# Date 2008-01-16 Time 01:38:48 PST -0800 (1200476328.58 s)
#phil __OFF__

Command line arguments: "../498.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12831
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 498

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.9914, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.96249
Completeness in resolution range: 0.965308
Completeness with d_max=infinity: 0.962321

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8986
                             d_min =   1.9625

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.96249
Completeness in resolution range: 0.965308
Completeness with d_max=infinity: 0.962321

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8990 -  4.1994 [2128/2152]  1915   213  10.0%
  bin  2:  4.1994 -  3.3456 [2041/2061]  1837   204  10.0%
  bin  3:  3.3456 -  2.9264 [2027/2046]  1824   203  10.0%
  bin  4:  2.9264 -  2.6605 [2006/2036]  1809   197   9.8%
  bin  5:  2.6605 -  2.4707 [2003/2022]  1803   200  10.0%
  bin  6:  2.4707 -  2.3256 [1967/1992]  1766   201  10.2%
  bin  7:  2.3256 -  2.2095 [1966/1994]  1766   200  10.2%
  bin  8:  2.2095 -  2.1136 [1973/2009]  1778   195   9.9%
  bin  9:  2.1136 -  2.0325 [1960/2002]  1767   193   9.8%
  bin 10:  2.0325 -  1.9625 [1518/1979]  1365   153  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_498/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 42
        2.42 -     3.04: 2259
        3.04 -     3.66: 4793
        3.66 -     4.28: 9195
        4.28 -     4.90: 12489
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.867 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.867 3.040 -x+1/2,-y+1,z-1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.907 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28773 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_498/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_498/model_refine_001.geo

CPU time processing inputs: 9.29


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.9914 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4823   r_free= 0.4742   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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: 6.285074                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6839 0.99   1386  155 0.4095 0.4089      6.6026      6.6558|
|  2:  4.6839 -  3.7371 0.99   1333  147 0.4152 0.3715      6.8128      6.7411|
|  3:  3.7371 -  3.2704 0.99   1307  143 0.4373 0.4196      6.6862      6.7308|
|  4:  3.2704 -  2.9740 0.99   1292  146 0.4678 0.4364      6.5478      6.4724|
|  5:  2.9740 -  2.7623 0.99   1289  145 0.5116 0.5311      6.3773      6.4105|
|  6:  2.7623 -  2.6003 0.99   1297  139 0.5051 0.5545      6.2932      6.2113|
|  7:  2.6003 -  2.4707 0.99   1284  142 0.5151 0.4522      6.2452      6.2218|
|  8:  2.4707 -  2.3636 0.98   1264  144 0.5368 0.4962      6.1955      6.1747|
|  9:  2.3636 -  2.2729 0.98   1266  140 0.5153 0.5445      6.1193      6.1494|
| 10:  2.2729 -  2.1947 1.00   1263  143 0.5180 0.5395       6.118      6.1375|
| 11:  2.1947 -  2.1263 0.98   1268  139 0.5110 0.4982      6.0414      6.0666|
| 12:  2.1263 -  2.0657 0.98   1246  142 0.5031 0.5326      5.9804      6.0156|
| 13:  2.0657 -  2.0114 0.99   1286  137 0.5398 0.5371      5.8945      5.8438|
| 14:  2.0114 -  1.9625 0.67    849   97 0.5574 0.4976      5.8607      5.7821|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.6839  1386   155  0.64  39.79   0.79     0.69      91000.10|
|  2:  4.6839 -  3.7371  1333   147  0.69  36.41   0.87     0.78     113894.65|
|  3:  3.7371 -  3.2704  1307   143  0.60  44.10   0.86     0.73     116847.84|
|  4:  3.2704 -  2.9740  1292   146  0.51  51.29   0.81     0.61     104287.54|
|  5:  2.9740 -  2.7623  1289   145  0.39  60.88   0.75     0.48      86948.91|
|  6:  2.7623 -  2.6003  1297   139  0.36  62.58   0.73     0.42      75930.46|
|  7:  2.6003 -  2.4707  1284   142  0.31  66.55   0.74     0.36      69868.02|
|  8:  2.4707 -  2.3636  1264   144  0.30  67.84   0.74     0.36      64334.30|
|  9:  2.3636 -  2.2729  1266   140  0.31  67.10   0.73     0.36      58057.01|
| 10:  2.2729 -  2.1947  1263   143  0.33  65.60   0.77     0.39      50568.08|
| 11:  2.1947 -  2.1263  1268   139  0.31  66.58   0.78     0.39      49210.35|
| 12:  2.1263 -  2.0657  1246   142  0.28  68.98   0.81     0.36      46503.44|
| 13:  2.0657 -  2.0114  1286   137  0.24  72.12   0.73     0.31      41078.31|
| 14:  2.0114 -  1.9625   849    97  0.26  70.51   0.72     0.29      31390.79|
|alpha:            min =        0.29 max =            0.78 mean =         0.47|
|beta:             min =    31390.79 max =       116847.84 mean =     72840.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.98 mean =        59.51|
|phase err.(test): min =        0.00 max =           89.99 mean =        59.55|
|-----------------------------------------------------------------------------|

============================== 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 = 17.120092             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.552   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.699768              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.708   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      709 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1558 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2693 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3993 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5165 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6627 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7864 |
|-----------------------------------------------------------------------------|
|-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 |       53.015 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.180 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    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 = 11.484)------------------------------------------|
|    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: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4879   r_free= 0.4762   ksol= 0.00   Bsol= 0.00   scale= 0.769    |
|                                                                             |
| 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: 6.286984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4735   r_free= 0.4616   ksol= 0.40   Bsol= 20.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.18,9.83,7.33,0.00,0.00,0.00); trace/3= 7.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.279339                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.632713             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.530   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.445688              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.059   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4735      final r-factor (work) = 0.4000          |
| start r-factor (free) = 0.4616      final r-factor (free) = 0.4233          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.8391 = 13.63 * 0.50 * 6.2825 + 1.00 * 53.0153                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.4717 = 13.63 * 0.50 * 6.2103 + 1.00 * 0.1403                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4000      final r-factor (work) = 0.3553          |
| start r-factor (free) = 0.4233      final r-factor (free) = 0.4059          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9925 = 1.45 * 1.00 * 6.2103 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8880 = 1.45 * 1.00 * 6.1346 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.81   13.98    None  None   None       |
|    all(noH): 2823   0      0.00    91.81   13.98    None  None   None       |
|    Sol.    : 438    0      0.00    91.81   25.48    None  None   None       |
|    Mac.    : 2385   0      0.00    90.84   11.87    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 -   9.181: 1242   |   5:    45.905 -  55.085:   41        |
|      1:     9.181 -  18.362:  778   |   6:    55.085 -  64.266:   14        |
|      2:    18.362 -  27.543:  446   |   7:    64.266 -  73.447:    5        |
|      3:    27.543 -  36.724:  205   |   8:    73.447 -  82.628:    0        |
|      4:    36.724 -  45.905:   88   |   9:    82.628 -  91.809:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3553 r_free = 0.4059             target_work(ml) = 6.117         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3548 r_free = 0.4061             target_work(ml) = 6.116         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3548   r_free= 0.4061   ksol= 0.40   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.18,9.83,7.33,0.00,0.00,0.00); trace/3= 7.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.115978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3521   r_free= 0.4018   ksol= 0.37   Bsol= 38.99   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.93,5.42,4.17,0.00,0.00,0.00); trace/3= 4.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.116383                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.043316             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.833   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.048  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3521      final r-factor (work) = 0.2698          |
| start r-factor (free) = 0.4018      final r-factor (free) = 0.3266          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.0505 = 12.04 * 0.50 * 6.1296 + 1.00 * 0.1403                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2814 = 12.04 * 0.50 * 6.0066 + 1.00 * 0.1114                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2698      final r-factor (work) = 0.2439          |
| start r-factor (free) = 0.3266      final r-factor (free) = 0.3104          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9819 = 0.66 * 1.00 * 6.0066 + 1.00 * 0.0193                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9003 = 0.66 * 1.00 * 5.8482 + 1.00 * 0.0423                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.00   13.92    None  None   None       |
|    all(noH): 2823   0      0.00    91.00   13.92    None  None   None       |
|    Sol.    : 438    0      0.00    89.93   29.89    None  None   None       |
|    Mac.    : 2385   0      0.00    91.00   10.99    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 -   9.100: 1264   |   5:    45.499 -  54.599:   45        |
|      1:     9.100 -  18.200:  779   |   6:    54.599 -  63.699:   14        |
|      2:    18.200 -  27.300:  391   |   7:    63.699 -  72.799:    5        |
|      3:    27.300 -  36.399:  227   |   8:    72.799 -  81.899:    0        |
|      4:    36.399 -  45.499:   94   |   9:    81.899 -  90.998:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2439 r_free = 0.3104             target_work(ml) = 5.822         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2434 r_free = 0.3111             target_work(ml) = 5.822         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2434   r_free= 0.3111   ksol= 0.37   Bsol= 38.99   scale= 1.059   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.93,5.42,4.17,0.00,0.00,0.00); trace/3= 4.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.821775                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2423   r_free= 0.3082   ksol= 0.34   Bsol= 38.99   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,3.15,3.11,0.00,0.00,0.00); trace/3= 2.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.817444                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.846339              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.330  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.701624              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.079   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2423      final r-factor (work) = 0.1992          |
| start r-factor (free) = 0.3082      final r-factor (free) = 0.2593          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4320 = 2.85 * 0.50 * 5.8465 + 1.00 * 0.1114                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2225 = 2.85 * 0.50 * 5.7365 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1992      final r-factor (work) = 0.1797          |
| start r-factor (free) = 0.2593      final r-factor (free) = 0.2368          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0569 = 0.70 * 1.00 * 5.7365 + 1.00 * 0.0320                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9443 = 0.70 * 1.00 * 5.6030 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.38   14.16    None  None   None       |
|    all(noH): 2823   0      0.00    97.38   14.16    None  None   None       |
|    Sol.    : 438    0      1.34    91.86   37.08    None  None   None       |
|    Mac.    : 2385   0      0.00    97.38   9.95     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 -   9.738: 1564   |   5:    48.689 -  58.426:   75        |
|      1:     9.738 -  19.475:  634   |   6:    58.426 -  68.164:   35        |
|      2:    19.475 -  29.213:  218   |   7:    68.164 -  77.902:    9        |
|      3:    29.213 -  38.951:  158   |   8:    77.902 -  87.639:    3        |
|      4:    38.951 -  48.689:  125   |   9:    87.639 -  97.377:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1797 r_free = 0.2368             target_work(ml) = 5.563         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1795 r_free = 0.2364             target_work(ml) = 5.562         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1795   r_free= 0.2364   ksol= 0.34   Bsol= 38.99   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,3.15,3.11,0.00,0.00,0.00); trace/3= 2.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.562357                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1793   r_free= 0.2362   ksol= 0.33   Bsol= 38.99   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,1.91,2.63,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.560896                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.306083              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.778  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.256112              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.140  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1793      final r-factor (work) = 0.1392          |
| start r-factor (free) = 0.2362      final r-factor (free) = 0.1931          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1235 = 4.31 * 0.50 * 5.6037 + 1.00 * 0.0585                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8088 = 4.31 * 0.50 * 5.4536 + 1.00 * 0.0669                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1392      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.1931      final r-factor (free) = 0.1797          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4097 = 0.26 * 1.00 * 5.4536 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3709 = 0.26 * 1.00 * 5.3144 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.42   13.61    None  None   None       |
|    all(noH): 2823   0      0.00    96.42   13.61    None  None   None       |
|    Sol.    : 438    0      3.01    89.18   36.64    None  None   None       |
|    Mac.    : 2385   0      0.00    96.42   9.38     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 -   9.642: 1667   |   5:    48.208 -  57.849:   76        |
|      1:     9.642 -  19.283:  602   |   6:    57.849 -  67.491:   34        |
|      2:    19.283 -  28.925:  174   |   7:    67.491 -  77.133:   11        |
|      3:    28.925 -  38.566:  131   |   8:    77.133 -  86.774:    2        |
|      4:    38.566 -  48.208:  123   |   9:    86.774 -  96.416:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1315 r_free = 0.1797             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1314 r_free = 0.1793             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: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1793   ksol= 0.33   Bsol= 38.99   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,1.91,2.63,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.274766                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1317   r_free= 0.1790   ksol= 0.33   Bsol= 38.99   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.18,1.26,2.38,0.00,0.00,0.00); trace/3= 1.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.274074                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.356376              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.501  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.209252              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.686  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1317      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1790      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3295 = 2.36 * 0.50 * 5.3155 + 1.00 * 0.0669                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2322 = 2.36 * 0.50 * 5.2409 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1679      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.0702 = 4.21 * 1.00 * 5.2409 + 1.00 * 0.0097                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.8726 = 4.21 * 1.00 * 5.1933 + 1.00 * 0.0127                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.00  13.95    None  None   None       |
|    all(noH): 2823   0      0.00    104.00  13.95    None  None   None       |
|    Sol.    : 438    0      2.66    93.69   39.31    None  None   None       |
|    Mac.    : 2385   0      0.00    104.00  9.29     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 -  10.400: 1773   |   5:    51.999 -  62.399:   84        |
|      1:    10.400 -  20.800:  543   |   6:    62.399 -  72.799:   36        |
|      2:    20.800 -  31.200:  139   |   7:    72.799 -  83.199:   15        |
|      3:    31.200 -  41.599:  124   |   8:    83.199 -  93.598:    5        |
|      4:    41.599 -  51.999:  102   |   9:    93.598 - 103.998:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1666             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1664             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1664   ksol= 0.33   Bsol= 38.99   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.18,1.26,2.38,0.00,0.00,0.00); trace/3= 1.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.188544                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6839 0.99   1386  155 0.1035 0.1282      5.4173      5.5486|
|  2:  4.6839 -  3.7371 0.99   1333  147 0.0886 0.1224      5.4742      5.6945|
|  3:  3.7371 -  3.2704 0.99   1307  143 0.1131 0.1500      5.5379      5.8761|
|  4:  3.2704 -  2.9740 0.99   1292  146 0.1292 0.1848      5.5212      5.6879|
|  5:  2.9740 -  2.7623 0.99   1289  145 0.1401 0.1870      5.3774      5.6188|
|  6:  2.7623 -  2.6003 0.99   1297  139 0.1245 0.1822      5.2545      5.4625|
|  7:  2.6003 -  2.4707 0.99   1284  142 0.1346 0.1708      5.2175      5.4455|
|  8:  2.4707 -  2.3636 0.98   1264  144 0.1240 0.1827      5.1254      5.3938|
|  9:  2.3636 -  2.2729 0.98   1266  140 0.1227 0.1805      5.0769      5.3054|
| 10:  2.2729 -  2.1947 1.00   1263  143 0.1168 0.1829      5.0111      5.2868|
| 11:  2.1947 -  2.1263 0.98   1268  139 0.1198 0.1985      5.0092       5.385|
| 12:  2.1263 -  2.0657 0.98   1246  142 0.1165 0.1791      4.9437      5.2259|
| 13:  2.0657 -  2.0114 0.99   1286  137 0.1118 0.1915      4.8037      5.1145|
| 14:  2.0114 -  1.9625 0.67    849   97 0.0952 0.1500       4.626       4.843|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.6839  1386   155  0.94   9.49   0.99     0.96       7630.61|
|  2:  4.6839 -  3.7371  1333   147  0.95   8.33   1.03     1.02       9753.03|
|  3:  3.7371 -  3.2704  1307   143  0.93  12.34   1.05     1.03      11645.76|
|  4:  3.2704 -  2.9740  1292   146  0.91  15.11   1.02     1.00      11907.69|
|  5:  2.9740 -  2.7623  1289   145  0.89  16.94   1.00     0.97       9269.74|
|  6:  2.7623 -  2.6003  1297   139  0.89  16.73   0.99     0.96       7866.42|
|  7:  2.6003 -  2.4707  1284   142  0.89  17.07   1.00     0.97       6971.09|
|  8:  2.4707 -  2.3636  1264   144  0.90  16.40   1.00     0.98       5988.83|
|  9:  2.3636 -  2.2729  1266   140  0.90  16.19   1.01     0.98       5504.25|
| 10:  2.2729 -  2.1947  1263   143  0.89  16.67   1.01     0.97       5003.46|
| 11:  2.1947 -  2.1263  1268   139  0.88  17.92   1.00     0.96       5157.29|
| 12:  2.1263 -  2.0657  1246   142  0.90  16.74   1.02     1.01       4684.95|
| 13:  2.0657 -  2.0114  1286   137  0.90  16.74   1.01     0.99       3528.26|
| 14:  2.0114 -  1.9625   849    97  0.92  13.83   1.01     0.98       2471.74|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2471.74 max =        11907.69 mean =      7098.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.00|
|phase err.(test): min =        0.00 max =           88.94 mean =        14.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1664   ksol= 0.32   Bsol= 42.78   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-0.41,0.78,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.187831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1664   ksol= 0.32   Bsol= 42.78   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-0.41,0.78,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.187831                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6839 0.99   1386  155 0.1033 0.1277      5.4117       5.544|
|  2:  4.6839 -  3.7371 0.99   1333  147 0.0889 0.1230      5.4756      5.6991|
|  3:  3.7371 -  3.2704 0.99   1307  143 0.1133 0.1502      5.5402      5.8784|
|  4:  3.2704 -  2.9740 0.99   1292  146 0.1291 0.1848      5.5212      5.6869|
|  5:  2.9740 -  2.7623 0.99   1289  145 0.1399 0.1866      5.3765      5.6169|
|  6:  2.7623 -  2.6003 0.99   1297  139 0.1243 0.1819      5.2533      5.4615|
|  7:  2.6003 -  2.4707 0.99   1284  142 0.1345 0.1710      5.2164      5.4459|
|  8:  2.4707 -  2.3636 0.98   1264  144 0.1240 0.1823      5.1247      5.3914|
|  9:  2.3636 -  2.2729 0.98   1266  140 0.1227 0.1805      5.0763      5.3057|
| 10:  2.2729 -  2.1947 1.00   1263  143 0.1168 0.1828      5.0107      5.2868|
| 11:  2.1947 -  2.1263 0.98   1268  139 0.1197 0.1981      5.0087      5.3841|
| 12:  2.1263 -  2.0657 0.98   1246  142 0.1163 0.1791      4.9431       5.226|
| 13:  2.0657 -  2.0114 0.99   1286  137 0.1117 0.1912      4.8028       5.113|
| 14:  2.0114 -  1.9625 0.67    849   97 0.0951 0.1496      4.6248      4.8412|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.6839  1386   155  0.94   9.42   0.98     0.96       7518.02|
|  2:  4.6839 -  3.7371  1333   147  0.95   8.33   1.03     1.02       9743.07|
|  3:  3.7371 -  3.2704  1307   143  0.93  12.38   1.05     1.03      11720.04|
|  4:  3.2704 -  2.9740  1292   146  0.91  15.11   1.02     1.00      11914.27|
|  5:  2.9740 -  2.7623  1289   145  0.89  16.91   1.00     0.98       9246.37|
|  6:  2.7623 -  2.6003  1297   139  0.89  16.70   0.99     0.96       7846.29|
|  7:  2.6003 -  2.4707  1284   142  0.89  17.04   1.00     0.97       6950.77|
|  8:  2.4707 -  2.3636  1264   144  0.90  16.38   1.00     0.98       5975.96|
|  9:  2.3636 -  2.2729  1266   140  0.90  16.18   1.01     0.98       5497.51|
| 10:  2.2729 -  2.1947  1263   143  0.89  16.67   1.01     0.97       5000.49|
| 11:  2.1947 -  2.1263  1268   139  0.88  17.92   1.01     0.96       5153.74|
| 12:  2.1263 -  2.0657  1246   142  0.90  16.72   1.02     1.01       4678.54|
| 13:  2.0657 -  2.0114  1286   137  0.90  16.72   1.02     1.00       3520.30|
| 14:  2.0114 -  1.9625   849    97  0.92  13.80   1.01     0.98       2463.00|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2463.00 max =        11914.27 mean =      7087.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.70 mean =        14.99|
|phase err.(test): min =        0.00 max =           89.87 mean =        14.44|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    105.66  15.62    None  None   None       |
|    all(noH): 2823   0      1.67    105.66  15.62    None  None   None       |
|    Sol.    : 438    0      4.33    95.36   40.97    None  None   None       |
|    Mac.    : 2385   0      1.67    105.66  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:     1.667 -  12.067: 1773   |   5:    53.666 -  64.066:   84        |
|      1:    12.067 -  22.466:  543   |   6:    64.066 -  74.465:   36        |
|      2:    22.466 -  32.866:  139   |   7:    74.465 -  84.865:   15        |
|      3:    32.866 -  43.266:  124   |   8:    84.865 -  95.265:    5        |
|      4:    43.266 -  53.666:  102   |   9:    95.265 - 105.665:    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)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.400 - 3.986
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 312
   mapped sites are within: 0.726 - 3.986

peak=    9.993 closest distance to " CB  VAL A 230 " =    1.398
peak=    9.858 closest distance to " CG2 VAL A 296 " =    1.516
peak=    7.700 closest distance to " O   HOH Z 130 " =    1.692
peak=    6.302 closest distance to " O   HOH Z  65 " =    1.407
peak=    5.891 closest distance to " CD2 LEU A   5 " =    1.302
peak=    5.884 closest distance to " NE2 GLN A  11 " =    1.153
peak=    5.663 closest distance to " O   HOH Z 124 " =    1.621
peak=    5.618 closest distance to " O   HOH Z   7 " =    1.634
peak=    5.409 closest distance to " CG  LEU A   5 " =    1.184
peak=    5.295 closest distance to " CB  VAL A 230 " =    1.183
peak=    5.287 closest distance to " CB  PRO A  54 " =    1.039
peak=    5.284 closest distance to " O   HOH Z 424 " =    1.264
peak=    5.279 closest distance to " CG  PRO A  54 " =    1.278
peak=    5.196 closest distance to " O   HOH Z   9 " =    1.525
peak=    5.169 closest distance to " O   HOH Z 142 " =    1.947
peak=    5.120 closest distance to " NH2 ARG A  56 " =    2.040
peak=    5.031 closest distance to " O   HOH Z  78 " =    1.654
peak=    4.921 closest distance to " O   HOH Z 369 " =    2.302
peak=    4.883 closest distance to " O   HOH Z 112 " =    1.364
peak=    4.877 closest distance to " O   HOH Z 427 " =    2.275
peak=    4.858 closest distance to " CB  ARG A 275 " =    0.959
peak=    4.847 closest distance to " O   HOH Z 425 " =    1.557
peak=    4.808 closest distance to " O   HOH Z 222 " =    1.268
peak=    4.805 closest distance to " O   HOH Z 193 " =    1.549
peak=    4.746 closest distance to " CG  PRO A 213 " =    1.219
peak=    4.723 closest distance to " CD2 LEU A 228 " =    1.145
peak=    4.714 closest distance to " O   HOH Z  63 " =    1.587
peak=    4.670 closest distance to " O   HOH Z 126 " =    1.940
peak=    4.587 closest distance to " O   HOH Z 423 " =    1.562
peak=    4.581 closest distance to " O   HOH Z 232 " =    2.261
peak=    4.560 closest distance to " CB  SER A   3 " =    1.313
peak=    4.518 closest distance to " CG  LEU A 228 " =    1.136
peak=    4.517 closest distance to " O   HOH Z 385 " =    1.076
peak=    4.459 closest distance to " CG  ARG A 138 " =    0.943
peak=    4.457 closest distance to " O   HOH Z 316 " =    2.884
peak=    4.444 closest distance to " O   HOH Z 380 " =    1.862
peak=    4.420 closest distance to " O   HOH Z 422 " =    2.473
peak=    4.406 closest distance to " O   SER A  87 " =    2.414
peak=    4.389 closest distance to " O   HOH Z 145 " =    1.743
peak=    4.376 closest distance to " O   HOH Z 209 " =    2.257
peak=    4.355 closest distance to " O   HOH Z   2 " =    1.808
peak=    4.342 closest distance to " O   HOH Z 403 " =    1.396
peak=    4.337 closest distance to " O   HOH Z 298 " =    1.872
peak=    4.336 closest distance to " O   HOH Z 287 " =    1.823
peak=    4.336 closest distance to " CB  SER A  63 " =    1.272
peak=    4.325 closest distance to " NH1 ARG A 138 " =    0.988
peak=    4.316 closest distance to " O   HOH Z 427 " =    1.146
peak=    4.312 closest distance to " O   HOH Z 419 " =    1.986
peak=    4.309 closest distance to " O   PRO A 198 " =    1.241
peak=    4.293 closest distance to " CB  GLN A 223 " =    1.582
peak=    4.257 closest distance to " O   HOH Z 272 " =    1.802
peak=    4.252 closest distance to " CB  GLN A 183 " =    1.214
peak=    4.189 closest distance to " OG  SER A  62 " =    3.059
peak=    4.183 closest distance to " CB  ASN A 148 " =    1.332
peak=    4.180 closest distance to " O   HOH Z 417 " =    1.284
peak=    4.153 closest distance to " O   HOH Z 236 " =    1.581
peak=    4.143 closest distance to " O   HOH Z 410 " =    1.401
peak=    4.127 closest distance to " O   HOH Z 214 " =    1.300
peak=    4.121 closest distance to " O   HOH Z 166 " =    1.401
peak=    4.107 closest distance to " O   HOH Z 405 " =    1.536
peak=    4.082 closest distance to " NZ  LYS A 117 " =    3.145
peak=    4.077 closest distance to " CD1AILE A 234 " =    0.968
peak=    4.053 closest distance to " O   HOH Z 389 " =    1.353
peak=    4.048 closest distance to " O   HOH Z 143 " =    1.181
peak=    4.021 closest distance to " CA  PHE A 283 " =    1.403
peak=    4.020 closest distance to " O   HOH Z 414 " =    1.139
peak=    4.017 closest distance to " O   HOH Z  30 " =    1.761
peak=    4.004 closest distance to " O   HOH Z 189 " =    2.548
peak=    4.002 closest distance to " CG2 VAL A 257 " =    0.882
peak=    3.988 closest distance to " CB  TRP A 179 " =    1.382
peak=    3.978 closest distance to " O   HOH Z 263 " =    1.520
peak=    3.977 closest distance to " CG  PRO A 198 " =    1.207
peak=    3.939 closest distance to " O   HOH Z  78 " =    1.897
peak=    3.935 closest distance to " O   HOH Z   1 " =    1.731
peak=    3.930 closest distance to " O   HOH Z 352 " =    1.763
peak=    3.923 closest distance to " CB BVAL A  41 " =    1.209
peak=    3.922 closest distance to " O   HOH Z 384 " =    1.443
peak=    3.905 closest distance to " CB  VAL A 265 " =    1.298
peak=    3.904 closest distance to " O   HOH Z 227 " =    1.855
peak=    3.895 closest distance to " CB  VAL A 202 " =    1.669
peak=    3.883 closest distance to " O   HOH Z 371 " =    2.858
peak=    3.880 closest distance to " O   HOH Z 278 " =    0.871
peak=    3.876 closest distance to " O   HOH Z 346 " =    1.581
peak=    3.857 closest distance to " CG  GLN A  11 " =    2.167
peak=    3.853 closest distance to " O   HOH Z 130 " =    2.087
peak=    3.818 closest distance to " O   HOH Z 411 " =    3.590
peak=    3.799 closest distance to " CB  SER A 216 " =    0.866
peak=    3.799 closest distance to " NE1 TRP A 274 " =    0.982
peak=    3.794 closest distance to " N   PHE A 130 " =    1.231
peak=    3.792 closest distance to " CG  LEU A 167 " =    1.166
peak=    3.791 closest distance to " O   HOH Z  59 " =    1.505
peak=    3.789 closest distance to " O   HOH Z 371 " =    1.964
peak=    3.753 closest distance to " CB  GLU A 128 " =    1.062
peak=    3.752 closest distance to " O   HOH Z 193 " =    1.714
peak=    3.749 closest distance to " O   HOH Z  22 " =    2.137
peak=    3.748 closest distance to " O   HOH Z 290 " =    0.990
peak=    3.743 closest distance to " O   HOH Z  51 " =    1.351
peak=    3.741 closest distance to " OD2 ASP A 286 " =    2.551
peak=    3.738 closest distance to " O   HOH Z 117 " =    1.909
peak=    3.732 closest distance to " CG2 THR A 221 " =    1.313
peak=    3.712 closest distance to " O   HOH Z 234 " =    3.465
peak=    3.691 closest distance to " O   HOH Z 361 " =    1.429
peak=    3.687 closest distance to " CA  ALA A 158 " =    1.145
peak=    3.687 closest distance to " O   HOH Z 392 " =    1.275
peak=    3.674 closest distance to " O   HOH Z 222 " =    1.920
peak=    3.671 closest distance to " O   HOH Z 139 " =    1.248
peak=    3.669 closest distance to " O   HOH Z 303 " =    2.255
peak=    3.666 closest distance to " O   HOH Z 418 " =    0.935
peak=    3.655 closest distance to " CG  GLN A  88 " =    1.124
peak=    3.650 closest distance to " O   HOH Z 368 " =    1.967
peak=    3.645 closest distance to " O   HOH Z  55 " =    1.767
peak=    3.641 closest distance to " O   HOH Z 359 " =    1.270
peak=    3.634 closest distance to " O   HOH Z  48 " =    1.606
peak=    3.634 closest distance to " O   HOH Z  28 " =    2.177
peak=    3.627 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.621 closest distance to " O   HOH Z 368 " =    3.703
peak=    3.615 closest distance to " O   HOH Z 143 " =    2.400
peak=    3.615 closest distance to " CA  ALA A 299 " =    0.984
peak=    3.612 closest distance to " OG BSER A 212 " =    2.811
peak=    3.610 closest distance to " O   HOH Z  61 " =    1.529
peak=    3.609 closest distance to " O   HOH Z  65 " =    1.638
peak=    3.605 closest distance to " OG  SER A  62 " =    2.707
peak=    3.599 closest distance to " O   HOH Z 108 " =    2.169
peak=    3.599 closest distance to " CB  GLU A 152 " =    1.253
peak=    3.591 closest distance to " CB  TYR A 169 " =    0.823
peak=    3.586 closest distance to " OD1 ASN A  69 " =    2.632
peak=    3.585 closest distance to " CE AMET A  47 " =    1.371
peak=    3.576 closest distance to " O   HOH Z 250 " =    1.349
peak=    3.575 closest distance to " CB  SER A 276 " =    1.175
peak=    3.574 closest distance to " O   HOH Z 366 " =    2.760
peak=    3.569 closest distance to " O   HOH Z   6 " =    2.108
peak=    3.568 closest distance to " O   HOH Z 425 " =    2.014
peak=    3.566 closest distance to " CD1 LEU A 281 " =    1.088
peak=    3.549 closest distance to " O   HOH Z 193 " =    1.921
peak=    3.548 closest distance to " NE2 GLN A  58 " =    3.455
peak=    3.548 closest distance to " CB  ASN A 148 " =    1.912
peak=    3.548 closest distance to " CB  ARG A 139 " =    0.985
peak=    3.543 closest distance to " CA  TYR A  30 " =    0.937
peak=    3.542 closest distance to " CB  TRP A 266 " =    1.122
peak=    3.541 closest distance to " OG BSER A  99 " =    2.131
peak=    3.539 closest distance to " CB  GLU A 277 " =    3.456
peak=    3.531 closest distance to " CA  ASN A 215 " =    1.140
peak=    3.511 closest distance to " CG1 VAL A 153 " =    0.831
peak=    3.510 closest distance to " CB  LEU A 237 " =    0.814
peak=    3.502 closest distance to " NZ  LYS A 117 " =    1.162
peak=    3.502 closest distance to " O   HOH Z 258 " =    2.235
peak=    3.500 closest distance to " N   ALA A   1 " =    1.093
peak=    3.498 closest distance to " CG1 ILE A 120 " =    1.358
peak=    3.497 closest distance to " O   HOH Z 305 " =    3.423
peak=    3.490 closest distance to " CB  ALA A 114 " =    1.497
peak=    3.489 closest distance to " O   HOH Z 123 " =    1.059
peak=    3.487 closest distance to " N   GLU A   2 " =    1.242
peak=    3.481 closest distance to " O   HOH Z  64 " =    2.155
peak=    3.477 closest distance to " OG BSER A 164 " =    2.072
peak=    3.477 closest distance to " O   ASN A 301 " =    2.328
peak=    3.476 closest distance to " O   HOH Z 327 " =    1.591
peak=    3.475 closest distance to " O   HOH Z 213 " =    1.965
peak=    3.474 closest distance to " O   HOH Z  47 " =    1.744
peak=    3.473 closest distance to " CB  LEU A 255 " =    0.815
peak=    3.469 closest distance to " CG1 ILE A  33 " =    1.334
peak=    3.464 closest distance to " NH1AARG A 145 " =    1.084
peak=    3.463 closest distance to " O   HOH Z   9 " =    1.697
peak=    3.457 closest distance to " CG1BVAL A  72 " =    1.298
peak=    3.455 closest distance to " O   HOH Z 383 " =    2.323
peak=    3.452 closest distance to " O   HOH Z 207 " =    2.231
peak=    3.449 closest distance to " CA  ILE A 234 " =    0.977
peak=    3.449 closest distance to " N   TYR A  15 " =    1.041
peak=    3.441 closest distance to " CB  THR A 157 " =    1.124
peak=    3.439 closest distance to " O   HOH Z 259 " =    2.255
peak=    3.437 closest distance to " O   HOH Z  66 " =    1.717
peak=    3.434 closest distance to " O   HOH Z 158 " =    2.781
peak=    3.432 closest distance to " O   HOH Z  50 " =    1.448
peak=    3.432 closest distance to " CA  ASN A 127 " =    1.066
peak=    3.431 closest distance to " O   HOH Z 214 " =    1.939
peak=    3.431 closest distance to " O   HOH Z  58 " =    1.786
peak=    3.430 closest distance to " CA  ALA A  51 " =    1.040
peak=    3.421 closest distance to " CG  GLN A  89 " =    1.399
peak=    3.412 closest distance to " O   HOH Z 129 " =    0.726
peak=    3.407 closest distance to " CB  ARG A  79 " =    1.297
peak=    3.404 closest distance to " O   HOH Z 423 " =    1.631
peak=    3.404 closest distance to " CE  MET A  93 " =    1.496
peak=    3.401 closest distance to " CB  LYS A 117 " =    1.223
peak=    3.400 closest distance to " O   HOH Z 402 " =    1.465
peak=    3.393 closest distance to " CG  LYS A  76 " =    1.547
peak=    3.393 closest distance to " O   HOH Z  88 " =    3.254
peak=    3.390 closest distance to " NE AARG A 275 " =    1.317
peak=    3.389 closest distance to " O   HOH Z 280 " =    2.565
peak=    3.387 closest distance to " O   HOH Z  93 " =    2.080
peak=    3.387 closest distance to " ND1 HIS A  86 " =    1.850
peak=    3.387 closest distance to " O   HOH Z 128 " =    2.017
peak=    3.384 closest distance to " O   HOH Z 128 " =    2.179
peak=    3.381 closest distance to " O   HOH Z  39 " =    1.195
peak=    3.379 closest distance to " O   GLN A  58 " =    1.461
peak=    3.378 closest distance to " O   HOH Z  59 " =    1.937
peak=    3.375 closest distance to " CB  MET A  40 " =    0.920
peak=    3.372 closest distance to " O   HOH Z 390 " =    2.274
peak=    3.369 closest distance to " O   HOH Z 344 " =    1.088
peak=    3.365 closest distance to " O   HOH Z 345 " =    3.236
peak=    3.364 closest distance to " OG1 THR A 221 " =    1.301
peak=    3.362 closest distance to " NH1 ARG A  14 " =    0.921
peak=    3.358 closest distance to " O   HOH Z 362 " =    2.102
peak=    3.344 closest distance to " CB  ASN A 142 " =    1.006
peak=    3.342 closest distance to " OE1 GLN A  58 " =    3.986
peak=    3.341 closest distance to " N   ARG A 156 " =    1.273
peak=    3.340 closest distance to " CA  LEU A 282 " =    1.063
peak=    3.339 closest distance to " OE1 GLN A 240 " =    1.482
peak=    3.338 closest distance to " O   HOH Z 175 " =    2.193
peak=    3.336 closest distance to " CB  ALA A 291 " =    1.392
peak=    3.332 closest distance to " O   HOH Z 152 " =    2.184
peak=    3.325 closest distance to " O   HOH Z 406 " =    1.531
peak=    3.324 closest distance to " CG1AVAL A 121 " =    0.944
peak=    3.322 closest distance to " O   HOH Z 251 " =    1.680
peak=    3.317 closest distance to " O   HOH Z 313 " =    1.563
peak=    3.315 closest distance to " O   HOH Z  43 " =    1.973
peak=    3.308 closest distance to " O   HOH Z 390 " =    1.236
peak=    3.308 closest distance to " N   GLN A 278 " =    1.200
peak=    3.304 closest distance to " O   ALA A   1 " =    1.539
peak=    3.302 closest distance to " O   HOH Z  89 " =    2.059
peak=    3.300 closest distance to " O   HOH Z 260 " =    1.136
peak=    3.299 closest distance to " NE2 GLN A 278 " =    3.709
peak=    3.293 closest distance to " O   HOH Z 119 " =    1.480
peak=    3.290 closest distance to " O   HOH Z 209 " =    2.379
peak=    3.285 closest distance to " O   HOH Z 244 " =    1.659
peak=    3.281 closest distance to " O   HOH Z  11 " =    1.505
peak=    3.280 closest distance to " O   HOH Z 385 " =    3.389
peak=    3.279 closest distance to " O   HOH Z 424 " =    2.379
peak=    3.278 closest distance to " O   HOH Z 126 " =    1.489
peak=    3.277 closest distance to " CG BARG A 102 " =    1.910
peak=    3.277 closest distance to " O   HOH Z  55 " =    1.822
peak=    3.275 closest distance to " CG1BVAL A 121 " =    2.184
peak=    3.273 closest distance to " CA  LEU A 101 " =    1.522
peak=    3.267 closest distance to " O   HOH Z 276 " =    1.260
peak=    3.262 closest distance to " O   HOH Z 147 " =    1.394
peak=    3.250 closest distance to " O   HOH Z 171 " =    2.718
peak=    3.248 closest distance to " CB  HIS A 108 " =    0.857
peak=    3.248 closest distance to " CG2 ILE A 106 " =    0.953
peak=    3.246 closest distance to " CA  ALA A 248 " =    1.311
peak=    3.240 closest distance to " CB  SER A  62 " =    1.076
peak=    3.239 closest distance to " O   HOH Z  10 " =    1.752
peak=    3.239 closest distance to " CA  SER A  87 " =    1.081
peak=    3.239 closest distance to " O   HOH Z 106 " =    2.492
peak=    3.234 closest distance to " O   HOH Z 329 " =    3.700
peak=    3.234 closest distance to " O   HOH Z 344 " =    2.775
peak=    3.231 closest distance to " O   HOH Z 293 " =    1.613
peak=    3.230 closest distance to " O   HOH Z 357 " =    1.984
peak=    3.224 closest distance to " N   ASN A  39 " =    1.113
peak=    3.224 closest distance to " CB  LEU A 300 " =    0.868
peak=    3.218 closest distance to " O   HOH Z 133 " =    1.450
peak=    3.214 closest distance to " ND1 HIS A  81 " =    1.629
peak=    3.214 closest distance to " NH2BARG A 145 " =    1.425
peak=    3.214 closest distance to " NH2AARG A 190 " =    1.783
peak=    3.208 closest distance to " O   HOH Z 109 " =    2.320
peak=    3.206 closest distance to " O   HOH Z 225 " =    1.560
peak=    3.202 closest distance to " CB  THR A  31 " =    1.659
peak=    3.201 closest distance to " O   HOH Z 184 " =    1.276
peak=    3.200 closest distance to " O   HOH Z   6 " =    1.555
peak=    3.191 closest distance to " O  BHOH Z  74 " =    1.410
peak=    3.191 closest distance to " CG1BVAL A  72 " =    1.093
peak=    3.188 closest distance to " N   ALA A   1 " =    2.777
peak=    3.186 closest distance to " O   HOH Z 220 " =    1.278
peak=    3.184 closest distance to " O   HOH Z  48 " =    1.285
peak=    3.183 closest distance to " O   HOH Z 303 " =    1.718
peak=    3.183 closest distance to " O   HOH Z 132 " =    2.238
peak=    3.183 closest distance to " O   HOH Z  28 " =    1.328
peak=    3.182 closest distance to " O   HOH Z 213 " =    1.602
peak=    3.182 closest distance to " O   HOH Z 323 " =    1.612
peak=    3.180 closest distance to " N   SER A 271 " =    0.993
peak=    3.179 closest distance to " O   HOH Z 358 " =    1.363
peak=    3.172 closest distance to " O   HOH Z 145 " =    1.861
peak=    3.172 closest distance to " NH1BARG A 145 " =    1.416
peak=    3.171 closest distance to " O   HOH Z 281 " =    1.736
peak=    3.170 closest distance to " O   HOH Z 410 " =    2.066
peak=    3.165 closest distance to " O   HOH Z 135 " =    1.781
peak=    3.164 closest distance to " O   HOH Z 233 " =    1.704
peak=    3.162 closest distance to " OD1 ASP A 286 " =    1.497
peak=    3.158 closest distance to " O   HOH Z 389 " =    1.501
peak=    3.150 closest distance to " CB  ASN A 215 " =    1.097
peak=    3.148 closest distance to " O   GLY A 302 " =    2.016
peak=    3.144 closest distance to " N   GLY A 196 " =    1.088
peak=    3.140 closest distance to " OE2 GLU A  53 " =    1.994
peak=    3.138 closest distance to " OG BSER A 134 " =    3.058
peak=    3.138 closest distance to " ND2 ASN A 249 " =    0.765
peak=    3.137 closest distance to " O   HOH Z 128 " =    2.045
peak=    3.133 closest distance to " O   HOH Z 118 " =    1.538
peak=    3.132 closest distance to " O   HOH Z 334 " =    1.559
peak=    3.129 closest distance to " O   HOH Z 153 " =    3.579
peak=    3.125 closest distance to " C   LYS A 290 " =    1.443
peak=    3.125 closest distance to " CG  GLU A 277 " =    1.906
peak=    3.124 closest distance to " O   HOH Z 289 " =    1.365
peak=    3.118 closest distance to " CB  TYR A  30 " =    1.756
peak=    3.117 closest distance to " CG2 ILE A  20 " =    1.714
peak=    3.115 closest distance to " O   HOH Z 374 " =    2.384
peak=    3.114 closest distance to " O   HOH Z 412 " =    1.573
peak=    3.101 closest distance to " CG2 ILE A 234 " =    0.891
peak=    3.101 closest distance to " O   HOH Z  64 " =    1.807
peak=    3.100 closest distance to " O   HOH Z 222 " =    2.157
peak=    3.099 closest distance to " NZ  LYS A  76 " =    1.357
peak=    3.096 closest distance to " O   HOH Z 110 " =    1.696
peak=    3.094 closest distance to " CG1 ILE A 151 " =    1.080
peak=    3.094 closest distance to " O   HOH Z 155 " =    1.447
peak=    3.093 closest distance to " ND2 ASN A 187 " =    1.669
peak=    3.090 closest distance to " CA  ARG A 102 " =    1.098
peak=    3.087 closest distance to " O   HOH Z 334 " =    2.876
peak=    3.082 closest distance to " CB  ASN A 187 " =    1.109
peak=    3.077 closest distance to " O   HOH Z 261 " =    1.914
peak=    3.071 closest distance to " N   VAL A 126 " =    1.208
peak=    3.071 closest distance to " O   HOH Z  71 " =    1.070
peak=    3.060 closest distance to " CG1 VAL A 126 " =    1.256
peak=    3.036 closest distance to " O   HOH Z 366 " =    3.440
peak=    3.010 closest distance to " O   HOH Z 392 " =    1.736

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.630 - 5.580
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 196
   mapped sites are within: 0.760 - 5.580

peak=   -4.399 closest distance to " CG2 VAL A 230 " =    0.834
peak=   -4.378 closest distance to " O   HOH Z  43 " =    1.849
peak=   -4.313 closest distance to " CD  ARG A  14 " =    3.016
peak=   -4.298 closest distance to " CA  GLY A 133 " =    1.920
peak=   -4.237 closest distance to " CD  ARG A 156 " =    1.934
peak=   -4.162 closest distance to " O   HOH Z 385 " =    1.115
peak=   -4.093 closest distance to " OG BSER A 134 " =    1.297
peak=   -4.068 closest distance to " O   HOH Z 412 " =    5.580
peak=   -4.054 closest distance to " CA  GLY A  98 " =    1.816
peak=   -4.014 closest distance to " O   VAL A  67 " =    2.656
peak=   -4.004 closest distance to " NH2 ARG A  79 " =    1.962
peak=   -3.998 closest distance to " O   HOH Z 185 " =    1.976
peak=   -3.975 closest distance to " CG2 VAL A 296 " =    1.842
peak=   -3.967 closest distance to " O   PRO A 198 " =    1.172
peak=   -3.939 closest distance to " CB  TYR A  15 " =    2.055
peak=   -3.917 closest distance to " O   HOH Z 103 " =    1.563
peak=   -3.905 closest distance to " OE1 GLU A 277 " =    2.205
peak=   -3.890 closest distance to " O   SER A 135 " =    1.456
peak=   -3.873 closest distance to " O   HOH Z 266 " =    4.643
peak=   -3.860 closest distance to " C   HIS A 108 " =    1.177
peak=   -3.853 closest distance to " O   HOH Z 351 " =    1.404
peak=   -3.851 closest distance to " O   HOH Z 131 " =    3.991
peak=   -3.815 closest distance to " CZ2 TRP A 274 " =    0.925
peak=   -3.813 closest distance to " CD1 LEU A 101 " =    2.259
peak=   -3.813 closest distance to " CE2 PHE A 218 " =    2.441
peak=   -3.802 closest distance to " CB  ASN A  39 " =    2.178
peak=   -3.797 closest distance to " O   HOH Z  11 " =    1.841
peak=   -3.788 closest distance to " O   HOH Z 191 " =    5.379
peak=   -3.776 closest distance to " CB  ALA A   7 " =    1.994
peak=   -3.776 closest distance to " O   HOH Z 407 " =    3.147
peak=   -3.764 closest distance to " O   HOH Z 231 " =    1.780
peak=   -3.761 closest distance to " CE2 TYR A 116 " =    2.955
peak=   -3.753 closest distance to " OG ASER A 134 " =    1.069
peak=   -3.750 closest distance to " N   GLN A  58 " =    1.644
peak=   -3.746 closest distance to " CE2 TYR A  30 " =    2.703
peak=   -3.739 closest distance to " CB  VAL A 230 " =    1.097
peak=   -3.735 closest distance to " CD1 LEU A 255 " =    2.804
peak=   -3.730 closest distance to " CD  GLN A  58 " =    1.118
peak=   -3.721 closest distance to " CB  PRO A 243 " =    2.563
peak=   -3.719 closest distance to " O   HOH Z 350 " =    1.851
peak=   -3.706 closest distance to " O   HOH Z 298 " =    1.153
peak=   -3.704 closest distance to " O   HOH Z 339 " =    1.739
peak=   -3.696 closest distance to " O   HOH Z 140 " =    1.224
peak=   -3.694 closest distance to " CB  ALA A 248 " =    2.036
peak=   -3.672 closest distance to " CG  ARG A 138 " =    1.038
peak=   -3.669 closest distance to " O   HOH Z 359 " =    1.684
peak=   -3.651 closest distance to " O   PRO A 243 " =    2.433
peak=   -3.639 closest distance to " O   HOH Z 166 " =    1.895
peak=   -3.616 closest distance to " CB  ALA A  43 " =    2.310
peak=   -3.614 closest distance to " O   HOH Z  65 " =    1.028
peak=   -3.610 closest distance to " CD  LYS A 289 " =    2.518
peak=   -3.608 closest distance to " C   ASN A 187 " =    1.900
peak=   -3.605 closest distance to " OG  SER A   3 " =    1.404
peak=   -3.597 closest distance to " O   HOH Z 313 " =    1.481
peak=   -3.587 closest distance to " CG  MET A 105 " =    0.905
peak=   -3.587 closest distance to " O   HOH Z 427 " =    1.607
peak=   -3.565 closest distance to " CD2 LEU A 237 " =    2.719
peak=   -3.556 closest distance to " O   HOH Z  13 " =    1.741
peak=   -3.554 closest distance to " O   HOH Z 143 " =    0.975
peak=   -3.553 closest distance to " C   ILE A 239 " =    2.143
peak=   -3.540 closest distance to " CG2 THR A 178 " =    2.080
peak=   -3.531 closest distance to " CG1 VAL A 197 " =    2.230
peak=   -3.524 closest distance to " N   ALA A 248 " =    1.654
peak=   -3.513 closest distance to " OD2 ASP A 191 " =    1.404
peak=   -3.507 closest distance to " C   ASN A 285 " =    2.024
peak=   -3.499 closest distance to " CD1 PHE A  59 " =    1.966
peak=   -3.495 closest distance to " ND2 ASN A  45 " =    1.144
peak=   -3.493 closest distance to " O   TYR A  30 " =    2.789
peak=   -3.491 closest distance to " O   SER A  22 " =    2.427
peak=   -3.485 closest distance to " N   ALA A   1 " =    1.219
peak=   -3.481 closest distance to " CE  LYS A  76 " =    2.952
peak=   -3.467 closest distance to " NH1 ARG A  56 " =    2.443
peak=   -3.466 closest distance to " O   HOH Z 389 " =    1.940
peak=   -3.466 closest distance to " O   HOH Z  56 " =    2.323
peak=   -3.463 closest distance to " CG  PHE A 283 " =    2.471
peak=   -3.460 closest distance to " ND2 ASN A 252 " =    1.903
peak=   -3.459 closest distance to " O   HOH Z  71 " =    1.138
peak=   -3.454 closest distance to " OG  SER A  87 " =    1.245
peak=   -3.452 closest distance to " CZ  PHE A  59 " =    1.420
peak=   -3.451 closest distance to " CD2 LEU A   5 " =    1.100
peak=   -3.448 closest distance to " O   HOH Z 137 " =    1.547
peak=   -3.443 closest distance to " O   VAL A  67 " =    2.928
peak=   -3.441 closest distance to " CB  PHE A 192 " =    1.637
peak=   -3.435 closest distance to " O   GLN A  11 " =    1.452
peak=   -3.433 closest distance to " O   HOH Z  90 " =    2.725
peak=   -3.420 closest distance to " O   HOH Z 111 " =    4.360
peak=   -3.418 closest distance to " OG  SER A 206 " =    1.718
peak=   -3.417 closest distance to " O   HOH Z 347 " =    1.010
peak=   -3.411 closest distance to " O   HOH Z 113 " =    2.509
peak=   -3.409 closest distance to " O   ALA A 161 " =    1.757
peak=   -3.406 closest distance to " N   VAL A  72 " =    1.630
peak=   -3.400 closest distance to " O   HOH Z 388 " =    2.124
peak=   -3.399 closest distance to " CB  ASP A 132 " =    2.318
peak=   -3.397 closest distance to " N   THR A 157 " =    1.422
peak=   -3.395 closest distance to " ND2 ASN A  60 " =    1.324
peak=   -3.394 closest distance to " CG  ASN A 301 " =    1.980
peak=   -3.392 closest distance to " OE2 GLU A 152 " =    1.073
peak=   -3.390 closest distance to " CG  GLU A 152 " =    2.172
peak=   -3.389 closest distance to " O   HOH Z 290 " =    1.182
peak=   -3.389 closest distance to " O   HOH Z 198 " =    2.204
peak=   -3.385 closest distance to " O   HOH Z 166 " =    1.667
peak=   -3.375 closest distance to " CG  ASP A 231 " =    0.760
peak=   -3.369 closest distance to " ND2 ASN A 187 " =    1.600
peak=   -3.367 closest distance to " O   HOH Z 211 " =    1.360
peak=   -3.364 closest distance to " O   HOH Z 385 " =    1.803
peak=   -3.360 closest distance to " O   HOH Z 368 " =    2.407
peak=   -3.357 closest distance to " CG  PRO A 163 " =    2.772
peak=   -3.355 closest distance to " O   HOH Z 435 " =    2.077
peak=   -3.351 closest distance to " O   HOH Z 426 " =    1.717
peak=   -3.349 closest distance to " O   HOH Z  60 " =    1.755
peak=   -3.334 closest distance to " O   HOH Z  93 " =    1.685
peak=   -3.331 closest distance to " OD2 ASP A  27 " =    1.517
peak=   -3.320 closest distance to " OG  SER A 245 " =    1.286
peak=   -3.317 closest distance to " O   HOH Z 389 " =    1.376
peak=   -3.314 closest distance to " O   HOH Z 414 " =    2.132
peak=   -3.309 closest distance to " O   HOH Z 208 " =    2.072
peak=   -3.308 closest distance to " CZ3 TRP A 123 " =    1.816
peak=   -3.306 closest distance to " CE  MET A 105 " =    2.193
peak=   -3.303 closest distance to " O   ILE A  49 " =    1.733
peak=   -3.300 closest distance to " O   ASN A 187 " =    1.436
peak=   -3.299 closest distance to " O   ARG A 145 " =    1.487
peak=   -3.289 closest distance to " O   GLY A  80 " =    2.385
peak=   -3.289 closest distance to " CA  ASN A 127 " =    1.315
peak=   -3.282 closest distance to " O   HOH Z 364 " =    1.917
peak=   -3.278 closest distance to " O   HOH Z 377 " =    1.184
peak=   -3.275 closest distance to " O   HOH Z 423 " =    2.458
peak=   -3.275 closest distance to " O   HOH Z 414 " =    2.068
peak=   -3.269 closest distance to " CD2 TYR A 293 " =    1.892
peak=   -3.267 closest distance to " O   HOH Z  60 " =    2.226
peak=   -3.257 closest distance to " N   HIS A 115 " =    2.012
peak=   -3.255 closest distance to " O   HOH Z 415 " =    1.258
peak=   -3.254 closest distance to " O   HOH Z 102 " =    1.538
peak=   -3.251 closest distance to " C   ALA A 158 " =    1.307
peak=   -3.251 closest distance to " O   HOH Z 125 " =    3.359
peak=   -3.248 closest distance to " O   HOH Z 231 " =    0.999
peak=   -3.245 closest distance to " CG  GLN A 223 " =    1.986
peak=   -3.242 closest distance to " O   HOH Z 222 " =    2.632
peak=   -3.241 closest distance to " N   THR A 235 " =    1.248
peak=   -3.241 closest distance to " CZ  PHE A  16 " =    1.664
peak=   -3.239 closest distance to " O   HOH Z  39 " =    1.328
peak=   -3.237 closest distance to " O   HOH Z 426 " =    2.177
peak=   -3.235 closest distance to " OE1 GLN A 183 " =    1.435
peak=   -3.234 closest distance to " O   HOH Z 275 " =    1.587
peak=   -3.234 closest distance to " O   HOH Z  68 " =    1.843
peak=   -3.232 closest distance to " O   HOH Z 134 " =    2.739
peak=   -3.226 closest distance to " C   LEU A 143 " =    1.209
peak=   -3.224 closest distance to " N   PRO A 163 " =    1.612
peak=   -3.224 closest distance to " OG ASER A 216 " =    1.332
peak=   -3.221 closest distance to " O   ALA A 180 " =    1.224
peak=   -3.209 closest distance to " CB  TYR A 172 " =    2.274
peak=   -3.208 closest distance to " O   HOH Z 235 " =    1.097
peak=   -3.207 closest distance to " O   HOH Z 207 " =    2.067
peak=   -3.207 closest distance to " O   HOH Z 134 " =    3.535
peak=   -3.206 closest distance to " OG  SER A  97 " =    2.152
peak=   -3.201 closest distance to " CZ2 TRP A 179 " =    2.443
peak=   -3.198 closest distance to " CB  ALA A 131 " =    1.930
peak=   -3.197 closest distance to " CB  PRO A  90 " =    1.523
peak=   -3.193 closest distance to " NH2 ARG A 219 " =    1.705
peak=   -3.190 closest distance to " O   HOH Z 165 " =    2.211
peak=   -3.187 closest distance to " N   SER A 276 " =    1.198
peak=   -3.186 closest distance to " N   VAL A 189 " =    1.602
peak=   -3.185 closest distance to " NE  ARG A 138 " =    1.566
peak=   -3.185 closest distance to " O   HOH Z 298 " =    2.517
peak=   -3.184 closest distance to " O   GLN A 240 " =    1.880
peak=   -3.180 closest distance to " CE BMET A  47 " =    1.356
peak=   -3.179 closest distance to " CG  GLN A  88 " =    0.908
peak=   -3.171 closest distance to " OH  TYR A 214 " =    1.191
peak=   -3.161 closest distance to " O   HOH Z 234 " =    3.747
peak=   -3.161 closest distance to " CG  ARG A 219 " =    2.454
peak=   -3.159 closest distance to " CB  GLN A  55 " =    1.182
peak=   -3.155 closest distance to " CG  GLU A 277 " =    1.202
peak=   -3.152 closest distance to " CZ  TYR A 169 " =    1.784
peak=   -3.151 closest distance to " O   TRP A  70 " =    1.319
peak=   -3.141 closest distance to " CD1 ILE A 239 " =    2.274
peak=   -3.141 closest distance to " CG  LEU A 228 " =    1.023
peak=   -3.140 closest distance to " O   ALA A  51 " =    1.289
peak=   -3.140 closest distance to " CD  LYS A 166 " =    2.488
peak=   -3.129 closest distance to " CG1 VAL A 230 " =    1.757
peak=   -3.128 closest distance to " CB  ALA A 248 " =    2.302
peak=   -3.112 closest distance to " CB  CYS A 201 " =    2.268
peak=   -3.110 closest distance to " CB  ASP A 132 " =    2.203
peak=   -3.107 closest distance to " O   HOH Z 364 " =    2.701
peak=   -3.100 closest distance to " OD1 ASP A 200 " =    1.290
peak=   -3.093 closest distance to " O   LEU A 261 " =    1.443
peak=   -3.088 closest distance to " CE2 TRP A  70 " =    2.333
peak=   -3.086 closest distance to " CD2 TRP A 150 " =    0.940
peak=   -3.078 closest distance to " O   ALA A   1 " =    1.344
peak=   -3.072 closest distance to " O   MET A  40 " =    2.849
peak=   -3.072 closest distance to " CA  VAL A 174 " =    1.752
peak=   -3.054 closest distance to " NH2AARG A 275 " =    5.339
peak=   -3.053 closest distance to " CG  ARG A  66 " =    2.112
peak=   -3.040 closest distance to " O   ASN A 249 " =    1.520
peak=   -3.032 closest distance to " CZ  ARG A  24 " =    1.753
peak=   -3.025 closest distance to " O   ALA A   8 " =    1.887
peak=   -3.004 closest distance to " O   ALA A 292 " =    2.001

================= 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    :  0.4823 0.4742   6.285074e+00   6.275201e+00
   1_bss:  0.4735 0.4616   6.279339e+00   6.264106e+00
   1_xyz:  0.4000 0.4233   6.185967e+00   6.214666e+00
   1_adp:  0.3553 0.4059   6.116604e+00   6.198544e+00
   1_occ:  0.3548 0.4061   6.115978e+00   6.198790e+00
   2_bss:  0.3521 0.4018   6.116383e+00   6.196384e+00
   2_xyz:  0.2698 0.3266   5.893787e+00   6.033952e+00
   2_adp:  0.2439 0.3104   5.822223e+00   5.987229e+00
   2_occ:  0.2434 0.3111   5.821775e+00   5.988050e+00
   3_bss:  0.2423 0.3082   5.817444e+00   5.982022e+00
   3_xyz:  0.1992 0.2593   5.650762e+00   5.839812e+00
   3_adp:  0.1797 0.2368   5.562977e+00   5.769094e+00
   3_occ:  0.1795 0.2364   5.562357e+00   5.768448e+00
   4_bss:  0.1793 0.2362   5.560896e+00   5.767435e+00
   4_xyz:  0.1392 0.1931   5.337170e+00   5.574740e+00
   4_adp:  0.1315 0.1797   5.275865e+00   5.508739e+00
   4_occ:  0.1314 0.1793   5.274766e+00   5.506930e+00
   5_bss:  0.1317 0.1790   5.274074e+00   5.505196e+00
   5_xyz:  0.1209 0.1679   5.207102e+00   5.447666e+00
   5_adp:  0.1170 0.1666   5.189173e+00   5.438284e+00
   5_occ:  0.1170 0.1664   5.188544e+00   5.437299e+00
   5_bss:  0.1169 0.1664   5.187831e+00   5.436772e+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:  0.399  19.999   6.185   9.830   7.327   0.000   0.000   0.000
   1_xyz:  0.399  19.999   6.185   9.830   7.327   0.000   0.000   0.000
   1_adp:  0.399  19.999   6.185   9.830   7.327   0.000   0.000   0.000
   1_occ:  0.399  19.999   6.185   9.830   7.327   0.000   0.000   0.000
   2_bss:  0.365  38.995   2.932   5.416   4.165   0.000   0.000   0.000
   2_xyz:  0.365  38.995   2.932   5.416   4.165   0.000   0.000   0.000
   2_adp:  0.365  38.995   2.932   5.416   4.165   0.000   0.000   0.000
   2_occ:  0.365  38.995   2.932   5.416   4.165   0.000   0.000   0.000
   3_bss:  0.343  38.995   1.996   3.154   3.106   0.000   0.000   0.000
   3_xyz:  0.343  38.995   1.996   3.154   3.106   0.000   0.000   0.000
   3_adp:  0.343  38.995   1.996   3.154   3.106   0.000   0.000   0.000
   3_occ:  0.343  38.995   1.996   3.154   3.106   0.000   0.000   0.000
   4_bss:  0.327  38.995   1.482   1.912   2.628   0.000   0.000   0.000
   4_xyz:  0.327  38.995   1.482   1.912   2.628   0.000   0.000   0.000
   4_adp:  0.327  38.995   1.482   1.912   2.628   0.000   0.000   0.000
   4_occ:  0.327  38.995   1.482   1.912   2.628   0.000   0.000   0.000
   5_bss:  0.327  38.995   1.180   1.260   2.382   0.000   0.000   0.000
   5_xyz:  0.327  38.995   1.180   1.260   2.382   0.000   0.000   0.000
   5_adp:  0.327  38.995   1.180   1.260   2.382   0.000   0.000   0.000
   5_occ:  0.327  38.995   1.180   1.260   2.382   0.000   0.000   0.000
   5_bss:  0.320  42.777  -0.366  -0.411   0.777   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.516 0.4001  0.4740    72836.194
   1_bss:  58.698 0.4093  0.6036    69375.730
   1_xyz:  49.815 0.5218  0.7597    54416.513
   1_adp:  46.458 0.5644  0.8749    50451.205
   1_occ:  46.508 0.5638  0.8731    50525.327
   2_bss:  46.125 0.5682  0.7747    49805.286
   2_xyz:  34.608 0.7054  0.9377    29391.815
   2_adp:  31.775 0.7383  0.9766    25717.438
   2_occ:  31.811 0.7379  0.9756    25757.319
   3_bss:  31.506 0.7409  0.9294    25201.409
   3_xyz:  25.600 0.8050  0.9828    17252.626
   3_adp:  23.009 0.8322  0.9958    14460.921
   3_occ:  22.986 0.8324  0.9956    14425.628
   4_bss:  22.944 0.8328  0.9691    14373.591
   4_xyz:  18.348 0.8767  0.9940     9437.929
   4_adp:  16.675 0.8923  0.9976     8353.833
   4_occ:  16.636 0.8926  0.9975     8305.161
   5_bss:  16.605 0.8928  0.9829     8255.143
   5_xyz:  15.212 0.9050  0.9888     7256.028
   5_adp:  14.962 0.9074  0.9835     7114.423
   5_occ:  14.947 0.9075  0.9835     7098.714
   5_bss:  14.932 0.9076  0.9858     7087.090
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3015e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3015e+01
   1_xyz:   1.690  0.013  0.105 18.215  0.006  4.106   1.4031e-01
   1_adp:   1.690  0.013  0.105 18.215  0.006  4.106   1.4031e-01
   1_occ:   1.690  0.013  0.105 18.215  0.006  4.106   1.4031e-01
   2_bss:   1.690  0.013  0.105 18.215  0.006  4.106   1.4031e-01
   2_xyz:   1.349  0.011  0.095 16.312  0.006  4.102   1.1141e-01
   2_adp:   1.349  0.011  0.095 16.312  0.006  4.102   1.1141e-01
   2_occ:   1.349  0.011  0.095 16.312  0.006  4.102   1.1141e-01
   3_bss:   1.349  0.011  0.095 16.312  0.006  4.102   1.1141e-01
   3_xyz:   0.950  0.006  0.068 15.496  0.003  4.114   5.8471e-02
   3_adp:   0.950  0.006  0.068 15.496  0.003  4.114   5.8471e-02
   3_occ:   0.950  0.006  0.068 15.496  0.003  4.114   5.8471e-02
   4_bss:   0.950  0.006  0.068 15.496  0.003  4.114   5.8471e-02
   4_xyz:   1.048  0.007  0.076 15.893  0.004  4.106   6.6892e-02
   4_adp:   1.048  0.007  0.076 15.893  0.004  4.106   6.6892e-02
   4_occ:   1.048  0.007  0.076 15.893  0.004  4.106   6.6892e-02
   5_bss:   1.048  0.007  0.076 15.893  0.004  4.106   6.6892e-02
   5_xyz:   0.954  0.006  0.073 15.504  0.004  4.108   5.7391e-02
   5_adp:   0.954  0.006  0.073 15.504  0.004  4.108   5.7391e-02
   5_occ:   0.954  0.006  0.073 15.504  0.004  4.108   5.7391e-02
   5_bss:   0.954  0.006  0.073 15.504  0.004  4.108   5.7391e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8702e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8702e+00
   1_xyz:  13.511  0.171  0.449 88.646  0.040  2.204   9.8183e-02
   1_adp:  13.511  0.171  0.449 88.646  0.040  2.204   9.8183e-02
   1_occ:  13.511  0.171  0.449 88.646  0.040  2.204   9.8183e-02
   2_bss:  13.511  0.171  0.449 88.646  0.040  2.204   9.8183e-02
   2_xyz:   8.662  0.134  0.381 82.136  0.049  2.042   1.1350e-01
   2_adp:   8.662  0.134  0.381 82.136  0.049  2.042   1.1350e-01
   2_occ:   8.662  0.134  0.381 82.136  0.049  2.042   1.1350e-01
   3_bss:   8.662  0.134  0.381 82.136  0.049  2.042   1.1350e-01
   3_xyz:   6.469  0.050  0.243 74.650  0.029  2.283   4.5245e-02
   3_adp:   6.469  0.050  0.243 74.650  0.029  2.283   4.5245e-02
   3_occ:   6.469  0.050  0.243 74.650  0.029  2.283   4.5245e-02
   4_bss:   6.469  0.050  0.243 74.650  0.029  2.283   4.5245e-02
   4_xyz:   7.679  0.048  0.330 83.512  0.029  2.236   4.8291e-02
   4_adp:   7.679  0.048  0.330 83.512  0.029  2.236   4.8291e-02
   4_occ:   7.679  0.048  0.330 83.512  0.029  2.236   4.8291e-02
   5_bss:   7.679  0.048  0.330 83.512  0.029  2.236   4.8291e-02
   5_xyz:   6.395  0.040  0.340 82.933  0.037  2.322   4.1672e-02
   5_adp:   6.395  0.040  0.340 82.933  0.037  2.322   4.1672e-02
   5_occ:   6.395  0.040  0.340 82.933  0.037  2.322   4.1672e-02
   5_bss:   6.395  0.040  0.340 82.933  0.037  2.322   4.1672e-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:  91.81   0.00  13.98  90.84   0.00  11.87  91.81   0.00  25.48
   1_occ:  91.81   0.00  13.98  90.84   0.00  11.87  91.81   0.00  25.48
   2_bss:  91.81   0.00  13.98  90.84   0.00  11.87  91.81   0.00  25.48
   2_xyz:  91.81   0.00  13.98  90.84   0.00  11.87  91.81   0.00  25.48
   2_adp:  91.00   0.00  13.92  91.00   0.00  10.99  89.93   0.00  29.89
   2_occ:  91.00   0.00  13.92  91.00   0.00  10.99  89.93   0.00  29.89
   3_bss:  91.00   0.00  13.92  91.00   0.00  10.99  89.93   0.00  29.89
   3_xyz:  91.00   0.00  13.92  91.00   0.00  10.99  89.93   0.00  29.89
   3_adp:  97.38   0.00  14.16  97.38   0.00   9.95  91.86   1.34  37.08
   3_occ:  97.38   0.00  14.16  97.38   0.00   9.95  91.86   1.34  37.08
   4_bss:  97.38   0.00  14.16  97.38   0.00   9.95  91.86   1.34  37.08
   4_xyz:  97.38   0.00  14.16  97.38   0.00   9.95  91.86   1.34  37.08
   4_adp:  96.42   0.00  13.61  96.42   0.00   9.38  89.18   3.01  36.64
   4_occ:  96.42   0.00  13.61  96.42   0.00   9.38  89.18   3.01  36.64
   5_bss:  96.42   0.00  13.61  96.42   0.00   9.38  89.18   3.01  36.64
   5_xyz:  96.42   0.00  13.61  96.42   0.00   9.38  89.18   3.01  36.64
   5_adp: 104.00   0.00  13.95 104.00   0.00   9.29  93.69   2.66  39.31
   5_occ: 104.00   0.00  13.95 104.00   0.00   9.29  93.69   2.66  39.31
   5_bss: 105.66   1.67  15.62 105.66   1.67  10.96  95.36   4.33  40.97
------------------------------------------------------------------------
 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:    1.242    0.019    0.411
   1_adp:    1.242    0.019    0.411
   1_occ:    1.242    0.019    0.411
   2_bss:    1.242    0.019    0.411
   2_xyz:    1.631    0.039    0.628
   2_adp:    1.631    0.039    0.628
   2_occ:    1.631    0.039    0.628
   3_bss:    1.631    0.039    0.628
   3_xyz:    1.642    0.044    0.670
   3_adp:    1.642    0.044    0.670
   3_occ:    1.642    0.044    0.670
   4_bss:    1.642    0.044    0.670
   4_xyz:    1.834    0.052    0.756
   4_adp:    1.834    0.052    0.756
   4_occ:    1.834    0.052    0.756
   5_bss:    1.834    0.052    0.756
   5_xyz:    1.891    0.038    0.774
   5_adp:    1.891    0.038    0.774
   5_occ:    1.891    0.038    0.774
   5_bss:    1.891    0.038    0.774
------------------------------------------------------------------------

CPU time actual refinement: 329.91


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_498/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_498/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_498/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_498/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_498/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.75 
  Macro-tasks:
    bulk solvent and scale       = 42.91  
    individual site refinement   = 130.46 
    weights calculation          = 32.31  
    collect and process          = 6.56   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 212.38 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 100.11 
    alpha_beta                      = 8.46   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 109.08 
    fmodel                         = 7.60   
    r_factors                      = 0.21   
    phase_errors                   = 10.50  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 239.76 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.722 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    631 calls, 99.71 s
gradients_fft:          577 calls, 96.43 s

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

# Date 2008-01-16 Time 01:44:32 PST -0800 (1200476672.05 s)
Start R-work = 0.4823, R-free = 0.4742 (no bulk solvent and anisotropic scale)
Final R-work = 0.1332, R-free = 0.1813 (no bulk solvent and anisotropic scale)

Start R-work = 0.4735, R-free = 0.4616
Final R-work = 0.1169, R-free = 0.1664