# Date 2008-01-16 Time 03:38:20 PST -0800 (1200483500.27 s)
#phil __OFF__

Command line arguments: "../1317.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6100
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1317

-------------------------------------------------------------------------------
  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, 47.8686, 87.6859, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3277 2.03104
Completeness in resolution range: 0.972835
Completeness with d_max=infinity: 0.969752

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3277
                             d_min =   2.0310

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, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3277 2.03104
Completeness in resolution range: 0.972835
Completeness with d_max=infinity: 0.969752

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3282 -  4.3456 [2104/2128]  1894   210  10.0%
  bin  2:  4.3456 -  3.4623 [2037/2056]  1833   204  10.0%
  bin  3:  3.4623 -  3.0285 [2006/2025]  1803   203  10.1%
  bin  4:  3.0285 -  2.7533 [1988/2018]  1793   195   9.8%
  bin  5:  2.7533 -  2.5570 [1979/1998]  1781   198  10.0%
  bin  6:  2.5570 -  2.4068 [1941/1966]  1747   194  10.0%
  bin  7:  2.4068 -  2.2867 [1970/1998]  1769   201  10.2%
  bin  8:  2.2867 -  2.1874 [1945/1981]  1754   191   9.8%
  bin  9:  2.1874 -  2.1035 [1935/1977]  1744   191   9.9%
  bin 10:  2.1035 -  2.0310 [1684/1989]  1512   172  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1317/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.24 -     1.97: 4
        1.97 -     2.71: 120
        2.71 -     3.44: 4421
        3.44 -     4.17: 9109
        4.17 -     4.90: 13921
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.243 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 277 " - " O   HOH Z 343 "  1.923 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  1.923 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.218 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27570 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_1317/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1317/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 47.8686 87.68585 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: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5179   r_free= 0.5004   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.99 A                  |
| x-ray target function (ml) for work reflections: 6.307720                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.8467 0.99   1376  152 0.4206 0.4095      6.6365      6.5773|
|  2:  4.8467 -  3.8673 0.99   1321  147 0.4578 0.4851      6.8844      6.9542|
|  3:  3.8673 -  3.3845 0.99   1298  144 0.4977 0.4649      6.7545      6.7327|
|  4:  3.3845 -  3.0778 0.99   1278  145 0.5196 0.4598      6.5908      6.5195|
|  5:  3.0778 -  2.8587 0.99   1283  141 0.5337 0.5285       6.403       6.417|
|  6:  2.8587 -  2.6911 0.99   1277  139 0.5506 0.5329      6.3176      6.2546|
|  7:  2.6911 -  2.5570 0.99   1271  142 0.5459 0.4855      6.2572      6.2394|
|  8:  2.5570 -  2.4461 0.98   1261  145 0.5572 0.5085      6.2098      6.1638|
|  9:  2.4461 -  2.3523 0.98   1258  136 0.5483 0.6370       6.133      6.1745|
| 10:  2.3523 -  2.2714 0.99   1240  142 0.5640 0.5543      6.1356      6.1743|
| 11:  2.2714 -  2.2006 0.98   1265  134 0.5448 0.5189      6.0612      6.0662|
| 12:  2.2006 -  2.1378 0.97   1236  140 0.5575 0.5145      6.0015      6.0256|
| 13:  2.1378 -  2.0817 1.00   1243  143 0.5426 0.4857      5.9003      5.8626|
| 14:  2.0817 -  2.0310 0.79   1023  109 0.5651 0.5295      5.8453      5.7602|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3282 -  4.8467  1376   152  0.65  38.30   0.77     0.69      87077.25|
|  2:  4.8467 -  3.8673  1321   147  0.64  40.60   0.84     0.69     131155.93|
|  3:  3.8673 -  3.3845  1298   144  0.52  50.23   0.76     0.61     142032.46|
|  4:  3.3845 -  3.0778  1278   145  0.41  58.60   0.76     0.50     123635.55|
|  5:  3.0778 -  2.8587  1283   141  0.34  64.74   0.69     0.40      96074.23|
|  6:  2.8587 -  2.6911  1277   139  0.32  65.92   0.68     0.36      78787.76|
|  7:  2.6911 -  2.5570  1271   142  0.27  69.79   0.69     0.30      73102.03|
|  8:  2.5570 -  2.4461  1261   145  0.19  76.01   0.70     0.22      70364.29|
|  9:  2.4461 -  2.3523  1258   136  0.12  81.30   0.67     0.13      66778.46|
| 10:  2.3523 -  2.2714  1240   142  0.11  82.17   0.68     0.12      61731.41|
| 11:  2.2714 -  2.2006  1265   134  0.19  76.06   0.73     0.22      53197.77|
| 12:  2.2006 -  2.1378  1236   140  0.25  71.71   0.71     0.30      47490.29|
| 13:  2.1378 -  2.0817  1243   143  0.23  72.66   0.69     0.27      39500.62|
| 14:  2.0817 -  2.0310  1023   109  0.08  84.09   0.66     0.09      35158.57|
|alpha:            min =        0.09 max =            0.69 mean =         0.36|
|beta:             min =    35158.57 max =       142032.46 mean =     80123.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           89.99 mean =        66.00|
|phase err.(test): min =        0.00 max =           89.93 mean =        65.67|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.961816             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.592   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.578790              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 85.252   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      670 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1464 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2548 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3814 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4946 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6377 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7548 |
|-----------------------------------------------------------------------------|
|-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 |       54.895 |
| 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 |       1.686 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.598)------------------------------------------|
|    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 = 12.598)------------------------------------------|
|    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: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5214   r_free= 0.5047   ksol= 0.00   Bsol= 0.00   scale= 0.721    |
|                                                                             |
| 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:   0.97 A                  |
| x-ray target function (ml) for work reflections: 6.308017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5121   r_free= 0.4976   ksol= 0.28   Bsol= 20.00   scale= 0.934   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.90,9.61,8.55,0.00,0.00,0.00); trace/3= 8.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.98 A                  |
| x-ray target function (ml) for work reflections: 6.305782                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.938094             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.195   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.032424              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.265   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5121      final r-factor (work) = 0.4499          |
| start r-factor (free) = 0.4976      final r-factor (free) = 0.4605          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 120.9167 = 20.94 * 0.50 * 6.3064 + 1.00 * 54.8952                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 65.6375 = 20.94 * 0.50 * 6.2536 + 1.00 * 0.1686                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4499      final r-factor (work) = 0.4100          |
| start r-factor (free) = 0.4605      final r-factor (free) = 0.4527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7247 = 2.03 * 1.00 * 6.2536 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6388 = 2.03 * 1.00 * 6.2053 + 1.00 * 0.0270                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.598)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    127.07  17.21    None  None   None       |
|    all(noH): 2823   0      0.00    127.07  17.21    None  None   None       |
|    Sol.    : 438    0      0.00    127.07  29.02    None  None   None       |
|    Mac.    : 2385   0      0.00    91.88   15.04    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 -  12.707: 1395   |   5:    63.533 -  76.239:   38        |
|      1:    12.707 -  25.413:  787   |   6:    76.239 -  88.946:   15        |
|      2:    25.413 -  38.120:  356   |   7:    88.946 - 101.653:    8        |
|      3:    38.120 -  50.826:  165   |   8:   101.653 - 114.359:    1        |
|      4:    50.826 -  63.533:   55   |   9:   114.359 - 127.066:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4100 r_free = 0.4527             target_work(ml) = 6.196         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4091 r_free = 0.4539             target_work(ml) = 6.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4091   r_free= 0.4539   ksol= 0.28   Bsol= 20.00   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.90,9.61,8.55,0.00,0.00,0.00); trace/3= 8.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.195521                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4083   r_free= 0.4520   ksol= 0.31   Bsol= 80.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.75,6.06,5.51,0.00,0.00,0.00); trace/3= 5.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.197191                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.890515             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.938  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.750119              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.787  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4083      final r-factor (work) = 0.3379          |
| start r-factor (free) = 0.4520      final r-factor (free) = 0.4081          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.2339 = 13.89 * 0.50 * 6.2007 + 1.00 * 0.1684                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.6727 = 13.89 * 0.50 * 6.1273 + 1.00 * 0.1173                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3379      final r-factor (work) = 0.3222          |
| start r-factor (free) = 0.4081      final r-factor (free) = 0.3871          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6244 = 0.75 * 1.00 * 6.1273 + 1.00 * 0.0283                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5755 = 0.75 * 1.00 * 6.0587 + 1.00 * 0.0307                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.598)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    137.93  14.97    None  None   None       |
|    all(noH): 2823   0      0.00    137.93  14.97    None  None   None       |
|    Sol.    : 438    0      0.00    137.93  30.90    None  None   None       |
|    Mac.    : 2385   0      0.00    101.12  12.04    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 -  13.793: 1714   |   5:    68.967 -  82.760:   14        |
|      1:    13.793 -  27.587:  726   |   6:    82.760 -  96.553:    6        |
|      2:    27.587 -  41.380:  239   |   7:    96.553 - 110.347:    3        |
|      3:    41.380 -  55.173:   86   |   8:   110.347 - 124.140:    1        |
|      4:    55.173 -  68.967:   33   |   9:   124.140 - 137.933:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3222 r_free = 0.3871             target_work(ml) = 6.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3220 r_free = 0.3879             target_work(ml) = 6.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3220   r_free= 0.3879   ksol= 0.31   Bsol= 80.00   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.75,6.06,5.51,0.00,0.00,0.00); trace/3= 5.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.038966                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3216   r_free= 0.3867   ksol= 0.32   Bsol= 80.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.48,4.52,4.07,0.00,0.00,0.00); trace/3= 4.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.038510                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.881467              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.217   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.943337              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.778   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3216      final r-factor (work) = 0.2527          |
| start r-factor (free) = 0.3867      final r-factor (free) = 0.3077          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9836 = 7.88 * 0.50 * 6.0563 + 1.00 * 0.1173                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5678 = 7.88 * 0.50 * 5.9557 + 1.00 * 0.0981                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2527      final r-factor (work) = 0.2365          |
| start r-factor (free) = 0.3077      final r-factor (free) = 0.2960          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6341 = 0.94 * 1.00 * 5.9557 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4994 = 0.94 * 1.00 * 5.8043 + 1.00 * 0.0239                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.598)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    137.61  14.82    None  None   None       |
|    all(noH): 2823   0      0.00    137.61  14.82    None  None   None       |
|    Sol.    : 438    0      0.00    137.61  33.46    None  None   None       |
|    Mac.    : 2385   0      0.00    102.23  11.40    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 -  13.761: 1710   |   5:    68.806 -  82.567:   12        |
|      1:    13.761 -  27.522:  716   |   6:    82.567 -  96.328:    7        |
|      2:    27.522 -  41.284:  242   |   7:    96.328 - 110.089:    3        |
|      3:    41.284 -  55.045:   92   |   8:   110.089 - 123.850:    1        |
|      4:    55.045 -  68.806:   39   |   9:   123.850 - 137.612:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2365 r_free = 0.2960             target_work(ml) = 5.790         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2363 r_free = 0.2961             target_work(ml) = 5.789         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2363   r_free= 0.2961   ksol= 0.32   Bsol= 80.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.48,4.52,4.07,0.00,0.00,0.00); trace/3= 4.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.788500                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2359   r_free= 0.2951   ksol= 0.34   Bsol= 80.18   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.22,2.96,2.79,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.787017                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.883538              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.571   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347367              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.189  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2359      final r-factor (work) = 0.1900          |
| start r-factor (free) = 0.2951      final r-factor (free) = 0.2461          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1784 = 5.88 * 0.50 * 5.8061 + 1.00 * 0.0981                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8553 = 5.88 * 0.50 * 5.6971 + 1.00 * 0.0957                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1900      final r-factor (work) = 0.1696          |
| start r-factor (free) = 0.2461      final r-factor (free) = 0.2191          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0174 = 0.35 * 1.00 * 5.6971 + 1.00 * 0.0384                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9414 = 0.35 * 1.00 * 5.5545 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.598)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.86  14.16    None  None   None       |
|    all(noH): 2823   0      0.00    123.86  14.16    None  None   None       |
|    Sol.    : 438    0      1.92    123.86  38.46    None  None   None       |
|    Mac.    : 2385   0      0.00    104.62  9.70     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 -  12.386: 1857   |   5:    61.932 -  74.318:   39        |
|      1:    12.386 -  24.773:  501   |   6:    74.318 -  86.704:    9        |
|      2:    24.773 -  37.159:  194   |   7:    86.704 -  99.091:    1        |
|      3:    37.159 -  49.545:  119   |   8:    99.091 - 111.477:    2        |
|      4:    49.545 -  61.932:  100   |   9:   111.477 - 123.863:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1696 r_free = 0.2191             target_work(ml) = 5.499         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1693 r_free = 0.2192             target_work(ml) = 5.498         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1693   r_free= 0.2192   ksol= 0.34   Bsol= 80.18   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.22,2.96,2.79,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.497803                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1696   r_free= 0.2201   ksol= 0.32   Bsol= 80.00   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,2.20,2.71,0.00,0.00,0.00); trace/3= 2.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.499473                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.109823              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.556  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553139              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.009  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1696      final r-factor (work) = 0.1432          |
| start r-factor (free) = 0.2201      final r-factor (free) = 0.1918          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5096 = 4.11 * 0.50 * 5.5545 + 1.00 * 0.0957                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2523 = 4.11 * 0.50 * 5.4304 + 1.00 * 0.0932                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1432      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.1918      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0156 = 0.55 * 1.00 * 5.4304 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9600 = 0.55 * 1.00 * 5.3259 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.598)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.84  14.35    None  None   None       |
|    all(noH): 2823   0      0.00    115.84  14.35    None  None   None       |
|    Sol.    : 438    0      2.04    115.84  41.04    None  None   None       |
|    Mac.    : 2385   0      0.00    105.67  9.45     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.584: 1829   |   5:    57.920 -  69.504:   66        |
|      1:    11.584 -  23.168:  517   |   6:    69.504 -  81.088:   29        |
|      2:    23.168 -  34.752:  144   |   7:    81.088 -  92.672:    7        |
|      3:    34.752 -  46.336:  126   |   8:    92.672 - 104.256:    2        |
|      4:    46.336 -  57.920:  101   |   9:   104.256 - 115.840:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1357 r_free = 0.1879             target_work(ml) = 5.313         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1356 r_free = 0.1877             target_work(ml) = 5.313         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1877   ksol= 0.32   Bsol= 80.00   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,2.20,2.71,0.00,0.00,0.00); trace/3= 2.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.312619                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.8467 0.99   1376  152 0.1084 0.1458       5.462      5.6248|
|  2:  4.8467 -  3.8673 0.99   1321  147 0.0945 0.1227      5.5401      5.7357|
|  3:  3.8673 -  3.3845 0.99   1298  144 0.1244 0.1770       5.625      5.9928|
|  4:  3.3845 -  3.0778 0.99   1278  145 0.1458 0.1741      5.6247      5.7613|
|  5:  3.0778 -  2.8587 0.99   1283  141 0.1670 0.2149      5.5398      5.7592|
|  6:  2.8587 -  2.6911 0.99   1277  139 0.1550 0.2354       5.429      5.6369|
|  7:  2.6911 -  2.5570 0.99   1271  142 0.1579 0.2095       5.364      5.5871|
|  8:  2.5570 -  2.4461 0.98   1261  145 0.1535 0.1982      5.2954      5.5146|
|  9:  2.4461 -  2.3523 0.98   1258  136 0.1491 0.2117      5.2302      5.4371|
| 10:  2.3523 -  2.2714 0.99   1240  142 0.1422 0.2082      5.1517      5.3928|
| 11:  2.2714 -  2.2006 0.98   1265  134 0.1455 0.2174       5.136       5.424|
| 12:  2.2006 -  2.1378 0.97   1236  140 0.1334 0.2072      5.0284       5.382|
| 13:  2.1378 -  2.0817 1.00   1243  143 0.1406 0.2031      4.9695      5.1985|
| 14:  2.0817 -  2.0310 0.79   1023  109 0.1317 0.2031      4.8342      5.0819|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3282 -  4.8467  1376   152  0.93  10.80   0.95     0.94       9172.62|
|  2:  4.8467 -  3.8673  1321   147  0.94   9.84   0.99     0.97      11373.35|
|  3:  3.8673 -  3.3845  1298   144  0.92  13.63   1.01     1.00      14106.89|
|  4:  3.3845 -  3.0778  1278   145  0.90  16.57   1.00     0.97      14411.34|
|  5:  3.0778 -  2.8587  1283   141  0.86  20.36   0.99     0.97      12949.03|
|  6:  2.8587 -  2.6911  1277   139  0.87  19.86   0.97     0.94      10785.53|
|  7:  2.6911 -  2.5570  1271   142  0.86  20.27   0.98     0.95       9568.43|
|  8:  2.5570 -  2.4461  1261   145  0.87  19.36   0.98     0.94       8114.72|
|  9:  2.4461 -  2.3523  1258   136  0.87  19.45   0.99     0.94       7466.02|
| 10:  2.3523 -  2.2714  1240   142  0.88  18.84   0.98     0.93       6148.07|
| 11:  2.2714 -  2.2006  1265   134  0.87  20.03   0.98     0.92       6202.02|
| 12:  2.2006 -  2.1378  1236   140  0.89  18.04   0.98     0.95       5321.22|
| 13:  2.1378 -  2.0817  1243   143  0.87  19.40   0.98     0.96       4760.70|
| 14:  2.0817 -  2.0310  1023   109  0.89  17.88   0.94     0.90       3418.47|
|alpha:            min =        0.90 max =            1.00 mean =         0.95|
|beta:             min =     3418.47 max =        14411.34 mean =      8962.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        17.37|
|phase err.(test): min =        0.00 max =           89.35 mean =        16.52|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1876   ksol= 0.33   Bsol= 79.10   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.14,0.67,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.312104                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1876   ksol= 0.33   Bsol= 79.10   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.14,0.67,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.312104                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.8467 0.99   1376  152 0.1071 0.1450      5.4536      5.6123|
|  2:  4.8467 -  3.8673 0.99   1321  147 0.0953 0.1231      5.5416      5.7352|
|  3:  3.8673 -  3.3845 0.99   1298  144 0.1247 0.1758      5.6262      5.9885|
|  4:  3.3845 -  3.0778 0.99   1278  145 0.1460 0.1743      5.6261       5.765|
|  5:  3.0778 -  2.8587 0.99   1283  141 0.1671 0.2153      5.5408        5.76|
|  6:  2.8587 -  2.6911 0.99   1277  139 0.1550 0.2350      5.4296      5.6356|
|  7:  2.6911 -  2.5570 0.99   1271  142 0.1579 0.2096      5.3636      5.5878|
|  8:  2.5570 -  2.4461 0.98   1261  145 0.1535 0.1983      5.2947      5.5139|
|  9:  2.4461 -  2.3523 0.98   1258  136 0.1489 0.2116      5.2293       5.436|
| 10:  2.3523 -  2.2714 0.99   1240  142 0.1421 0.2085      5.1514      5.3929|
| 11:  2.2714 -  2.2006 0.98   1265  134 0.1453 0.2175      5.1356      5.4249|
| 12:  2.2006 -  2.1378 0.97   1236  140 0.1333 0.2075      5.0283      5.3832|
| 13:  2.1378 -  2.0817 1.00   1243  143 0.1405 0.2030      4.9691      5.1982|
| 14:  2.0817 -  2.0310 0.79   1023  109 0.1317 0.2023      4.8332      5.0793|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3282 -  4.8467  1376   152  0.93  10.58   0.95     0.93       8885.86|
|  2:  4.8467 -  3.8673  1321   147  0.94   9.76   1.00     0.97      11226.82|
|  3:  3.8673 -  3.3845  1298   144  0.92  13.62   1.01     1.00      14104.48|
|  4:  3.3845 -  3.0778  1278   145  0.90  16.57   1.00     0.98      14427.09|
|  5:  3.0778 -  2.8587  1283   141  0.86  20.37   0.99     0.97      12964.54|
|  6:  2.8587 -  2.6911  1277   139  0.87  19.86   0.98     0.94      10800.36|
|  7:  2.6911 -  2.5570  1271   142  0.86  20.25   0.99     0.95       9555.79|
|  8:  2.5570 -  2.4461  1261   145  0.87  19.33   0.98     0.94       8096.15|
|  9:  2.4461 -  2.3523  1258   136  0.87  19.42   1.00     0.94       7449.90|
| 10:  2.3523 -  2.2714  1240   142  0.88  18.83   0.99     0.94       6137.25|
| 11:  2.2714 -  2.2006  1265   134  0.87  20.04   0.98     0.92       6211.37|
| 12:  2.2006 -  2.1378  1236   140  0.89  18.05   0.98     0.95       5322.05|
| 13:  2.1378 -  2.0817  1243   143  0.87  19.39   0.98     0.96       4755.89|
| 14:  2.0817 -  2.0310  1023   109  0.89  17.84   0.95     0.90       3404.35|
|alpha:            min =        0.90 max =            1.00 mean =         0.95|
|beta:             min =     3404.35 max =        14427.09 mean =      8927.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.34|
|phase err.(test): min =        0.00 max =           89.35 mean =        16.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.598)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.26    118.10  16.60    None  None   None       |
|    all(noH): 2823   0      2.26    118.10  16.60    None  None   None       |
|    Sol.    : 438    0      4.29    118.10  43.29    None  None   None       |
|    Mac.    : 2385   0      2.26    107.93  11.70    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:     2.256 -  13.840: 1829   |   5:    60.176 -  71.760:   66        |
|      1:    13.840 -  25.424:  517   |   6:    71.760 -  83.344:   29        |
|      2:    25.424 -  37.008:  144   |   7:    83.344 -  94.928:    7        |
|      3:    37.008 -  48.592:  126   |   8:    94.928 - 106.512:    2        |
|      4:    48.592 -  60.176:  101   |   9:   106.512 - 118.096:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.276 - 4.951
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 326 from: 332
   mapped sites are within: 0.712 - 4.951

peak=    7.768 closest distance to " CG2 VAL A 230 " =    1.377
peak=    6.900 closest distance to " O   HOH Z 400 " =    1.068
peak=    6.425 closest distance to " CD1AILE A 234 " =    1.256
peak=    6.211 closest distance to " O   HOH Z 120 " =    1.341
peak=    6.195 closest distance to " O   HOH Z 117 " =    1.639
peak=    6.028 closest distance to " CG  ARG A 138 " =    1.358
peak=    5.999 closest distance to " O   HOH Z 210 " =    1.552
peak=    5.972 closest distance to " CG2 VAL A 296 " =    1.063
peak=    5.943 closest distance to " NH1BARG A 275 " =    1.243
peak=    5.330 closest distance to " O   HOH Z 102 " =    1.515
peak=    5.313 closest distance to " O   HOH Z  84 " =    1.001
peak=    5.307 closest distance to " CG  LEU A   5 " =    1.224
peak=    5.251 closest distance to " O   HOH Z 425 " =    1.975
peak=    5.163 closest distance to " CB  SER A  63 " =    1.328
peak=    5.144 closest distance to " NH1 ARG A 138 " =    1.071
peak=    5.006 closest distance to " O   HOH Z 394 " =    1.692
peak=    4.902 closest distance to " CG  LEU A 228 " =    1.295
peak=    4.889 closest distance to " CB  GLN A 223 " =    1.508
peak=    4.856 closest distance to " CZ  PHE A 218 " =    1.160
peak=    4.849 closest distance to " CG  PRO A 280 " =    0.945
peak=    4.842 closest distance to " CG  PRO A  54 " =    1.281
peak=    4.790 closest distance to " CB  VAL A 230 " =    1.322
peak=    4.609 closest distance to " O   HOH Z 184 " =    1.920
peak=    4.564 closest distance to " O   HOH Z 111 " =    1.902
peak=    4.540 closest distance to " O   PRO A 198 " =    1.601
peak=    4.452 closest distance to " CG AARG A 275 " =    1.301
peak=    4.411 closest distance to " NH1 ARG A  56 " =    1.129
peak=    4.399 closest distance to " CB  ASP A 124 " =    0.811
peak=    4.368 closest distance to " O   HOH Z  47 " =    1.723
peak=    4.342 closest distance to " O   HOH Z 411 " =    3.674
peak=    4.324 closest distance to " O   HOH Z 154 " =    1.630
peak=    4.306 closest distance to " O   HOH Z  68 " =    2.053
peak=    4.248 closest distance to " CA  TYR A  30 " =    1.047
peak=    4.227 closest distance to " OE1 GLN A  88 " =    0.952
peak=    4.224 closest distance to " O   HOH Z  49 " =    1.488
peak=    4.217 closest distance to " CD  ARG A 138 " =    1.168
peak=    4.176 closest distance to " O   HOH Z  37 " =    1.045
peak=    4.171 closest distance to " N   SER A 164 " =    0.979
peak=    4.166 closest distance to " CA  ARG A 195 " =    1.242
peak=    4.152 closest distance to " O   HOH Z  48 " =    1.973
peak=    4.133 closest distance to " O   HOH Z 146 " =    1.840
peak=    4.124 closest distance to " O   HOH Z 406 " =    1.573
peak=    4.116 closest distance to " CG1 VAL A 153 " =    1.139
peak=    4.096 closest distance to " CG2 THR A 221 " =    1.056
peak=    4.087 closest distance to " CG2 ILE A 234 " =    1.172
peak=    4.085 closest distance to " CB  PRO A  54 " =    0.848
peak=    4.056 closest distance to " CB  ALA A 100 " =    1.549
peak=    4.053 closest distance to " O   HOH Z 303 " =    2.478
peak=    4.053 closest distance to " O   HOH Z 410 " =    1.151
peak=    4.031 closest distance to " O   HOH Z  54 " =    1.151
peak=    4.012 closest distance to " O   HOH Z 433 " =    2.093
peak=    4.000 closest distance to " NH1AARG A 145 " =    1.189
peak=    3.996 closest distance to " O   HOH Z 369 " =    1.634
peak=    3.996 closest distance to " O   HOH Z   4 " =    1.710
peak=    3.976 closest distance to " O   HOH Z 250 " =    1.343
peak=    3.976 closest distance to " O   HOH Z  56 " =    1.913
peak=    3.973 closest distance to " CB  PRO A 198 " =    1.128
peak=    3.973 closest distance to " O   HOH Z 261 " =    1.640
peak=    3.968 closest distance to " CB  GLN A 183 " =    1.205
peak=    3.964 closest distance to " O   HOH Z 404 " =    1.451
peak=    3.948 closest distance to " CA  MET A  40 " =    1.247
peak=    3.943 closest distance to " CD  LYS A 166 " =    1.528
peak=    3.941 closest distance to " CB  ASP A 140 " =    0.831
peak=    3.941 closest distance to " CD2 LEU A   5 " =    1.082
peak=    3.935 closest distance to " O   HOH Z 403 " =    1.891
peak=    3.926 closest distance to " CD ALYS A 290 " =    1.163
peak=    3.925 closest distance to " CG  PRO A 213 " =    1.297
peak=    3.925 closest distance to " CD2 LEU A 228 " =    1.240
peak=    3.917 closest distance to " O   HOH Z 402 " =    1.598
peak=    3.915 closest distance to " OD1 ASN A 301 " =    1.185
peak=    3.904 closest distance to " O   HOH Z 126 " =    1.734
peak=    3.898 closest distance to " CB  TYR A 169 " =    0.712
peak=    3.888 closest distance to " NE2 GLN A  11 " =    1.064
peak=    3.884 closest distance to " O   HOH Z 182 " =    1.369
peak=    3.882 closest distance to " O   HOH Z 234 " =    3.786
peak=    3.845 closest distance to " O   ASP A 124 " =    1.106
peak=    3.840 closest distance to " CB  MET A  40 " =    0.816
peak=    3.833 closest distance to " CB  TRP A 266 " =    1.045
peak=    3.832 closest distance to " CG  PRO A 198 " =    1.325
peak=    3.827 closest distance to " O   THR A 294 " =    1.623
peak=    3.823 closest distance to " O   HOH Z 126 " =    2.362
peak=    3.823 closest distance to " O   HOH Z  80 " =    2.439
peak=    3.807 closest distance to " CB  ASN A 148 " =    1.422
peak=    3.787 closest distance to " CG  PRO A 243 " =    1.128
peak=    3.784 closest distance to " ND2 ASN A 249 " =    2.177
peak=    3.774 closest distance to " O   ALA A 165 " =    1.381
peak=    3.774 closest distance to " OD1 ASN A 217 " =    1.617
peak=    3.773 closest distance to " O   HOH Z 359 " =    1.722
peak=    3.765 closest distance to " O   HOH Z 395 " =    1.433
peak=    3.742 closest distance to " O   HOH Z 377 " =    1.780
peak=    3.720 closest distance to " CB  VAL A 202 " =    1.421
peak=    3.712 closest distance to " CA  ALA A 295 " =    1.106
peak=    3.711 closest distance to " N   PHE A 130 " =    1.197
peak=    3.709 closest distance to " CG  GLN A  77 " =    0.853
peak=    3.709 closest distance to " O   HOH Z 247 " =    1.635
peak=    3.707 closest distance to " CB  ASN A 285 " =    0.838
peak=    3.703 closest distance to " CB  GLN A  88 " =    1.242
peak=    3.701 closest distance to " O   HOH Z 174 " =    1.411
peak=    3.685 closest distance to " O   HOH Z  57 " =    2.190
peak=    3.678 closest distance to " O   HOH Z 437 " =    2.103
peak=    3.674 closest distance to " O   HOH Z 183 " =    1.393
peak=    3.674 closest distance to " OG  SER A  22 " =    2.916
peak=    3.671 closest distance to " O   HOH Z 158 " =    3.335
peak=    3.663 closest distance to " CA  PRO A  54 " =    0.959
peak=    3.657 closest distance to " CB  TRP A 179 " =    1.363
peak=    3.655 closest distance to " O  BHOH Z  74 " =    1.337
peak=    3.654 closest distance to " O   HOH Z 393 " =    3.503
peak=    3.652 closest distance to " CA  ARG A 139 " =    1.668
peak=    3.648 closest distance to " N   TYR A  15 " =    0.856
peak=    3.645 closest distance to " O   HOH Z 134 " =    1.744
peak=    3.638 closest distance to " CA  ILE A 106 " =    0.804
peak=    3.637 closest distance to " CA  SER A  87 " =    0.948
peak=    3.637 closest distance to " CB  GLU A 128 " =    1.191
peak=    3.634 closest distance to " O   HOH Z  92 " =    1.273
peak=    3.625 closest distance to " O   HOH Z 281 " =    4.388
peak=    3.623 closest distance to " CE3 TRP A  85 " =    1.203
peak=    3.614 closest distance to " NH2 ARG A 156 " =    1.241
peak=    3.608 closest distance to " O   HOH Z  38 " =    2.589
peak=    3.607 closest distance to " NE2 HIS A 115 " =    1.177
peak=    3.600 closest distance to " O   HOH Z 368 " =    2.386
peak=    3.595 closest distance to " O   GLU A   2 " =    1.751
peak=    3.586 closest distance to " CB  ALA A 137 " =    1.103
peak=    3.585 closest distance to " CA  ALA A  21 " =    1.376
peak=    3.584 closest distance to " CB  VAL A 296 " =    1.176
peak=    3.575 closest distance to " CE  LYS A 119 " =    1.230
peak=    3.570 closest distance to " CB  ARG A 275 " =    0.779
peak=    3.561 closest distance to " O   HOH Z  43 " =    2.258
peak=    3.555 closest distance to " CG2 VAL A 296 " =    1.617
peak=    3.554 closest distance to " CD2 TRP A 179 " =    1.305
peak=    3.553 closest distance to " N   GLU A 152 " =    1.585
peak=    3.552 closest distance to " O   HOH Z 128 " =    2.308
peak=    3.551 closest distance to " CA  ALA A 160 " =    0.977
peak=    3.547 closest distance to " O   HOH Z 418 " =    1.613
peak=    3.533 closest distance to " O   HOH Z   5 " =    1.738
peak=    3.533 closest distance to " O   HOH Z 423 " =    1.592
peak=    3.526 closest distance to " CA  ARG A 102 " =    1.304
peak=    3.526 closest distance to " O   HOH Z  54 " =    1.461
peak=    3.526 closest distance to " O   HOH Z  32 " =    1.025
peak=    3.520 closest distance to " NH1 ARG A  14 " =    1.092
peak=    3.516 closest distance to " O   HOH Z  58 " =    1.847
peak=    3.513 closest distance to " CA  ASP A 162 " =    1.019
peak=    3.511 closest distance to " OE1 GLN A  11 " =    2.119
peak=    3.510 closest distance to " O   HOH Z 214 " =    1.607
peak=    3.502 closest distance to " O   HOH Z 193 " =    2.454
peak=    3.501 closest distance to " O   HOH Z 131 " =    2.248
peak=    3.498 closest distance to " CB  PRO A  54 " =    1.377
peak=    3.496 closest distance to " CA  ASN A 127 " =    1.152
peak=    3.495 closest distance to " O   ASP A 200 " =    1.546
peak=    3.492 closest distance to " CB AVAL A  41 " =    1.148
peak=    3.486 closest distance to " O   HOH Z   9 " =    2.189
peak=    3.485 closest distance to " CG1 ILE A  49 " =    1.667
peak=    3.478 closest distance to " O   HOH Z 426 " =    1.142
peak=    3.474 closest distance to " O   HOH Z 232 " =    2.043
peak=    3.471 closest distance to " CB  ARG A 190 " =    1.713
peak=    3.468 closest distance to " O   HOH Z 215 " =    1.398
peak=    3.465 closest distance to " CD1 LEU A   5 " =    1.351
peak=    3.464 closest distance to " CB  ASN A 187 " =    1.121
peak=    3.464 closest distance to " O   HOH Z  94 " =    2.187
peak=    3.462 closest distance to " CD  ARG A  66 " =    2.474
peak=    3.462 closest distance to " O   HOH Z 285 " =    2.713
peak=    3.459 closest distance to " N   SER A 271 " =    1.008
peak=    3.456 closest distance to " O   HOH Z 298 " =    2.072
peak=    3.454 closest distance to " CB  ALA A 104 " =    0.990
peak=    3.453 closest distance to " CA  GLY A 196 " =    0.760
peak=    3.446 closest distance to " CA  GLU A 152 " =    0.968
peak=    3.445 closest distance to " O   HOH Z 186 " =    1.985
peak=    3.445 closest distance to " CG  MET A 185 " =    1.291
peak=    3.445 closest distance to " CD1 LEU A 300 " =    1.198
peak=    3.441 closest distance to " NE2 GLN A 278 " =    2.254
peak=    3.440 closest distance to " O   HOH Z 117 " =    1.880
peak=    3.430 closest distance to " O   HOH Z 346 " =    1.682
peak=    3.425 closest distance to " CG1 ILE A 120 " =    1.113
peak=    3.423 closest distance to " O   HOH Z 431 " =    1.300
peak=    3.412 closest distance to " CA  MET A 105 " =    1.016
peak=    3.411 closest distance to " O   HOH Z  95 " =    1.854
peak=    3.400 closest distance to " C   ASN A 209 " =    1.448
peak=    3.400 closest distance to " CD  ARG A 269 " =    0.865
peak=    3.398 closest distance to " CE  LYS A  76 " =    0.952
peak=    3.396 closest distance to " O   SER A  87 " =    2.433
peak=    3.395 closest distance to " CZ3 TRP A 266 " =    1.147
peak=    3.392 closest distance to " O   HOH Z 374 " =    2.956
peak=    3.392 closest distance to " O   HOH Z 343 " =    2.776
peak=    3.392 closest distance to " CG1 ILE A  33 " =    1.248
peak=    3.388 closest distance to " CB  GLN A  89 " =    1.143
peak=    3.386 closest distance to " OD1 ASN A  69 " =    2.543
peak=    3.371 closest distance to " O   HOH Z 133 " =    2.028
peak=    3.369 closest distance to " O   HOH Z 301 " =    1.486
peak=    3.367 closest distance to " CB  ALA A 248 " =    1.098
peak=    3.365 closest distance to " O   HOH Z 272 " =    2.079
peak=    3.358 closest distance to " O   HOH Z 112 " =    1.415
peak=    3.347 closest distance to " CB  SER A 141 " =    1.080
peak=    3.347 closest distance to " CD1 LEU A 222 " =    0.809
peak=    3.346 closest distance to " CB  ASN A  39 " =    0.737
peak=    3.346 closest distance to " CD1 LEU A 101 " =    1.052
peak=    3.345 closest distance to " CB  GLN A 103 " =    1.036
peak=    3.341 closest distance to " O   HOH Z 327 " =    2.259
peak=    3.338 closest distance to " O   HOH Z 250 " =    1.067
peak=    3.333 closest distance to " O   HOH Z 227 " =    1.653
peak=    3.332 closest distance to " CG  MET A 188 " =    0.832
peak=    3.330 closest distance to " CG2AVAL A 121 " =    1.978
peak=    3.329 closest distance to " CA  ASP A 140 " =    1.366
peak=    3.327 closest distance to " O   HOH Z 422 " =    1.249
peak=    3.327 closest distance to " O   HOH Z 153 " =    2.344
peak=    3.327 closest distance to " CB  THR A  31 " =    1.474
peak=    3.323 closest distance to " OG  SER A 245 " =    1.627
peak=    3.322 closest distance to " O   HOH Z 427 " =    3.324
peak=    3.316 closest distance to " CA  ARG A 156 " =    1.120
peak=    3.315 closest distance to " NZ  LYS A 181 " =    0.905
peak=    3.313 closest distance to " O   HOH Z 174 " =    1.879
peak=    3.312 closest distance to " O   HOH Z 367 " =    1.769
peak=    3.310 closest distance to " CB  LEU A 228 " =    1.250
peak=    3.310 closest distance to " CB  PRO A 243 " =    1.142
peak=    3.310 closest distance to " CA  ILE A  33 " =    1.763
peak=    3.309 closest distance to " O   HOH Z 417 " =    1.144
peak=    3.307 closest distance to " O   HOH Z 290 " =    1.364
peak=    3.306 closest distance to " O   ASN A  74 " =    1.904
peak=    3.306 closest distance to " CB  GLU A 152 " =    1.083
peak=    3.303 closest distance to " CA  TRP A  92 " =    1.090
peak=    3.298 closest distance to " CE1 PHE A  16 " =    1.076
peak=    3.298 closest distance to " O   HOH Z 417 " =    3.262
peak=    3.296 closest distance to " CB  ASP A 140 " =    0.774
peak=    3.296 closest distance to " CB  SER A  62 " =    0.911
peak=    3.295 closest distance to " C   ILE A 106 " =    1.921
peak=    3.294 closest distance to " CD  LYS A 289 " =    1.236
peak=    3.289 closest distance to " OE1 GLU A   2 " =    1.766
peak=    3.287 closest distance to " O   HOH Z 125 " =    3.822
peak=    3.286 closest distance to " CD  ARG A 159 " =    0.769
peak=    3.286 closest distance to " O   HOH Z 167 " =    1.597
peak=    3.284 closest distance to " O   HOH Z 256 " =    1.986
peak=    3.283 closest distance to " OG  SER A  28 " =    1.524
peak=    3.278 closest distance to " O   HOH Z  59 " =    2.256
peak=    3.273 closest distance to " CD  PRO A  54 " =    1.016
peak=    3.271 closest distance to " O   HOH Z 344 " =    2.908
peak=    3.268 closest distance to " OH  TYR A 186 " =    0.995
peak=    3.265 closest distance to " O   HOH Z 350 " =    1.523
peak=    3.264 closest distance to " CZ3 TRP A  92 " =    1.410
peak=    3.260 closest distance to " CB  PHE A 283 " =    0.877
peak=    3.260 closest distance to " O   HOH Z 139 " =    4.951
peak=    3.256 closest distance to " O   HOH Z 368 " =    3.431
peak=    3.251 closest distance to " CB  SER A   3 " =    1.791
peak=    3.251 closest distance to " CB  LEU A 143 " =    1.158
peak=    3.251 closest distance to " O   HOH Z 201 " =    3.012
peak=    3.249 closest distance to " O   HOH Z 313 " =    1.802
peak=    3.247 closest distance to " O   HOH Z 316 " =    3.352
peak=    3.243 closest distance to " CZ3 TRP A  85 " =    0.909
peak=    3.239 closest distance to " O   HOH Z  14 " =    1.575
peak=    3.238 closest distance to " O   HOH Z 146 " =    1.592
peak=    3.238 closest distance to " NZ  LYS A 193 " =    1.570
peak=    3.235 closest distance to " CB  TYR A  30 " =    1.086
peak=    3.232 closest distance to " CA  ALA A  51 " =    0.928
peak=    3.230 closest distance to " CD1 TRP A 266 " =    1.202
peak=    3.229 closest distance to " C   TYR A 214 " =    1.474
peak=    3.228 closest distance to " CB  ALA A 161 " =    0.865
peak=    3.226 closest distance to " CG  GLU A  37 " =    0.909
peak=    3.225 closest distance to " CG  GLN A 278 " =    0.963
peak=    3.224 closest distance to " N   LYS A 166 " =    0.941
peak=    3.223 closest distance to " CB  ALA A 256 " =    1.658
peak=    3.222 closest distance to " O   HOH Z  85 " =    2.088
peak=    3.221 closest distance to " O   THR A 251 " =    1.352
peak=    3.219 closest distance to " O   HOH Z  88 " =    2.533
peak=    3.215 closest distance to " CB  ILE A 199 " =    0.902
peak=    3.213 closest distance to " NE AARG A 275 " =    1.658
peak=    3.212 closest distance to " CB  ARG A 259 " =    1.855
peak=    3.211 closest distance to " CB  ASN A 142 " =    1.147
peak=    3.208 closest distance to " O   HOH Z  99 " =    2.470
peak=    3.208 closest distance to " CA  TYR A 116 " =    1.502
peak=    3.204 closest distance to " CA  GLY A 241 " =    0.935
peak=    3.202 closest distance to " CG1BVAL A 121 " =    1.148
peak=    3.199 closest distance to " O   HOH Z  78 " =    1.262
peak=    3.198 closest distance to " O   HOH Z 379 " =    1.522
peak=    3.196 closest distance to " N   ALA A 256 " =    1.247
peak=    3.191 closest distance to " O   HOH Z 422 " =    2.466
peak=    3.189 closest distance to " CA  GLN A 223 " =    0.894
peak=    3.185 closest distance to " O   HOH Z 175 " =    3.784
peak=    3.182 closest distance to " O   HOH Z 258 " =    2.295
peak=    3.180 closest distance to " N   VAL A 126 " =    1.726
peak=    3.170 closest distance to " CA  SER A  12 " =    1.366
peak=    3.169 closest distance to " CA  ALA A 100 " =    1.214
peak=    3.168 closest distance to " CB  ALA A 242 " =    0.832
peak=    3.164 closest distance to " O   HOH Z 203 " =    1.920
peak=    3.160 closest distance to " CA  GLN A  88 " =    1.230
peak=    3.159 closest distance to " O   HOH Z 265 " =    2.113
peak=    3.157 closest distance to " OE2 GLU A   2 " =    2.230
peak=    3.154 closest distance to " O   HOH Z 361 " =    2.617
peak=    3.151 closest distance to " CB  ALA A   9 " =    1.656
peak=    3.146 closest distance to " CB  ARG A  79 " =    1.306
peak=    3.140 closest distance to " ND1 HIS A  81 " =    1.624
peak=    3.140 closest distance to " CB  VAL A 265 " =    1.245
peak=    3.138 closest distance to " CG2 ILE A 106 " =    0.975
peak=    3.138 closest distance to " CG  ASP A 253 " =    1.245
peak=    3.135 closest distance to " O   HOH Z 388 " =    1.208
peak=    3.134 closest distance to " CB  ILE A 120 " =    1.457
peak=    3.133 closest distance to " CZ  PHE A 192 " =    0.960
peak=    3.132 closest distance to " O   HOH Z 407 " =    2.563
peak=    3.131 closest distance to " NH2AARG A 145 " =    0.955
peak=    3.130 closest distance to " O   HOH Z 136 " =    1.474
peak=    3.129 closest distance to " O   HOH Z 196 " =    1.891
peak=    3.129 closest distance to " O   HOH Z 419 " =    1.844
peak=    3.127 closest distance to " O   HOH Z 188 " =    3.248
peak=    3.127 closest distance to " O   HOH Z  76 " =    1.421
peak=    3.125 closest distance to " O   HOH Z  53 " =    1.614
peak=    3.125 closest distance to " CA  CYS A 254 " =    1.381
peak=    3.124 closest distance to " CB  SER A  26 " =    1.794
peak=    3.121 closest distance to " O   HOH Z 261 " =    1.815
peak=    3.117 closest distance to " CA  ALA A 299 " =    0.982
peak=    3.116 closest distance to " CA  GLY A   6 " =    0.777
peak=    3.113 closest distance to " CZ3 TRP A 274 " =    4.731
peak=    3.111 closest distance to " CG1 VAL A 257 " =    1.003
peak=    3.110 closest distance to " O   HOH Z 162 " =    2.609
peak=    3.106 closest distance to " NH2 ARG A 269 " =    1.326
peak=    3.103 closest distance to " O   HOH Z 128 " =    2.407
peak=    3.102 closest distance to " O   HOH Z  33 " =    2.404
peak=    3.101 closest distance to " CA  ASP A 191 " =    0.797
peak=    3.099 closest distance to " CA  CYS A 260 " =    0.911
peak=    3.093 closest distance to " CD  ARG A  56 " =    1.231
peak=    3.080 closest distance to " O   HOH Z 191 " =    1.601
peak=    3.077 closest distance to " O   HOH Z 313 " =    1.909
peak=    3.076 closest distance to " CB  GLU A 277 " =    3.893
peak=    3.074 closest distance to " CG  LYS A 119 " =    1.044
peak=    3.074 closest distance to " O   HOH Z 134 " =    2.123
peak=    3.061 closest distance to " CB  VAL A 257 " =    0.827
peak=    3.058 closest distance to " O   HOH Z 131 " =    1.640
peak=    3.048 closest distance to " O   HOH Z  21 " =    1.784
peak=    3.046 closest distance to " O   HOH Z 327 " =    1.903
peak=    3.043 closest distance to " O   HOH Z 299 " =    4.399
peak=    3.034 closest distance to " O   ALA A 158 " =    1.318

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.690 - 5.203
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 221
   mapped sites are within: 0.706 - 5.203

peak=   -5.147 closest distance to " O   HOH Z 166 " =    1.288
peak=   -4.836 closest distance to " CG2 VAL A 230 " =    0.901
peak=   -4.779 closest distance to " CD  ARG A 138 " =    1.289
peak=   -4.471 closest distance to " O   HOH Z 400 " =    1.077
peak=   -4.469 closest distance to " O   HOH Z 155 " =    1.614
peak=   -4.408 closest distance to " O   HOH Z 103 " =    1.824
peak=   -4.359 closest distance to " O   HOH Z 216 " =    1.354
peak=   -4.275 closest distance to " N   ARG A 275 " =    1.172
peak=   -4.229 closest distance to " CA  TYR A  68 " =    2.887
peak=   -4.214 closest distance to " O   HOH Z  19 " =    2.271
peak=   -4.213 closest distance to " O   HOH Z 102 " =    1.338
peak=   -4.202 closest distance to " O   HOH Z  10 " =    1.656
peak=   -4.141 closest distance to " CD2 LEU A 237 " =    2.630
peak=   -4.106 closest distance to " O   HOH Z 183 " =    1.340
peak=   -4.099 closest distance to " CB  ALA A 291 " =    2.464
peak=   -4.098 closest distance to " CA  ASP A 298 " =    1.080
peak=   -4.097 closest distance to " CG  ARG A 269 " =    2.475
peak=   -4.092 closest distance to " CD1 PHE A  59 " =    1.995
peak=   -4.040 closest distance to " CD  GLN A  88 " =    0.974
peak=   -4.037 closest distance to " N   ALA A 226 " =    2.312
peak=   -4.035 closest distance to " O   HOH Z 211 " =    0.895
peak=   -3.993 closest distance to " O   HOH Z 411 " =    5.203
peak=   -3.960 closest distance to " NE2 GLN A  55 " =    2.415
peak=   -3.939 closest distance to " CB  ALA A 161 " =    2.728
peak=   -3.934 closest distance to " CG2 ILE A  49 " =    2.804
peak=   -3.919 closest distance to " O   HOH Z 117 " =    0.748
peak=   -3.911 closest distance to " CG  ARG A 138 " =    0.876
peak=   -3.890 closest distance to " O   HOH Z 150 " =    1.330
peak=   -3.880 closest distance to " CD2 PHE A  59 " =    2.433
peak=   -3.869 closest distance to " NH2 ARG A  66 " =    1.645
peak=   -3.818 closest distance to " O   HOH Z 231 " =    1.904
peak=   -3.817 closest distance to " O   HOH Z  43 " =    1.588
peak=   -3.796 closest distance to " CH2 TRP A 179 " =    1.149
peak=   -3.788 closest distance to " OG  SER A  26 " =    1.322
peak=   -3.771 closest distance to " CD1 LEU A   5 " =    2.546
peak=   -3.769 closest distance to " CD  GLN A 223 " =    1.232
peak=   -3.763 closest distance to " CD2 TYR A 293 " =    1.933
peak=   -3.761 closest distance to " O   HOH Z 113 " =    2.165
peak=   -3.747 closest distance to " N   SER A 134 " =    1.227
peak=   -3.739 closest distance to " OG  SER A  97 " =    2.194
peak=   -3.735 closest distance to " OE1 GLN A  88 " =    0.948
peak=   -3.729 closest distance to " O   HOH Z  33 " =    1.939
peak=   -3.713 closest distance to " CG2 VAL A 230 " =    2.694
peak=   -3.713 closest distance to " O   HOH Z 400 " =    0.880
peak=   -3.705 closest distance to " O   HOH Z  73 " =    2.398
peak=   -3.703 closest distance to " O   HOH Z 407 " =    3.704
peak=   -3.703 closest distance to " CA  GLU A 277 " =    1.299
peak=   -3.670 closest distance to " O   HOH Z 438 " =    2.907
peak=   -3.661 closest distance to " CB  PRO A 243 " =    2.876
peak=   -3.654 closest distance to " CD  GLN A  58 " =    0.882
peak=   -3.653 closest distance to " CD2 PHE A  61 " =    2.075
peak=   -3.647 closest distance to " CG1 VAL A 296 " =    1.271
peak=   -3.644 closest distance to " O   HOH Z 136 " =    1.175
peak=   -3.643 closest distance to " O   HOH Z 210 " =    1.326
peak=   -3.640 closest distance to " O   HOH Z 388 " =    1.872
peak=   -3.638 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.636 closest distance to " O   HOH Z  37 " =    1.297
peak=   -3.634 closest distance to " OD2 ASP A  50 " =    2.238
peak=   -3.627 closest distance to " O   HOH Z 179 " =    2.212
peak=   -3.626 closest distance to " CD  GLN A 223 " =    0.876
peak=   -3.612 closest distance to " CG  ASP A 231 " =    0.771
peak=   -3.611 closest distance to " CA  GLY A 203 " =    2.471
peak=   -3.601 closest distance to " O   SER A 276 " =    1.684
peak=   -3.599 closest distance to " O   HOH Z  52 " =    2.249
peak=   -3.591 closest distance to " CB  SER A 146 " =    2.204
peak=   -3.588 closest distance to " CG1BVAL A  72 " =    2.603
peak=   -3.584 closest distance to " O   PRO A 198 " =    1.313
peak=   -3.559 closest distance to " O   HOH Z 234 " =    4.609
peak=   -3.550 closest distance to " CD1 LEU A  25 " =    2.467
peak=   -3.548 closest distance to " O   HOH Z 261 " =    1.144
peak=   -3.545 closest distance to " SG ACYS A 201 " =    1.003
peak=   -3.544 closest distance to " O   HOH Z 120 " =    4.565
peak=   -3.544 closest distance to " O   HOH Z  60 " =    1.914
peak=   -3.543 closest distance to " O   HOH Z  39 " =    0.758
peak=   -3.520 closest distance to " O   HOH Z 177 " =    1.848
peak=   -3.515 closest distance to " O   HOH Z  49 " =    0.706
peak=   -3.514 closest distance to " NH1 ARG A 195 " =    0.916
peak=   -3.514 closest distance to " CE2 TYR A  30 " =    2.801
peak=   -3.514 closest distance to " N   ILE A 120 " =    0.992
peak=   -3.513 closest distance to " O   HOH Z  92 " =    1.139
peak=   -3.511 closest distance to " OD1 ASN A 173 " =    1.336
peak=   -3.502 closest distance to " O   SER A 135 " =    2.111
peak=   -3.495 closest distance to " CG2 THR A  18 " =    2.820
peak=   -3.488 closest distance to " CG  ARG A 219 " =    2.572
peak=   -3.486 closest distance to " O   HOH Z 275 " =    1.737
peak=   -3.480 closest distance to " NE2 GLN A 103 " =    1.892
peak=   -3.475 closest distance to " CD  GLN A  73 " =    0.725
peak=   -3.472 closest distance to " CE3 TRP A  70 " =    1.828
peak=   -3.472 closest distance to " CG  LEU A 101 " =    2.604
peak=   -3.472 closest distance to " CD  GLU A 236 " =    1.046
peak=   -3.460 closest distance to " O   HOH Z 246 " =    1.098
peak=   -3.459 closest distance to " CD1 ILE A 263 " =    2.479
peak=   -3.458 closest distance to " CG2 THR A 221 " =    2.360
peak=   -3.453 closest distance to " OD2 ASP A 298 " =    1.075
peak=   -3.449 closest distance to " O   HOH Z 377 " =    1.732
peak=   -3.447 closest distance to " O   HOH Z 387 " =    3.692
peak=   -3.447 closest distance to " OG1 THR A  82 " =    2.123
peak=   -3.442 closest distance to " O   HOH Z 285 " =    1.579
peak=   -3.438 closest distance to " OD1 ASN A 148 " =    1.425
peak=   -3.438 closest distance to " O   HOH Z 368 " =    1.888
peak=   -3.432 closest distance to " CZ  ARG A  79 " =    1.785
peak=   -3.423 closest distance to " O   HOH Z 351 " =    1.740
peak=   -3.421 closest distance to " O   SER A 164 " =    1.964
peak=   -3.420 closest distance to " NH2 ARG A 156 " =    1.175
peak=   -3.419 closest distance to " O   HOH Z 200 " =    1.455
peak=   -3.417 closest distance to " O   HOH Z 394 " =    1.817
peak=   -3.410 closest distance to " CA  SER A 164 " =    2.220
peak=   -3.407 closest distance to " CD2 LEU A 167 " =    1.860
peak=   -3.407 closest distance to " O   HOH Z  82 " =    1.145
peak=   -3.403 closest distance to " O   HOH Z 120 " =    1.001
peak=   -3.399 closest distance to " O   HOH Z  83 " =    1.496
peak=   -3.398 closest distance to " O   HOH Z 250 " =    1.443
peak=   -3.395 closest distance to " O   HOH Z  38 " =    0.946
peak=   -3.392 closest distance to " O   HOH Z  57 " =    0.753
peak=   -3.390 closest distance to " CD1 TYR A 247 " =    2.479
peak=   -3.389 closest distance to " O   HOH Z   6 " =    1.534
peak=   -3.385 closest distance to " CA  ASN A 127 " =    1.041
peak=   -3.369 closest distance to " O   HOH Z 151 " =    0.771
peak=   -3.361 closest distance to " CG1 VAL A 197 " =    2.581
peak=   -3.360 closest distance to " O   HOH Z 150 " =    1.327
peak=   -3.357 closest distance to " O   HOH Z 198 " =    1.627
peak=   -3.355 closest distance to " CG  LEU A   5 " =    1.615
peak=   -3.353 closest distance to " O   HOH Z 157 " =    3.481
peak=   -3.352 closest distance to " CD  GLN A  58 " =    1.212
peak=   -3.344 closest distance to " O   HOH Z 231 " =    1.363
peak=   -3.344 closest distance to " O   HOH Z 109 " =    0.975
peak=   -3.344 closest distance to " CB  PHE A 130 " =    1.238
peak=   -3.339 closest distance to " CB  SER A  63 " =    3.382
peak=   -3.339 closest distance to " O   HOH Z  70 " =    2.277
peak=   -3.333 closest distance to " O   HOH Z 165 " =    1.961
peak=   -3.330 closest distance to " CG1 VAL A 112 " =    2.926
peak=   -3.330 closest distance to " CD2 LEU A 228 " =    2.589
peak=   -3.329 closest distance to " O   HOH Z 252 " =    3.644
peak=   -3.329 closest distance to " O   VAL A  67 " =    2.527
peak=   -3.327 closest distance to " O   HOH Z 174 " =    2.289
peak=   -3.325 closest distance to " O   THR A 251 " =    1.755
peak=   -3.325 closest distance to " CA  GLY A 229 " =    2.477
peak=   -3.324 closest distance to " NH2 ARG A  66 " =    0.930
peak=   -3.323 closest distance to " O   HOH Z 407 " =    1.174
peak=   -3.320 closest distance to " N   ASP A 272 " =    1.330
peak=   -3.318 closest distance to " NE2 HIS A  86 " =    0.950
peak=   -3.318 closest distance to " O   HOH Z 189 " =    2.448
peak=   -3.317 closest distance to " N   THR A  52 " =    1.618
peak=   -3.315 closest distance to " O   HOH Z 418 " =    1.329
peak=   -3.312 closest distance to " CG  ARG A 259 " =    2.499
peak=   -3.310 closest distance to " CG  LEU A   5 " =    0.924
peak=   -3.308 closest distance to " O   HOH Z 105 " =    2.168
peak=   -3.306 closest distance to " CB  ALA A  10 " =    2.104
peak=   -3.302 closest distance to " O   HOH Z  94 " =    1.724
peak=   -3.291 closest distance to " CA  ASN A 110 " =    1.022
peak=   -3.286 closest distance to " O   HOH Z 424 " =    2.999
peak=   -3.281 closest distance to " O   HOH Z 277 " =    1.434
peak=   -3.275 closest distance to " CG  TRP A 266 " =    1.909
peak=   -3.274 closest distance to " O   GLY A  17 " =    1.301
peak=   -3.271 closest distance to " OD2 ASP A 171 " =    1.991
peak=   -3.266 closest distance to " O   HOH Z 435 " =    1.744
peak=   -3.265 closest distance to " O   HOH Z 118 " =    1.210
peak=   -3.259 closest distance to " CB  ALA A 291 " =    2.407
peak=   -3.259 closest distance to " C   ALA A 158 " =    1.317
peak=   -3.257 closest distance to " CH2 TRP A 177 " =    2.266
peak=   -3.256 closest distance to " O   HOH Z 184 " =    1.168
peak=   -3.253 closest distance to " CA  GLY A 133 " =    2.425
peak=   -3.251 closest distance to " CA  PRO A 198 " =    0.874
peak=   -3.247 closest distance to " O   HOH Z 265 " =    1.531
peak=   -3.244 closest distance to " O   HOH Z 410 " =    1.514
peak=   -3.236 closest distance to " CD  GLN A  77 " =    0.972
peak=   -3.225 closest distance to " O   HOH Z 287 " =    2.168
peak=   -3.224 closest distance to " O   HOH Z 140 " =    2.136
peak=   -3.220 closest distance to " CZ  ARG A 259 " =    0.920
peak=   -3.214 closest distance to " CD2 HIS A 115 " =    0.989
peak=   -3.213 closest distance to " CD2 TRP A 274 " =    2.531
peak=   -3.213 closest distance to " O   HOH Z 166 " =    1.492
peak=   -3.210 closest distance to " CB  THR A  18 " =    1.316
peak=   -3.208 closest distance to " OG1 THR A 157 " =    1.772
peak=   -3.204 closest distance to " O   HOH Z 134 " =    2.022
peak=   -3.203 closest distance to " O   LEU A 255 " =    1.724
peak=   -3.200 closest distance to " OG1 THR A  82 " =    1.332
peak=   -3.195 closest distance to " CD  ARG A  14 " =    3.244
peak=   -3.194 closest distance to " O   HOH Z 110 " =    1.398
peak=   -3.191 closest distance to " O   HOH Z 115 " =    3.884
peak=   -3.187 closest distance to " CB  PRO A 163 " =    2.537
peak=   -3.183 closest distance to " CG2 VAL A 202 " =    2.191
peak=   -3.183 closest distance to " OD1 ASN A 301 " =    0.796
peak=   -3.178 closest distance to " O   HOH Z 396 " =    1.826
peak=   -3.174 closest distance to " O   HOH Z 317 " =    2.040
peak=   -3.173 closest distance to " OG  SER A  22 " =    2.182
peak=   -3.173 closest distance to " O   HOH Z 196 " =    2.021
peak=   -3.171 closest distance to " O   PHE A 218 " =    1.520
peak=   -3.170 closest distance to " O   HOH Z 165 " =    2.308
peak=   -3.170 closest distance to " O   HOH Z 384 " =    1.946
peak=   -3.167 closest distance to " O   HOH Z 137 " =    1.474
peak=   -3.166 closest distance to " O   HOH Z  54 " =    1.207
peak=   -3.159 closest distance to " O   HOH Z 350 " =    1.801
peak=   -3.155 closest distance to " CB  ALA A   9 " =    2.650
peak=   -3.155 closest distance to " CD1 LEU A 101 " =    2.561
peak=   -3.148 closest distance to " O   HOH Z 280 " =    1.968
peak=   -3.141 closest distance to " NH1AARG A 102 " =    1.784
peak=   -3.139 closest distance to " O   HOH Z 393 " =    5.059
peak=   -3.137 closest distance to " O   HOH Z 313 " =    0.890
peak=   -3.133 closest distance to " O   SER A 210 " =    2.061
peak=   -3.132 closest distance to " OG  SER A  87 " =    1.863
peak=   -3.129 closest distance to " O   HOH Z  64 " =    1.850
peak=   -3.108 closest distance to " OG  SER A 245 " =    0.978
peak=   -3.101 closest distance to " O   LEU A 101 " =    2.780
peak=   -3.099 closest distance to " CE2 PHE A  61 " =    2.557
peak=   -3.099 closest distance to " CG  ARG A 219 " =    2.822
peak=   -3.094 closest distance to " O   ASP A 253 " =    2.015
peak=   -3.094 closest distance to " O   HOH Z 151 " =    1.000
peak=   -3.092 closest distance to " CD1 ILE A 151 " =    2.447
peak=   -3.086 closest distance to " CA  GLY A 241 " =    3.263
peak=   -3.082 closest distance to " CG1 VAL A 112 " =    2.729
peak=   -3.079 closest distance to " OE1 GLN A  88 " =    0.924
peak=   -3.075 closest distance to " O   HOH Z 429 " =    1.354
peak=   -3.063 closest distance to " N   GLN A  58 " =    1.338
peak=   -3.053 closest distance to " O   HOH Z 290 " =    1.404
peak=   -3.042 closest distance to " O   HOH Z  44 " =    0.827
peak=   -3.041 closest distance to " O   HOH Z  69 " =    1.744
peak=   -3.035 closest distance to " CD  PRO A 243 " =    1.911
peak=   -3.034 closest distance to " O   ASP A 107 " =    2.138
peak=   -3.018 closest distance to " CD1 LEU A 101 " =    2.551

================= 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    :  0.5179 0.5004   6.307720e+00   6.293989e+00
   1_bss:  0.5121 0.4976   6.305782e+00   6.289611e+00
   1_xyz:  0.4499 0.4605   6.242842e+00   6.256027e+00
   1_adp:  0.4100 0.4527   6.195595e+00   6.246556e+00
   1_occ:  0.4091 0.4539   6.195521e+00   6.247209e+00
   2_bss:  0.4083 0.4520   6.197191e+00   6.247196e+00
   2_xyz:  0.3379 0.4081   6.072829e+00   6.181150e+00
   2_adp:  0.3222 0.3871   6.039218e+00   6.150944e+00
   2_occ:  0.3220 0.3879   6.038966e+00   6.152021e+00
   3_bss:  0.3216 0.3867   6.038510e+00   6.150930e+00
   3_xyz:  0.2527 0.3077   5.838740e+00   5.985283e+00
   3_adp:  0.2365 0.2960   5.789667e+00   5.954642e+00
   3_occ:  0.2363 0.2961   5.788500e+00   5.953787e+00
   4_bss:  0.2359 0.2951   5.787017e+00   5.952730e+00
   4_xyz:  0.1900 0.2461   5.603139e+00   5.803296e+00
   4_adp:  0.1696 0.2191   5.498559e+00   5.703774e+00
   4_occ:  0.1693 0.2192   5.497803e+00   5.703348e+00
   5_bss:  0.1696 0.2201   5.499473e+00   5.705115e+00
   5_xyz:  0.1432 0.1918   5.350217e+00   5.572954e+00
   5_adp:  0.1357 0.1879   5.313183e+00   5.548233e+00
   5_occ:  0.1356 0.1877   5.312619e+00   5.547648e+00
   5_bss:  0.1356 0.1876   5.312104e+00   5.546483e+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:  0.278  20.001   7.902   9.608   8.552   0.000   0.000   0.000
   1_xyz:  0.278  20.001   7.902   9.608   8.552   0.000   0.000   0.000
   1_adp:  0.278  20.001   7.902   9.608   8.552   0.000   0.000   0.000
   1_occ:  0.278  20.001   7.902   9.608   8.552   0.000   0.000   0.000
   2_bss:  0.311  80.000   4.749   6.061   5.507   0.000   0.000   0.000
   2_xyz:  0.311  80.000   4.749   6.061   5.507   0.000   0.000   0.000
   2_adp:  0.311  80.000   4.749   6.061   5.507   0.000   0.000   0.000
   2_occ:  0.311  80.000   4.749   6.061   5.507   0.000   0.000   0.000
   3_bss:  0.324  80.000   3.481   4.525   4.065   0.000   0.000   0.000
   3_xyz:  0.324  80.000   3.481   4.525   4.065   0.000   0.000   0.000
   3_adp:  0.324  80.000   3.481   4.525   4.065   0.000   0.000   0.000
   3_occ:  0.324  80.000   3.481   4.525   4.065   0.000   0.000   0.000
   4_bss:  0.335  80.179   2.220   2.962   2.789   0.000   0.000   0.000
   4_xyz:  0.335  80.179   2.220   2.962   2.789   0.000   0.000   0.000
   4_adp:  0.335  80.179   2.220   2.962   2.789   0.000   0.000   0.000
   4_occ:  0.335  80.179   2.220   2.962   2.789   0.000   0.000   0.000
   5_bss:  0.321  80.000   1.637   2.203   2.705   0.000   0.000   0.000
   5_xyz:  0.321  80.000   1.637   2.203   2.705   0.000   0.000   0.000
   5_adp:  0.321  80.000   1.637   2.203   2.705   0.000   0.000   0.000
   5_occ:  0.321  80.000   1.637   2.203   2.705   0.000   0.000   0.000
   5_bss:  0.326  79.099  -0.528  -0.144   0.672   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.967 0.3155  0.3572    80129.326
   1_bss:  65.291 0.3236  0.4672    79089.594
   1_xyz:  57.744 0.4205  0.5958    65262.274
   1_adp:  55.436 0.4505  0.6970    62416.385
   1_occ:  55.665 0.4476  0.6917    62893.230
   2_bss:  55.590 0.4486  0.6260    62856.766
   2_xyz:  47.802 0.5458  0.7662    48748.773
   2_adp:  44.031 0.5929  0.8164    43428.157
   2_occ:  44.092 0.5922  0.8154    43532.774
   3_bss:  43.973 0.5935  0.7788    43220.330
   3_xyz:  32.442 0.7303  0.9285    25932.688
   3_adp:  30.663 0.7507  0.9369    23849.048
   3_occ:  30.616 0.7512  0.9372    23773.473
   4_bss:  30.494 0.7523  0.8942    23562.416
   4_xyz:  24.928 0.8114  0.9392    15935.341
   4_adp:  21.558 0.8461  0.9456    12534.212
   4_occ:  21.547 0.8463  0.9455    12534.680
   5_bss:  21.594 0.8459  0.9294    12603.937
   5_xyz:  18.028 0.8803  0.9532     9407.527
   5_adp:  17.299 0.8874  0.9499     8975.863
   5_occ:  17.286 0.8875  0.9499     8962.859
   5_bss:  17.255 0.8877  0.9522     8928.091
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4895e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4895e+01
   1_xyz:   1.853  0.015  0.116 18.342  0.008  4.128   1.6859e-01
   1_adp:   1.853  0.015  0.116 18.342  0.008  4.128   1.6859e-01
   1_occ:   1.853  0.015  0.116 18.342  0.008  4.128   1.6859e-01
   2_bss:   1.853  0.015  0.116 18.342  0.008  4.128   1.6859e-01
   2_xyz:   1.387  0.011  0.092 16.894  0.005  4.114   1.1730e-01
   2_adp:   1.387  0.011  0.092 16.894  0.005  4.114   1.1730e-01
   2_occ:   1.387  0.011  0.092 16.894  0.005  4.114   1.1730e-01
   3_bss:   1.387  0.011  0.092 16.894  0.005  4.114   1.1730e-01
   3_xyz:   1.263  0.010  0.090 15.931  0.004  4.110   9.8144e-02
   3_adp:   1.263  0.010  0.090 15.931  0.004  4.110   9.8144e-02
   3_occ:   1.263  0.010  0.090 15.931  0.004  4.110   9.8144e-02
   4_bss:   1.263  0.010  0.090 15.931  0.004  4.110   9.8144e-02
   4_xyz:   1.242  0.011  0.088 15.799  0.004  4.133   9.5674e-02
   4_adp:   1.242  0.011  0.088 15.799  0.004  4.133   9.5674e-02
   4_occ:   1.242  0.011  0.088 15.799  0.004  4.133   9.5674e-02
   5_bss:   1.242  0.011  0.088 15.799  0.004  4.133   9.5674e-02
   5_xyz:   1.249  0.012  0.092 15.794  0.004  4.121   9.3229e-02
   5_adp:   1.249  0.012  0.092 15.794  0.004  4.121   9.3229e-02
   5_occ:   1.249  0.012  0.092 15.794  0.004  4.121   9.3229e-02
   5_bss:   1.249  0.012  0.092 15.794  0.004  4.121   9.3229e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1175e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1175e+00
   1_xyz:  15.682  0.139  0.481 86.373  0.056  2.082   1.1702e-01
   1_adp:  15.682  0.139  0.481 86.373  0.056  2.082   1.1702e-01
   1_occ:  15.682  0.139  0.481 86.373  0.056  2.082   1.1702e-01
   2_bss:  15.682  0.139  0.481 86.373  0.056  2.082   1.1702e-01
   2_xyz:   8.196  0.148  0.295 81.016  0.052  2.032   1.3511e-01
   2_adp:   8.196  0.148  0.295 81.016  0.052  2.032   1.3511e-01
   2_occ:   8.196  0.148  0.295 81.016  0.052  2.032   1.3511e-01
   3_bss:   8.196  0.148  0.295 81.016  0.052  2.032   1.3511e-01
   3_xyz:   8.837  0.063  0.299 78.055  0.028  2.200   1.8322e-01
   3_adp:   8.837  0.063  0.299 78.055  0.028  2.200   1.8322e-01
   3_occ:   8.837  0.063  0.299 78.055  0.028  2.200   1.8322e-01
   4_bss:   8.837  0.063  0.299 78.055  0.028  2.200   1.8322e-01
   4_xyz:   8.888  0.065  0.287 80.177  0.049  2.223   1.6397e-01
   4_adp:   8.888  0.065  0.287 80.177  0.049  2.223   1.6397e-01
   4_occ:   8.888  0.065  0.287 80.177  0.049  2.223   1.6397e-01
   5_bss:   8.888  0.065  0.287 80.177  0.049  2.223   1.6397e-01
   5_xyz:   9.334  0.075  0.533 80.575  0.041  2.191   7.6025e-02
   5_adp:   9.334  0.075  0.533 80.575  0.041  2.191   7.6025e-02
   5_occ:   9.334  0.075  0.533 80.575  0.041  2.191   7.6025e-02
   5_bss:   9.334  0.075  0.533 80.575  0.041  2.191   7.6025e-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: 127.07   0.00  17.21  91.88   0.00  15.04 127.07   0.00  29.02
   1_occ: 127.07   0.00  17.21  91.88   0.00  15.04 127.07   0.00  29.02
   2_bss: 127.07   0.00  17.21  91.88   0.00  15.04 127.07   0.00  29.02
   2_xyz: 127.07   0.00  17.21  91.88   0.00  15.04 127.07   0.00  29.02
   2_adp: 137.93   0.00  14.97 101.12   0.00  12.04 137.93   0.00  30.90
   2_occ: 137.93   0.00  14.97 101.12   0.00  12.04 137.93   0.00  30.90
   3_bss: 137.93   0.00  14.97 101.12   0.00  12.04 137.93   0.00  30.90
   3_xyz: 137.93   0.00  14.97 101.12   0.00  12.04 137.93   0.00  30.90
   3_adp: 137.61   0.00  14.82 102.23   0.00  11.40 137.61   0.00  33.46
   3_occ: 137.61   0.00  14.82 102.23   0.00  11.40 137.61   0.00  33.46
   4_bss: 137.61   0.00  14.82 102.23   0.00  11.40 137.61   0.00  33.46
   4_xyz: 137.61   0.00  14.82 102.23   0.00  11.40 137.61   0.00  33.46
   4_adp: 123.86   0.00  14.16 104.62   0.00   9.70 123.86   1.92  38.46
   4_occ: 123.86   0.00  14.16 104.62   0.00   9.70 123.86   1.92  38.46
   5_bss: 123.86   0.00  14.16 104.62   0.00   9.70 123.86   1.92  38.46
   5_xyz: 123.86   0.00  14.16 104.62   0.00   9.70 123.86   1.92  38.46
   5_adp: 115.84   0.00  14.35 105.67   0.00   9.45 115.84   2.04  41.04
   5_occ: 115.84   0.00  14.35 105.67   0.00   9.45 115.84   2.04  41.04
   5_bss: 118.10   2.26  16.60 107.93   2.26  11.70 118.10   4.29  43.29
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.191    0.020    0.419
   1_adp:    1.191    0.020    0.419
   1_occ:    1.191    0.020    0.419
   2_bss:    1.191    0.020    0.419
   2_xyz:    1.647    0.018    0.612
   2_adp:    1.647    0.018    0.612
   2_occ:    1.647    0.018    0.612
   3_bss:    1.647    0.018    0.612
   3_xyz:    1.667    0.030    0.754
   3_adp:    1.667    0.030    0.754
   3_occ:    1.667    0.030    0.754
   4_bss:    1.667    0.030    0.754
   4_xyz:    1.826    0.075    0.864
   4_adp:    1.826    0.075    0.864
   4_occ:    1.826    0.075    0.864
   5_bss:    1.826    0.075    0.864
   5_xyz:    1.936    0.078    0.916
   5_adp:    1.936    0.078    0.916
   5_occ:    1.936    0.078    0.916
   5_bss:    1.936    0.078    0.916
------------------------------------------------------------------------

CPU time actual refinement: 356.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1317/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_1317/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1317/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1317/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1317/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.54 
  Macro-tasks:
    bulk solvent and scale       = 64.08  
    individual site refinement   = 131.77 
    weights calculation          = 32.23  
    collect and process          = 6.40   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 234.61 
  Micro-tasks:
    mask                            = 2.88   
    f_calc                          = 103.26 
    alpha_beta                      = 8.54   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 112.06 
    fmodel                         = 10.88  
    r_factors                      = 0.52   
    phase_errors                   = 10.09  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 249.58 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.031 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    648 calls, 102.94 s
gradients_fft:          592 calls,  99.75 s

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

# Date 2008-01-16 Time 03:44:29 PST -0800 (1200483869.41 s)
Start R-work = 0.5179, R-free = 0.5004 (no bulk solvent and anisotropic scale)
Final R-work = 0.1506, R-free = 0.2020 (no bulk solvent and anisotropic scale)

Start R-work = 0.5121, R-free = 0.4976
Final R-work = 0.1356, R-free = 0.1876