# Date 2008-01-16 Time 03:36:18 PST -0800 (1200483378.37 s)
#phil __OFF__

Command line arguments: "../1301.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25168
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1301

-------------------------------------------------------------------------------
  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: (72.0062, 47.6339, 85.5261, 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: 3.33, per 1000 atoms: 1.18


================================== 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: (72.0062, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.98133
Completeness in resolution range: 0.931169
Completeness with d_max=infinity: 0.928389

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2211
                             d_min =   1.9813

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: (72.0062, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.98133
Completeness in resolution range: 0.931169
Completeness with d_max=infinity: 0.928389

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2215 -  4.2408 [2209/2238]  1990   219   9.9%
  bin  2:  4.2408 -  3.3781 [2112/2135]  1901   211  10.0%
  bin  3:  3.3781 -  2.9547 [2092/2114]  1877   215  10.3%
  bin  4:  2.9547 -  2.6861 [2078/2097]  1882   196   9.4%
  bin  5:  2.6861 -  2.4945 [2065/2094]  1849   216  10.5%
  bin  6:  2.4945 -  2.3480 [2034/2075]  1836   198   9.7%
  bin  7:  2.3480 -  2.2308 [2048/2084]  1841   207  10.1%
  bin  8:  2.2308 -  2.1339 [2015/2053]  1814   201  10.0%
  bin  9:  2.1339 -  2.0520 [2051/2083]  1846   205  10.0%
  bin 10:  2.0520 -  1.9813 [ 885/2064]   794    91  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1301/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.31 -     2.03: 5
        2.03 -     2.75: 301
        2.75 -     3.47: 4535
        3.47 -     4.18: 9282
        4.18 -     4.90: 13886
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.315 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.841 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.951 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.988 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28004 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_1301/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1301/model_refine_001.geo

CPU time processing inputs: 8.97


============================ 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 = 72.00625 47.63395 85.5261 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: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4913   r_free= 0.4811   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.291904                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7305 0.99   1427  159 0.4037 0.3895      6.6098      6.5751|
|  2:  4.7305 -  3.7736 0.99   1388  150 0.4103 0.4371      6.8171      6.8916|
|  3:  3.7736 -  3.3021 0.99   1348  155 0.4652 0.4095      6.6864      6.6221|
|  4:  3.3021 -  3.0027 0.99   1347  149 0.4803 0.4660      6.5289      6.5168|
|  5:  3.0027 -  2.7889 0.99   1321  146 0.5181 0.5385      6.3765      6.3695|
|  6:  2.7889 -  2.6254 0.98   1330  152 0.5235 0.5160      6.2847      6.2407|
|  7:  2.6254 -  2.4945 0.99   1338  146 0.5258 0.4800      6.2527      6.1813|
|  8:  2.4945 -  2.3863 0.99   1310  145 0.5349 0.5477      6.1671      6.2051|
|  9:  2.3863 -  2.2948 0.98   1313  145 0.5436 0.5233      6.1349      6.1033|
| 10:  2.2948 -  2.2158 0.98   1312  152 0.5144 0.5183      6.0845       6.115|
| 11:  2.2158 -  2.1467 0.98   1313  137 0.5264 0.5276      6.0335      6.0352|
| 12:  2.1467 -  2.0855 0.99   1301  141 0.5423 0.5203      5.9572      5.9875|
| 13:  2.0855 -  2.0308 0.91   1212  147 0.5520 0.5254      5.8855      5.8371|
| 14:  2.0308 -  1.9813 0.28    370   35 0.5722 0.4993      5.8208      5.7644|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2215 -  4.7305  1427   159  0.69  34.77   0.79     0.72      73950.53|
|  2:  4.7305 -  3.7736  1388   150  0.69  36.46   0.87     0.74     109395.10|
|  3:  3.7736 -  3.3021  1348   155  0.56  46.92   0.80     0.67     122093.99|
|  4:  3.3021 -  3.0027  1347   149  0.45  55.87   0.78     0.54     112781.94|
|  5:  3.0027 -  2.7889  1321   146  0.35  63.87   0.71     0.42      93197.88|
|  6:  2.7889 -  2.6254  1330   152  0.33  65.47   0.72     0.40      78587.35|
|  7:  2.6254 -  2.4945  1338   146  0.34  64.40   0.72     0.37      66895.12|
|  8:  2.4945 -  2.3863  1310   145  0.32  66.37   0.69     0.38      63226.94|
|  9:  2.3863 -  2.2948  1313   145  0.28  68.94   0.72     0.34      57729.72|
| 10:  2.2948 -  2.2158  1312   152  0.27  70.01   0.73     0.31      56177.53|
| 11:  2.2158 -  2.1467  1313   137  0.24  71.77   0.75     0.30      50739.11|
| 12:  2.1467 -  2.0855  1301   141  0.23  72.64   0.73     0.30      47144.41|
| 13:  2.0855 -  2.0308  1212   147  0.26  70.59   0.70     0.33      39183.75|
| 14:  2.0308 -  1.9813   370    35  0.30  67.60   0.68     0.36      31068.51|
|alpha:            min =        0.30 max =            0.74 mean =         0.45|
|beta:             min =    31068.51 max =       122093.99 mean =     74321.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.41|
|phase err.(test): min =        0.00 max =           89.94 mean =        60.28|
|-----------------------------------------------------------------------------|

============================== 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 = 18.829669             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.546   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.676191              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.700   (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:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1499 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2589 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3874 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5007 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6484 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7674 |
|-----------------------------------------------------------------------------|
|-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 |       54.216 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.807 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.241)------------------------------------------|
|    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 = 12.241)------------------------------------------|
|    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: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4947   r_free= 0.4861   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.292591                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4832   r_free= 0.4705   ksol= 0.30   Bsol= 22.58   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.08,9.43,6.71,0.00,0.00,0.00); trace/3= 8.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.288698                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.603141             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.385   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.377276              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.272   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4832      final r-factor (work) = 0.4090          |
| start r-factor (free) = 0.4705      final r-factor (free) = 0.4320          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.2790 = 15.60 * 0.50 * 6.2888 + 1.00 * 54.2164                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.6242 = 15.60 * 0.50 * 6.2121 + 1.00 * 0.1600                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4090      final r-factor (work) = 0.3684          |
| start r-factor (free) = 0.4320      final r-factor (free) = 0.4203          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5702 = 1.38 * 1.00 * 6.2121 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4889 = 1.38 * 1.00 * 6.1511 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.241)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.57   12.77    None  None   None       |
|    all(noH): 2823   0      0.00    82.57   12.77    None  None   None       |
|    Sol.    : 438    0      0.00    82.57   23.85    None  None   None       |
|    Mac.    : 2385   0      0.00    63.98   10.73    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 -   8.257: 1216   |   5:    41.283 -  49.540:   52        |
|      1:     8.257 -  16.513:  819   |   6:    49.540 -  57.796:   23        |
|      2:    16.513 -  24.770:  435   |   7:    57.796 -  66.053:    6        |
|      3:    24.770 -  33.026:  171   |   8:    66.053 -  74.309:    2        |
|      4:    33.026 -  41.283:   98   |   9:    74.309 -  82.566:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3684 r_free = 0.4203             target_work(ml) = 6.136         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3679 r_free = 0.4212             target_work(ml) = 6.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3679   r_free= 0.4212   ksol= 0.30   Bsol= 22.58   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.08,9.43,6.71,0.00,0.00,0.00); trace/3= 8.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.135340                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3673   r_free= 0.4176   ksol= 0.32   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.08,6.30,4.79,0.00,0.00,0.00); trace/3= 5.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.137543                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.157204             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.635  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.782503              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.373  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3673      final r-factor (work) = 0.2829          |
| start r-factor (free) = 0.4176      final r-factor (free) = 0.3536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.3868 = 10.16 * 0.50 * 6.1487 + 1.00 * 0.1600                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.7668 = 10.16 * 0.50 * 6.0385 + 1.00 * 0.0996                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2829      final r-factor (work) = 0.2595          |
| start r-factor (free) = 0.3536      final r-factor (free) = 0.3253          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7436 = 0.78 * 1.00 * 6.0385 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6346 = 0.78 * 1.00 * 5.9056 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.241)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.48   13.31    None  None   None       |
|    all(noH): 2823   0      0.00    84.48   13.31    None  None   None       |
|    Sol.    : 438    0      0.00    84.48   32.78    None  None   None       |
|    Mac.    : 2385   0      0.00    79.03   9.73     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 -   8.449: 1368   |   5:    42.242 -  50.691:   61        |
|      1:     8.449 -  16.897:  740   |   6:    50.691 -  59.139:   44        |
|      2:    16.897 -  25.345:  309   |   7:    59.139 -  67.587:   28        |
|      3:    25.345 -  33.794:  158   |   8:    67.587 -  76.036:    9        |
|      4:    33.794 -  42.242:  100   |   9:    76.036 -  84.484:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2595 r_free = 0.3253             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2593 r_free = 0.3252             target_work(ml) = 5.868         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2593   r_free= 0.3252   ksol= 0.32   Bsol= 50.00   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.08,6.30,4.79,0.00,0.00,0.00); trace/3= 5.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.868337                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2575   r_free= 0.3224   ksol= 0.32   Bsol= 70.38   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,3.90,3.20,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.868413                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.586325              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.656   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.389991              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.202  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2575      final r-factor (work) = 0.1879          |
| start r-factor (free) = 0.3224      final r-factor (free) = 0.2407          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5524 = 6.59 * 0.50 * 5.9070 + 1.00 * 0.0996                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0389 = 6.59 * 0.50 * 5.7562 + 1.00 * 0.0829                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1879      final r-factor (work) = 0.1693          |
| start r-factor (free) = 0.2407      final r-factor (free) = 0.2207          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2584 = 0.39 * 1.00 * 5.7562 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1701 = 0.39 * 1.00 * 5.5341 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.241)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.19   13.60    None  None   None       |
|    all(noH): 2823   0      0.00    85.19   13.60    None  None   None       |
|    Sol.    : 438    0      0.00    81.74   37.71    None  None   None       |
|    Mac.    : 2385   0      0.00    85.19   9.17     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 -   8.519: 1503   |   5:    42.593 -  51.111:   90        |
|      1:     8.519 -  17.037:  682   |   6:    51.111 -  59.630:   68        |
|      2:    17.037 -  25.556:  202   |   7:    59.630 -  68.148:   31        |
|      3:    25.556 -  34.074:  118   |   8:    68.148 -  76.667:   14        |
|      4:    34.074 -  42.593:  108   |   9:    76.667 -  85.185:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1693 r_free = 0.2207             target_work(ml) = 5.491         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1689 r_free = 0.2205             target_work(ml) = 5.490         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1689   r_free= 0.2205   ksol= 0.32   Bsol= 70.38   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,3.90,3.20,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.489797                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1681   r_free= 0.2202   ksol= 0.35   Bsol= 70.38   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.30,2.61,2.34,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.491597                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.911158              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.460  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.379264              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.472  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1681      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.2202      final r-factor (free) = 0.1899          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1464 = 2.91 * 0.50 * 5.5398 + 1.00 * 0.0829                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9652 = 2.91 * 0.50 * 5.4242 + 1.00 * 0.0698                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1422      final r-factor (work) = 0.1367          |
| start r-factor (free) = 0.1899      final r-factor (free) = 0.1860          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0690 = 0.38 * 1.00 * 5.4242 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0339 = 0.38 * 1.00 * 5.3310 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.241)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.03   13.62    None  None   None       |
|    all(noH): 2823   0      0.00    87.03   13.62    None  None   None       |
|    Sol.    : 438    0      1.20    82.74   38.28    None  None   None       |
|    Mac.    : 2385   0      0.00    87.03   9.09     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 -   8.703: 1541   |   5:    43.513 -  52.215:   92        |
|      1:     8.703 -  17.405:  684   |   6:    52.215 -  60.918:   69        |
|      2:    17.405 -  26.108:  175   |   7:    60.918 -  69.620:   30        |
|      3:    26.108 -  34.810:  111   |   8:    69.620 -  78.323:   11        |
|      4:    34.810 -  43.513:  102   |   9:    78.323 -  87.025:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1367 r_free = 0.1860             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1366 r_free = 0.1859             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1366   r_free= 0.1859   ksol= 0.35   Bsol= 70.38   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.30,2.61,2.34,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.321200                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1858   ksol= 0.33   Bsol= 60.63   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,2.19,2.27,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.321125                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.354623              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.664  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.802682              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.333  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1367      final r-factor (work) = 0.1267          |
| start r-factor (free) = 0.1858      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3467 = 2.35 * 0.50 * 5.3316 + 1.00 * 0.0698                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2989 = 2.35 * 0.50 * 5.2904 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1267      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1748      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.8392 = 2.80 * 1.00 * 5.2904 + 1.00 * 0.0119                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.7181 = 2.80 * 1.00 * 5.2459 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.241)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.16  13.99    None  None   None       |
|    all(noH): 2823   0      0.00    100.16  13.99    None  None   None       |
|    Sol.    : 438    0      0.94    98.64   40.47    None  None   None       |
|    Mac.    : 2385   0      0.00    100.16  9.13     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.017: 1737   |   5:    50.082 -  60.099:   74        |
|      1:    10.017 -  20.033:  549   |   6:    60.099 -  70.115:   55        |
|      2:    20.033 -  30.049:  153   |   7:    70.115 -  80.131:   24        |
|      3:    30.049 -  40.066:  116   |   8:    80.131 -  90.148:   10        |
|      4:    40.066 -  50.082:   99   |   9:    90.148 - 100.164:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1751             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1235 r_free = 0.1750             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1750   ksol= 0.33   Bsol= 60.63   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,2.19,2.27,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.249575                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7305 0.99   1427  159 0.1005 0.1301        5.39      5.5407|
|  2:  4.7305 -  3.7736 0.99   1388  150 0.0894 0.1140      5.4637       5.677|
|  3:  3.7736 -  3.3021 0.99   1348  155 0.1147 0.1774      5.5457      5.9434|
|  4:  3.3021 -  3.0027 0.99   1347  149 0.1388 0.1699      5.5574      5.7075|
|  5:  3.0027 -  2.7889 0.99   1321  146 0.1522 0.2023      5.4594      5.6433|
|  6:  2.7889 -  2.6254 0.98   1330  152 0.1425 0.2138      5.3447      5.5822|
|  7:  2.6254 -  2.4945 0.99   1338  146 0.1388 0.1874      5.2735      5.4657|
|  8:  2.4945 -  2.3863 0.99   1310  145 0.1278 0.1879      5.1475      5.3953|
|  9:  2.3863 -  2.2948 0.98   1313  145 0.1310 0.2189      5.1267      5.4281|
| 10:  2.2948 -  2.2158 0.98   1312  152 0.1261 0.1811      5.0807      5.2962|
| 11:  2.2158 -  2.1467 0.98   1313  137 0.1287 0.2035      5.0541      5.4155|
| 12:  2.1467 -  2.0855 0.99   1301  141 0.1282 0.1957      4.9923      5.2001|
| 13:  2.0855 -  2.0308 0.91   1212  147 0.1286 0.1917      4.8853      5.1303|
| 14:  2.0308 -  1.9813 0.28    370   35 0.1120 0.1927      4.7156      5.0264|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2215 -  4.7305  1427   159  0.94   9.05   0.96     0.94       7308.77|
|  2:  4.7305 -  3.7736  1388   150  0.95   8.49   1.00     0.98       9383.26|
|  3:  3.7736 -  3.3021  1348   155  0.92  12.61   1.02     1.02      12080.35|
|  4:  3.3021 -  3.0027  1347   149  0.90  16.20   1.00     0.97      12856.36|
|  5:  3.0027 -  2.7889  1321   146  0.87  19.16   0.99     0.97      11342.31|
|  6:  2.7889 -  2.6254  1330   152  0.87  19.07   0.98     0.95       9477.33|
|  7:  2.6254 -  2.4945  1338   146  0.89  17.71   0.98     0.95       7891.78|
|  8:  2.4945 -  2.3863  1310   145  0.89  17.64   0.97     0.92       6414.60|
|  9:  2.3863 -  2.2948  1313   145  0.88  18.34   0.99     0.94       6177.75|
| 10:  2.2948 -  2.2158  1312   152  0.89  17.82   0.98     0.94       5787.56|
| 11:  2.2158 -  2.1467  1313   137  0.88  18.85   0.97     0.92       5571.91|
| 12:  2.1467 -  2.0855  1301   141  0.88  18.43   0.98     0.97       5170.74|
| 13:  2.0855 -  2.0308  1212   147  0.88  18.58   0.97     0.95       4162.08|
| 14:  2.0308 -  1.9813   370    35  0.88  17.95   0.97     0.93       3091.12|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     3091.12 max =        12856.36 mean =      7915.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.24|
|phase err.(test): min =        0.00 max =           89.94 mean =        15.58|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1750   ksol= 0.32   Bsol= 62.71   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,-0.01,0.15,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.249537                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1750   ksol= 0.32   Bsol= 62.71   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,-0.01,0.15,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.249537                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7305 0.99   1427  159 0.1003 0.1304      5.3885      5.5421|
|  2:  4.7305 -  3.7736 0.99   1388  150 0.0895 0.1143      5.4653       5.679|
|  3:  3.7736 -  3.3021 0.99   1348  155 0.1147 0.1775      5.5464      5.9437|
|  4:  3.3021 -  3.0027 0.99   1347  149 0.1387 0.1698      5.5574      5.7073|
|  5:  3.0027 -  2.7889 0.99   1321  146 0.1521 0.2024      5.4591      5.6431|
|  6:  2.7889 -  2.6254 0.98   1330  152 0.1424 0.2137      5.3444      5.5816|
|  7:  2.6254 -  2.4945 0.99   1338  146 0.1388 0.1875      5.2734      5.4659|
|  8:  2.4945 -  2.3863 0.99   1310  145 0.1278 0.1879      5.1475      5.3954|
|  9:  2.3863 -  2.2948 0.98   1313  145 0.1310 0.2189      5.1267      5.4278|
| 10:  2.2948 -  2.2158 0.98   1312  152 0.1261 0.1812      5.0808      5.2962|
| 11:  2.2158 -  2.1467 0.98   1313  137 0.1286 0.2033      5.0539       5.415|
| 12:  2.1467 -  2.0855 0.99   1301  141 0.1282 0.1958       4.992      5.2003|
| 13:  2.0855 -  2.0308 0.91   1212  147 0.1287 0.1917      4.8852      5.1299|
| 14:  2.0308 -  1.9813 0.28    370   35 0.1120 0.1925      4.7152      5.0257|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2215 -  4.7305  1427   159  0.94   9.07   0.96     0.94       7330.17|
|  2:  4.7305 -  3.7736  1388   150  0.95   8.51   1.00     0.98       9420.49|
|  3:  3.7736 -  3.3021  1348   155  0.92  12.64   1.02     1.02      12119.92|
|  4:  3.3021 -  3.0027  1347   149  0.90  16.20   1.00     0.97      12857.61|
|  5:  3.0027 -  2.7889  1321   146  0.87  19.15   0.99     0.97      11335.19|
|  6:  2.7889 -  2.6254  1330   152  0.87  19.07   0.98     0.95       9471.60|
|  7:  2.6254 -  2.4945  1338   146  0.89  17.70   0.99     0.96       7886.25|
|  8:  2.4945 -  2.3863  1310   145  0.89  17.64   0.98     0.93       6413.18|
|  9:  2.3863 -  2.2948  1313   145  0.88  18.34   0.99     0.95       6175.62|
| 10:  2.2948 -  2.2158  1312   152  0.89  17.82   0.99     0.94       5787.25|
| 11:  2.2158 -  2.1467  1313   137  0.88  18.85   0.98     0.92       5569.63|
| 12:  2.1467 -  2.0855  1301   141  0.88  18.43   0.99     0.98       5168.58|
| 13:  2.0855 -  2.0308  1212   147  0.88  18.58   0.98     0.96       4158.67|
| 14:  2.0308 -  1.9813   370    35  0.88  17.95   0.98     0.94       3087.53|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     3087.53 max =        12857.61 mean =      7920.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.25|
|phase err.(test): min =        0.00 max =           89.92 mean =        15.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.241)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.28    102.44  16.27    None  None   None       |
|    all(noH): 2823   0      2.28    102.44  16.27    None  None   None       |
|    Sol.    : 438    0      3.22    100.91  42.75    None  None   None       |
|    Mac.    : 2385   0      2.28    102.44  11.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.277 -  12.294: 1737   |   5:    52.359 -  62.376:   74        |
|      1:    12.294 -  22.310:  549   |   6:    62.376 -  72.392:   55        |
|      2:    22.310 -  32.327:  153   |   7:    72.392 -  82.409:   24        |
|      3:    32.327 -  42.343:  116   |   8:    82.409 -  92.425:   10        |
|      4:    42.343 -  52.359:   99   |   9:    92.425 - 102.442:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 357         
Filter by distance & map next to the model:
   mapped sites are within: 0.425 - 5.964
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 350 from: 357
   mapped sites are within: 0.709 - 5.964

peak=    9.141 closest distance to " CG2 VAL A 230 " =    1.387
peak=    8.910 closest distance to " CG2 VAL A 296 " =    1.353
peak=    7.021 closest distance to " CG  ARG A 138 " =    1.225
peak=    6.093 closest distance to " CG  LEU A   5 " =    1.177
peak=    5.407 closest distance to " O   HOH Z 111 " =    1.896
peak=    5.374 closest distance to " CB  GLN A 223 " =    1.413
peak=    5.314 closest distance to " CD1AILE A 234 " =    1.100
peak=    5.160 closest distance to " O   HOH Z  37 " =    1.207
peak=    5.134 closest distance to " O   HOH Z 102 " =    1.498
peak=    5.114 closest distance to " CB  VAL A 230 " =    1.291
peak=    5.053 closest distance to " NH1 ARG A 138 " =    1.026
peak=    5.003 closest distance to " CG  PRO A  54 " =    1.260
peak=    4.994 closest distance to " CG  LEU A 228 " =    1.215
peak=    4.980 closest distance to " CB  SER A  63 " =    1.355
peak=    4.807 closest distance to " CB  PRO A  54 " =    0.889
peak=    4.752 closest distance to " CG  PRO A 213 " =    1.328
peak=    4.712 closest distance to " CG2 THR A 221 " =    1.026
peak=    4.698 closest distance to " O   HOH Z 186 " =    1.399
peak=    4.690 closest distance to " CG  PRO A 198 " =    1.269
peak=    4.678 closest distance to " CG  PRO A 280 " =    1.037
peak=    4.559 closest distance to " CD2 LEU A   5 " =    1.063
peak=    4.556 closest distance to " O   HOH Z 247 " =    1.676
peak=    4.467 closest distance to " O   HOH Z 112 " =    1.478
peak=    4.459 closest distance to " CA  TYR A  30 " =    0.985
peak=    4.440 closest distance to " O   HOH Z 232 " =    2.144
peak=    4.411 closest distance to " O   HOH Z  68 " =    1.882
peak=    4.408 closest distance to " O   HOH Z 126 " =    1.668
peak=    4.391 closest distance to " O   HOH Z  63 " =    1.545
peak=    4.344 closest distance to " O   HOH Z 433 " =    1.663
peak=    4.308 closest distance to " O   HOH Z  80 " =    2.029
peak=    4.270 closest distance to " CD  ARG A 159 " =    0.839
peak=    4.267 closest distance to " CB  ASN A 148 " =    1.282
peak=    4.261 closest distance to " O   HOH Z 411 " =    3.354
peak=    4.254 closest distance to " O  BHOH Z 338 " =    1.107
peak=    4.252 closest distance to " O   PRO A 198 " =    1.486
peak=    4.244 closest distance to " O   HOH Z  47 " =    1.844
peak=    4.242 closest distance to " O   HOH Z  15 " =    2.175
peak=    4.231 closest distance to " CB  GLU A 128 " =    1.232
peak=    4.211 closest distance to " O   HOH Z 425 " =    1.568
peak=    4.210 closest distance to " CB  GLN A 183 " =    1.283
peak=    4.188 closest distance to " O   HOH Z 163 " =    1.769
peak=    4.165 closest distance to " O   HOH Z   4 " =    1.924
peak=    4.162 closest distance to " CA  ALA A 160 " =    0.976
peak=    4.159 closest distance to " CZ  PHE A 192 " =    1.053
peak=    4.131 closest distance to " O   HOH Z 133 " =    2.238
peak=    4.123 closest distance to " OD1 ASN A 217 " =    1.577
peak=    4.117 closest distance to " O   HOH Z 394 " =    1.670
peak=    4.099 closest distance to " O   HOH Z 369 " =    2.016
peak=    4.092 closest distance to " CD  ARG A  66 " =    2.641
peak=    4.092 closest distance to " O   HOH Z 134 " =    1.646
peak=    4.087 closest distance to " O   HOH Z 120 " =    1.039
peak=    4.076 closest distance to " CG1 ILE A  33 " =    1.336
peak=    4.076 closest distance to " O   HOH Z 403 " =    1.881
peak=    4.061 closest distance to " CA  ALA A  21 " =    1.273
peak=    4.055 closest distance to " CD  ARG A 138 " =    1.202
peak=    4.043 closest distance to " NH1 ARG A  56 " =    1.075
peak=    4.032 closest distance to " O   HOH Z  78 " =    2.256
peak=    4.029 closest distance to " CA  MET A  40 " =    1.138
peak=    4.021 closest distance to " O   HOH Z 316 " =    2.984
peak=    4.012 closest distance to " CD1 LEU A 300 " =    1.167
peak=    3.949 closest distance to " CD ALYS A 290 " =    1.016
peak=    3.945 closest distance to " CG1 VAL A 153 " =    1.110
peak=    3.944 closest distance to " O   HOH Z 183 " =    1.567
peak=    3.939 closest distance to " O   HOH Z 298 " =    1.713
peak=    3.937 closest distance to " O   HOH Z 234 " =    3.736
peak=    3.937 closest distance to " NE2 GLN A  11 " =    1.034
peak=    3.933 closest distance to " O   HOH Z  91 " =    2.452
peak=    3.927 closest distance to " CG AARG A 275 " =    1.175
peak=    3.924 closest distance to " CD1 LEU A   5 " =    1.371
peak=    3.921 closest distance to " CB  TRP A 266 " =    1.012
peak=    3.919 closest distance to " O   HOH Z 368 " =    2.180
peak=    3.912 closest distance to " CB  ASP A 124 " =    0.772
peak=    3.899 closest distance to " O   HOH Z 271 " =    2.529
peak=    3.894 closest distance to " CB  ARG A 275 " =    0.849
peak=    3.873 closest distance to " O   HOH Z 284 " =    3.030
peak=    3.865 closest distance to " O   HOH Z 389 " =    1.953
peak=    3.854 closest distance to " O   HOH Z 174 " =    1.375
peak=    3.835 closest distance to " O   HOH Z 184 " =    1.665
peak=    3.827 closest distance to " CD  ARG A 269 " =    0.865
peak=    3.808 closest distance to " OE1 GLN A  11 " =    1.832
peak=    3.806 closest distance to " CB  TRP A 179 " =    1.414
peak=    3.803 closest distance to " CB  LEU A 228 " =    1.298
peak=    3.801 closest distance to " O   HOH Z 236 " =    1.806
peak=    3.793 closest distance to " O   HOH Z  54 " =    2.149
peak=    3.788 closest distance to " CA  ALA A 295 " =    1.083
peak=    3.786 closest distance to " CD2 LEU A 255 " =    1.577
peak=    3.782 closest distance to " CB  LEU A 143 " =    1.159
peak=    3.779 closest distance to " O   HOH Z 124 " =    1.138
peak=    3.770 closest distance to " O   HOH Z 303 " =    2.231
peak=    3.769 closest distance to " CA  ASP A 191 " =    0.785
peak=    3.768 closest distance to " CD2 LEU A 228 " =    1.199
peak=    3.766 closest distance to " O   HOH Z  97 " =    1.941
peak=    3.756 closest distance to " CB  SER A   3 " =    1.476
peak=    3.755 closest distance to " CG  PRO A 243 " =    1.144
peak=    3.752 closest distance to " O   HOH Z 118 " =    1.675
peak=    3.743 closest distance to " NH1AARG A 145 " =    1.113
peak=    3.737 closest distance to " CB  ALA A   9 " =    1.604
peak=    3.735 closest distance to " O   HOH Z  47 " =    1.474
peak=    3.733 closest distance to " CB  GLU A 152 " =    1.191
peak=    3.726 closest distance to " CB  SER A 216 " =    0.862
peak=    3.726 closest distance to " O   HOH Z 386 " =    2.149
peak=    3.714 closest distance to " O   HOH Z 437 " =    2.340
peak=    3.711 closest distance to " CA  ASP A 124 " =    0.709
peak=    3.702 closest distance to " CE1 PHE A 208 " =    1.101
peak=    3.702 closest distance to " ND1 HIS A  81 " =    1.683
peak=    3.696 closest distance to " O   ASP A 124 " =    1.151
peak=    3.691 closest distance to " O   HOH Z 427 " =    3.323
peak=    3.690 closest distance to " O   HOH Z  48 " =    1.713
peak=    3.676 closest distance to " CA  GLY A 267 " =    0.939
peak=    3.674 closest distance to " O   HOH Z  19 " =    2.450
peak=    3.668 closest distance to " CA  GLU A 152 " =    0.860
peak=    3.657 closest distance to " O   HOH Z 114 " =    1.506
peak=    3.656 closest distance to " O   HOH Z 383 " =    2.086
peak=    3.652 closest distance to " O   HOH Z 404 " =    1.443
peak=    3.652 closest distance to " OD2 ASP A 286 " =    2.965
peak=    3.651 closest distance to " OD1 ASN A  69 " =    2.578
peak=    3.650 closest distance to " O   HOH Z  40 " =    1.646
peak=    3.646 closest distance to " NZ  LYS A 117 " =    3.186
peak=    3.644 closest distance to " O   HOH Z 245 " =    1.288
peak=    3.643 closest distance to " CB  ALA A 100 " =    1.543
peak=    3.643 closest distance to " O   HOH Z  61 " =    1.477
peak=    3.640 closest distance to " O   HOH Z 272 " =    1.908
peak=    3.634 closest distance to " CB  TYR A 169 " =    0.916
peak=    3.633 closest distance to " CB  VAL A 265 " =    1.273
peak=    3.631 closest distance to " O   HOH Z 295 " =    1.564
peak=    3.618 closest distance to " N   HIS A 108 " =    1.926
peak=    3.608 closest distance to " O   HOH Z  99 " =    2.475
peak=    3.606 closest distance to " O   HOH Z  88 " =    3.158
peak=    3.600 closest distance to " O   HOH Z  20 " =    2.327
peak=    3.598 closest distance to " O   HOH Z 131 " =    2.395
peak=    3.593 closest distance to " NH2BARG A 102 " =    1.114
peak=    3.590 closest distance to " CB  VAL A 202 " =    1.521
peak=    3.584 closest distance to " O   HOH Z  54 " =    1.508
peak=    3.578 closest distance to " O   HOH Z 128 " =    2.117
peak=    3.575 closest distance to " O   HOH Z 281 " =    4.162
peak=    3.571 closest distance to " O   HOH Z 132 " =    2.623
peak=    3.551 closest distance to " O   HOH Z 387 " =    2.895
peak=    3.550 closest distance to " CD1 TRP A 266 " =    1.114
peak=    3.548 closest distance to " CZ  PHE A 218 " =    1.110
peak=    3.544 closest distance to " CG2BVAL A  41 " =    1.244
peak=    3.537 closest distance to " CB  SER A 141 " =    1.000
peak=    3.534 closest distance to " CA  LYS A 117 " =    1.214
peak=    3.530 closest distance to " O   HOH Z  21 " =    1.761
peak=    3.520 closest distance to " O   HOH Z 180 " =    2.187
peak=    3.519 closest distance to " C   SER A  32 " =    1.093
peak=    3.514 closest distance to " NH2 ARG A 156 " =    1.115
peak=    3.512 closest distance to " CD1 LEU A 101 " =    1.142
peak=    3.512 closest distance to " O   HOH Z 410 " =    1.294
peak=    3.506 closest distance to " O   HOH Z 244 " =    1.688
peak=    3.505 closest distance to " CB  SER A 212 " =    1.078
peak=    3.503 closest distance to " CB  ASP A 140 " =    0.809
peak=    3.502 closest distance to " CB  ASN A 187 " =    1.102
peak=    3.502 closest distance to " CG2 THR A  42 " =    0.950
peak=    3.499 closest distance to " O   HOH Z 371 " =    3.379
peak=    3.498 closest distance to " O   HOH Z 227 " =    1.789
peak=    3.484 closest distance to " O   HOH Z 426 " =    1.446
peak=    3.481 closest distance to " CB  ARG A 259 " =    1.874
peak=    3.479 closest distance to " CA  ALA A  51 " =    1.048
peak=    3.470 closest distance to " CA  ARG A  36 " =    1.138
peak=    3.467 closest distance to " CD  ARG A 195 " =    0.978
peak=    3.466 closest distance to " O   HOH Z 392 " =    1.383
peak=    3.465 closest distance to " O   HOH Z 221 " =    1.220
peak=    3.463 closest distance to " O   HOH Z 214 " =    2.243
peak=    3.457 closest distance to " O   HOH Z 189 " =    2.915
peak=    3.455 closest distance to " CD  LYS A 119 " =    1.418
peak=    3.454 closest distance to " CG1 ILE A  49 " =    1.744
peak=    3.453 closest distance to " CG  MET A 188 " =    0.905
peak=    3.453 closest distance to " CD  ARG A  14 " =    1.243
peak=    3.452 closest distance to " OE1 GLU A   2 " =    2.102
peak=    3.451 closest distance to " O   HOH Z  22 " =    2.549
peak=    3.450 closest distance to " O   HOH Z 402 " =    1.530
peak=    3.449 closest distance to " CA  ARG A 102 " =    1.389
peak=    3.448 closest distance to " CB  GLU A 277 " =    3.835
peak=    3.445 closest distance to " CZ3 TRP A  92 " =    1.329
peak=    3.443 closest distance to " CG1BVAL A  72 " =    1.730
peak=    3.441 closest distance to " O   HOH Z 345 " =    3.645
peak=    3.439 closest distance to " O   HOH Z 344 " =    3.081
peak=    3.438 closest distance to " O   HOH Z 261 " =    1.859
peak=    3.437 closest distance to " O   HOH Z 420 " =    5.964
peak=    3.437 closest distance to " CA  GLY A 196 " =    0.978
peak=    3.437 closest distance to " CG BARG A 275 " =    1.428
peak=    3.435 closest distance to " O   HOH Z 355 " =    1.823
peak=    3.434 closest distance to " C   GLY A  80 " =    1.209
peak=    3.428 closest distance to " O   HOH Z 377 " =    1.391
peak=    3.427 closest distance to " O   HOH Z 271 " =    1.960
peak=    3.425 closest distance to " O   HOH Z 193 " =    1.648
peak=    3.423 closest distance to " O   HOH Z 196 " =    1.157
peak=    3.417 closest distance to " CB  LYS A 193 " =    1.124
peak=    3.413 closest distance to " CB  MET A  40 " =    0.753
peak=    3.411 closest distance to " NZ  LYS A  76 " =    1.493
peak=    3.409 closest distance to " CA  ASP A 140 " =    1.336
peak=    3.408 closest distance to " CA  ARG A 195 " =    1.251
peak=    3.404 closest distance to " O   HOH Z  57 " =    1.508
peak=    3.404 closest distance to " CB  ASN A 142 " =    1.044
peak=    3.404 closest distance to " CB  ILE A 199 " =    0.942
peak=    3.402 closest distance to " O   HOH Z 104 " =    3.077
peak=    3.397 closest distance to " O   HOH Z  11 " =    1.282
peak=    3.391 closest distance to " CA  ILE A  33 " =    1.630
peak=    3.390 closest distance to " CE1 TYR A 186 " =    1.312
peak=    3.388 closest distance to " O   HOH Z  32 " =    1.843
peak=    3.383 closest distance to " O   HOH Z 116 " =    1.819
peak=    3.380 closest distance to " CZ3 TRP A  85 " =    0.931
peak=    3.380 closest distance to " CG  GLN A  88 " =    1.115
peak=    3.376 closest distance to " CB  ALA A 291 " =    1.430
peak=    3.375 closest distance to " CB  LEU A 255 " =    0.910
peak=    3.375 closest distance to " CG  GLN A  58 " =    2.435
peak=    3.374 closest distance to " OD2 ASP A 286 " =    2.376
peak=    3.373 closest distance to " O   HOH Z 193 " =    1.713
peak=    3.373 closest distance to " CE2 TYR A 186 " =    0.893
peak=    3.365 closest distance to " NH2BARG A 145 " =    2.049
peak=    3.364 closest distance to " CB  MET A  47 " =    1.029
peak=    3.364 closest distance to " O   HOH Z 374 " =    2.733
peak=    3.361 closest distance to " O   HOH Z 185 " =    1.850
peak=    3.358 closest distance to " OG BSER A 164 " =    1.999
peak=    3.355 closest distance to " CB  ARG A 190 " =    1.721
peak=    3.354 closest distance to " OE1 GLN A  58 " =    1.256
peak=    3.353 closest distance to " O   HOH Z  43 " =    2.284
peak=    3.352 closest distance to " CD  ARG A  66 " =    2.939
peak=    3.347 closest distance to " O   HOH Z  13 " =    1.567
peak=    3.346 closest distance to " O   HOH Z 279 " =    2.375
peak=    3.343 closest distance to " CB  THR A 235 " =    0.931
peak=    3.343 closest distance to " O   GLN A 278 " =    1.304
peak=    3.342 closest distance to " OG  SER A  97 " =    3.506
peak=    3.342 closest distance to " O   HOH Z 422 " =    2.674
peak=    3.337 closest distance to " OG  SER A 206 " =    1.177
peak=    3.330 closest distance to " CB  ALA A 242 " =    1.047
peak=    3.328 closest distance to " N   TYR A  15 " =    0.872
peak=    3.328 closest distance to " O   HOH Z 132 " =    2.454
peak=    3.327 closest distance to " CB  TYR A 247 " =    0.981
peak=    3.324 closest distance to " O   HOH Z 423 " =    3.001
peak=    3.320 closest distance to " O   HOH Z 346 " =    1.500
peak=    3.315 closest distance to " O   HOH Z 109 " =    2.410
peak=    3.314 closest distance to " CE  LYS A  76 " =    0.866
peak=    3.314 closest distance to " CB  ALA A 248 " =    1.262
peak=    3.312 closest distance to " CG  LEU A 167 " =    1.099
peak=    3.310 closest distance to " CB  PHE A 204 " =    1.042
peak=    3.309 closest distance to " CE3 TRP A 274 " =    3.915
peak=    3.309 closest distance to " CG  MET A 185 " =    1.343
peak=    3.309 closest distance to " NH1 ARG A  14 " =    1.194
peak=    3.304 closest distance to " O   ALA A 158 " =    1.357
peak=    3.301 closest distance to " CB  ARG A  79 " =    1.478
peak=    3.301 closest distance to " CB  ALA A 137 " =    1.108
peak=    3.300 closest distance to " CB  GLN A  89 " =    1.124
peak=    3.297 closest distance to " O   HOH Z  58 " =    1.607
peak=    3.295 closest distance to " CB  ALA A  34 " =    0.879
peak=    3.294 closest distance to " CE2 PHE A 204 " =    0.809
peak=    3.294 closest distance to " O   HOH Z 352 " =    1.802
peak=    3.293 closest distance to " CA  LEU A 282 " =    1.054
peak=    3.286 closest distance to " CA  ASN A 127 " =    1.029
peak=    3.285 closest distance to " O   HOH Z 192 " =    1.420
peak=    3.285 closest distance to " CB  PHE A  16 " =    0.939
peak=    3.283 closest distance to " O   ALA A 165 " =    1.345
peak=    3.283 closest distance to " OD1 ASN A 252 " =    1.244
peak=    3.282 closest distance to " O   HOH Z 298 " =    2.373
peak=    3.276 closest distance to " O   HOH Z 374 " =    3.142
peak=    3.275 closest distance to " N   ALA A 256 " =    1.017
peak=    3.273 closest distance to " CB  ALA A 256 " =    1.326
peak=    3.272 closest distance to " CB  PRO A 198 " =    0.989
peak=    3.267 closest distance to " CA  MET A 105 " =    1.161
peak=    3.266 closest distance to " CG1BVAL A 121 " =    1.123
peak=    3.263 closest distance to " CA  TYR A 116 " =    1.602
peak=    3.260 closest distance to " O   HOH Z  44 " =    2.269
peak=    3.258 closest distance to " CD1 LEU A  96 " =    0.763
peak=    3.248 closest distance to " O   GLY A  57 " =    2.504
peak=    3.248 closest distance to " O   HOH Z 290 " =    1.198
peak=    3.246 closest distance to " CG1 ILE A 151 " =    1.211
peak=    3.243 closest distance to " O   HOH Z 240 " =    1.974
peak=    3.242 closest distance to " O   HOH Z 197 " =    2.080
peak=    3.241 closest distance to " CB  SER A 273 " =    0.842
peak=    3.241 closest distance to " CE3 TRP A  85 " =    1.217
peak=    3.239 closest distance to " CB  LEU A 237 " =    0.850
peak=    3.239 closest distance to " O   HOH Z  50 " =    2.086
peak=    3.238 closest distance to " OH  TYR A 186 " =    1.039
peak=    3.237 closest distance to " CD1 LEU A 222 " =    0.794
peak=    3.230 closest distance to " CG2 ILE A 106 " =    0.855
peak=    3.228 closest distance to " N   SER A 164 " =    1.037
peak=    3.228 closest distance to " CD  PRO A 280 " =    0.933
peak=    3.224 closest distance to " O   HOH Z 171 " =    3.981
peak=    3.224 closest distance to " O   HOH Z 301 " =    1.962
peak=    3.221 closest distance to " O   HOH Z 313 " =    1.911
peak=    3.220 closest distance to " CB  GLU A 277 " =    1.020
peak=    3.217 closest distance to " O   HOH Z 135 " =    2.173
peak=    3.217 closest distance to " O   HOH Z 395 " =    1.378
peak=    3.216 closest distance to " NZ  LYS A 181 " =    1.292
peak=    3.214 closest distance to " CD  LYS A 166 " =    1.453
peak=    3.211 closest distance to " ND1 HIS A  86 " =    1.633
peak=    3.207 closest distance to " O   HOH Z 128 " =    1.716
peak=    3.207 closest distance to " CG2 THR A 220 " =    0.934
peak=    3.206 closest distance to " O   HOH Z 407 " =    2.627
peak=    3.206 closest distance to " CD  GLU A 152 " =    0.830
peak=    3.206 closest distance to " O   HOH Z 263 " =    1.498
peak=    3.206 closest distance to " O   HOH Z 125 " =    3.715
peak=    3.205 closest distance to " CB  ALA A  71 " =    1.245
peak=    3.205 closest distance to " O   HOH Z  78 " =    1.162
peak=    3.195 closest distance to " O   TRP A 274 " =    1.809
peak=    3.195 closest distance to " NE2 HIS A 115 " =    0.939
peak=    3.192 closest distance to " CG2 VAL A 257 " =    0.879
peak=    3.188 closest distance to " CG BARG A 102 " =    1.893
peak=    3.187 closest distance to " CD  ARG A 219 " =    1.045
peak=    3.185 closest distance to " CG2 VAL A 197 " =    1.185
peak=    3.185 closest distance to " O   HOH Z 327 " =    2.251
peak=    3.183 closest distance to " OG  SER A  22 " =    2.942
peak=    3.183 closest distance to " CA  ILE A 106 " =    0.857
peak=    3.177 closest distance to " O   HOH Z 368 " =    3.363
peak=    3.177 closest distance to " CA  LEU A 101 " =    1.621
peak=    3.177 closest distance to " O   HOH Z 417 " =    3.050
peak=    3.176 closest distance to " CB  ARG A 139 " =    0.842
peak=    3.175 closest distance to " O   HOH Z 175 " =    3.790
peak=    3.175 closest distance to " O   HOH Z 155 " =    1.519
peak=    3.174 closest distance to " O   HOH Z  85 " =    1.238
peak=    3.173 closest distance to " CA  ALA A 291 " =    0.937
peak=    3.170 closest distance to " CG2 ILE A 234 " =    0.872
peak=    3.166 closest distance to " CA  LYS A 290 " =    1.310
peak=    3.165 closest distance to " CG2 THR A  29 " =    1.498
peak=    3.165 closest distance to " CB  SER A  28 " =    1.052
peak=    3.164 closest distance to " CB  ALA A 154 " =    1.360
peak=    3.164 closest distance to " O   HOH Z 214 " =    2.414
peak=    3.160 closest distance to " O   HOH Z 282 " =    2.189
peak=    3.159 closest distance to " O   HOH Z 144 " =    1.414
peak=    3.158 closest distance to " CG  ASP A 231 " =    0.984
peak=    3.156 closest distance to " O   HOH Z 211 " =    2.709
peak=    3.155 closest distance to " O   HOH Z 327 " =    1.737
peak=    3.155 closest distance to " O   HOH Z 276 " =    1.267
peak=    3.154 closest distance to " O   HOH Z 216 " =    2.729
peak=    3.153 closest distance to " N   VAL A 126 " =    1.468
peak=    3.151 closest distance to " CB  ILE A 120 " =    1.404
peak=    3.146 closest distance to " O   HOH Z 359 " =    1.386
peak=    3.144 closest distance to " CB  PRO A 243 " =    1.213
peak=    3.143 closest distance to " O   HOH Z  66 " =    2.194
peak=    3.143 closest distance to " OE1 GLN A  58 " =    5.960
peak=    3.142 closest distance to " CB  TYR A  30 " =    1.422
peak=    3.136 closest distance to " CB  ASN A  39 " =    0.872
peak=    3.134 closest distance to " N   TYR A 247 " =    1.304
peak=    3.132 closest distance to " CD2 TYR A  15 " =    1.546
peak=    3.129 closest distance to " O   HOH Z 215 " =    1.500
peak=    3.124 closest distance to " O   HOH Z 147 " =    1.698
peak=    3.120 closest distance to " CG2 VAL A  78 " =    0.999
peak=    3.107 closest distance to " CA  GLU A  46 " =    0.750
peak=    3.098 closest distance to " OD2 ASP A 298 " =    4.078
peak=    3.096 closest distance to " O   HOH Z 128 " =    2.295
peak=    3.092 closest distance to " CA  ALA A 100 " =    1.073
peak=    3.090 closest distance to " CG2AVAL A 121 " =    2.349
peak=    3.088 closest distance to " NE1 TRP A  85 " =    2.087
peak=    3.082 closest distance to " CA  ARG A 156 " =    0.981
peak=    3.067 closest distance to " CA  TRP A 274 " =    0.918
peak=    3.055 closest distance to " O   HOH Z 329 " =    3.790
peak=    3.054 closest distance to " CD1 ILE A 106 " =    0.927
peak=    3.053 closest distance to " O   HOH Z  49 " =    0.969
peak=    3.052 closest distance to " O   HOH Z 391 " =    3.026
peak=    3.026 closest distance to " CB  VAL A 296 " =    0.863

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.787 - 5.411
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 218
   mapped sites are within: 0.787 - 5.411

peak=   -4.575 closest distance to " CD  ARG A 138 " =    1.287
peak=   -4.522 closest distance to " O   HOH Z 231 " =    1.617
peak=   -4.504 closest distance to " CG2 VAL A 230 " =    0.974
peak=   -4.396 closest distance to " NH2 ARG A  66 " =    1.617
peak=   -4.340 closest distance to " O   HOH Z 103 " =    1.837
peak=   -4.336 closest distance to " O   HOH Z  19 " =    2.090
peak=   -4.191 closest distance to " O   HOH Z  13 " =    1.583
peak=   -4.185 closest distance to " CD2 LEU A 167 " =    1.783
peak=   -4.183 closest distance to " OG ASER A 134 " =    1.148
peak=   -4.143 closest distance to " O   ILE A 109 " =    2.675
peak=   -4.121 closest distance to " O   HOH Z 166 " =    1.801
peak=   -4.116 closest distance to " O   HOH Z 407 " =    3.574
peak=   -3.996 closest distance to " CD1 PHE A  59 " =    1.858
peak=   -3.981 closest distance to " N   ALA A 226 " =    2.152
peak=   -3.971 closest distance to " CD2 LEU A 143 " =    2.542
peak=   -3.961 closest distance to " O   HOH Z  43 " =    1.407
peak=   -3.949 closest distance to " O   HOH Z  52 " =    1.810
peak=   -3.947 closest distance to " CG  ASP A 231 " =    0.846
peak=   -3.943 closest distance to " O   HOH Z 184 " =    1.083
peak=   -3.921 closest distance to " CD2 LEU A 237 " =    2.597
peak=   -3.918 closest distance to " CD  ARG A 156 " =    2.046
peak=   -3.894 closest distance to " O   HOH Z 102 " =    1.598
peak=   -3.882 closest distance to " CD  LYS A 289 " =    2.457
peak=   -3.854 closest distance to " CE2 TYR A  30 " =    2.735
peak=   -3.847 closest distance to " O   HOH Z 266 " =    4.722
peak=   -3.846 closest distance to " O   HOH Z  38 " =    0.956
peak=   -3.837 closest distance to " CG  ARG A 138 " =    0.907
peak=   -3.818 closest distance to " OG  SER A  87 " =    1.703
peak=   -3.815 closest distance to " CG2 VAL A 112 " =    2.587
peak=   -3.815 closest distance to " O   HOH Z 177 " =    1.406
peak=   -3.785 closest distance to " O   HOH Z 210 " =    0.787
peak=   -3.779 closest distance to " O   HOH Z 275 " =    1.545
peak=   -3.773 closest distance to " OG1 THR A  82 " =    1.984
peak=   -3.745 closest distance to " CD1 LEU A   5 " =    2.637
peak=   -3.712 closest distance to " NE2 GLN A  55 " =    2.576
peak=   -3.707 closest distance to " O   HOH Z 351 " =    1.552
peak=   -3.702 closest distance to " OE1 GLN A 223 " =    2.428
peak=   -3.700 closest distance to " CB  CYS A 254 " =    2.107
peak=   -3.699 closest distance to " O   HOH Z 385 " =    3.951
peak=   -3.696 closest distance to " C   GLN A 240 " =    2.287
peak=   -3.666 closest distance to " OG  SER A  97 " =    2.277
peak=   -3.663 closest distance to " CG  ARG A  66 " =    2.407
peak=   -3.659 closest distance to " CA  ASN A 127 " =    1.013
peak=   -3.657 closest distance to " CB  GLU A 277 " =    1.321
peak=   -3.650 closest distance to " O   HOH Z  17 " =    1.381
peak=   -3.647 closest distance to " CG  GLU A  53 " =    1.605
peak=   -3.643 closest distance to " OD2 ASP A 171 " =    1.881
peak=   -3.617 closest distance to " O   HOH Z 234 " =    4.413
peak=   -3.614 closest distance to " OG  SER A  26 " =    1.359
peak=   -3.610 closest distance to " O   HOH Z  94 " =    2.062
peak=   -3.608 closest distance to " OG  SER A  63 " =    1.393
peak=   -3.605 closest distance to " O   HOH Z 151 " =    1.420
peak=   -3.599 closest distance to " O   HOH Z 292 " =    4.452
peak=   -3.597 closest distance to " O   HOH Z 308 " =    1.674
peak=   -3.584 closest distance to " OE1 GLN A  88 " =    0.982
peak=   -3.578 closest distance to " O   HOH Z 231 " =    1.278
peak=   -3.575 closest distance to " O   HOH Z 396 " =    1.546
peak=   -3.574 closest distance to " O   HOH Z 377 " =    1.884
peak=   -3.573 closest distance to " O   HOH Z 283 " =    2.184
peak=   -3.570 closest distance to " C   ALA A 158 " =    1.132
peak=   -3.565 closest distance to " O   HOH Z 243 " =    2.027
peak=   -3.554 closest distance to " C   ASN A 187 " =    1.761
peak=   -3.546 closest distance to " CG  ARG A 269 " =    2.326
peak=   -3.540 closest distance to " CG  TRP A 266 " =    1.849
peak=   -3.536 closest distance to " N   GLN A  58 " =    1.535
peak=   -3.535 closest distance to " OG1 THR A   4 " =    1.960
peak=   -3.530 closest distance to " O   HOH Z 388 " =    1.699
peak=   -3.517 closest distance to " O   HOH Z   5 " =    1.572
peak=   -3.515 closest distance to " O   HOH Z  71 " =    1.250
peak=   -3.514 closest distance to " O   PRO A 163 " =    2.093
peak=   -3.505 closest distance to " N   SER A   3 " =    2.312
peak=   -3.503 closest distance to " CZ3 TRP A 179 " =    1.173
peak=   -3.499 closest distance to " O   PRO A 198 " =    1.308
peak=   -3.495 closest distance to " CD  ARG A 139 " =    1.645
peak=   -3.490 closest distance to " O   HOH Z 380 " =    4.643
peak=   -3.488 closest distance to " CG  GLN A  88 " =    0.893
peak=   -3.478 closest distance to " CA  GLY A 241 " =    3.130
peak=   -3.477 closest distance to " O   HOH Z 179 " =    2.169
peak=   -3.476 closest distance to " CG  GLU A   2 " =    1.792
peak=   -3.474 closest distance to " CG2 ILE A  49 " =    2.793
peak=   -3.468 closest distance to " O   HOH Z 165 " =    2.024
peak=   -3.467 closest distance to " CD1 LEU A 228 " =    2.569
peak=   -3.458 closest distance to " CG1 VAL A 296 " =    1.382
peak=   -3.450 closest distance to " CA  TYR A  68 " =    2.763
peak=   -3.448 closest distance to " OXT GLY A 302 " =    2.954
peak=   -3.444 closest distance to " O   HOH Z 156 " =    1.694
peak=   -3.435 closest distance to " N   THR A 235 " =    1.227
peak=   -3.431 closest distance to " CD2 LEU A 300 " =    3.011
peak=   -3.430 closest distance to " O   HOH Z  69 " =    1.064
peak=   -3.428 closest distance to " CA  GLY A 203 " =    2.289
peak=   -3.427 closest distance to " CB  ALA A 227 " =    2.376
peak=   -3.426 closest distance to " O   HOH Z 290 " =    1.347
peak=   -3.424 closest distance to " NH1 ARG A 195 " =    2.332
peak=   -3.422 closest distance to " CB  ALA A 248 " =    1.976
peak=   -3.417 closest distance to " O   HOH Z  55 " =    2.651
peak=   -3.412 closest distance to " O   VAL A  67 " =    2.494
peak=   -3.405 closest distance to " OD1 ASN A 249 " =    1.245
peak=   -3.404 closest distance to " OD1 ASP A 191 " =    1.600
peak=   -3.402 closest distance to " CE3 TRP A  70 " =    1.747
peak=   -3.401 closest distance to " NH2AARG A 275 " =    5.411
peak=   -3.397 closest distance to " OD1 ASN A 148 " =    1.547
peak=   -3.396 closest distance to " O   HOH Z 124 " =    1.292
peak=   -3.396 closest distance to " O   HOH Z  37 " =    1.432
peak=   -3.392 closest distance to " O   HOH Z 186 " =    1.550
peak=   -3.391 closest distance to " CG1 VAL A  78 " =    2.393
peak=   -3.384 closest distance to " O   HOH Z 350 " =    1.687
peak=   -3.384 closest distance to " CZ  ARG A  66 " =    0.911
peak=   -3.382 closest distance to " O   HOH Z 426 " =    1.837
peak=   -3.379 closest distance to " N   ILE A 120 " =    1.078
peak=   -3.377 closest distance to " O   HOH Z 222 " =    1.466
peak=   -3.373 closest distance to " O   GLY A  80 " =    2.486
peak=   -3.368 closest distance to " O   SER A 135 " =    1.412
peak=   -3.367 closest distance to " O   HOH Z 189 " =    2.242
peak=   -3.367 closest distance to " CD2 HIS A  86 " =    1.111
peak=   -3.362 closest distance to " CG  MET A 105 " =    0.932
peak=   -3.353 closest distance to " CA  ALA A   8 " =    1.463
peak=   -3.344 closest distance to " O   HOH Z  92 " =    1.327
peak=   -3.342 closest distance to " O   HOH Z 241 " =    1.174
peak=   -3.342 closest distance to " CE  MET A  93 " =    1.245
peak=   -3.335 closest distance to " OD2 ASP A 171 " =    2.044
peak=   -3.335 closest distance to " N   ALA A  43 " =    2.833
peak=   -3.325 closest distance to " O   HOH Z 423 " =    1.079
peak=   -3.321 closest distance to " O   HOH Z 185 " =    2.478
peak=   -3.306 closest distance to " OG  SER A  62 " =    4.468
peak=   -3.305 closest distance to " C   GLY A  23 " =    2.158
peak=   -3.302 closest distance to " CD1 TYR A 247 " =    2.332
peak=   -3.301 closest distance to " CE  MET A 105 " =    2.209
peak=   -3.300 closest distance to " CA  ASP A 298 " =    1.067
peak=   -3.299 closest distance to " O   HOH Z 246 " =    1.399
peak=   -3.296 closest distance to " O   HOH Z 111 " =    2.334
peak=   -3.295 closest distance to " SG ACYS A 201 " =    2.213
peak=   -3.288 closest distance to " C   THR A 279 " =    1.266
peak=   -3.286 closest distance to " CG1 VAL A 112 " =    2.820
peak=   -3.279 closest distance to " O   HOH Z  15 " =    1.649
peak=   -3.272 closest distance to " C   HIS A 108 " =    1.128
peak=   -3.270 closest distance to " O   HOH Z 221 " =    1.531
peak=   -3.270 closest distance to " CD1 LEU A 101 " =    2.890
peak=   -3.269 closest distance to " OG BSER A 212 " =    1.680
peak=   -3.267 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -3.266 closest distance to " CB  GLN A  55 " =    1.354
peak=   -3.264 closest distance to " O   GLY A 203 " =    2.451
peak=   -3.264 closest distance to " OD1 ASN A  39 " =    2.251
peak=   -3.263 closest distance to " OH  TYR A 169 " =    1.095
peak=   -3.260 closest distance to " O   HOH Z 149 " =    1.947
peak=   -3.257 closest distance to " CD  ARG A  14 " =    3.229
peak=   -3.253 closest distance to " O   GLY A 118 " =    2.200
peak=   -3.250 closest distance to " CG  LYS A 166 " =    2.108
peak=   -3.250 closest distance to " CE3 TRP A 150 " =    2.463
peak=   -3.248 closest distance to " CZ2 TRP A 274 " =    1.036
peak=   -3.246 closest distance to " O   HOH Z 198 " =    1.711
peak=   -3.241 closest distance to " O   HOH Z  48 " =    1.027
peak=   -3.239 closest distance to " CB  PRO A 163 " =    2.685
peak=   -3.235 closest distance to " C   LEU A 255 " =    1.773
peak=   -3.233 closest distance to " OH  TYR A 172 " =    1.589
peak=   -3.230 closest distance to " O   HOH Z 348 " =    2.333
peak=   -3.230 closest distance to " OE1 GLN A 278 " =    1.165
peak=   -3.229 closest distance to " O   HOH Z 252 " =    4.158
peak=   -3.226 closest distance to " C   LEU A 143 " =    1.258
peak=   -3.222 closest distance to " O   HOH Z  91 " =    1.903
peak=   -3.220 closest distance to " CD2 TYR A 293 " =    2.079
peak=   -3.219 closest distance to " O   HOH Z  11 " =    1.648
peak=   -3.219 closest distance to " ND2 ASN A  60 " =    1.555
peak=   -3.217 closest distance to " O   HOH Z 252 " =    1.180
peak=   -3.216 closest distance to " CA  GLY A 133 " =    2.304
peak=   -3.216 closest distance to " O   HOH Z 118 " =    4.866
peak=   -3.214 closest distance to " C   LEU A 101 " =    1.044
peak=   -3.210 closest distance to " CD1 LEU A 167 " =    2.230
peak=   -3.209 closest distance to " CB  ARG A  79 " =    2.537
peak=   -3.207 closest distance to " O   HOH Z 389 " =    1.880
peak=   -3.203 closest distance to " O   HOH Z 367 " =    3.923
peak=   -3.200 closest distance to " C   SER A 206 " =    1.365
peak=   -3.200 closest distance to " N   THR A 157 " =    1.607
peak=   -3.196 closest distance to " CB  TRP A  85 " =    2.418
peak=   -3.194 closest distance to " O   HOH Z 221 " =    1.374
peak=   -3.194 closest distance to " O   GLY A 211 " =    1.621
peak=   -3.194 closest distance to " NE2 GLN A  88 " =    1.089
peak=   -3.194 closest distance to " CZ3 TRP A  92 " =    1.267
peak=   -3.193 closest distance to " OG BSER A 134 " =    1.471
peak=   -3.188 closest distance to " CB  ALA A  43 " =    2.680
peak=   -3.181 closest distance to " CB  ASN A  39 " =    1.980
peak=   -3.172 closest distance to " CD1 ILE A 151 " =    2.225
peak=   -3.171 closest distance to " O   HOH Z 389 " =    4.319
peak=   -3.170 closest distance to " CD  ARG A 259 " =    2.595
peak=   -3.165 closest distance to " CD  GLN A 223 " =    1.599
peak=   -3.164 closest distance to " O   HOH Z 418 " =    1.855
peak=   -3.163 closest distance to " O   SER A 210 " =    1.949
peak=   -3.155 closest distance to " O   HOH Z 105 " =    1.989
peak=   -3.148 closest distance to " O   HOH Z 423 " =    2.211
peak=   -3.147 closest distance to " O   GLY A 262 " =    2.457
peak=   -3.141 closest distance to " O   ALA A 100 " =    2.498
peak=   -3.132 closest distance to " O   HOH Z 236 " =    1.334
peak=   -3.131 closest distance to " O   HOH Z 120 " =    4.186
peak=   -3.126 closest distance to " NH1BARG A 145 " =    1.811
peak=   -3.120 closest distance to " N   SER A 134 " =    1.271
peak=   -3.108 closest distance to " O   HOH Z 399 " =    2.244
peak=   -3.107 closest distance to " O   THR A 251 " =    1.676
peak=   -3.104 closest distance to " O   PHE A 218 " =    1.452
peak=   -3.102 closest distance to " O   HOH Z 156 " =    3.622
peak=   -3.101 closest distance to " O   HOH Z 402 " =    1.471
peak=   -3.095 closest distance to " OD1 ASN A 173 " =    1.285
peak=   -3.090 closest distance to " NH2 ARG A  66 " =    5.285
peak=   -3.090 closest distance to " OD2 ASP A 132 " =    1.631
peak=   -3.088 closest distance to " O   HOH Z 416 " =    1.041
peak=   -3.088 closest distance to " O   HOH Z  60 " =    2.011
peak=   -3.084 closest distance to " CE2 PHE A 283 " =    2.591
peak=   -3.081 closest distance to " OG1 THR A  82 " =    1.476
peak=   -3.079 closest distance to " O   HOH Z 410 " =    1.465
peak=   -3.076 closest distance to " CB  ALA A 291 " =    2.259
peak=   -3.073 closest distance to " O   GLN A 194 " =    1.304
peak=   -3.063 closest distance to " CB  ALA A  10 " =    2.039
peak=   -3.053 closest distance to " NH2BARG A 145 " =    2.620
peak=   -3.053 closest distance to " O   HOH Z   6 " =    1.948
peak=   -3.050 closest distance to " O   HOH Z 171 " =    2.397
peak=   -3.050 closest distance to " O   HOH Z 295 " =    1.301
peak=   -3.033 closest distance to " ND2 ASN A  60 " =    1.799
peak=   -3.033 closest distance to " O   ASN A 187 " =    1.677
peak=   -3.022 closest distance to " CD  PRO A 213 " =    2.249
peak=   -3.006 closest distance to " CB  ARG A 138 " =    1.367

================= 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    :  0.4913 0.4811   6.291904e+00   6.280069e+00
   1_bss:  0.4832 0.4705   6.288698e+00   6.275863e+00
   1_xyz:  0.4090 0.4320   6.192690e+00   6.234957e+00
   1_adp:  0.3684 0.4203   6.135625e+00   6.213993e+00
   1_occ:  0.3679 0.4212   6.135340e+00   6.214959e+00
   2_bss:  0.3673 0.4176   6.137543e+00   6.214940e+00
   2_xyz:  0.2829 0.3536   5.939948e+00   6.097716e+00
   2_adp:  0.2595 0.3253   5.869833e+00   6.038274e+00
   2_occ:  0.2593 0.3252   5.868337e+00   6.036883e+00
   3_bss:  0.2575 0.3224   5.868413e+00   6.035817e+00
   3_xyz:  0.1879 0.2407   5.580087e+00   5.781342e+00
   3_adp:  0.1693 0.2207   5.491020e+00   5.698576e+00
   3_occ:  0.1689 0.2205   5.489797e+00   5.697326e+00
   4_bss:  0.1681 0.2202   5.491597e+00   5.697149e+00
   4_xyz:  0.1422 0.1899   5.346790e+00   5.564724e+00
   4_adp:  0.1367 0.1860   5.321491e+00   5.545158e+00
   4_occ:  0.1366 0.1859   5.321200e+00   5.544897e+00
   5_bss:  0.1367 0.1858   5.321125e+00   5.543830e+00
   5_xyz:  0.1267 0.1748   5.257353e+00   5.486944e+00
   5_adp:  0.1235 0.1751   5.249572e+00   5.489416e+00
   5_occ:  0.1235 0.1750   5.249575e+00   5.489636e+00
   5_bss:  0.1235 0.1750   5.249537e+00   5.489792e+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:  0.299  22.582   9.079   9.433   6.709   0.000   0.000   0.000
   1_xyz:  0.299  22.582   9.079   9.433   6.709   0.000   0.000   0.000
   1_adp:  0.299  22.582   9.079   9.433   6.709   0.000   0.000   0.000
   1_occ:  0.299  22.582   9.079   9.433   6.709   0.000   0.000   0.000
   2_bss:  0.324  50.000   6.084   6.297   4.789   0.000   0.000   0.000
   2_xyz:  0.324  50.000   6.084   6.297   4.789   0.000   0.000   0.000
   2_adp:  0.324  50.000   6.084   6.297   4.789   0.000   0.000   0.000
   2_occ:  0.324  50.000   6.084   6.297   4.789   0.000   0.000   0.000
   3_bss:  0.317  70.378   3.680   3.896   3.196   0.000   0.000   0.000
   3_xyz:  0.317  70.378   3.680   3.896   3.196   0.000   0.000   0.000
   3_adp:  0.317  70.378   3.680   3.896   3.196   0.000   0.000   0.000
   3_occ:  0.317  70.378   3.680   3.896   3.196   0.000   0.000   0.000
   4_bss:  0.346  70.378   2.304   2.606   2.343   0.000   0.000   0.000
   4_xyz:  0.346  70.378   2.304   2.606   2.343   0.000   0.000   0.000
   4_adp:  0.346  70.378   2.304   2.606   2.343   0.000   0.000   0.000
   4_occ:  0.346  70.378   2.304   2.606   2.343   0.000   0.000   0.000
   5_bss:  0.329  60.633   1.952   2.193   2.273   0.000   0.000   0.000
   5_xyz:  0.329  60.633   1.952   2.193   2.273   0.000   0.000   0.000
   5_adp:  0.329  60.633   1.952   2.193   2.273   0.000   0.000   0.000
   5_occ:  0.329  60.633   1.952   2.193   2.273   0.000   0.000   0.000
   5_bss:  0.322  62.713  -0.140  -0.007   0.147  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.394 0.3882  0.4515    74328.490
   1_bss:  61.020 0.3780  0.5529    72360.556
   1_xyz:  53.391 0.4752  0.6854    58573.448
   1_adp:  50.106 0.5168  0.7789    53343.464
   1_occ:  50.302 0.5142  0.7743    53646.185
   2_bss:  50.158 0.5160  0.7123    53468.486
   2_xyz:  39.145 0.6509  0.8946    35342.393
   2_adp:  34.848 0.7023  0.9494    29544.804
   2_occ:  34.745 0.7034  0.9505    29362.568
   3_bss:  34.590 0.7052  0.8841    29211.017
   3_xyz:  24.113 0.8194  0.9730    15018.676
   3_adp:  21.439 0.8470  0.9839    12472.822
   3_occ:  21.405 0.8474  0.9838    12455.486
   4_bss:  21.417 0.8474  0.9445    12488.000
   4_xyz:  17.961 0.8807  0.9673     9282.968
   4_adp:  17.447 0.8857  0.9682     8983.254
   4_occ:  17.441 0.8858  0.9681     8982.387
   5_bss:  17.409 0.8860  0.9585     8942.527
   5_xyz:  16.097 0.8977  0.9626     7875.555
   5_adp:  16.171 0.8971  0.9556     7916.930
   5_occ:  16.176 0.8970  0.9554     7915.976
   5_bss:  16.180 0.8970  0.9599     7921.452
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4216e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4216e+01
   1_xyz:   1.814  0.014  0.114 18.178  0.008  4.110   1.6004e-01
   1_adp:   1.814  0.014  0.114 18.178  0.008  4.110   1.6004e-01
   1_occ:   1.814  0.014  0.114 18.178  0.008  4.110   1.6004e-01
   2_bss:   1.814  0.014  0.114 18.178  0.008  4.110   1.6004e-01
   2_xyz:   1.288  0.010  0.086 16.365  0.006  4.110   9.9561e-02
   2_adp:   1.288  0.010  0.086 16.365  0.006  4.110   9.9561e-02
   2_occ:   1.288  0.010  0.086 16.365  0.006  4.110   9.9561e-02
   3_bss:   1.288  0.010  0.086 16.365  0.006  4.110   9.9561e-02
   3_xyz:   1.198  0.009  0.087 15.776  0.005  4.137   8.2868e-02
   3_adp:   1.198  0.009  0.087 15.776  0.005  4.137   8.2868e-02
   3_occ:   1.198  0.009  0.087 15.776  0.005  4.137   8.2868e-02
   4_bss:   1.198  0.009  0.087 15.776  0.005  4.137   8.2868e-02
   4_xyz:   1.071  0.008  0.080 15.573  0.004  4.116   6.9775e-02
   4_adp:   1.071  0.008  0.080 15.573  0.004  4.116   6.9775e-02
   4_occ:   1.071  0.008  0.080 15.573  0.004  4.116   6.9775e-02
   5_bss:   1.071  0.008  0.080 15.573  0.004  4.116   6.9775e-02
   5_xyz:   1.100  0.009  0.082 15.532  0.004  4.123   7.0497e-02
   5_adp:   1.100  0.009  0.082 15.532  0.004  4.123   7.0497e-02
   5_occ:   1.100  0.009  0.082 15.532  0.004  4.123   7.0497e-02
   5_bss:   1.100  0.009  0.082 15.532  0.004  4.123   7.0497e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0286e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0286e+00
   1_xyz:  16.188  0.183  0.530 87.227  0.052  2.162   1.1176e-01
   1_adp:  16.188  0.183  0.530 87.227  0.052  2.162   1.1176e-01
   1_occ:  16.188  0.183  0.530 87.227  0.052  2.162   1.1176e-01
   2_bss:  16.188  0.183  0.530 87.227  0.052  2.162   1.1176e-01
   2_xyz:   8.415  0.090  0.301 84.283  0.043  2.111   8.9002e-02
   2_adp:   8.415  0.090  0.301 84.283  0.043  2.111   8.9002e-02
   2_occ:   8.415  0.090  0.301 84.283  0.043  2.111   8.9002e-02
   3_bss:   8.415  0.090  0.301 84.283  0.043  2.111   8.9002e-02
   3_xyz:   7.795  0.080  0.287 82.404  0.050  2.212   7.7528e-02
   3_adp:   7.795  0.080  0.287 82.404  0.050  2.212   7.7528e-02
   3_occ:   7.795  0.080  0.287 82.404  0.050  2.212   7.7528e-02
   4_bss:   7.795  0.080  0.287 82.404  0.050  2.212   7.7528e-02
   4_xyz:   8.150  0.053  0.389 83.926  0.041  2.313   4.7713e-02
   4_adp:   8.150  0.053  0.389 83.926  0.041  2.313   4.7713e-02
   4_occ:   8.150  0.053  0.389 83.926  0.041  2.313   4.7713e-02
   5_bss:   8.150  0.053  0.389 83.926  0.041  2.313   4.7713e-02
   5_xyz:   8.444  0.059  0.417 83.852  0.034  2.382   4.3404e-02
   5_adp:   8.444  0.059  0.417 83.852  0.034  2.382   4.3404e-02
   5_occ:   8.444  0.059  0.417 83.852  0.034  2.382   4.3404e-02
   5_bss:   8.444  0.059  0.417 83.852  0.034  2.382   4.3404e-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:  82.57   0.00  12.77  63.98   0.00  10.73  82.57   0.00  23.85
   1_occ:  82.57   0.00  12.77  63.98   0.00  10.73  82.57   0.00  23.85
   2_bss:  82.57   0.00  12.77  63.98   0.00  10.73  82.57   0.00  23.85
   2_xyz:  82.57   0.00  12.77  63.98   0.00  10.73  82.57   0.00  23.85
   2_adp:  84.48   0.00  13.31  79.03   0.00   9.73  84.48   0.00  32.78
   2_occ:  84.48   0.00  13.31  79.03   0.00   9.73  84.48   0.00  32.78
   3_bss:  84.48   0.00  13.31  79.03   0.00   9.73  84.48   0.00  32.78
   3_xyz:  84.48   0.00  13.31  79.03   0.00   9.73  84.48   0.00  32.78
   3_adp:  85.19   0.00  13.60  85.19   0.00   9.17  81.74   0.00  37.71
   3_occ:  85.19   0.00  13.60  85.19   0.00   9.17  81.74   0.00  37.71
   4_bss:  85.19   0.00  13.60  85.19   0.00   9.17  81.74   0.00  37.71
   4_xyz:  85.19   0.00  13.60  85.19   0.00   9.17  81.74   0.00  37.71
   4_adp:  87.03   0.00  13.62  87.03   0.00   9.09  82.74   1.20  38.28
   4_occ:  87.03   0.00  13.62  87.03   0.00   9.09  82.74   1.20  38.28
   5_bss:  87.03   0.00  13.62  87.03   0.00   9.09  82.74   1.20  38.28
   5_xyz:  87.03   0.00  13.62  87.03   0.00   9.09  82.74   1.20  38.28
   5_adp: 100.16   0.00  13.99 100.16   0.00   9.13  98.64   0.94  40.47
   5_occ: 100.16   0.00  13.99 100.16   0.00   9.13  98.64   0.94  40.47
   5_bss: 102.44   2.28  16.27 102.44   2.28  11.41 100.91   3.22  42.75
------------------------------------------------------------------------
 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:    1.183    0.020    0.421
   1_adp:    1.183    0.020    0.421
   1_occ:    1.183    0.020    0.421
   2_bss:    1.183    0.020    0.421
   2_xyz:    1.686    0.052    0.619
   2_adp:    1.686    0.052    0.619
   2_occ:    1.686    0.052    0.619
   3_bss:    1.686    0.052    0.619
   3_xyz:    1.625    0.056    0.734
   3_adp:    1.625    0.056    0.734
   3_occ:    1.625    0.056    0.734
   4_bss:    1.625    0.056    0.734
   4_xyz:    1.707    0.026    0.781
   4_adp:    1.707    0.026    0.781
   4_occ:    1.707    0.026    0.781
   5_bss:    1.707    0.026    0.781
   5_xyz:    1.764    0.032    0.809
   5_adp:    1.764    0.032    0.809
   5_occ:    1.764    0.032    0.809
   5_bss:    1.764    0.032    0.809
------------------------------------------------------------------------

CPU time actual refinement: 345.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1301/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_1301/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1301/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1301/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1301/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.46 
  Macro-tasks:
    bulk solvent and scale       = 42.65  
    individual site refinement   = 145.13 
    weights calculation          = 31.77  
    collect and process          = 6.51   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 226.16 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 110.56 
    alpha_beta                      = 8.31   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 115.28 
    fmodel                         = 7.57   
    r_factors                      = 0.17   
    phase_errors                   = 10.96  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 256.59 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.893 micro seconds
Total CPU time: 5.98 minutes
from_scatterers_fft:    622 calls, 110.16 s
gradients_fft:          567 calls, 104.14 s

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

# Date 2008-01-16 Time 03:42:18 PST -0800 (1200483738.28 s)
Start R-work = 0.4913, R-free = 0.4811 (no bulk solvent and anisotropic scale)
Final R-work = 0.1389, R-free = 0.1905 (no bulk solvent and anisotropic scale)

Start R-work = 0.4832, R-free = 0.4705
Final R-work = 0.1235, R-free = 0.1750