# Date 2008-01-16 Time 02:52:20 PST -0800 (1200480740.48 s)
#phil __OFF__

Command line arguments: "../1012.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 779
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1012

-------------------------------------------------------------------------------
  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: (71.3037, 46.6953, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.81, per 1000 atoms: 1.00


================================== 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: (71.3037, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95125
Completeness in resolution range: 0.930638
Completeness with d_max=infinity: 0.927905

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0490
                             d_min =   1.9513

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: (71.3037, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95125
Completeness in resolution range: 0.930638
Completeness with d_max=infinity: 0.927905

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0495 -  4.1767 [2205/2235]  1988   217   9.8%
  bin  2:  4.1767 -  3.3270 [2121/2140]  1906   215  10.1%
  bin  3:  3.3270 -  2.9099 [2096/2116]  1884   212  10.1%
  bin  4:  2.9099 -  2.6454 [2081/2106]  1880   201   9.7%
  bin  5:  2.6454 -  2.4566 [2056/2075]  1845   211  10.3%
  bin  6:  2.4566 -  2.3123 [2056/2103]  1855   201   9.8%
  bin  7:  2.3123 -  2.1969 [2046/2078]  1834   212  10.4%
  bin  8:  2.1969 -  2.1015 [2015/2052]  1819   196   9.7%
  bin  9:  2.1015 -  2.0208 [2039/2084]  1833   206  10.1%
  bin 10:  2.0208 -  1.9513 [ 874/2060]   786    88  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1012/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: 0.11 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:
        1.59 -     2.25: 24
        2.25 -     2.91: 1495
        2.91 -     3.58: 4521
        3.58 -     4.24: 9270
        4.24 -     4.90: 13267
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.589 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.688 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.744 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.757 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28572 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_1012/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1012/model_refine_001.geo

CPU time processing inputs: 8.22


============================ 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 = 71.30375 46.69535 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4808   r_free= 0.4731   ksol= 0.00   Bsol= 0.00   scale= 0.796    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.282486                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6592 0.99   1429  161 0.3991 0.4068      6.5962      6.6144|
|  2:  4.6592 -  3.7165 0.99   1386  149 0.4026 0.4082      6.7905      6.8419|
|  3:  3.7165 -  3.2521 0.99   1348  154 0.4528 0.3973      6.6743      6.6982|
|  4:  3.2521 -  2.9572 0.99   1358  151 0.4675 0.4520      6.5193      6.5074|
|  5:  2.9572 -  2.7466 0.99   1327  144 0.5050 0.4942      6.3655      6.3468|
|  6:  2.7466 -  2.5855 0.98   1326  151 0.5136 0.5433      6.2737      6.2443|
|  7:  2.5855 -  2.4566 0.99   1329  146 0.5150 0.4755      6.2504      6.1658|
|  8:  2.4566 -  2.3501 0.98   1306  148 0.5325 0.5325      6.1614      6.1833|
|  9:  2.3501 -  2.2600 0.98   1322  146 0.5204 0.4832      6.1251       6.065|
| 10:  2.2600 -  2.1822 0.98   1307  149 0.5229 0.5404      6.0815      6.1139|
| 11:  2.1822 -  2.1142 0.99   1339  143 0.5216 0.5329      6.0355      6.0369|
| 12:  2.1142 -  2.0539 0.98   1297  143 0.5293 0.5472      5.9452      5.9779|
| 13:  2.0539 -  1.9999 0.88   1159  140 0.5327 0.5127      5.8759      5.8369|
| 14:  1.9999 -  1.9513 0.29    397   34 0.5438 0.5504      5.8048      5.8048|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6592  1429   161  0.68  36.19   0.80     0.72      77457.93|
|  2:  4.6592 -  3.7165  1386   149  0.69  36.30   0.87     0.77     112383.29|
|  3:  3.7165 -  3.2521  1348   154  0.57  45.96   0.83     0.72     121445.84|
|  4:  3.2521 -  2.9572  1358   151  0.49  52.88   0.81     0.62     108986.48|
|  5:  2.9572 -  2.7466  1327   144  0.39  60.57   0.74     0.48      88242.77|
|  6:  2.7466 -  2.5855  1326   151  0.37  61.87   0.72     0.46      74956.57|
|  7:  2.5855 -  2.4566  1329   146  0.37  62.00   0.74     0.42      64352.74|
|  8:  2.4566 -  2.3501  1306   148  0.37  62.23   0.72     0.45      58035.45|
|  9:  2.3501 -  2.2600  1322   146  0.36  63.08   0.75     0.43      52456.45|
| 10:  2.2600 -  2.1822  1307   149  0.34  64.57   0.75     0.42      50509.41|
| 11:  2.1822 -  2.1142  1339   143  0.30  67.77   0.78     0.37      48520.81|
| 12:  2.1142 -  2.0539  1297   143  0.25  71.55   0.75     0.32      45971.67|
| 13:  2.0539 -  1.9999  1159   140  0.22  73.35   0.74     0.29      40607.73|
| 14:  1.9999 -  1.9513   397    34  0.21  74.54   0.70     0.26      34703.27|
|alpha:            min =        0.26 max =            0.77 mean =         0.50|
|beta:             min =    34703.27 max =       121445.84 mean =     72420.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.30|
|phase err.(test): min =        0.00 max =           90.00 mean =        58.45|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.103613             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.128   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.331940              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.317   (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:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      703 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1533 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2669 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3931 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5131 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6610 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7788 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.368 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.963 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4860   r_free= 0.4807   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.284870                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4731   r_free= 0.4647   ksol= 0.37   Bsol= 20.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.79,7.16,9.12,0.00,0.00,0.00); trace/3= 8.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.279748                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.023141             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.783   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.187456              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.708   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4731      final r-factor (work) = 0.4003          |
| start r-factor (free) = 0.4647      final r-factor (free) = 0.4259          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.1164 = 12.02 * 0.50 * 6.2794 + 1.00 * 53.3676                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.4347 = 12.02 * 0.50 * 6.2043 + 1.00 * 0.1374                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4003      final r-factor (work) = 0.3570          |
| start r-factor (free) = 0.4259      final r-factor (free) = 0.4152          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3816 = 1.19 * 1.00 * 6.2043 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2919 = 1.19 * 1.00 * 6.1273 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.13  13.68    None  None   None       |
|    all(noH): 2823   0      0.00    104.13  13.68    None  None   None       |
|    Sol.    : 438    0      0.00    78.18   26.59    None  None   None       |
|    Mac.    : 2385   0      0.00    104.13  11.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.413: 1429   |   5:    52.064 -  62.477:   26        |
|      1:    10.413 -  20.826:  778   |   6:    62.477 -  72.889:    8        |
|      2:    20.826 -  31.238:  364   |   7:    72.889 -  83.302:    4        |
|      3:    31.238 -  41.651:  142   |   8:    83.302 -  93.715:    1        |
|      4:    41.651 -  52.064:   69   |   9:    93.715 - 104.128:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3570 r_free = 0.4152             target_work(ml) = 6.114         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3565 r_free = 0.4151             target_work(ml) = 6.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3565   r_free= 0.4151   ksol= 0.37   Bsol= 20.00   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.79,7.16,9.12,0.00,0.00,0.00); trace/3= 8.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.112883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3536   r_free= 0.4117   ksol= 0.33   Bsol= 34.18   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.24,3.61,6.12,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.113016                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.218082              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.901   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553537              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.108  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3536      final r-factor (work) = 0.2720          |
| start r-factor (free) = 0.4117      final r-factor (free) = 0.3339          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2984 = 8.22 * 0.50 * 6.1233 + 1.00 * 0.1374                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7867 = 8.22 * 0.50 * 6.0125 + 1.00 * 0.0812                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2720      final r-factor (work) = 0.2516          |
| start r-factor (free) = 0.3339      final r-factor (free) = 0.3168          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3441 = 0.55 * 1.00 * 6.0125 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2759 = 0.55 * 1.00 * 5.8763 + 1.00 * 0.0232                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.92   13.83    None  None   None       |
|    all(noH): 2823   0      0.00    99.92   13.83    None  None   None       |
|    Sol.    : 438    0      0.00    78.85   31.61    None  None   None       |
|    Mac.    : 2385   0      0.00    99.92   10.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.992: 1482   |   5:    49.962 -  59.954:   25        |
|      1:     9.992 -  19.985:  695   |   6:    59.954 -  69.946:   12        |
|      2:    19.985 -  29.977:  300   |   7:    69.946 -  79.939:    3        |
|      3:    29.977 -  39.969:  199   |   8:    79.939 -  89.931:    1        |
|      4:    39.969 -  49.962:  104   |   9:    89.931 -  99.923:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2516 r_free = 0.3168             target_work(ml) = 5.852         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2514 r_free = 0.3168             target_work(ml) = 5.852         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2514   r_free= 0.3168   ksol= 0.33   Bsol= 34.18   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.24,3.61,6.12,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.851694                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2499   r_free= 0.3142   ksol= 0.32   Bsol= 34.18   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,1.93,3.68,0.00,0.00,0.00); trace/3= 2.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.850183                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.492559              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.870  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.841233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.516   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2499      final r-factor (work) = 0.1828          |
| start r-factor (free) = 0.3142      final r-factor (free) = 0.2403          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2255 = 5.49 * 0.50 * 5.8786 + 1.00 * 0.0812                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8197 = 5.49 * 0.50 * 5.7344 + 1.00 * 0.0714                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1828      final r-factor (work) = 0.1599          |
| start r-factor (free) = 0.2403      final r-factor (free) = 0.2195          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.0399 = 3.84 * 1.00 * 5.7344 + 1.00 * 0.0126                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.2125 = 3.84 * 1.00 * 5.5182 + 1.00 * 0.0158                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.97  14.96    None  None   None       |
|    all(noH): 2823   0      0.00    110.97  14.96    None  None   None       |
|    Sol.    : 438    0      1.90    94.69   41.37    None  None   None       |
|    Mac.    : 2385   0      0.00    110.97  10.11    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 -  11.097: 1715   |   5:    55.487 -  66.584:   84        |
|      1:    11.097 -  22.195:  565   |   6:    66.584 -  77.682:   36        |
|      2:    22.195 -  33.292:  156   |   7:    77.682 -  88.779:    8        |
|      3:    33.292 -  44.390:  147   |   8:    88.779 -  99.877:    5        |
|      4:    44.390 -  55.487:  106   |   9:    99.877 - 110.974:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1599 r_free = 0.2195             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1598 r_free = 0.2193             target_work(ml) = 5.471         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1598   r_free= 0.2193   ksol= 0.32   Bsol= 34.18   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,1.93,3.68,0.00,0.00,0.00); trace/3= 2.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.470740                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1591   r_free= 0.2178   ksol= 0.32   Bsol= 42.50   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,1.31,2.16,0.00,0.00,0.00); trace/3= 1.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.465917                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.802263              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.589  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.659  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1591      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.2178      final r-factor (free) = 0.1883          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8092 = 2.80 * 0.50 * 5.5225 + 1.00 * 0.0714                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6392 = 2.80 * 0.50 * 5.4097 + 1.00 * 0.0595                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1317          |
| start r-factor (free) = 0.1883      final r-factor (free) = 0.1772          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5385 = 0.28 * 1.00 * 5.4097 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5059 = 0.28 * 1.00 * 5.3113 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.26  14.24    None  None   None       |
|    all(noH): 2823   0      0.00    107.26  14.24    None  None   None       |
|    Sol.    : 438    0      3.07    91.32   39.04    None  None   None       |
|    Mac.    : 2385   0      0.00    107.26  9.69     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.726: 1766   |   5:    53.632 -  64.358:   66        |
|      1:    10.726 -  21.453:  556   |   6:    64.358 -  75.084:   33        |
|      2:    21.453 -  32.179:  135   |   7:    75.084 -  85.811:   10        |
|      3:    32.179 -  42.905:  137   |   8:    85.811 -  96.537:    3        |
|      4:    42.905 -  53.632:  115   |   9:    96.537 - 107.263:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1317 r_free = 0.1772             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1315 r_free = 0.1768             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1315   r_free= 0.1768   ksol= 0.32   Bsol= 42.50   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,1.31,2.16,0.00,0.00,0.00); trace/3= 1.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.274855                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1317   r_free= 0.1775   ksol= 0.32   Bsol= 42.49   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.32,1.03,1.63,0.00,0.00,0.00); trace/3= 1.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.277550                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.373644              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.805  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.882224              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.055  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1317      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1775      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3651 = 2.37 * 0.50 * 5.3130 + 1.00 * 0.0595                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2837 = 2.37 * 0.50 * 5.2415 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6350 = 0.88 * 1.00 * 5.2415 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5935 = 0.88 * 1.00 * 5.1933 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.74  14.19    None  None   None       |
|    all(noH): 2823   0      0.00    111.74  14.19    None  None   None       |
|    Sol.    : 438    0      2.89    92.28   39.06    None  None   None       |
|    Mac.    : 2385   0      0.00    111.74  9.62     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 -  11.174: 1809   |   5:    55.868 -  67.042:   62        |
|      1:    11.174 -  22.347:  528   |   6:    67.042 -  78.216:   23        |
|      2:    22.347 -  33.521:  152   |   7:    78.216 -  89.389:    7        |
|      3:    33.521 -  44.695:  129   |   8:    89.389 - 100.563:    6        |
|      4:    44.695 -  55.868:  105   |   9:   100.563 - 111.737:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1643             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1641             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1641   ksol= 0.32   Bsol= 42.49   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.32,1.03,1.63,0.00,0.00,0.00); trace/3= 1.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.191582                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6592 0.99   1429  161 0.1003 0.1303      5.3969      5.5494|
|  2:  4.6592 -  3.7165 0.99   1386  149 0.0897 0.1160       5.461      5.6815|
|  3:  3.7165 -  3.2521 0.99   1348  154 0.1125 0.1651      5.5032      5.8803|
|  4:  3.2521 -  2.9572 0.99   1358  151 0.1333 0.1592      5.5052      5.6354|
|  5:  2.9572 -  2.7466 0.99   1327  144 0.1363 0.1687      5.3574      5.5077|
|  6:  2.7466 -  2.5855 0.98   1326  151 0.1325 0.2022      5.2631      5.5221|
|  7:  2.5855 -  2.4566 0.99   1329  146 0.1336 0.1820      5.2279      5.4626|
|  8:  2.4566 -  2.3501 0.98   1306  148 0.1188 0.1691      5.0754      5.2956|
|  9:  2.3501 -  2.2600 0.98   1322  146 0.1172 0.1990      5.0356        5.36|
| 10:  2.2600 -  2.1822 0.98   1307  149 0.1180 0.1681      4.9939      5.2019|
| 11:  2.1822 -  2.1142 0.99   1339  143 0.1218 0.1911      4.9922      5.3341|
| 12:  2.1142 -  2.0539 0.98   1297  143 0.1190 0.1801       4.927      5.1372|
| 13:  2.0539 -  1.9999 0.88   1159  140 0.1230 0.1788      4.8193      5.0652|
| 14:  1.9999 -  1.9513 0.29    397   34 0.1074 0.1737      4.6421       4.898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6592  1429   161  0.94   8.98   0.98     0.96       7324.07|
|  2:  4.6592 -  3.7165  1386   149  0.95   8.09   1.02     1.01       9092.62|
|  3:  3.7165 -  3.2521  1348   154  0.93  11.90   1.04     1.03      10851.46|
|  4:  3.2521 -  2.9572  1358   151  0.91  15.04   1.01     0.99      11234.20|
|  5:  2.9572 -  2.7466  1327   144  0.90  16.55   0.99     0.97       8874.36|
|  6:  2.7466 -  2.5855  1326   151  0.89  17.52   0.99     0.96       7939.41|
|  7:  2.5855 -  2.4566  1329   146  0.90  16.34   1.00     0.97       6975.88|
|  8:  2.4566 -  2.3501  1306   148  0.90  16.41   0.98     0.95       5528.10|
|  9:  2.3501 -  2.2600  1322   146  0.90  16.41   1.01     0.99       5220.69|
| 10:  2.2600 -  2.1822  1307   149  0.90  15.86   1.00     0.97       4705.63|
| 11:  2.1822 -  2.1142  1339   143  0.89  17.44   1.00     0.96       4955.22|
| 12:  2.1142 -  2.0539  1297   143  0.89  17.28   1.01     1.00       4534.43|
| 13:  2.0539 -  1.9999  1159   140  0.90  16.74   1.00     0.98       3535.21|
| 14:  1.9999 -  1.9513   397    34  0.90  16.14   0.99     0.97       2552.86|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2552.86 max =        11234.20 mean =      6944.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.91|
|phase err.(test): min =        0.00 max =           88.42 mean =        14.35|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1641   ksol= 0.32   Bsol= 44.64   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.02,-0.24,0.22,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.191519                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1641   ksol= 0.32   Bsol= 44.64   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.02,-0.24,0.22,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.191519                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6592 0.99   1429  161 0.1003 0.1304      5.3967      5.5502|
|  2:  4.6592 -  3.7165 0.99   1386  149 0.0898 0.1163      5.4617      5.6828|
|  3:  3.7165 -  3.2521 0.99   1348  154 0.1126 0.1652      5.5036      5.8804|
|  4:  3.2521 -  2.9572 0.99   1358  151 0.1333 0.1592      5.5052      5.6353|
|  5:  2.9572 -  2.7466 0.99   1327  144 0.1363 0.1687      5.3572      5.5072|
|  6:  2.7466 -  2.5855 0.98   1326  151 0.1324 0.2024      5.2631       5.523|
|  7:  2.5855 -  2.4566 0.99   1329  146 0.1337 0.1819      5.2281      5.4627|
|  8:  2.4566 -  2.3501 0.98   1306  148 0.1187 0.1688      5.0754      5.2949|
|  9:  2.3501 -  2.2600 0.98   1322  146 0.1173 0.1991      5.0356      5.3604|
| 10:  2.2600 -  2.1822 0.98   1307  149 0.1179 0.1679      4.9935      5.2007|
| 11:  2.1822 -  2.1142 0.99   1339  143 0.1218 0.1913      4.9918      5.3339|
| 12:  2.1142 -  2.0539 0.98   1297  143 0.1189 0.1799      4.9263      5.1362|
| 13:  2.0539 -  1.9999 0.88   1159  140 0.1229 0.1784      4.8191      5.0643|
| 14:  1.9999 -  1.9513 0.29    397   34 0.1075 0.1747      4.6426      4.9018|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6592  1429   161  0.94   8.99   0.98     0.96       7331.20|
|  2:  4.6592 -  3.7165  1386   149  0.95   8.10   1.02     1.01       9106.85|
|  3:  3.7165 -  3.2521  1348   154  0.93  11.91   1.04     1.03      10866.72|
|  4:  3.2521 -  2.9572  1358   151  0.91  15.04   1.01     0.99      11234.28|
|  5:  2.9572 -  2.7466  1327   144  0.90  16.55   0.99     0.97       8877.42|
|  6:  2.7466 -  2.5855  1326   151  0.89  17.53   0.99     0.96       7942.84|
|  7:  2.5855 -  2.4566  1329   146  0.90  16.35   1.00     0.97       6978.69|
|  8:  2.4566 -  2.3501  1306   148  0.90  16.41   0.98     0.95       5529.60|
|  9:  2.3501 -  2.2600  1322   146  0.90  16.41   1.01     0.99       5217.51|
| 10:  2.2600 -  2.1822  1307   149  0.90  15.86   1.00     0.97       4704.92|
| 11:  2.1822 -  2.1142  1339   143  0.89  17.43   1.00     0.97       4949.03|
| 12:  2.1142 -  2.0539  1297   143  0.89  17.26   1.01     1.00       4526.42|
| 13:  2.0539 -  1.9999  1159   140  0.90  16.74   1.00     0.99       3533.77|
| 14:  1.9999 -  1.9513   397    34  0.90  16.14   0.99     0.97       2555.91|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2555.91 max =        11234.28 mean =      6946.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.91|
|phase err.(test): min =        0.00 max =           88.39 mean =        14.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.723)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.34    113.08  15.53    None  None   None       |
|    all(noH): 2823   0      1.34    113.08  15.53    None  None   None       |
|    Sol.    : 438    0      4.23    93.62   40.40    None  None   None       |
|    Mac.    : 2385   0      1.34    113.08  10.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.339 -  12.513: 1809   |   5:    57.207 -  68.381:   62        |
|      1:    12.513 -  23.686:  528   |   6:    68.381 -  79.555:   23        |
|      2:    23.686 -  34.860:  152   |   7:    79.555 -  90.728:    7        |
|      3:    34.860 -  46.034:  129   |   8:    90.728 - 101.902:    6        |
|      4:    46.034 -  57.207:  105   |   9:   101.902 - 113.076:    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)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.450 - 5.758
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 313
   mapped sites are within: 0.724 - 5.758

peak=   10.120 closest distance to " CB  VAL A 230 " =    1.440
peak=    8.734 closest distance to " CG2 VAL A 296 " =    1.309
peak=    6.491 closest distance to " CD1AILE A 234 " =    1.088
peak=    6.476 closest distance to " O   HOH Z  37 " =    1.660
peak=    6.346 closest distance to " O   HOH Z 278 " =    1.526
peak=    6.206 closest distance to " NH2 ARG A  56 " =    2.238
peak=    6.170 closest distance to " CG  ARG A 138 " =    1.062
peak=    5.848 closest distance to " CG  LEU A   5 " =    1.195
peak=    5.622 closest distance to " O   HOH Z 132 " =    1.578
peak=    5.577 closest distance to " CD2 LEU A   5 " =    1.219
peak=    5.464 closest distance to " NE2 GLN A  11 " =    1.196
peak=    5.402 closest distance to " CB  GLN A 223 " =    1.452
peak=    5.122 closest distance to " CG  PRO A  54 " =    1.238
peak=    5.079 closest distance to " CG  PRO A 213 " =    1.239
peak=    5.063 closest distance to " O   HOH Z 202 " =    1.573
peak=    5.057 closest distance to " NH2BARG A 102 " =    1.014
peak=    5.030 closest distance to " CB  SER A  63 " =    1.331
peak=    4.928 closest distance to " O   HOH Z 120 " =    1.065
peak=    4.900 closest distance to " CG  PRO A 198 " =    1.330
peak=    4.751 closest distance to " O   HOH Z 144 " =    1.755
peak=    4.737 closest distance to " O   HOH Z 427 " =    3.000
peak=    4.697 closest distance to " O   HOH Z 247 " =    1.336
peak=    4.626 closest distance to " CG  LEU A 228 " =    1.244
peak=    4.612 closest distance to " O   HOH Z  48 " =    1.685
peak=    4.591 closest distance to " O   HOH Z 126 " =    1.888
peak=    4.575 closest distance to " O   HOH Z 124 " =    1.348
peak=    4.567 closest distance to " O   HOH Z 205 " =    1.071
peak=    4.565 closest distance to " CB  ASN A 148 " =    1.337
peak=    4.542 closest distance to " CB  TYR A 169 " =    0.905
peak=    4.504 closest distance to " CB  GLN A 183 " =    1.261
peak=    4.485 closest distance to " CA  GLY A 241 " =    3.831
peak=    4.451 closest distance to " O   HOH Z 232 " =    2.238
peak=    4.444 closest distance to " CB  PRO A  54 " =    0.894
peak=    4.439 closest distance to " CB  VAL A 230 " =    1.187
peak=    4.429 closest distance to " O   HOH Z  97 " =    1.147
peak=    4.423 closest distance to " O   HOH Z 117 " =    2.117
peak=    4.390 closest distance to " NH1 ARG A 138 " =    1.027
peak=    4.373 closest distance to " O   HOH Z 371 " =    3.152
peak=    4.368 closest distance to " CB  SER A   3 " =    1.420
peak=    4.362 closest distance to " O   HOH Z 260 " =    1.262
peak=    4.352 closest distance to " O   HOH Z 214 " =    1.288
peak=    4.349 closest distance to " O   HOH Z 263 " =    1.506
peak=    4.326 closest distance to " O   HOH Z  15 " =    2.251
peak=    4.323 closest distance to " O   HOH Z   3 " =    1.947
peak=    4.320 closest distance to " O   HOH Z 193 " =    1.641
peak=    4.316 closest distance to " O   HOH Z 344 " =    1.276
peak=    4.300 closest distance to " O   HOH Z  78 " =    2.155
peak=    4.293 closest distance to " O   HOH Z 126 " =    2.091
peak=    4.291 closest distance to " O   PRO A 198 " =    1.529
peak=    4.283 closest distance to " CB  ARG A 275 " =    0.878
peak=    4.281 closest distance to " CD2 LEU A 228 " =    1.173
peak=    4.280 closest distance to " O   HOH Z 134 " =    1.485
peak=    4.244 closest distance to " CA  VAL A  41 " =    0.981
peak=    4.217 closest distance to " O   HOH Z 272 " =    1.889
peak=    4.203 closest distance to " O   HOH Z 316 " =    2.727
peak=    4.191 closest distance to " O   HOH Z 368 " =    2.010
peak=    4.188 closest distance to " O   HOH Z 303 " =    2.158
peak=    4.186 closest distance to " CA  ALA A  21 " =    1.193
peak=    4.170 closest distance to " O   HOH Z 128 " =    1.897
peak=    4.169 closest distance to " O   HOH Z 108 " =    1.737
peak=    4.124 closest distance to " O   HOH Z 133 " =    1.552
peak=    4.118 closest distance to " O   HOH Z 298 " =    1.897
peak=    4.109 closest distance to " O   HOH Z 217 " =    1.499
peak=    4.097 closest distance to " O   HOH Z 199 " =    1.009
peak=    4.075 closest distance to " O   HOH Z 126 " =    1.601
peak=    4.068 closest distance to " CG2 VAL A 257 " =    0.859
peak=    4.063 closest distance to " CB  LEU A 228 " =    1.313
peak=    4.058 closest distance to " O   HOH Z 346 " =    1.486
peak=    4.056 closest distance to " O   HOH Z 425 " =    1.382
peak=    4.041 closest distance to " OD2 ASP A 286 " =    2.775
peak=    4.040 closest distance to " O   HOH Z 280 " =    3.023
peak=    4.033 closest distance to " CA  LEU A 282 " =    1.076
peak=    4.029 closest distance to " O   HOH Z  88 " =    3.150
peak=    4.024 closest distance to " CB  GLU A 152 " =    1.160
peak=    4.004 closest distance to " O   HOH Z  92 " =    0.895
peak=    4.001 closest distance to " CB  VAL A 265 " =    1.167
peak=    3.993 closest distance to " O   HOH Z 236 " =    1.955
peak=    3.991 closest distance to " NZ  LYS A 117 " =    3.228
peak=    3.990 closest distance to " O   SER A  87 " =    2.374
peak=    3.979 closest distance to " O   HOH Z 369 " =    2.040
peak=    3.969 closest distance to " CG  PRO A 243 " =    1.164
peak=    3.964 closest distance to " CG  LEU A 167 " =    1.114
peak=    3.960 closest distance to " O   HOH Z 389 " =    1.830
peak=    3.947 closest distance to " O   HOH Z 180 " =    2.219
peak=    3.937 closest distance to " O   HOH Z 209 " =    2.337
peak=    3.936 closest distance to " O   HOH Z 112 " =    1.293
peak=    3.933 closest distance to " O   HOH Z  59 " =    1.935
peak=    3.932 closest distance to " NH1 ARG A  56 " =    0.999
peak=    3.928 closest distance to " O   HOH Z 193 " =    1.619
peak=    3.909 closest distance to " CB  GLU A 128 " =    1.149
peak=    3.902 closest distance to " OD1 ASN A  69 " =    2.636
peak=    3.900 closest distance to " CB  VAL A 202 " =    1.594
peak=    3.899 closest distance to " O   HOH Z 227 " =    1.685
peak=    3.896 closest distance to " O   HOH Z 284 " =    1.420
peak=    3.887 closest distance to " O   HOH Z  93 " =    2.667
peak=    3.868 closest distance to " CG  GLN A  88 " =    1.089
peak=    3.867 closest distance to " O   HOH Z  58 " =    1.670
peak=    3.861 closest distance to " O   HOH Z 116 " =    1.718
peak=    3.849 closest distance to " O   HOH Z 326 " =    1.399
peak=    3.848 closest distance to " CD  ARG A 138 " =    1.165
peak=    3.844 closest distance to " O   HOH Z 183 " =    1.285
peak=    3.833 closest distance to " CD1 LEU A 300 " =    1.148
peak=    3.830 closest distance to " CB  ALA A 161 " =    0.945
peak=    3.826 closest distance to " CB  LEU A 237 " =    0.945
peak=    3.826 closest distance to " CA  TYR A  30 " =    1.025
peak=    3.820 closest distance to " CG1BVAL A  72 " =    1.538
peak=    3.804 closest distance to " CA  THR A 221 " =    0.947
peak=    3.801 closest distance to " O   MET A 105 " =    1.699
peak=    3.799 closest distance to " CG2 THR A 221 " =    1.031
peak=    3.798 closest distance to " O   HOH Z 403 " =    1.768
peak=    3.793 closest distance to " O   HOH Z  80 " =    1.715
peak=    3.792 closest distance to " CA  ASN A 215 " =    1.285
peak=    3.778 closest distance to " O   HOH Z  68 " =    1.665
peak=    3.772 closest distance to " O   HOH Z 189 " =    2.689
peak=    3.759 closest distance to " CB  ARG A 139 " =    0.911
peak=    3.757 closest distance to " O   HOH Z 203 " =    1.712
peak=    3.747 closest distance to " OE1 GLU A   2 " =    2.164
peak=    3.742 closest distance to " O   HOH Z 234 " =    3.727
peak=    3.725 closest distance to " CD2 LEU A 255 " =    1.370
peak=    3.723 closest distance to " CA  ALA A 154 " =    1.186
peak=    3.706 closest distance to " CB  TYR A  30 " =    1.623
peak=    3.694 closest distance to " O   HOH Z 193 " =    1.967
peak=    3.680 closest distance to " O   HOH Z 276 " =    1.343
peak=    3.678 closest distance to " CB  LEU A 255 " =    0.824
peak=    3.677 closest distance to " O   HOH Z 357 " =    1.484
peak=    3.674 closest distance to " CB  GLU A 277 " =    3.587
peak=    3.667 closest distance to " O   HOH Z 147 " =    1.171
peak=    3.660 closest distance to " CB  TRP A 179 " =    1.364
peak=    3.655 closest distance to " CG1 ILE A  33 " =    1.318
peak=    3.652 closest distance to " CB  SER A 273 " =    0.914
peak=    3.647 closest distance to " O   HOH Z  20 " =    1.835
peak=    3.639 closest distance to " CA  TYR A 186 " =    1.510
peak=    3.631 closest distance to " CA  ASN A  74 " =    1.333
peak=    3.620 closest distance to " O   HOH Z 186 " =    1.063
peak=    3.619 closest distance to " O   HOH Z 295 " =    1.569
peak=    3.619 closest distance to " O   HOH Z 271 " =    2.058
peak=    3.608 closest distance to " O   HOH Z 281 " =    4.311
peak=    3.601 closest distance to " CB  ARG A  79 " =    1.428
peak=    3.597 closest distance to " NE2 GLN A  58 " =    5.459
peak=    3.596 closest distance to " O   HOH Z  54 " =    1.569
peak=    3.592 closest distance to " O   HOH Z 344 " =    2.795
peak=    3.591 closest distance to " O   HOH Z 192 " =    1.091
peak=    3.588 closest distance to " O   HOH Z 282 " =    1.420
peak=    3.572 closest distance to " CB  GLN A  88 " =    1.264
peak=    3.564 closest distance to " CD BLYS A 290 " =    1.029
peak=    3.561 closest distance to " O   HOH Z 214 " =    1.880
peak=    3.558 closest distance to " O   HOH Z  30 " =    2.009
peak=    3.558 closest distance to " O   HOH Z  30 " =    1.401
peak=    3.557 closest distance to " O   HOH Z 127 " =    1.223
peak=    3.554 closest distance to " CD1 ILE A  33 " =    1.482
peak=    3.548 closest distance to " CZ  PHE A 192 " =    1.109
peak=    3.537 closest distance to " O   HOH Z 236 " =    1.640
peak=    3.530 closest distance to " O   ALA A 158 " =    1.367
peak=    3.516 closest distance to " O   HOH Z 184 " =    1.307
peak=    3.514 closest distance to " CA  ALA A  51 " =    1.071
peak=    3.509 closest distance to " O   HOH Z 345 " =    3.233
peak=    3.509 closest distance to " O   HOH Z 118 " =    1.918
peak=    3.509 closest distance to " O   HOH Z  49 " =    2.330
peak=    3.505 closest distance to " O   HOH Z  61 " =    1.579
peak=    3.501 closest distance to " O   HOH Z  44 " =    1.808
peak=    3.491 closest distance to " CB  TRP A 266 " =    1.026
peak=    3.490 closest distance to " O   HOH Z 261 " =    1.760
peak=    3.489 closest distance to " O   HOH Z  53 " =    2.461
peak=    3.489 closest distance to " O   HOH Z 133 " =    2.178
peak=    3.488 closest distance to " O   HOH Z  49 " =    1.871
peak=    3.483 closest distance to " CG1 VAL A 153 " =    1.025
peak=    3.479 closest distance to " NH1 ARG A  14 " =    1.014
peak=    3.479 closest distance to " CD  ARG A 269 " =    0.888
peak=    3.468 closest distance to " CA  THR A 264 " =    0.767
peak=    3.465 closest distance to " CG BARG A 102 " =    1.910
peak=    3.457 closest distance to " CA  VAL A 126 " =    1.178
peak=    3.457 closest distance to " CB  SER A 216 " =    0.876
peak=    3.449 closest distance to " CA  MET A  40 " =    1.034
peak=    3.445 closest distance to " OD1 ASN A 217 " =    1.595
peak=    3.443 closest distance to " SG ACYS A 201 " =    0.995
peak=    3.441 closest distance to " CB  SER A  62 " =    1.302
peak=    3.426 closest distance to " O   HOH Z 255 " =    1.734
peak=    3.425 closest distance to " CD  LYS A 119 " =    1.498
peak=    3.420 closest distance to " O   HOH Z 355 " =    1.869
peak=    3.412 closest distance to " CA  ARG A  36 " =    1.122
peak=    3.409 closest distance to " CB  LEU A 143 " =    1.125
peak=    3.406 closest distance to " O   HOH Z 332 " =    1.598
peak=    3.400 closest distance to " O   HOH Z 273 " =    2.882
peak=    3.400 closest distance to " CB  ILE A 234 " =    0.980
peak=    3.399 closest distance to " O   HOH Z 151 " =    1.792
peak=    3.397 closest distance to " CG2 VAL A 174 " =    1.375
peak=    3.395 closest distance to " CA  ALA A 295 " =    1.095
peak=    3.394 closest distance to " CA  LEU A 101 " =    1.527
peak=    3.394 closest distance to " CB  THR A 157 " =    0.991
peak=    3.393 closest distance to " CB  THR A  82 " =    1.270
peak=    3.391 closest distance to " O   HOH Z 158 " =    2.733
peak=    3.390 closest distance to " CE1 TYR A 186 " =    1.217
peak=    3.389 closest distance to " CB  LYS A 117 " =    1.190
peak=    3.389 closest distance to " O   HOH Z 359 " =    3.697
peak=    3.387 closest distance to " O   HOH Z 108 " =    1.581
peak=    3.383 closest distance to " OE1 GLN A  11 " =    1.657
peak=    3.372 closest distance to " OG  SER A  22 " =    3.001
peak=    3.369 closest distance to " NH2 ARG A 156 " =    1.117
peak=    3.362 closest distance to " C   ALA A 299 " =    0.959
peak=    3.360 closest distance to " CG  ARG A  66 " =    2.457
peak=    3.352 closest distance to " O   HOH Z 278 " =    1.195
peak=    3.351 closest distance to " O   HOH Z 130 " =    2.247
peak=    3.350 closest distance to " OE2 GLU A  53 " =    1.984
peak=    3.348 closest distance to " O   HOH Z 280 " =    1.628
peak=    3.348 closest distance to " CB  ALA A 291 " =    1.426
peak=    3.347 closest distance to " O   HOH Z  37 " =    2.737
peak=    3.343 closest distance to " O   HOH Z 329 " =    3.373
peak=    3.341 closest distance to " O   HOH Z 422 " =    2.638
peak=    3.340 closest distance to " O   HOH Z  59 " =    1.949
peak=    3.338 closest distance to " NH2BARG A 190 " =    1.611
peak=    3.338 closest distance to " O   HOH Z   9 " =    1.621
peak=    3.336 closest distance to " O   HOH Z  21 " =    1.689
peak=    3.335 closest distance to " CB  VAL A 296 " =    1.038
peak=    3.333 closest distance to " CB  ASP A 124 " =    0.724
peak=    3.331 closest distance to " O   HOH Z 291 " =    1.566
peak=    3.331 closest distance to " O   HOH Z 392 " =    2.896
peak=    3.328 closest distance to " CG  LYS A  76 " =    1.807
peak=    3.324 closest distance to " O   HOH Z 132 " =    2.851
peak=    3.316 closest distance to " CB  GLU A 236 " =    1.306
peak=    3.316 closest distance to " CB  SER A 212 " =    1.060
peak=    3.313 closest distance to " NH1AARG A 145 " =    1.005
peak=    3.310 closest distance to " O   GLN A  58 " =    1.570
peak=    3.304 closest distance to " O   HOH Z 152 " =    2.946
peak=    3.302 closest distance to " CB  ASN A 187 " =    1.129
peak=    3.298 closest distance to " CD  LYS A 166 " =    1.411
peak=    3.293 closest distance to " O   HOH Z 189 " =    3.261
peak=    3.290 closest distance to " CA  ALA A 158 " =    1.078
peak=    3.288 closest distance to " CB  TRP A 150 " =    1.409
peak=    3.287 closest distance to " O   HOH Z 426 " =    1.409
peak=    3.287 closest distance to " CB BVAL A  41 " =    1.290
peak=    3.286 closest distance to " O   VAL A 232 " =    1.955
peak=    3.286 closest distance to " O   HOH Z 244 " =    1.583
peak=    3.283 closest distance to " O   HOH Z 423 " =    1.740
peak=    3.283 closest distance to " O   HOH Z 213 " =    1.939
peak=    3.283 closest distance to " CB  ALA A 248 " =    0.942
peak=    3.279 closest distance to " CB  MET A  40 " =    0.828
peak=    3.276 closest distance to " O   HOH Z 303 " =    1.728
peak=    3.271 closest distance to " O   HOH Z 331 " =    1.235
peak=    3.270 closest distance to " CE  LYS A  76 " =    0.890
peak=    3.269 closest distance to " OG BSER A 164 " =    2.238
peak=    3.266 closest distance to " N   PHE A 130 " =    1.332
peak=    3.264 closest distance to " O   HOH Z 148 " =    3.601
peak=    3.263 closest distance to " CA  GLY A 267 " =    1.254
peak=    3.260 closest distance to " O   HOH Z 207 " =    2.336
peak=    3.257 closest distance to " O   ALA A 291 " =    1.706
peak=    3.253 closest distance to " OG  SER A  97 " =    2.581
peak=    3.252 closest distance to " O   TRP A 274 " =    1.845
peak=    3.250 closest distance to " NZ  LYS A  76 " =    1.276
peak=    3.243 closest distance to " CA  ASP A 140 " =    1.204
peak=    3.241 closest distance to " CA  ALA A 160 " =    0.758
peak=    3.238 closest distance to " CD2 HIS A  81 " =    1.031
peak=    3.238 closest distance to " O   HOH Z 136 " =    1.074
peak=    3.235 closest distance to " NE AARG A 275 " =    1.416
peak=    3.232 closest distance to " N   ALA A 256 " =    1.046
peak=    3.228 closest distance to " C   LYS A 290 " =    1.274
peak=    3.226 closest distance to " O   HOH Z 425 " =    2.328
peak=    3.226 closest distance to " O   HOH Z 374 " =    2.489
peak=    3.225 closest distance to " O   HOH Z   7 " =    1.229
peak=    3.222 closest distance to " CD BARG A 102 " =    1.200
peak=    3.219 closest distance to " CG  MET A 185 " =    1.269
peak=    3.218 closest distance to " NE2 GLN A 278 " =    2.530
peak=    3.215 closest distance to " O   HOH Z 148 " =    2.075
peak=    3.205 closest distance to " CA  ILE A 234 " =    0.868
peak=    3.204 closest distance to " O   HOH Z 227 " =    2.008
peak=    3.200 closest distance to " O   HOH Z 285 " =    3.214
peak=    3.195 closest distance to " O   ALA A   1 " =    1.502
peak=    3.195 closest distance to " OD1 ASP A 286 " =    1.543
peak=    3.192 closest distance to " O   HOH Z 272 " =    2.428
peak=    3.189 closest distance to " O   GLY A  57 " =    2.514
peak=    3.189 closest distance to " O   HOH Z 175 " =    3.532
peak=    3.187 closest distance to " CG  MET A 188 " =    1.325
peak=    3.186 closest distance to " O   ALA A  10 " =    1.538
peak=    3.185 closest distance to " O   HOH Z  55 " =    2.161
peak=    3.183 closest distance to " CA  LYS A 117 " =    1.223
peak=    3.177 closest distance to " O   HOH Z 426 " =    2.987
peak=    3.177 closest distance to " O   HOH Z 420 " =    1.868
peak=    3.176 closest distance to " O   HOH Z 266 " =    1.509
peak=    3.175 closest distance to " N   ASN A  39 " =    1.237
peak=    3.170 closest distance to " O   HOH Z 407 " =    2.143
peak=    3.167 closest distance to " OD1 ASP A 231 " =    1.778
peak=    3.150 closest distance to " OG  SER A  62 " =    2.918
peak=    3.148 closest distance to " NH2BARG A 145 " =    2.164
peak=    3.147 closest distance to " CG2 ILE A 120 " =    1.318
peak=    3.147 closest distance to " CA  ASP A 191 " =    0.762
peak=    3.144 closest distance to " O   HOH Z 365 " =    5.758
peak=    3.143 closest distance to " NZ ALYS A 290 " =    1.150
peak=    3.143 closest distance to " CB  LYS A 193 " =    1.094
peak=    3.142 closest distance to " O   HOH Z 172 " =    3.802
peak=    3.140 closest distance to " CH2 TRP A 274 " =    2.198
peak=    3.138 closest distance to " O   HOH Z  10 " =    1.898
peak=    3.136 closest distance to " O   HOH Z 171 " =    2.301
peak=    3.133 closest distance to " NE  ARG A 156 " =    1.081
peak=    3.132 closest distance to " CB  ALA A  34 " =    1.003
peak=    3.129 closest distance to " O   HOH Z 313 " =    1.842
peak=    3.126 closest distance to " O   HOH Z  68 " =    2.594
peak=    3.113 closest distance to " O   HOH Z 119 " =    1.403
peak=    3.112 closest distance to " O   HOH Z 277 " =    1.080
peak=    3.108 closest distance to " O   HOH Z 409 " =    3.282
peak=    3.102 closest distance to " O   HOH Z   4 " =    1.724
peak=    3.093 closest distance to " O   HOH Z 366 " =    3.069
peak=    3.089 closest distance to " O   HOH Z 197 " =    1.806
peak=    3.088 closest distance to " O   HOH Z 388 " =    1.965
peak=    3.084 closest distance to " O   HOH Z 128 " =    2.088
peak=    3.067 closest distance to " O   HOH Z 156 " =    2.858
peak=    3.057 closest distance to " O   HOH Z  11 " =    1.673
peak=    3.048 closest distance to " CB  ALA A 180 " =    1.322
peak=    3.037 closest distance to " CA  ARG A 195 " =    1.240

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.599 - 5.346
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 203
   mapped sites are within: 0.793 - 5.346

peak=   -4.998 closest distance to " CG2 VAL A 230 " =    0.900
peak=   -4.599 closest distance to " O   HOH Z 198 " =    2.525
peak=   -4.446 closest distance to " O   HOH Z 377 " =    1.550
peak=   -4.254 closest distance to " CG  ARG A 138 " =    0.996
peak=   -4.252 closest distance to " CD  ARG A 156 " =    1.977
peak=   -4.239 closest distance to " CD  ARG A 138 " =    1.393
peak=   -4.205 closest distance to " O   HOH Z 231 " =    1.616
peak=   -4.199 closest distance to " OG ASER A 134 " =    1.165
peak=   -4.180 closest distance to " O   HOH Z  92 " =    1.333
peak=   -4.098 closest distance to " O   ILE A 109 " =    2.655
peak=   -4.044 closest distance to " O   HOH Z 266 " =    4.423
peak=   -4.016 closest distance to " O   HOH Z 388 " =    1.805
peak=   -3.966 closest distance to " CD  ARG A  14 " =    3.320
peak=   -3.935 closest distance to " CG  ASP A 231 " =    0.793
peak=   -3.924 closest distance to " O   HOH Z  98 " =    1.712
peak=   -3.903 closest distance to " CA  ASP A  27 " =    2.473
peak=   -3.879 closest distance to " CB  TYR A  15 " =    2.167
peak=   -3.851 closest distance to " NH2 ARG A  66 " =    1.956
peak=   -3.845 closest distance to " N   SER A 276 " =    1.323
peak=   -3.833 closest distance to " C   ASN A 187 " =    1.729
peak=   -3.825 closest distance to " O   PRO A 163 " =    2.004
peak=   -3.811 closest distance to " OG1 THR A   4 " =    1.861
peak=   -3.807 closest distance to " CB  ALA A  43 " =    2.371
peak=   -3.796 closest distance to " O   HOH Z 166 " =    1.477
peak=   -3.789 closest distance to " O   HOH Z 166 " =    1.894
peak=   -3.786 closest distance to " CG1 VAL A 250 " =    2.662
peak=   -3.775 closest distance to " OG BSER A 134 " =    1.156
peak=   -3.764 closest distance to " CG  GLN A 223 " =    2.045
peak=   -3.759 closest distance to " CB  PRO A 163 " =    2.660
peak=   -3.749 closest distance to " NH2AARG A 275 " =    5.346
peak=   -3.743 closest distance to " CD1 LEU A 101 " =    2.512
peak=   -3.735 closest distance to " O   HOH Z  97 " =    1.465
peak=   -3.734 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.729 closest distance to " O   PRO A 198 " =    1.323
peak=   -3.704 closest distance to " CD  LYS A 289 " =    2.610
peak=   -3.702 closest distance to " O   HOH Z 103 " =    1.834
peak=   -3.700 closest distance to " OG  SER A  87 " =    1.332
peak=   -3.692 closest distance to " O   HOH Z 290 " =    1.059
peak=   -3.662 closest distance to " NH1 ARG A  56 " =    2.440
peak=   -3.661 closest distance to " CG  GLU A 152 " =    2.498
peak=   -3.659 closest distance to " O   HOH Z  93 " =    2.035
peak=   -3.656 closest distance to " CD  GLN A  88 " =    0.849
peak=   -3.631 closest distance to " CG  TRP A 266 " =    1.565
peak=   -3.630 closest distance to " O   HOH Z 407 " =    3.094
peak=   -3.629 closest distance to " OG  SER A 206 " =    1.837
peak=   -3.629 closest distance to " N   GLN A  58 " =    1.768
peak=   -3.628 closest distance to " CB  SER A 134 " =    1.735
peak=   -3.621 closest distance to " CB  ALA A 248 " =    1.923
peak=   -3.598 closest distance to " CB  ALA A  51 " =    1.798
peak=   -3.593 closest distance to " O   GLY A 211 " =    1.302
peak=   -3.578 closest distance to " O   VAL A  67 " =    2.618
peak=   -3.575 closest distance to " O   HOH Z  43 " =    1.838
peak=   -3.575 closest distance to " CG  ASN A  45 " =    1.725
peak=   -3.570 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -3.565 closest distance to " NH2 ARG A  79 " =    1.861
peak=   -3.564 closest distance to " O   SER A 135 " =    1.506
peak=   -3.563 closest distance to " CD  ARG A 139 " =    1.758
peak=   -3.560 closest distance to " O   HOH Z 266 " =    4.622
peak=   -3.555 closest distance to " O   HOH Z  13 " =    1.262
peak=   -3.551 closest distance to " CD1 LEU A 228 " =    2.283
peak=   -3.534 closest distance to " CB  ASN A  39 " =    2.020
peak=   -3.530 closest distance to " OD2 ASP A  50 " =    1.495
peak=   -3.526 closest distance to " N   GLN A 122 " =    1.516
peak=   -3.521 closest distance to " CB  PRO A 243 " =    2.730
peak=   -3.520 closest distance to " O   HOH Z 274 " =    2.672
peak=   -3.520 closest distance to " O   ALA A 158 " =    0.990
peak=   -3.517 closest distance to " CD  GLN A  88 " =    2.324
peak=   -3.516 closest distance to " O   HOH Z  97 " =    2.218
peak=   -3.513 closest distance to " CA  GLY A 133 " =    1.877
peak=   -3.501 closest distance to " O   HOH Z 292 " =    4.390
peak=   -3.499 closest distance to " CE  MET A 105 " =    2.047
peak=   -3.495 closest distance to " OH  TYR A 214 " =    1.204
peak=   -3.495 closest distance to " CZ  PHE A  59 " =    1.560
peak=   -3.489 closest distance to " N   THR A 157 " =    1.575
peak=   -3.487 closest distance to " O   HOH Z 350 " =    2.191
peak=   -3.483 closest distance to " OH  TYR A 172 " =    1.635
peak=   -3.473 closest distance to " CE2 PHE A 218 " =    2.584
peak=   -3.471 closest distance to " ND2 ASN A  60 " =    1.378
peak=   -3.464 closest distance to " CG  PHE A 283 " =    2.651
peak=   -3.462 closest distance to " CA  GLY A  35 " =    2.001
peak=   -3.460 closest distance to " O   HOH Z 389 " =    1.649
peak=   -3.450 closest distance to " C   ASN A 285 " =    2.479
peak=   -3.443 closest distance to " O   HOH Z  63 " =    0.879
peak=   -3.434 closest distance to " O   HOH Z 275 " =    1.825
peak=   -3.422 closest distance to " O   HOH Z 168 " =    1.756
peak=   -3.421 closest distance to " O   HOH Z  15 " =    1.635
peak=   -3.419 closest distance to " N   ALA A 248 " =    1.675
peak=   -3.419 closest distance to " O   HOH Z 165 " =    1.989
peak=   -3.416 closest distance to " OE1 GLN A  88 " =    1.006
peak=   -3.415 closest distance to " N   ALA A 226 " =    2.086
peak=   -3.408 closest distance to " O   VAL A 197 " =    1.390
peak=   -3.403 closest distance to " OD2 ASP A 171 " =    1.721
peak=   -3.398 closest distance to " CG  ASP A  50 " =    2.039
peak=   -3.385 closest distance to " C   ALA A 158 " =    1.209
peak=   -3.380 closest distance to " CA  ASN A 127 " =    1.024
peak=   -3.377 closest distance to " O   HOH Z  17 " =    1.468
peak=   -3.377 closest distance to " O   HOH Z 281 " =    2.905
peak=   -3.375 closest distance to " CH2 TRP A 179 " =    1.331
peak=   -3.373 closest distance to " CE  MET A  93 " =    1.172
peak=   -3.371 closest distance to " OG  SER A  87 " =    1.514
peak=   -3.369 closest distance to " O   HOH Z  98 " =    1.415
peak=   -3.367 closest distance to " O   HOH Z 250 " =    1.420
peak=   -3.367 closest distance to " O   HOH Z 426 " =    2.219
peak=   -3.366 closest distance to " ND2 ASN A  45 " =    1.012
peak=   -3.366 closest distance to " OG1 THR A 178 " =    1.131
peak=   -3.363 closest distance to " O   PRO A 198 " =    1.339
peak=   -3.361 closest distance to " N   ALA A   9 " =    1.462
peak=   -3.360 closest distance to " O   HOH Z   3 " =    2.065
peak=   -3.355 closest distance to " CG  PRO A 163 " =    2.505
peak=   -3.349 closest distance to " O   HOH Z 365 " =    1.544
peak=   -3.347 closest distance to " O   HOH Z 423 " =    1.028
peak=   -3.342 closest distance to " O   HOH Z 396 " =    1.631
peak=   -3.340 closest distance to " CG2 VAL A 296 " =    1.864
peak=   -3.339 closest distance to " O   GLY A  98 " =    2.050
peak=   -3.338 closest distance to " CE BMET A  47 " =    1.424
peak=   -3.335 closest distance to " CB  CYS A 254 " =    2.233
peak=   -3.334 closest distance to " O   HOH Z 148 " =    1.778
peak=   -3.334 closest distance to " O   GLY A 196 " =    1.101
peak=   -3.328 closest distance to " O   HOH Z 275 " =    1.547
peak=   -3.321 closest distance to " OD1 ASP A 200 " =    1.224
peak=   -3.320 closest distance to " N   HIS A 115 " =    1.958
peak=   -3.319 closest distance to " O   HOH Z  71 " =    1.031
peak=   -3.313 closest distance to " CD1 PHE A  59 " =    1.867
peak=   -3.310 closest distance to " CA  TYR A  68 " =    2.684
peak=   -3.309 closest distance to " CZ  TYR A 169 " =    1.747
peak=   -3.307 closest distance to " O   HOH Z 143 " =    1.368
peak=   -3.301 closest distance to " C   HIS A 108 " =    1.094
peak=   -3.298 closest distance to " O   LEU A 228 " =    2.370
peak=   -3.297 closest distance to " O   ASP A 231 " =    2.456
peak=   -3.294 closest distance to " O   HOH Z 108 " =    2.451
peak=   -3.294 closest distance to " O   HOH Z 213 " =    1.168
peak=   -3.293 closest distance to " O   HOH Z 351 " =    1.294
peak=   -3.291 closest distance to " CB  ALA A 227 " =    2.341
peak=   -3.289 closest distance to " CE3 TRP A 150 " =    2.049
peak=   -3.285 closest distance to " O   HOH Z 411 " =    3.658
peak=   -3.283 closest distance to " CG  GLU A 277 " =    1.254
peak=   -3.282 closest distance to " CG1 VAL A 296 " =    1.337
peak=   -3.280 closest distance to " O   HOH Z 205 " =    0.934
peak=   -3.277 closest distance to " O   GLY A  80 " =    2.443
peak=   -3.277 closest distance to " O   HOH Z 345 " =    2.047
peak=   -3.276 closest distance to " CB  TRP A  85 " =    2.421
peak=   -3.275 closest distance to " CG  LYS A 193 " =    2.354
peak=   -3.272 closest distance to " O   THR A  29 " =    2.807
peak=   -3.270 closest distance to " O   ASP A 191 " =    1.720
peak=   -3.260 closest distance to " O   HOH Z 410 " =    2.018
peak=   -3.258 closest distance to " N   GLN A  55 " =    1.512
peak=   -3.256 closest distance to " OG1 THR A  82 " =    1.579
peak=   -3.252 closest distance to " O   HOH Z  11 " =    1.798
peak=   -3.245 closest distance to " O   HOH Z 189 " =    2.255
peak=   -3.244 closest distance to " ND2BASN A 224 " =    1.560
peak=   -3.244 closest distance to " OH  TYR A 169 " =    0.998
peak=   -3.242 closest distance to " O   HOH Z 238 " =    1.682
peak=   -3.241 closest distance to " OD1 ASN A 187 " =    1.540
peak=   -3.238 closest distance to " O   HOH Z 348 " =    1.871
peak=   -3.231 closest distance to " O   HOH Z  52 " =    1.570
peak=   -3.219 closest distance to " CG2 VAL A 112 " =    2.508
peak=   -3.219 closest distance to " NH2 ARG A  66 " =    2.776
peak=   -3.217 closest distance to " OD1 ASN A 249 " =    1.113
peak=   -3.216 closest distance to " O   HOH Z  60 " =    2.329
peak=   -3.216 closest distance to " CD2 LEU A 300 " =    2.911
peak=   -3.212 closest distance to " O   HOH Z 366 " =    1.807
peak=   -3.210 closest distance to " C   MET A 188 " =    1.628
peak=   -3.198 closest distance to " OE1 GLN A  73 " =    2.387
peak=   -3.197 closest distance to " ND2 ASN A 249 " =    2.209
peak=   -3.185 closest distance to " CB  ASP A 132 " =    2.293
peak=   -3.176 closest distance to " CG2 ILE A 151 " =    2.566
peak=   -3.175 closest distance to " O   HOH Z 310 " =    1.793
peak=   -3.174 closest distance to " CG  GLU A 152 " =    0.899
peak=   -3.173 closest distance to " CD2 TYR A 293 " =    2.113
peak=   -3.173 closest distance to " O   HOH Z 234 " =    4.172
peak=   -3.170 closest distance to " O   HOH Z 353 " =    2.232
peak=   -3.169 closest distance to " O   GLU A  44 " =    1.548
peak=   -3.160 closest distance to " O   SER A 271 " =    2.179
peak=   -3.154 closest distance to " O   HOH Z 430 " =    1.839
peak=   -3.150 closest distance to " C   LEU A 143 " =    1.379
peak=   -3.150 closest distance to " OXT GLY A 302 " =    3.265
peak=   -3.150 closest distance to " OG  SER A  97 " =    2.193
peak=   -3.148 closest distance to " O   HOH Z 435 " =    2.797
peak=   -3.142 closest distance to " O   HOH Z 341 " =    1.217
peak=   -3.139 closest distance to " O   HOH Z 138 " =    1.073
peak=   -3.135 closest distance to " CD  PRO A 198 " =    1.306
peak=   -3.130 closest distance to " O   ASN A 187 " =    1.448
peak=   -3.127 closest distance to " O   HOH Z 389 " =    4.464
peak=   -3.126 closest distance to " CE  LYS A  76 " =    2.923
peak=   -3.122 closest distance to " O   HOH Z  12 " =    3.173
peak=   -3.119 closest distance to " O   MET A  40 " =    2.773
peak=   -3.110 closest distance to " OD1 ASP A 191 " =    1.621
peak=   -3.109 closest distance to " O   ALA A   1 " =    1.310
peak=   -3.107 closest distance to " N   ASN A  60 " =    1.364
peak=   -3.101 closest distance to " O   HOH Z 147 " =    1.045
peak=   -3.092 closest distance to " N   PHE A  59 " =    2.093
peak=   -3.092 closest distance to " O   HOH Z  44 " =    1.924
peak=   -3.091 closest distance to " CB  TYR A 172 " =    2.248
peak=   -3.084 closest distance to " CG  LEU A 228 " =    1.019
peak=   -3.071 closest distance to " CD2 LEU A 300 " =    3.137
peak=   -3.063 closest distance to " O   GLN A 194 " =    1.261
peak=   -3.059 closest distance to " O   HOH Z 218 " =    3.000
peak=   -3.056 closest distance to " CE3 TRP A  70 " =    2.546
peak=   -3.049 closest distance to " O   HOH Z 198 " =    1.638
peak=   -3.046 closest distance to " O   HOH Z  97 " =    0.967
peak=   -3.025 closest distance to " O   ALA A 161 " =    1.782

================= 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    :  0.4808 0.4731   6.282486e+00   6.278605e+00
   1_bss:  0.4731 0.4647   6.279748e+00   6.271324e+00
   1_xyz:  0.4003 0.4259   6.182631e+00   6.221377e+00
   1_adp:  0.3570 0.4152   6.113513e+00   6.202355e+00
   1_occ:  0.3565 0.4151   6.112883e+00   6.202013e+00
   2_bss:  0.3536 0.4117   6.113016e+00   6.199699e+00
   2_xyz:  0.2720 0.3339   5.909481e+00   6.060164e+00
   2_adp:  0.2516 0.3168   5.852318e+00   6.021288e+00
   2_occ:  0.2514 0.3168   5.851694e+00   6.021040e+00
   3_bss:  0.2499 0.3142   5.850183e+00   6.017416e+00
   3_xyz:  0.1828 0.2403   5.578156e+00   5.780554e+00
   3_adp:  0.1599 0.2195   5.471736e+00   5.702981e+00
   3_occ:  0.1598 0.2193   5.470740e+00   5.702070e+00
   4_bss:  0.1591 0.2178   5.465917e+00   5.696462e+00
   4_xyz:  0.1366 0.1883   5.323231e+00   5.561751e+00
   4_adp:  0.1317 0.1772   5.276078e+00   5.498848e+00
   4_occ:  0.1315 0.1768   5.274855e+00   5.497383e+00
   5_bss:  0.1317 0.1775   5.277550e+00   5.499297e+00
   5_xyz:  0.1208 0.1647   5.203680e+00   5.431893e+00
   5_adp:  0.1179 0.1643   5.191985e+00   5.429251e+00
   5_occ:  0.1178 0.1641   5.191582e+00   5.429008e+00
   5_bss:  0.1178 0.1641   5.191519e+00   5.429020e+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:  0.366  20.000   7.785   7.165   9.116   0.000   0.000   0.000
   1_xyz:  0.366  20.000   7.785   7.165   9.116   0.000   0.000   0.000
   1_adp:  0.366  20.000   7.785   7.165   9.116   0.000   0.000   0.000
   1_occ:  0.366  20.000   7.785   7.165   9.116   0.000   0.000   0.000
   2_bss:  0.325  34.183   4.243   3.613   6.119   0.000   0.000   0.000
   2_xyz:  0.325  34.183   4.243   3.613   6.119   0.000   0.000   0.000
   2_adp:  0.325  34.183   4.243   3.613   6.119   0.000   0.000   0.000
   2_occ:  0.325  34.183   4.243   3.613   6.119   0.000   0.000   0.000
   3_bss:  0.324  34.183   2.318   1.929   3.678   0.000   0.000   0.000
   3_xyz:  0.324  34.183   2.318   1.929   3.678   0.000   0.000   0.000
   3_adp:  0.324  34.183   2.318   1.929   3.678   0.000   0.000   0.000
   3_occ:  0.324  34.183   2.318   1.929   3.678   0.000   0.000   0.000
   4_bss:  0.323  42.496   1.737   1.311   2.158   0.000   0.000   0.000
   4_xyz:  0.323  42.496   1.737   1.311   2.158   0.000   0.000   0.000
   4_adp:  0.323  42.496   1.737   1.311   2.158   0.000   0.000   0.000
   4_occ:  0.323  42.496   1.737   1.311   2.158   0.000   0.000   0.000
   5_bss:  0.320  42.488   1.318   1.027   1.626   0.000   0.000   0.000
   5_xyz:  0.320  42.488   1.318   1.027   1.626   0.000   0.000   0.000
   5_adp:  0.320  42.488   1.318   1.027   1.626   0.000   0.000   0.000
   5_occ:  0.320  42.488   1.318   1.027   1.626   0.000   0.000   0.000
   5_bss:  0.319  44.642   0.021  -0.245   0.224   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.315 0.4154  0.4972    72424.314
   1_bss:  58.996 0.4042  0.6014    69478.051
   1_xyz:  50.142 0.5167  0.7599    54336.530
   1_adp:  47.454 0.5506  0.8600    50570.392
   1_occ:  47.499 0.5501  0.8585    50634.617
   2_bss:  47.241 0.5531  0.7696    50273.981
   2_xyz:  36.250 0.6856  0.9301    31238.386
   2_adp:  33.696 0.7156  0.9706    27968.558
   2_occ:  33.670 0.7158  0.9705    27913.126
   3_bss:  33.378 0.7188  0.9056    27529.484
   3_xyz:  24.033 0.8213  0.9918    15295.194
   3_adp:  21.663 0.8454  1.0024    12857.995
   3_occ:  21.631 0.8457  1.0023    12806.539
   4_bss:  21.437 0.8474  0.9713    12603.280
   4_xyz:  17.959 0.8803  0.9877     9202.222
   4_adp:  16.404 0.8948  0.9925     8140.679
   4_occ:  16.365 0.8952  0.9926     8112.759
   5_bss:  16.421 0.8948  0.9773     8192.975
   5_xyz:  14.981 0.9069  0.9825     7016.175
   5_adp:  14.866 0.9082  0.9797     6951.608
   5_occ:  14.855 0.9082  0.9796     6944.858
   5_bss:  14.856 0.9082  0.9801     6947.163
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3368e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3368e+01
   1_xyz:   1.646  0.013  0.105 18.334  0.006  4.108   1.3735e-01
   1_adp:   1.646  0.013  0.105 18.334  0.006  4.108   1.3735e-01
   1_occ:   1.646  0.013  0.105 18.334  0.006  4.108   1.3735e-01
   2_bss:   1.646  0.013  0.105 18.334  0.006  4.108   1.3735e-01
   2_xyz:   1.104  0.008  0.080 16.435  0.005  4.108   8.1244e-02
   2_adp:   1.104  0.008  0.080 16.435  0.005  4.108   8.1244e-02
   2_occ:   1.104  0.008  0.080 16.435  0.005  4.108   8.1244e-02
   3_bss:   1.104  0.008  0.080 16.435  0.005  4.108   8.1244e-02
   3_xyz:   1.109  0.008  0.080 15.889  0.004  4.110   7.1380e-02
   3_adp:   1.109  0.008  0.080 15.889  0.004  4.110   7.1380e-02
   3_occ:   1.109  0.008  0.080 15.889  0.004  4.110   7.1380e-02
   4_bss:   1.109  0.008  0.080 15.889  0.004  4.110   7.1380e-02
   4_xyz:   0.985  0.006  0.074 15.535  0.003  4.113   5.9523e-02
   4_adp:   0.985  0.006  0.074 15.535  0.003  4.113   5.9523e-02
   4_occ:   0.985  0.006  0.074 15.535  0.003  4.113   5.9523e-02
   5_bss:   0.985  0.006  0.074 15.535  0.003  4.113   5.9523e-02
   5_xyz:   1.035  0.007  0.078 15.629  0.004  4.112   6.3007e-02
   5_adp:   1.035  0.007  0.078 15.629  0.004  4.112   6.3007e-02
   5_occ:   1.035  0.007  0.078 15.629  0.004  4.112   6.3007e-02
   5_bss:   1.035  0.007  0.078 15.629  0.004  4.112   6.3007e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9175e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9175e+00
   1_xyz:  13.390  0.167  0.431 84.777  0.048  2.236   9.4629e-02
   1_adp:  13.390  0.167  0.431 84.777  0.048  2.236   9.4629e-02
   1_occ:  13.390  0.167  0.431 84.777  0.048  2.236   9.4629e-02
   2_bss:  13.390  0.167  0.431 84.777  0.048  2.236   9.4629e-02
   2_xyz:   7.843  0.052  0.250 82.788  0.038  2.128   6.1266e-02
   2_adp:   7.843  0.052  0.250 82.788  0.038  2.128   6.1266e-02
   2_occ:   7.843  0.052  0.250 82.788  0.038  2.128   6.1266e-02
   3_bss:   7.843  0.052  0.250 82.788  0.038  2.128   6.1266e-02
   3_xyz:   7.478  0.048  0.383 89.782  0.034  2.321   5.2709e-02
   3_adp:   7.478  0.048  0.383 89.782  0.034  2.321   5.2709e-02
   3_occ:   7.478  0.048  0.383 89.782  0.034  2.321   5.2709e-02
   4_bss:   7.478  0.048  0.383 89.782  0.034  2.321   5.2709e-02
   4_xyz:   7.502  0.043  0.367 81.104  0.036  2.305   4.6130e-02
   4_adp:   7.502  0.043  0.367 81.104  0.036  2.305   4.6130e-02
   4_occ:   7.502  0.043  0.367 81.104  0.036  2.305   4.6130e-02
   5_bss:   7.502  0.043  0.367 81.104  0.036  2.305   4.6130e-02
   5_xyz:   7.545  0.057  0.454 85.384  0.037  2.363   4.3268e-02
   5_adp:   7.545  0.057  0.454 85.384  0.037  2.363   4.3268e-02
   5_occ:   7.545  0.057  0.454 85.384  0.037  2.363   4.3268e-02
   5_bss:   7.545  0.057  0.454 85.384  0.037  2.363   4.3268e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp: 104.13   0.00  13.68 104.13   0.00  11.31  78.18   0.00  26.59
   1_occ: 104.13   0.00  13.68 104.13   0.00  11.31  78.18   0.00  26.59
   2_bss: 104.13   0.00  13.68 104.13   0.00  11.31  78.18   0.00  26.59
   2_xyz: 104.13   0.00  13.68 104.13   0.00  11.31  78.18   0.00  26.59
   2_adp:  99.92   0.00  13.83  99.92   0.00  10.56  78.85   0.00  31.61
   2_occ:  99.92   0.00  13.83  99.92   0.00  10.56  78.85   0.00  31.61
   3_bss:  99.92   0.00  13.83  99.92   0.00  10.56  78.85   0.00  31.61
   3_xyz:  99.92   0.00  13.83  99.92   0.00  10.56  78.85   0.00  31.61
   3_adp: 110.97   0.00  14.96 110.97   0.00  10.11  94.69   1.90  41.37
   3_occ: 110.97   0.00  14.96 110.97   0.00  10.11  94.69   1.90  41.37
   4_bss: 110.97   0.00  14.96 110.97   0.00  10.11  94.69   1.90  41.37
   4_xyz: 110.97   0.00  14.96 110.97   0.00  10.11  94.69   1.90  41.37
   4_adp: 107.26   0.00  14.24 107.26   0.00   9.69  91.32   3.07  39.04
   4_occ: 107.26   0.00  14.24 107.26   0.00   9.69  91.32   3.07  39.04
   5_bss: 107.26   0.00  14.24 107.26   0.00   9.69  91.32   3.07  39.04
   5_xyz: 107.26   0.00  14.24 107.26   0.00   9.69  91.32   3.07  39.04
   5_adp: 111.74   0.00  14.19 111.74   0.00   9.62  92.28   2.89  39.06
   5_occ: 111.74   0.00  14.19 111.74   0.00   9.62  92.28   2.89  39.06
   5_bss: 113.08   1.34  15.53 113.08   1.34  10.96  93.62   4.23  40.40
------------------------------------------------------------------------
 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:    1.233    0.025    0.406
   1_adp:    1.233    0.025    0.406
   1_occ:    1.233    0.025    0.406
   2_bss:    1.233    0.025    0.406
   2_xyz:    1.571    0.033    0.577
   2_adp:    1.571    0.033    0.577
   2_occ:    1.571    0.033    0.577
   3_bss:    1.571    0.033    0.577
   3_xyz:    1.697    0.048    0.685
   3_adp:    1.697    0.048    0.685
   3_occ:    1.697    0.048    0.685
   4_bss:    1.697    0.048    0.685
   4_xyz:    1.809    0.059    0.723
   4_adp:    1.809    0.059    0.723
   4_occ:    1.809    0.059    0.723
   5_bss:    1.809    0.059    0.723
   5_xyz:    1.943    0.039    0.743
   5_adp:    1.943    0.039    0.743
   5_occ:    1.943    0.039    0.743
   5_bss:    1.943    0.039    0.743
------------------------------------------------------------------------

CPU time actual refinement: 286.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1012/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_1012/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1012/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1012/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1012/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 286.69 
  Macro-tasks:
    bulk solvent and scale       = 33.92  
    individual site refinement   = 121.99 
    weights calculation          = 26.72  
    collect and process          = 5.31   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 188.03 
  Micro-tasks:
    mask                            = 2.06   
    f_calc                          = 90.48  
    alpha_beta                      = 6.78   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 99.12  
    fmodel                         = 5.77   
    r_factors                      = 0.22   
    phase_errors                   = 8.54   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 214.18 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.048 micro seconds
Total CPU time: 4.98 minutes
from_scatterers_fft:    632 calls, 90.20 s
gradients_fft:          576 calls, 87.88 s

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

# Date 2008-01-16 Time 02:57:17 PST -0800 (1200481037.90 s)
Start R-work = 0.4808, R-free = 0.4731 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1806 (no bulk solvent and anisotropic scale)

Start R-work = 0.4731, R-free = 0.4647
Final R-work = 0.1178, R-free = 0.1641