
peak=   -3.184 closest distance to " O   ALA A   1 " =    1.709
peak=   -3.184 closest distance to " OG  SER A  62 " =    1.510
peak=   -3.184 closest distance to " CD1 LEU A 228 " =    2.039
peak=   -3.182 closest distance to " O   VAL A 174 " =    2.043
peak=   -3.182 closest distance to " O   HOH Z 353 " =    2.117
peak=   -3.181 closest distance to " O   HOH Z 256 " =    1.340
peak=   -3.178 closest distance to " CA  GLY A  23 " =    1.920
peak=   -3.178 closest distance to " ND2 ASN A  60 " =    1.297
peak=   -3.167 closest distance to " C   ASN A 187 " =    1.873
peak=   -3.159 closest distance to " O   HOH Z 411 " =    3.943
peak=   -3.159 closest distance to " O   HOH Z 200 " =    4.574
peak=   -3.155 closest distance to " O   GLY A  80 " =    2.539
peak=   -3.154 closest distance to " CB  SER A 210 " =    1.188
peak=   -3.136 closest distance to " O   HOH Z 216 " =    1.626
peak=   -3.133 closest distance to " O   HOH Z 210 " =    1.113
peak=   -3.129 closest distance to " O   ALA A  10 " =    1.743
peak=   -3.128 closest distance to " CG  GLU A   2 " =    2.039
peak=   -3.125 closest distance to " C   ALA A 158 " =    1.363
peak=   -3.122 closest distance to " CD  GLN A 223 " =    0.820
peak=   -3.117 closest distance to " CB  ASP A 286 " =    2.222
peak=   -3.111 closest distance to " N   ALA A 248 " =    2.300
peak=   -3.104 closest distance to " CA  TRP A 274 " =    1.283
peak=   -3.097 closest distance to " O   HOH Z 111 " =    4.820
peak=   -3.096 closest distance to " CB  ASP A 132 " =    2.254
peak=   -3.093 closest distance to " CA  PRO A 243 " =    2.243
peak=   -3.088 closest distance to " O   HOH Z 198 " =    1.993
peak=   -3.086 closest distance to " CG  GLU A 277 " =    1.247
peak=   -3.082 closest distance to " O   HOH Z 265 " =    1.614
peak=   -3.072 closest distance to " O   HOH Z 149 " =    2.156
peak=   -3.046 closest distance to " CE1 HIS A  81 " =    1.499
peak=   -3.038 closest distance to " CG  GLU A 152 " =    1.248
peak=   -3.028 closest distance to " O   GLY A  75 " =    1.701

================= 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    :  0.4316 0.4212   6.225025e+00   6.202552e+00
   1_bss:  0.4235 0.4099   6.216080e+00   6.189000e+00
   1_xyz:  0.3138 0.3306   6.001127e+00   6.042933e+00
   1_adp:  0.2474 0.2801   5.797960e+00   5.906660e+00
   1_occ:  0.2469 0.2802   5.796606e+00   5.907079e+00
   2_bss:  0.2414 0.2741   5.795254e+00   5.904976e+00
   2_xyz:  0.1600 0.1963   5.428763e+00   5.608385e+00
   2_adp:  0.1449 0.1836   5.342325e+00   5.535065e+00
   2_occ:  0.1448 0.1835   5.341662e+00   5.534457e+00
   3_bss:  0.1440 0.1831   5.340276e+00   5.531355e+00
   3_xyz:  0.1255 0.1646   5.223186e+00   5.429098e+00
   3_adp:  0.1209 0.1626   5.200124e+00   5.418593e+00
   3_occ:  0.1208 0.1625   5.199558e+00   5.418063e+00
   4_bss:  0.1208 0.1625   5.199116e+00   5.417619e+00
   4_xyz:  0.1130 0.1570   5.154147e+00   5.391756e+00
   4_adp:  0.1126 0.1552   5.147677e+00   5.381853e+00
   4_occ:  0.1124 0.1552   5.146236e+00   5.380994e+00
   5_bss:  0.1124 0.1558   5.148193e+00   5.382152e+00
   5_xyz:  0.1097 0.1550   5.131529e+00   5.375346e+00
   5_adp:  0.1100 0.1546   5.130111e+00   5.370320e+00
   5_occ:  0.1100 0.1546   5.129975e+00   5.370284e+00
   5_bss:  0.1100 0.1545   5.129998e+00   5.370221e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.357  20.000   8.104   8.029   8.677   0.000   0.000   0.000
   1_xyz:  0.357  20.000   8.104   8.029   8.677   0.000   0.000   0.000
   1_adp:  0.357  20.000   8.104   8.029   8.677   0.000   0.000   0.000
   1_occ:  0.357  20.000   8.104   8.029   8.677   0.000   0.000   0.000
   2_bss:  0.331  37.401   4.356   4.076   5.323   0.000   0.000   0.000
   2_xyz:  0.331  37.401   4.356   4.076   5.323   0.000   0.000   0.000
   2_adp:  0.331  37.401   4.356   4.076   5.323   0.000   0.000   0.000
   2_occ:  0.331  37.401   4.356   4.076   5.323   0.000   0.000   0.000
   3_bss:  0.322  37.401   2.833   3.406   4.537   0.000   0.000   0.000
   3_xyz:  0.322  37.401   2.833   3.406   4.537   0.000   0.000   0.000
   3_adp:  0.322  37.401   2.833   3.406   4.537   0.000   0.000   0.000
   3_occ:  0.322  37.401   2.833   3.406   4.537   0.000   0.000   0.000
   4_bss:  0.324  44.097   2.833   3.406   4.537   0.000   0.000   0.000
   4_xyz:  0.324  44.097   2.833   3.406   4.537   0.000   0.000   0.000
   4_adp:  0.324  44.097   2.833   3.406   4.537   0.000   0.000   0.000
   4_occ:  0.324  44.097   2.833   3.406   4.537   0.000   0.000   0.000
   5_bss:  0.325  43.876   2.833   3.406   4.537   0.000   0.000   0.000
   5_xyz:  0.325  43.876   2.833   3.406   4.537   0.000   0.000   0.000
   5_adp:  0.325  43.876   2.833   3.406   4.537   0.000   0.000   0.000
   5_occ:  0.325  43.876   2.833   3.406   4.537   0.000   0.000   0.000
   5_bss:  0.325  45.675  -0.851  -0.174   1.025   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.730 0.5632  0.6358    52196.369
   1_bss:  46.511 0.5639  0.8199    49408.128
   1_xyz:  35.333 0.6970  0.9758    29799.670
   1_adp:  28.148 0.7788  1.0635    20590.943
   1_occ:  28.136 0.7789  1.0630    20572.617
   2_bss:  27.913 0.7813  0.9327    20324.055
   2_xyz:  18.987 0.8711  1.0009    10009.494
   2_adp:  17.223 0.8877  1.0127     8702.684
   2_occ:  17.211 0.8878  1.0126     8685.719
   3_bss:  17.151 0.8883  0.9753     8613.965
   3_xyz:  14.972 0.9070  0.9828     6951.625
   3_adp:  14.754 0.9090  0.9815     6787.400
   3_occ:  14.744 0.9090  0.9815     6777.904
   4_bss:  14.732 0.9091  0.9818     6776.206
   4_xyz:  14.134 0.9140  0.9828     6401.808
   4_adp:  13.896 0.9161  0.9815     6275.862
   4_occ:  13.880 0.9162  0.9813     6265.786
   5_bss:  13.939 0.9158  0.9808     6323.420
   5_xyz:  13.775 0.9170  0.9821     6215.808
   5_adp:  13.645 0.9181  0.9804     6159.076
   5_occ:  13.646 0.9181  0.9803     6158.078
   5_bss:  13.649 0.9180  0.9796     6155.689
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3477e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3477e+01
   1_xyz:   1.513  0.011  0.101 17.729  0.006  4.120   1.1606e-01
   1_adp:   1.513  0.011  0.101 17.729  0.006  4.120   1.1606e-01
   1_occ:   1.513  0.011  0.101 17.729  0.006  4.120   1.1606e-01
   2_bss:   1.513  0.011  0.101 17.729  0.006  4.120   1.1606e-01
   2_xyz:   1.029  0.007  0.078 15.888  0.004  4.120   6.4053e-02
   2_adp:   1.029  0.007  0.078 15.888  0.004  4.120   6.4053e-02
   2_occ:   1.029  0.007  0.078 15.888  0.004  4.120   6.4053e-02
   3_bss:   1.029  0.007  0.078 15.888  0.004  4.120   6.4053e-02
   3_xyz:   0.919  0.006  0.072 15.464  0.003  4.117   5.4238e-02
   3_adp:   0.919  0.006  0.072 15.464  0.003  4.117   5.4238e-02
   3_occ:   0.919  0.006  0.072 15.464  0.003  4.117   5.4238e-02
   4_bss:   0.919  0.006  0.072 15.464  0.003  4.117   5.4238e-02
   4_xyz:   1.012  0.007  0.081 15.520  0.004  4.121   6.1325e-02
   4_adp:   1.012  0.007  0.081 15.520  0.004  4.121   6.1325e-02
   4_occ:   1.012  0.007  0.081 15.520  0.004  4.121   6.1325e-02
   5_bss:   1.012  0.007  0.081 15.520  0.004  4.121   6.1325e-02
   5_xyz:   1.036  0.008  0.083 15.459  0.004  4.120   6.4466e-02
   5_adp:   1.036  0.008  0.083 15.459  0.004  4.120   6.4466e-02
   5_occ:   1.036  0.008  0.083 15.459  0.004  4.120   6.4466e-02
   5_bss:   1.036  0.008  0.083 15.459  0.004  4.120   6.4466e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9315e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9315e+00
   1_xyz:  12.814  0.136  0.408 86.843  0.036  2.286   8.5648e-02
   1_adp:  12.814  0.136  0.408 86.843  0.036  2.286   8.5648e-02
   1_occ:  12.814  0.136  0.408 86.843  0.036  2.286   8.5648e-02
   2_bss:  12.814  0.136  0.408 86.843  0.036  2.286   8.5648e-02
   2_xyz:   6.538  0.061  0.421 85.531  0.029  2.263   4.3113e-02
   2_adp:   6.538  0.061  0.421 85.531  0.029  2.263   4.3113e-02
   2_occ:   6.538  0.061  0.421 85.531  0.029  2.263   4.3113e-02
   3_bss:   6.538  0.061  0.421 85.531  0.029  2.263   4.3113e-02
   3_xyz:   6.191  0.043  0.423 82.916  0.032  2.351   5.8489e-02
   3_adp:   6.191  0.043  0.423 82.916  0.032  2.351   5.8489e-02
   3_occ:   6.191  0.043  0.423 82.916  0.032  2.351   5.8489e-02
   4_bss:   6.191  0.043  0.423 82.916  0.032  2.351   5.8489e-02
   4_xyz:   6.847  0.045  0.517 83.169  0.037  2.343   4.6124e-02
   4_adp:   6.847  0.045  0.517 83.169  0.037  2.343   4.6124e-02
   4_occ:   6.847  0.045  0.517 83.169  0.037  2.343   4.6124e-02
   5_bss:   6.847  0.045  0.517 83.169  0.037  2.343   4.6124e-02
   5_xyz:   6.917  0.050  0.528 83.604  0.036  2.325   4.5309e-02
   5_adp:   6.917  0.050  0.528 83.604  0.036  2.325   4.5309e-02
   5_occ:   6.917  0.050  0.528 83.604  0.036  2.325   4.5309e-02
   5_bss:   6.917  0.050  0.528 83.604  0.036  2.325   4.5309e-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:  57.61   0.00  10.67  57.61   0.00   7.63  55.02   0.00  27.20
   1_occ:  57.61   0.00  10.67  57.61   0.00   7.63  55.02   0.00  27.20
   2_bss:  57.61   0.00  10.67  57.61   0.00   7.63  55.02   0.00  27.20
   2_xyz:  57.61   0.00  10.67  57.61   0.00   7.63  55.02   0.00  27.20
   2_adp:  67.85   0.00  10.99  67.85   0.00   7.32  56.79   0.20  30.98
   2_occ:  67.85   0.00  10.99  67.85   0.00   7.32  56.79   0.20  30.98
   3_bss:  67.85   0.00  10.99  67.85   0.00   7.32  56.79   0.20  30.98
   3_xyz:  67.85   0.00  10.99  67.85   0.00   7.32  56.79   0.20  30.98
   3_adp:  80.65   0.00  11.98  80.65   0.00   7.60  74.32   0.45  35.84
   3_occ:  80.65   0.00  11.98  80.65   0.00   7.60  74.32   0.45  35.84
   4_bss:  80.65   0.00  11.98  80.65   0.00   7.60  74.32   0.45  35.84
   4_xyz:  80.65   0.00  11.98  80.65   0.00   7.60  74.32   0.45  35.84
   4_adp:  84.13   0.00  11.56  84.13   0.00   7.42  74.12   0.44  34.14
   4_occ:  84.13   0.00  11.56  84.13   0.00   7.42  74.12   0.44  34.14
   5_bss:  84.13   0.00  11.56  84.13   0.00   7.42  74.12   0.44  34.14
   5_xyz:  84.13   0.00  11.56  84.13   0.00   7.42  74.12   0.44  34.14
   5_adp:  83.93   0.00  11.20  83.93   0.00   7.25  72.65   0.87  32.71
   5_occ:  83.93   0.00  11.20  83.93   0.00   7.25  72.65   0.87  32.71
   5_bss:  87.51   3.58  14.78  87.51   3.58  10.83  76.23   4.45  36.29
------------------------------------------------------------------------
 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:    1.219    0.018    0.402
   1_adp:    1.219    0.018    0.402
   1_occ:    1.219    0.018    0.402
   2_bss:    1.219    0.018    0.402
   2_xyz:    1.494    0.025    0.499
   2_adp:    1.494    0.025    0.499
   2_occ:    1.494    0.025    0.499
   3_bss:    1.494    0.025    0.499
   3_xyz:    1.533    0.056    0.522
   3_adp:    1.533    0.056    0.522
   3_occ:    1.533    0.056    0.522
   4_bss:    1.533    0.056    0.522
   4_xyz:    1.669    0.042    0.542
   4_adp:    1.669    0.042    0.542
   4_occ:    1.669    0.042    0.542
   5_bss:    1.669    0.042    0.542
   5_xyz:    1.673    0.046    0.551
   5_adp:    1.673    0.046    0.551
   5_occ:    1.673    0.046    0.551
   5_bss:    1.673    0.046    0.551
------------------------------------------------------------------------

CPU time actual refinement: 335.14


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_303/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_303/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_303/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_303/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_303/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.99 
  Macro-tasks:
    bulk solvent and scale       = 41.05  
    individual site refinement   = 141.41 
    weights calculation          = 32.23  
    collect and process          = 6.46   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 221.25 
  Micro-tasks:
    mask                            = 1.71   
    f_calc                          = 102.36 
    alpha_beta                      = 7.94   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 115.49 
    fmodel                         = 7.14   
    r_factors                      = 0.23   
    phase_errors                   = 10.87  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 247.16 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.613 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    679 calls, 101.97 s
gradients_fft:          624 calls, 101.06 s

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

# Date 2008-01-16 Time 01:15:23 PST -0800 (1200474923.34 s)
Start R-work = 0.4316, R-free = 0.4212 (no bulk solvent and anisotropic scale)
Final R-work = 0.1283, R-free = 0.1711 (no bulk solvent and anisotropic scale)

Start R-work = 0.4235, R-free = 0.4099
Final R-work = 0.1100, R-free = 0.1545