# Date 2008-01-16 Time 01:03:12 PST -0800 (1200474192.24 s)
#phil __OFF__

Command line arguments: "../253.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 = 26864
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 253

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 45.9914, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.951
Completeness in resolution range: 0.9724
Completeness with d_max=infinity: 0.969321

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7280
                             d_min =   1.9510

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.951
Completeness in resolution range: 0.9724
Completeness with d_max=infinity: 0.969321

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7284 -  4.1744 [2105/2129]  1895   210  10.0%
  bin  2:  4.1744 -  3.3259 [2037/2056]  1833   204  10.0%
  bin  3:  3.3259 -  2.9092 [2011/2030]  1807   204  10.1%
  bin  4:  2.9092 -  2.6448 [1989/2019]  1795   194   9.8%
  bin  5:  2.6448 -  2.4562 [1978/1997]  1779   199  10.1%
  bin  6:  2.4562 -  2.3120 [1944/1969]  1750   194  10.0%
  bin  7:  2.3120 -  2.1966 [1969/1997]  1769   200  10.2%
  bin  8:  2.1966 -  2.1012 [1948/1984]  1756   192   9.9%
  bin  9:  2.1012 -  2.0206 [1940/1982]  1748   192   9.9%
  bin 10:  2.0206 -  1.9510 [1668/1982]  1498   170  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_253/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.03 -     1.80: 8
        1.80 -     2.58: 114
        2.58 -     3.35: 4220
        3.35 -     4.13: 9695
        4.13 -     4.90: 15190
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.030 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.279 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.315 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.426 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.546 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29222 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_253/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_253/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 45.9914 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5191   r_free= 0.5209   ksol= 0.00   Bsol= 0.00   scale= 0.781    |
|                                                                             |
| 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:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.309412                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6558 0.99   1376  153 0.4395 0.4518      6.6584      6.7021|
|  2:  4.6558 -  3.7149 0.99   1324  146 0.4760 0.4529      6.8802       6.871|
|  3:  3.7149 -  3.2511 0.99   1295  145 0.4981 0.4879      6.7534      6.8134|
|  4:  3.2511 -  2.9565 0.99   1282  144 0.5057 0.4722      6.5873      6.5306|
|  5:  2.9565 -  2.7460 0.99   1282  143 0.5475 0.5295      6.4102      6.3913|
|  6:  2.7460 -  2.5850 0.99   1280  137 0.5459 0.6058      6.3115      6.2809|
|  7:  2.5850 -  2.4562 0.99   1270  143 0.5383 0.4938       6.261       6.227|
|  8:  2.4562 -  2.3497 0.98   1259  146 0.5599 0.5800       6.211       6.189|
|  9:  2.3497 -  2.2596 0.98   1262  135 0.5456 0.5920      6.1308      6.1636|
| 10:  2.2596 -  2.1819 0.99   1243  142 0.5631 0.5284      6.1314      6.1614|
| 11:  2.1819 -  2.1139 0.98   1260  135 0.5436 0.5829      6.0649      6.0638|
| 12:  2.1139 -  2.0536 0.97   1237  138 0.5369 0.5642      5.9929      6.0399|
| 13:  2.0536 -  1.9997 1.00   1251  145 0.5555 0.5002      5.9047      5.8692|
| 14:  1.9997 -  1.9510 0.78   1009  107 0.5490 0.5415      5.8523      5.7584|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6558  1376   153  0.57  45.29   0.78     0.63     111663.65|
|  2:  4.6558 -  3.7149  1324   146  0.58  44.96   0.84     0.68     157908.92|
|  3:  3.7149 -  3.2511  1295   145  0.47  53.90   0.83     0.63     162026.70|
|  4:  3.2511 -  2.9565  1282   144  0.40  59.96   0.80     0.51     133643.13|
|  5:  2.9565 -  2.7460  1282   143  0.30  67.13   0.72     0.39     100724.65|
|  6:  2.7460 -  2.5850  1280   137  0.26  70.21   0.72     0.31      84334.72|
|  7:  2.5850 -  2.4562  1270   143  0.19  75.67   0.73     0.22      77855.41|
|  8:  2.4562 -  2.3497  1259   146  0.17  77.06   0.73     0.22      71638.55|
|  9:  2.3497 -  2.2596  1262   135  0.17  77.30   0.72     0.21      65107.87|
| 10:  2.2596 -  2.1819  1243   142  0.18  76.42   0.74     0.23      58912.18|
| 11:  2.1819 -  2.1139  1260   135  0.15  78.54   0.78     0.20      55299.62|
| 12:  2.1139 -  2.0536  1237   138  0.18  76.66   0.78     0.24      50753.00|
| 13:  2.0536 -  1.9997  1251   145  0.21  74.25   0.75     0.28      41601.36|
| 14:  1.9997 -  1.9510  1009   107  0.29  68.34   0.73     0.33      30856.32|
|alpha:            min =        0.20 max =            0.68 mean =         0.37|
|beta:             min =    30856.32 max =       162026.70 mean =     87410.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.30|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.26|
|phase err.(test): min =        0.00 max =           89.81 mean =        67.66|
|-----------------------------------------------------------------------------|

============================== 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 = 33.933093             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.130   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.147184              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.785   (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 |  0.542 -  0.978:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  0.978 -  1.414:        3 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.414 -  1.849:       25 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.849 -  2.285:      208 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.285 -  2.721:      871 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.721 -  3.157:     2171 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.157 -  3.593:     3755 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.593 -  4.028:     5580 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.028 -  4.464:     7479 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.464 -  4.900:     9176 |
|-----------------------------------------------------------------------------|
|-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 |       52.430 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  0.542 |       3.180 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.182)------------------------------------------|
|    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 = 11.182)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5224   r_free= 0.5224   ksol= 0.00   Bsol= 0.00   scale= 0.750    |
|                                                                             |
| 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:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.309535                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5117   r_free= 0.5092   ksol= 0.42   Bsol= 20.00   scale= 0.947   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.51,8.15,7.84,0.00,0.00,0.00); trace/3= 7.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.304795                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 24.459609             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.814   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.384814              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.683   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5117      final r-factor (work) = 0.4587          |
| start r-factor (free) = 0.5092      final r-factor (free) = 0.4824          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 129.5473 = 24.46 * 0.50 * 6.3057 + 1.00 * 52.4295                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.7888 = 24.46 * 0.50 * 6.2648 + 1.00 * 0.1710                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4587      final r-factor (work) = 0.4195          |
| start r-factor (free) = 0.4824      final r-factor (free) = 0.4802          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.9549 = 2.38 * 1.00 * 6.2648 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.8771 = 2.38 * 1.00 * 6.2276 + 1.00 * 0.0255                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.182)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.96   16.60    None  None   None       |
|    all(noH): 2823   0      0.00    89.96   16.60    None  None   None       |
|    Sol.    : 438    0      0.00    89.96   22.02    None  None   None       |
|    Mac.    : 2385   0      0.00    80.99   15.60    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.996:  937   |   5:    44.978 -  53.974:   69        |
|      1:     8.996 -  17.991:  800   |   6:    53.974 -  62.969:   32        |
|      2:    17.991 -  26.987:  540   |   7:    62.969 -  71.965:    7        |
|      3:    26.987 -  35.983:  289   |   8:    71.965 -  80.961:    2        |
|      4:    35.983 -  44.978:  144   |   9:    80.961 -  89.956:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4195 r_free = 0.4802             target_work(ml) = 6.222         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4190 r_free = 0.4815             target_work(ml) = 6.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4190   r_free= 0.4815   ksol= 0.42   Bsol= 20.00   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.51,8.15,7.84,0.00,0.00,0.00); trace/3= 7.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.221443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4184   r_free= 0.4801   ksol= 0.40   Bsol= 50.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.36,5.12,5.79,0.00,0.00,0.00); trace/3= 4.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.222718                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.786941             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.114  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.075400              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.706  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4184      final r-factor (work) = 0.3709          |
| start r-factor (free) = 0.4801      final r-factor (free) = 0.4443          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0813 = 13.79 * 0.50 * 6.2248 + 1.00 * 0.1710                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.7242 = 13.79 * 0.50 * 6.1805 + 1.00 * 0.1194                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3709      final r-factor (work) = 0.3547          |
| start r-factor (free) = 0.4443      final r-factor (free) = 0.4350          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6842 = 1.08 * 1.00 * 6.1805 + 1.00 * 0.0377                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6256 = 1.08 * 1.00 * 6.1254 + 1.00 * 0.0384                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.182)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.84  15.66    None  None   None       |
|    all(noH): 2823   0      0.00    102.84  15.66    None  None   None       |
|    Sol.    : 438    0      0.00    102.84  24.70    None  None   None       |
|    Mac.    : 2385   0      0.00    91.97   14.00    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:     0.000 -  10.284: 1122   |   5:    51.422 -  61.706:   29        |
|      1:    10.284 -  20.569:  941   |   6:    61.706 -  71.991:   10        |
|      2:    20.569 -  30.853:  459   |   7:    71.991 -  82.275:    2        |
|      3:    30.853 -  41.137:  182   |   8:    82.275 -  92.559:    3        |
|      4:    41.137 -  51.422:   74   |   9:    92.559 - 102.844:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3547 r_free = 0.4350             target_work(ml) = 6.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3543 r_free = 0.4352             target_work(ml) = 6.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3543   r_free= 0.4352   ksol= 0.40   Bsol= 50.00   scale= 1.077   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.36,5.12,5.79,0.00,0.00,0.00); trace/3= 4.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.111765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3538   r_free= 0.4347   ksol= 0.34   Bsol= 50.00   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,3.23,3.82,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.111082                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.000040             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.374   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.581857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.573   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3538      final r-factor (work) = 0.2911          |
| start r-factor (free) = 0.4347      final r-factor (free) = 0.3622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.7345 = 10.00 * 0.50 * 6.1230 + 1.00 * 0.1194                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.3214 = 10.00 * 0.50 * 6.0441 + 1.00 * 0.1010                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2911      final r-factor (work) = 0.2612          |
| start r-factor (free) = 0.3622      final r-factor (free) = 0.3470          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.6654 = 3.58 * 1.00 * 6.0441 + 1.00 * 0.0165                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.2072 = 3.58 * 1.00 * 5.9135 + 1.00 * 0.0257                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.182)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.56  17.24    None  None   None       |
|    all(noH): 2823   0      0.00    112.56  17.24    None  None   None       |
|    Sol.    : 438    0      0.29    109.90  37.59    None  None   None       |
|    Mac.    : 2385   0      0.00    112.56  13.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.256: 1355   |   5:    56.278 -  67.534:   69        |
|      1:    11.256 -  22.511:  703   |   6:    67.534 -  78.790:   33        |
|      2:    22.511 -  33.767:  346   |   7:    78.790 -  90.045:   14        |
|      3:    33.767 -  45.023:  175   |   8:    90.045 - 101.301:    3        |
|      4:    45.023 -  56.278:  122   |   9:   101.301 - 112.556:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2612 r_free = 0.3470             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2610 r_free = 0.3471             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2610   r_free= 0.3471   ksol= 0.34   Bsol= 50.00   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,3.23,3.82,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.890142                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2604   r_free= 0.3460   ksol= 0.33   Bsol= 49.08   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,1.71,2.72,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.887807                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.600885              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.911  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211293              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.534  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2604      final r-factor (work) = 0.2170          |
| start r-factor (free) = 0.3460      final r-factor (free) = 0.2925          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6582 = 5.60 * 0.50 * 5.9124 + 1.00 * 0.1010                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3737 = 5.60 * 0.50 * 5.8226 + 1.00 * 0.0677                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2170      final r-factor (work) = 0.2071          |
| start r-factor (free) = 0.2925      final r-factor (free) = 0.2678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2562 = 0.21 * 1.00 * 5.8226 + 1.00 * 0.0260                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2174 = 0.21 * 1.00 * 5.7210 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.182)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.79  14.72    None  None   None       |
|    all(noH): 2823   0      0.00    105.79  14.72    None  None   None       |
|    Sol.    : 438    0      2.29    105.79  35.79    None  None   None       |
|    Mac.    : 2385   0      0.00    105.07  10.85    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 -  10.579: 1570   |   5:    52.896 -  63.476:   42        |
|      1:    10.579 -  21.159:  674   |   6:    63.476 -  74.055:   13        |
|      2:    21.159 -  31.738:  244   |   7:    74.055 -  84.634:    9        |
|      3:    31.738 -  42.317:  159   |   8:    84.634 -  95.213:    2        |
|      4:    42.317 -  52.896:  107   |   9:    95.213 - 105.793:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2071 r_free = 0.2678             target_work(ml) = 5.674         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2066 r_free = 0.2671             target_work(ml) = 5.672         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2066   r_free= 0.2671   ksol= 0.33   Bsol= 49.08   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,1.71,2.72,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.671578                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2063   r_free= 0.2658   ksol= 0.32   Bsol= 37.88   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.74,1.19,1.89,0.00,0.00,0.00); trace/3= 1.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.669781                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.758139              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.105  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.381594              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.560  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2063      final r-factor (work) = 0.1593          |
| start r-factor (free) = 0.2658      final r-factor (free) = 0.2054          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8150 = 3.76 * 0.50 * 5.7195 + 1.00 * 0.0677                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5182 = 3.76 * 0.50 * 5.5595 + 1.00 * 0.0716                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1593      final r-factor (work) = 0.1462          |
| start r-factor (free) = 0.2054      final r-factor (free) = 0.1954          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1300 = 0.38 * 1.00 * 5.5595 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0639 = 0.38 * 1.00 * 5.3828 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.182)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.04  14.90    None  None   None       |
|    all(noH): 2823   0      0.00    104.04  14.90    None  None   None       |
|    Sol.    : 438    0      3.87    104.04  39.54    None  None   None       |
|    Mac.    : 2385   0      0.00    103.99  10.37    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 -  10.404: 1651   |   5:    52.021 -  62.425:   76        |
|      1:    10.404 -  20.808:  623   |   6:    62.425 -  72.829:   30        |
|      2:    20.808 -  31.213:  162   |   7:    72.829 -  83.234:    9        |
|      3:    31.213 -  41.617:  136   |   8:    83.234 -  93.638:    1        |
|      4:    41.617 -  52.021:  132   |   9:    93.638 - 104.042:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1462 r_free = 0.1954             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1459 r_free = 0.1948             target_work(ml) = 5.353         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1948   ksol= 0.32   Bsol= 37.88   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.74,1.19,1.89,0.00,0.00,0.00); trace/3= 1.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.353464                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6558 0.99   1376  153 0.1197 0.1558      5.5845      5.7555|
|  2:  4.6558 -  3.7149 0.99   1324  146 0.1116 0.1556      5.6774       5.963|
|  3:  3.7149 -  3.2511 0.99   1295  145 0.1436 0.1613      5.7376      5.9168|
|  4:  3.2511 -  2.9565 0.99   1282  144 0.1609 0.2165      5.7073      5.9001|
|  5:  2.9565 -  2.7460 0.99   1282  143 0.1728 0.2161      5.5492      5.7121|
|  6:  2.7460 -  2.5850 0.99   1280  137 0.1592 0.2181      5.4311      5.5796|
|  7:  2.5850 -  2.4562 0.99   1270  143 0.1580 0.2118      5.3602      5.6236|
|  8:  2.4562 -  2.3497 0.98   1259  146 0.1597 0.2161      5.3191      5.5514|
|  9:  2.3497 -  2.2596 0.98   1262  135 0.1536 0.2130      5.2454      5.4804|
| 10:  2.2596 -  2.1819 0.99   1243  142 0.1433 0.2121      5.1608      5.3897|
| 11:  2.1819 -  2.1139 0.98   1260  135 0.1434 0.2193      5.1151      5.4418|
| 12:  2.1139 -  2.0536 0.97   1237  138 0.1420 0.1680      5.0553      5.2749|
| 13:  2.0536 -  1.9997 1.00   1251  145 0.1428 0.2153      4.9706      5.2477|
| 14:  1.9997 -  1.9510 0.78   1009  107 0.1429 0.1973      4.8682      5.0869|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6558  1376   153  0.91  12.99   0.99     0.96      12038.89|
|  2:  4.6558 -  3.7149  1324   146  0.93  11.45   1.06     1.04      14654.26|
|  3:  3.7149 -  3.2511  1295   145  0.90  15.64   1.07     1.05      16997.76|
|  4:  3.2511 -  2.9565  1282   144  0.89  17.81   1.04     1.03      16510.34|
|  5:  2.9565 -  2.7460  1282   143  0.87  19.49   1.02     0.97      11845.86|
|  6:  2.7460 -  2.5850  1280   137  0.87  19.94   1.02     0.97      10653.33|
|  7:  2.5850 -  2.4562  1270   143  0.86  20.64   1.03     1.01       9582.72|
|  8:  2.4562 -  2.3497  1259   146  0.86  20.71   1.04     1.01       8842.46|
|  9:  2.3497 -  2.2596  1262   135  0.88  19.07   1.05     1.03       7486.79|
| 10:  2.2596 -  2.1819  1243   142  0.87  19.37   1.05     1.01       6516.17|
| 11:  2.1819 -  2.1139  1260   135  0.87  19.92   1.06     1.02       6143.78|
| 12:  2.1139 -  2.0536  1237   138  0.88  18.85   1.07     1.04       5481.51|
| 13:  2.0536 -  1.9997  1251   145  0.88  19.14   1.07     1.06       4599.39|
| 14:  1.9997 -  1.9510  1009   107  0.88  18.02   1.05     1.01       3513.54|
|alpha:            min =        0.96 max =            1.06 mean =         1.01|
|beta:             min =     3513.54 max =        16997.76 mean =      9792.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        18.01|
|phase err.(test): min =        0.00 max =           89.53 mean =        17.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1455   r_free= 0.1946   ksol= 0.32   Bsol= 38.46   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.20,0.62,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.352139                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1455   r_free= 0.1946   ksol= 0.32   Bsol= 38.46   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.20,0.62,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.352139                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6558 0.99   1376  153 0.1195 0.1562      5.5719      5.7279|
|  2:  4.6558 -  3.7149 0.99   1324  146 0.1129 0.1567      5.6787      5.9657|
|  3:  3.7149 -  3.2511 0.99   1295  145 0.1441 0.1601       5.739        5.92|
|  4:  3.2511 -  2.9565 0.99   1282  144 0.1612 0.2208      5.7096      5.9123|
|  5:  2.9565 -  2.7460 0.99   1282  143 0.1727 0.2173      5.5507      5.7147|
|  6:  2.7460 -  2.5850 0.99   1280  137 0.1591 0.2182      5.4306      5.5795|
|  7:  2.5850 -  2.4562 0.99   1270  143 0.1580 0.2117      5.3595      5.6214|
|  8:  2.4562 -  2.3497 0.98   1259  146 0.1592 0.2164      5.3169      5.5518|
|  9:  2.3497 -  2.2596 0.98   1262  135 0.1531 0.2129      5.2442      5.4835|
| 10:  2.2596 -  2.1819 0.99   1243  142 0.1431 0.2117      5.1593       5.388|
| 11:  2.1819 -  2.1139 0.98   1260  135 0.1430 0.2196      5.1136      5.4417|
| 12:  2.1139 -  2.0536 0.97   1237  138 0.1415 0.1677      5.0544      5.2738|
| 13:  2.0536 -  1.9997 1.00   1251  145 0.1428 0.2156      4.9699      5.2471|
| 14:  1.9997 -  1.9510 0.78   1009  107 0.1428 0.1966      4.8657      5.0829|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6558  1376   153  0.91  12.60   0.98     0.96      11398.45|
|  2:  4.6558 -  3.7149  1324   146  0.93  11.35   1.04     1.03      14351.24|
|  3:  3.7149 -  3.2511  1295   145  0.90  15.72   1.06     1.03      17174.18|
|  4:  3.2511 -  2.9565  1282   144  0.88  17.92   1.03     1.01      16668.80|
|  5:  2.9565 -  2.7460  1282   143  0.87  19.60   1.00     0.95      11963.46|
|  6:  2.7460 -  2.5850  1280   137  0.87  19.94   0.99     0.94      10643.71|
|  7:  2.5850 -  2.4562  1270   143  0.86  20.61   1.00     0.98       9566.34|
|  8:  2.4562 -  2.3497  1259   146  0.86  20.68   1.01     0.98       8820.64|
|  9:  2.3497 -  2.2596  1262   135  0.88  19.06   1.01     1.00       7475.14|
| 10:  2.2596 -  2.1819  1243   142  0.87  19.35   1.01     0.97       6499.21|
| 11:  2.1819 -  2.1139  1260   135  0.87  19.90   1.02     0.99       6134.58|
| 12:  2.1139 -  2.0536  1237   138  0.88  18.83   1.03     1.00       5480.94|
| 13:  2.0536 -  1.9997  1251   145  0.88  19.11   1.02     1.01       4583.68|
| 14:  1.9997 -  1.9510  1009   107  0.89  17.93   1.00     0.97       3479.91|
|alpha:            min =        0.94 max =            1.03 mean =         0.99|
|beta:             min =     3479.91 max =        17174.18 mean =      9743.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.98|
|phase err.(test): min =        0.00 max =           89.53 mean =        17.21|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.182)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.58    104.62  15.48    None  None   None       |
|    all(noH): 2823   0      0.58    104.62  15.48    None  None   None       |
|    Sol.    : 438    0      4.44    104.62  40.12    None  None   None       |
|    Mac.    : 2385   0      0.58    104.57  10.95    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:     0.575 -  10.979: 1651   |   5:    52.596 -  63.000:   76        |
|      1:    10.979 -  21.384:  623   |   6:    63.000 -  73.404:   30        |
|      2:    21.384 -  31.788:  162   |   7:    73.404 -  83.809:    9        |
|      3:    31.788 -  42.192:  136   |   8:    83.809 -  94.213:    1        |
|      4:    42.192 -  52.596:  132   |   9:    94.213 - 104.617:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.620 - 5.215
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 330
   mapped sites are within: 0.725 - 5.215

peak=    9.361 closest distance to " CB  VAL A 230 " =    1.491
peak=    9.172 closest distance to " CB  VAL A 296 " =    1.455
peak=    8.669 closest distance to " O   HOH Z 390 " =    1.542
peak=    6.875 closest distance to " O   HOH Z 381 " =    1.577
peak=    6.872 closest distance to " O   HOH Z 120 " =    1.261
peak=    6.797 closest distance to " O   HOH Z 429 " =    1.478
peak=    6.574 closest distance to " OD1 ASN A  60 " =    1.204
peak=    6.459 closest distance to " O   HOH Z 199 " =    1.744
peak=    6.433 closest distance to " O   HOH Z 130 " =    1.749
peak=    6.392 closest distance to " O   HOH Z 205 " =    2.187
peak=    6.151 closest distance to " O   HOH Z 385 " =    1.537
peak=    6.029 closest distance to " CD2 LEU A   5 " =    1.466
peak=    6.009 closest distance to " O   HOH Z 363 " =    1.546
peak=    5.824 closest distance to " O   HOH Z  65 " =    2.143
peak=    5.775 closest distance to " CD  ARG A 138 " =    1.061
peak=    5.728 closest distance to " O   HOH Z  69 " =    1.568
peak=    5.724 closest distance to " O   HOH Z  61 " =    1.393
peak=    5.655 closest distance to " O   HOH Z 316 " =    1.187
peak=    5.638 closest distance to " O   PRO A 198 " =    1.414
peak=    5.570 closest distance to " CG1AVAL A 121 " =    0.949
peak=    5.500 closest distance to " O   HOH Z 193 " =    2.028
peak=    5.357 closest distance to " O   HOH Z 326 " =    1.643
peak=    5.350 closest distance to " O   HOH Z 410 " =    1.424
peak=    5.320 closest distance to " O   HOH Z 214 " =    1.767
peak=    5.218 closest distance to " O   HOH Z 289 " =    1.387
peak=    5.160 closest distance to " O   HOH Z 321 " =    0.925
peak=    5.153 closest distance to " O   HOH Z 375 " =    1.328
peak=    5.142 closest distance to " O   HOH Z 358 " =    1.470
peak=    5.136 closest distance to " CD2 LEU A 228 " =    1.298
peak=    5.077 closest distance to " CB  ASN A  60 " =    0.964
peak=    5.073 closest distance to " CB  ARG A 275 " =    1.149
peak=    5.052 closest distance to " CD1AILE A 234 " =    0.945
peak=    5.044 closest distance to " CD  ARG A 138 " =    1.237
peak=    5.004 closest distance to " O   HOH Z 278 " =    2.395
peak=    4.985 closest distance to " O   HOH Z 138 " =    1.030
peak=    4.940 closest distance to " O   HOH Z 279 " =    1.263
peak=    4.912 closest distance to " O   HOH Z 142 " =    2.002
peak=    4.882 closest distance to " O   HOH Z 403 " =    1.846
peak=    4.780 closest distance to " NE2 GLN A  11 " =    1.110
peak=    4.772 closest distance to " O   HOH Z 124 " =    1.663
peak=    4.772 closest distance to " O   HOH Z   7 " =    1.904
peak=    4.770 closest distance to " O   HOH Z 423 " =    2.061
peak=    4.698 closest distance to " CE AMET A  47 " =    1.211
peak=    4.685 closest distance to " O   HOH Z 414 " =    1.735
peak=    4.683 closest distance to " NE1 TRP A 266 " =    1.903
peak=    4.678 closest distance to " O   HOH Z 428 " =    1.622
peak=    4.676 closest distance to " O   HOH Z 426 " =    1.345
peak=    4.671 closest distance to " O   HOH Z  54 " =    1.280
peak=    4.606 closest distance to " O   HOH Z 316 " =    2.080
peak=    4.586 closest distance to " O   HOH Z 123 " =    1.372
peak=    4.542 closest distance to " O   HOH Z 112 " =    1.368
peak=    4.512 closest distance to " CG2 ILE A 234 " =    1.019
peak=    4.495 closest distance to " O   HOH Z 344 " =    1.454
peak=    4.491 closest distance to " N   PHE A  59 " =    0.764
peak=    4.486 closest distance to " O   HOH Z  63 " =    1.736
peak=    4.441 closest distance to " O   HOH Z 427 " =    2.324
peak=    4.440 closest distance to " O   HOH Z 388 " =    1.138
peak=    4.435 closest distance to " O   HOH Z 134 " =    1.475
peak=    4.427 closest distance to " O   HOH Z  59 " =    1.841
peak=    4.419 closest distance to " OG ASER A 134 " =    1.537
peak=    4.410 closest distance to " CB  PRO A  54 " =    1.139
peak=    4.382 closest distance to " O   HOH Z  28 " =    2.243
peak=    4.370 closest distance to " O   HOH Z 334 " =    1.835
peak=    4.368 closest distance to " O   HOH Z 400 " =    0.912
peak=    4.367 closest distance to " O   HOH Z 347 " =    1.095
peak=    4.358 closest distance to " NH2 ARG A  56 " =    2.095
peak=    4.353 closest distance to " O   HOH Z 269 " =    1.441
peak=    4.315 closest distance to " O   HOH Z 236 " =    1.738
peak=    4.305 closest distance to " O   HOH Z 261 " =    1.948
peak=    4.305 closest distance to " O   HOH Z 291 " =    1.618
peak=    4.273 closest distance to " O   HOH Z 222 " =    1.375
peak=    4.267 closest distance to " OE1 GLN A  58 " =    5.215
peak=    4.242 closest distance to " O   HOH Z 117 " =    1.366
peak=    4.236 closest distance to " OD1 ASN A  45 " =    1.166
peak=    4.201 closest distance to " O   HOH Z 202 " =    1.813
peak=    4.181 closest distance to " N   ASN A  60 " =    1.040
peak=    4.172 closest distance to " O   SER A  62 " =    0.918
peak=    4.152 closest distance to " CB  ALA A   1 " =    1.179
peak=    4.145 closest distance to " O   HOH Z 126 " =    1.852
peak=    4.131 closest distance to " CG2 THR A 246 " =    1.006
peak=    4.102 closest distance to " O   HOH Z  53 " =    2.192
peak=    4.087 closest distance to " O   HOH Z 287 " =    1.475
peak=    4.083 closest distance to " O   HOH Z 132 " =    1.595
peak=    4.078 closest distance to " O   HOH Z 108 " =    1.671
peak=    4.047 closest distance to " NH2BARG A 145 " =    1.443
peak=    4.039 closest distance to " O   HOH Z 223 " =    1.158
peak=    4.032 closest distance to " O   HOH Z  89 " =    1.642
peak=    4.005 closest distance to " O   HOH Z   9 " =    1.254
peak=    3.998 closest distance to " CB  TYR A 169 " =    0.725
peak=    3.995 closest distance to " O   HOH Z 139 " =    1.388
peak=    3.995 closest distance to " O   HOH Z  97 " =    1.466
peak=    3.991 closest distance to " NE2 GLN A  55 " =    1.409
peak=    3.988 closest distance to " O   HOH Z 302 " =    1.571
peak=    3.965 closest distance to " NE2 GLN A  73 " =    1.836
peak=    3.964 closest distance to " CB  SER A   3 " =    1.237
peak=    3.957 closest distance to " O   HOH Z 273 " =    1.440
peak=    3.955 closest distance to " OG BSER A 216 " =    1.007
peak=    3.952 closest distance to " O   HOH Z 428 " =    1.373
peak=    3.948 closest distance to " CA  GLY A 241 " =    3.611
peak=    3.939 closest distance to " O   HOH Z 360 " =    1.251
peak=    3.934 closest distance to " O   HOH Z 357 " =    1.684
peak=    3.933 closest distance to " OD2 ASP A 286 " =    2.423
peak=    3.928 closest distance to " O   HOH Z  51 " =    2.301
peak=    3.918 closest distance to " CG  PRO A  54 " =    1.149
peak=    3.912 closest distance to " O   HOH Z 188 " =    1.203
peak=    3.911 closest distance to " NZ  LYS A 117 " =    1.307
peak=    3.900 closest distance to " O   HOH Z 133 " =    2.316
peak=    3.900 closest distance to " NH2BARG A 190 " =    1.550
peak=    3.892 closest distance to " O   HOH Z  39 " =    1.520
peak=    3.888 closest distance to " O   HOH Z 249 " =    1.308
peak=    3.867 closest distance to " NH1 ARG A 138 " =    0.957
peak=    3.852 closest distance to " O   ALA A 165 " =    1.050
peak=    3.848 closest distance to " O   HOH Z 130 " =    1.904
peak=    3.847 closest distance to " O   HOH Z 145 " =    2.472
peak=    3.836 closest distance to " O   HOH Z  24 " =    1.608
peak=    3.811 closest distance to " O   HOH Z 366 " =    2.097
peak=    3.797 closest distance to " CD2 TRP A 179 " =    2.190
peak=    3.788 closest distance to " O   HOH Z  46 " =    1.221
peak=    3.778 closest distance to " O   HOH Z 116 " =    1.261
peak=    3.773 closest distance to " O   HOH Z 133 " =    1.394
peak=    3.771 closest distance to " O   HOH Z 217 " =    1.914
peak=    3.762 closest distance to " O   HOH Z 194 " =    1.573
peak=    3.755 closest distance to " O   HOH Z 361 " =    1.519
peak=    3.751 closest distance to " O   HOH Z 251 " =    1.812
peak=    3.738 closest distance to " O   HOH Z  58 " =    1.630
peak=    3.734 closest distance to " CA  LEU A 282 " =    1.032
peak=    3.724 closest distance to " CG  GLN A  11 " =    2.047
peak=    3.724 closest distance to " O   HOH Z 269 " =    2.799
peak=    3.717 closest distance to " O   SER A 164 " =    1.301
peak=    3.715 closest distance to " O   HOH Z 220 " =    1.391
peak=    3.708 closest distance to " O   HOH Z 250 " =    2.112
peak=    3.697 closest distance to " O   HOH Z 270 " =    1.516
peak=    3.692 closest distance to " CG  PRO A 213 " =    1.208
peak=    3.683 closest distance to " OD1 ASP A 286 " =    1.249
peak=    3.683 closest distance to " O   HOH Z  28 " =    2.079
peak=    3.679 closest distance to " O   HOH Z 331 " =    1.573
peak=    3.673 closest distance to " O   HOH Z 363 " =    2.870
peak=    3.665 closest distance to " N   TYR A  15 " =    1.149
peak=    3.662 closest distance to " CG  LEU A   5 " =    1.246
peak=    3.662 closest distance to " CD1 LEU A   5 " =    1.686
peak=    3.660 closest distance to " O   HOH Z  88 " =    2.812
peak=    3.659 closest distance to " O   HOH Z 247 " =    1.259
peak=    3.645 closest distance to " OD1 ASN A 148 " =    2.054
peak=    3.641 closest distance to " O   HOH Z 158 " =    1.420
peak=    3.639 closest distance to " O   HOH Z 130 " =    1.990
peak=    3.635 closest distance to " CA  ARG A  66 " =    0.879
peak=    3.632 closest distance to " O   HOH Z 366 " =    2.269
peak=    3.628 closest distance to " NH1 ARG A  14 " =    1.023
peak=    3.625 closest distance to " O   HOH Z 152 " =    2.421
peak=    3.623 closest distance to " CB  VAL A 265 " =    1.328
peak=    3.617 closest distance to " O   GLY A 302 " =    1.723
peak=    3.578 closest distance to " O   HOH Z 356 " =    1.513
peak=    3.576 closest distance to " O   HOH Z 260 " =    1.721
peak=    3.576 closest distance to " CG  GLN A  88 " =    1.056
peak=    3.574 closest distance to " O   HOH Z 262 " =    1.425
peak=    3.573 closest distance to " O   HOH Z 426 " =    3.181
peak=    3.570 closest distance to " O   HOH Z   6 " =    1.517
peak=    3.569 closest distance to " NE1 TRP A 274 " =    1.000
peak=    3.564 closest distance to " O   HOH Z  89 " =    2.209
peak=    3.562 closest distance to " CG2 THR A 279 " =    1.242
peak=    3.553 closest distance to " O   HOH Z 425 " =    1.561
peak=    3.549 closest distance to " CB  ASN A 187 " =    1.023
peak=    3.545 closest distance to " O   HOH Z 227 " =    2.104
peak=    3.542 closest distance to " O   HOH Z 196 " =    1.429
peak=    3.539 closest distance to " O   HOH Z 250 " =    1.379
peak=    3.534 closest distance to " CG  LYS A 166 " =    1.377
peak=    3.521 closest distance to " CB  ASP A 200 " =    1.014
peak=    3.514 closest distance to " O   HOH Z 364 " =    1.897
peak=    3.512 closest distance to " ND1 HIS A  81 " =    1.198
peak=    3.507 closest distance to " O   HOH Z 276 " =    1.876
peak=    3.504 closest distance to " SD BMET A  47 " =    1.719
peak=    3.503 closest distance to " O   HOH Z 137 " =    1.477
peak=    3.502 closest distance to " CA  ILE A 234 " =    1.101
peak=    3.497 closest distance to " O   HOH Z 280 " =    1.502
peak=    3.497 closest distance to " CA  PHE A 283 " =    1.173
peak=    3.496 closest distance to " CB  ASN A 187 " =    1.135
peak=    3.494 closest distance to " O   HOH Z  15 " =    1.379
peak=    3.493 closest distance to " O   HOH Z 128 " =    1.783
peak=    3.488 closest distance to " CG2 ILE A  20 " =    1.301
peak=    3.482 closest distance to " O   HOH Z 132 " =    2.117
peak=    3.482 closest distance to " N   PHE A 130 " =    1.374
peak=    3.476 closest distance to " O   HOH Z 264 " =    1.185
peak=    3.474 closest distance to " O   HOH Z 332 " =    1.431
peak=    3.473 closest distance to " O   HOH Z 253 " =    1.478
peak=    3.467 closest distance to " O   HOH Z 393 " =    1.441
peak=    3.466 closest distance to " O   HOH Z  88 " =    2.606
peak=    3.460 closest distance to " CD2 LEU A  25 " =    1.084
peak=    3.459 closest distance to " CB  ASN A 148 " =    1.365
peak=    3.446 closest distance to " O   HOH Z 334 " =    1.813
peak=    3.445 closest distance to " OE1 GLU A  44 " =    1.227
peak=    3.445 closest distance to " OD1 ASN A  45 " =    1.471
peak=    3.445 closest distance to " SG ACYS A 201 " =    0.734
peak=    3.443 closest distance to " O   HOH Z 258 " =    1.495
peak=    3.440 closest distance to " O   HOH Z 245 " =    1.450
peak=    3.440 closest distance to " O   HOH Z 272 " =    1.946
peak=    3.437 closest distance to " O   HOH Z  66 " =    1.208
peak=    3.435 closest distance to " OE1 GLN A  77 " =    1.177
peak=    3.434 closest distance to " CA  ASN A 284 " =    1.109
peak=    3.433 closest distance to " O   HOH Z 367 " =    3.935
peak=    3.428 closest distance to " CG  GLN A  77 " =    2.052
peak=    3.427 closest distance to " O   HOH Z   1 " =    1.830
peak=    3.427 closest distance to " N   PHE A 130 " =    1.246
peak=    3.424 closest distance to " O   HOH Z 389 " =    1.368
peak=    3.422 closest distance to " O   HOH Z 162 " =    1.606
peak=    3.412 closest distance to " CB  ILE A 234 " =    0.922
peak=    3.411 closest distance to " C   PHE A 208 " =    1.497
peak=    3.409 closest distance to " CG  PRO A 198 " =    1.430
peak=    3.405 closest distance to " O   HOH Z 427 " =    1.269
peak=    3.402 closest distance to " CB  TRP A  85 " =    1.544
peak=    3.399 closest distance to " O   HOH Z   2 " =    1.858
peak=    3.397 closest distance to " CG  LYS A 119 " =    1.020
peak=    3.391 closest distance to " O   HOH Z 226 " =    1.098
peak=    3.389 closest distance to " O   HOH Z 172 " =    2.738
peak=    3.387 closest distance to " O   HOH Z  11 " =    1.774
peak=    3.381 closest distance to " O   HOH Z 371 " =    1.697
peak=    3.380 closest distance to " O   HOH Z 234 " =    2.438
peak=    3.365 closest distance to " CB  ARG A 102 " =    0.841
peak=    3.354 closest distance to " CB  PRO A 198 " =    1.026
peak=    3.354 closest distance to " O   SER A  26 " =    1.868
peak=    3.353 closest distance to " CA  PRO A 163 " =    0.930
peak=    3.352 closest distance to " O   HOH Z 284 " =    2.289
peak=    3.348 closest distance to " O   HOH Z 179 " =    1.245
peak=    3.344 closest distance to " O   HOH Z 211 " =    1.347
peak=    3.341 closest distance to " O   HOH Z 305 " =    3.265
peak=    3.340 closest distance to " O   HOH Z 111 " =    1.702
peak=    3.337 closest distance to " CB  LYS A 290 " =    1.423
peak=    3.331 closest distance to " CA  ARG A  36 " =    1.309
peak=    3.329 closest distance to " O   HOH Z 215 " =    2.529
peak=    3.318 closest distance to " CA  THR A 264 " =    0.777
peak=    3.317 closest distance to " OG  SER A  62 " =    3.219
peak=    3.314 closest distance to " CB  GLN A 223 " =    1.412
peak=    3.313 closest distance to " CG  LEU A 167 " =    1.130
peak=    3.313 closest distance to " CA  ASN A 127 " =    1.057
peak=    3.309 closest distance to " O   HOH Z  95 " =    1.808
peak=    3.309 closest distance to " O   HOH Z 272 " =    1.843
peak=    3.304 closest distance to " O   HOH Z  47 " =    1.539
peak=    3.303 closest distance to " NZ  LYS A  48 " =    1.806
peak=    3.302 closest distance to " O   HOH Z  51 " =    2.330
peak=    3.301 closest distance to " O   HOH Z 248 " =    2.320
peak=    3.300 closest distance to " CE  MET A  40 " =    0.938
peak=    3.299 closest distance to " O   HOH Z 422 " =    2.586
peak=    3.295 closest distance to " CD BARG A 145 " =    1.181
peak=    3.294 closest distance to " CB  VAL A 202 " =    1.795
peak=    3.293 closest distance to " CZ AARG A 102 " =    1.563
peak=    3.290 closest distance to " O   GLY A 111 " =    1.367
peak=    3.283 closest distance to " CB  ASN A  69 " =    1.747
peak=    3.283 closest distance to " CZ  PHE A  59 " =    1.031
peak=    3.282 closest distance to " O   HOH Z 419 " =    1.983
peak=    3.280 closest distance to " O   ARG A  14 " =    0.992
peak=    3.274 closest distance to " CB  ALA A 114 " =    1.359
peak=    3.270 closest distance to " CG2AVAL A  72 " =    2.832
peak=    3.269 closest distance to " O   HOH Z 299 " =    2.616
peak=    3.269 closest distance to " CB  ASN A 142 " =    1.164
peak=    3.267 closest distance to " CG1BVAL A 121 " =    2.158
peak=    3.266 closest distance to " CG  PRO A 243 " =    1.193
peak=    3.266 closest distance to " O   HOH Z 384 " =    1.623
peak=    3.259 closest distance to " O   HOH Z 324 " =    1.507
peak=    3.258 closest distance to " CG  ASP A 238 " =    0.761
peak=    3.251 closest distance to " N   ALA A 154 " =    0.767
peak=    3.249 closest distance to " CB  ARG A  79 " =    0.737
peak=    3.248 closest distance to " O   ALA A   1 " =    1.412
peak=    3.246 closest distance to " O   HOH Z  50 " =    1.859
peak=    3.244 closest distance to " CB  TRP A 179 " =    1.138
peak=    3.244 closest distance to " O   HOH Z 371 " =    1.645
peak=    3.231 closest distance to " CB  ALA A  10 " =    0.749
peak=    3.230 closest distance to " CE  MET A  93 " =    1.470
peak=    3.222 closest distance to " O   HOH Z 143 " =    1.503
peak=    3.219 closest distance to " N   GLY A 136 " =    1.449
peak=    3.209 closest distance to " O   HOH Z   8 " =    1.457
peak=    3.208 closest distance to " O   HOH Z 186 " =    1.150
peak=    3.198 closest distance to " O   HOH Z 218 " =    4.700
peak=    3.192 closest distance to " O   HOH Z  43 " =    1.583
peak=    3.190 closest distance to " O   HOH Z 222 " =    2.110
peak=    3.189 closest distance to " CA  ALA A  21 " =    1.124
peak=    3.189 closest distance to " CG  ARG A  66 " =    1.041
peak=    3.188 closest distance to " CB  THR A  29 " =    1.257
peak=    3.188 closest distance to " NZ  LYS A  76 " =    1.556
peak=    3.186 closest distance to " CB  SER A  12 " =    1.467
peak=    3.185 closest distance to " CD1 LEU A 281 " =    1.066
peak=    3.184 closest distance to " CB  SER A 276 " =    1.251
peak=    3.184 closest distance to " O   HOH Z 392 " =    1.322
peak=    3.183 closest distance to " N   PHE A  59 " =    1.236
peak=    3.183 closest distance to " CE2 PHE A  16 " =    0.952
peak=    3.171 closest distance to " N   LYS A 119 " =    0.861
peak=    3.169 closest distance to " CB  ARG A  79 " =    1.453
peak=    3.168 closest distance to " O   HOH Z 325 " =    1.201
peak=    3.166 closest distance to " O   HOH Z 166 " =    1.017
peak=    3.164 closest distance to " O   HOH Z 234 " =    3.632
peak=    3.162 closest distance to " O   HOH Z 383 " =    2.264
peak=    3.162 closest distance to " O   HOH Z 209 " =    1.185
peak=    3.162 closest distance to " O   HOH Z   6 " =    1.274
peak=    3.161 closest distance to " O   HOH Z  69 " =    1.812
peak=    3.159 closest distance to " CD1 PHE A 130 " =    0.946
peak=    3.159 closest distance to " O   HOH Z 126 " =    1.516
peak=    3.154 closest distance to " O   HOH Z 222 " =    1.906
peak=    3.151 closest distance to " CG  PHE A  59 " =    1.084
peak=    3.144 closest distance to " N   MET A  40 " =    1.549
peak=    3.143 closest distance to " O   HOH Z 232 " =    1.314
peak=    3.138 closest distance to " OG BSER A 216 " =    1.868
peak=    3.136 closest distance to " CA  ARG A 159 " =    1.252
peak=    3.132 closest distance to " O   HOH Z  33 " =    1.965
peak=    3.132 closest distance to " O   HOH Z 365 " =    1.928
peak=    3.131 closest distance to " CB  GLN A 278 " =    0.822
peak=    3.127 closest distance to " O   ALA A 242 " =    1.204
peak=    3.127 closest distance to " O   HOH Z 191 " =    3.840
peak=    3.125 closest distance to " O   HOH Z 214 " =    1.733
peak=    3.121 closest distance to " O   HOH Z  37 " =    1.180
peak=    3.118 closest distance to " OE1 GLN A  58 " =    1.264
peak=    3.117 closest distance to " CD2 LEU A 255 " =    1.013
peak=    3.113 closest distance to " CG BARG A 145 " =    0.737
peak=    3.113 closest distance to " C   TRP A 177 " =    1.213
peak=    3.111 closest distance to " O   HOH Z 353 " =    1.805
peak=    3.111 closest distance to " CD1 TYR A  15 " =    1.035
peak=    3.108 closest distance to " O   HOH Z  28 " =    1.598
peak=    3.107 closest distance to " CG  ASN A 301 " =    0.874
peak=    3.104 closest distance to " N   ILE A  33 " =    1.192
peak=    3.097 closest distance to " O   HOH Z 119 " =    1.604
peak=    3.090 closest distance to " O   HOH Z 102 " =    1.793
peak=    3.088 closest distance to " O   HOH Z 380 " =    2.300
peak=    3.086 closest distance to " O   HOH Z  88 " =    4.665
peak=    3.080 closest distance to " O   HOH Z  72 " =    0.983
peak=    3.077 closest distance to " O   HOH Z 162 " =    3.495
peak=    3.070 closest distance to " O   HOH Z 191 " =    1.969
peak=    3.063 closest distance to " CD1 ILE A  33 " =    1.662
peak=    3.063 closest distance to " O   HOH Z 189 " =    2.238
peak=    3.048 closest distance to " O   HOH Z 417 " =    1.316
peak=    3.044 closest distance to " CE BMET A  47 " =    1.399
peak=    3.023 closest distance to " O   HOH Z 413 " =    1.536

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.452 - 5.108
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 194
   mapped sites are within: 0.711 - 5.108

peak=   -6.002 closest distance to " CD  ARG A 138 " =    0.985
peak=   -4.875 closest distance to " N   GLN A  58 " =    1.028
peak=   -4.336 closest distance to " O   PRO A 198 " =    1.012
peak=   -4.333 closest distance to " OG ASER A 134 " =    1.063
peak=   -4.120 closest distance to " OG1 THR A 178 " =    1.046
peak=   -4.096 closest distance to " N   THR A  52 " =    1.693
peak=   -4.093 closest distance to " CG2 VAL A 230 " =    0.798
peak=   -4.085 closest distance to " CE2 PHE A 218 " =    2.777
peak=   -4.056 closest distance to " N   ASN A  60 " =    0.965
peak=   -4.022 closest distance to " O   HOH Z  93 " =    1.226
peak=   -3.947 closest distance to " O   HOH Z 347 " =    0.753
peak=   -3.939 closest distance to " O   HOH Z  24 " =    1.327
peak=   -3.886 closest distance to " C   ASN A 285 " =    2.134
peak=   -3.885 closest distance to " O   HOH Z 388 " =    1.695
peak=   -3.880 closest distance to " O   SER A  62 " =    1.143
peak=   -3.866 closest distance to " CG2BVAL A 121 " =    0.799
peak=   -3.861 closest distance to " N   GLN A  58 " =    2.165
peak=   -3.819 closest distance to " NE1 TRP A  70 " =    1.428
peak=   -3.813 closest distance to " CD  ARG A  14 " =    3.004
peak=   -3.810 closest distance to " O   SER A 135 " =    1.558
peak=   -3.803 closest distance to " CD2 LEU A   5 " =    0.854
peak=   -3.782 closest distance to " N   VAL A 125 " =    1.237
peak=   -3.769 closest distance to " O   TRP A  92 " =    1.456
peak=   -3.759 closest distance to " CB  ALA A 100 " =    2.523
peak=   -3.737 closest distance to " N   HIS A 115 " =    1.916
peak=   -3.737 closest distance to " NH2 ARG A  79 " =    1.877
peak=   -3.733 closest distance to " OG1 THR A 246 " =    1.595
peak=   -3.726 closest distance to " O   HOH Z 385 " =    1.088
peak=   -3.723 closest distance to " O   HOH Z 166 " =    1.934
peak=   -3.703 closest distance to " O   HOH Z 290 " =    0.919
peak=   -3.691 closest distance to " O   VAL A 125 " =    1.895
peak=   -3.683 closest distance to " O   HOH Z 413 " =    3.912
peak=   -3.675 closest distance to " O   GLY A  98 " =    2.181
peak=   -3.666 closest distance to " O   HOH Z  11 " =    2.059
peak=   -3.632 closest distance to " CG AARG A 145 " =    0.718
peak=   -3.617 closest distance to " O   HOH Z 412 " =    5.108
peak=   -3.617 closest distance to " O   HOH Z 134 " =    1.676
peak=   -3.610 closest distance to " CG1BVAL A  72 " =    4.320
peak=   -3.604 closest distance to " O   HOH Z 125 " =    3.270
peak=   -3.586 closest distance to " CA  GLY A 133 " =    1.942
peak=   -3.583 closest distance to " CB  ALA A 244 " =    2.146
peak=   -3.580 closest distance to " O   HOH Z  22 " =    0.939
peak=   -3.578 closest distance to " CZ  PHE A  16 " =    1.097
peak=   -3.577 closest distance to " CD1 TRP A 179 " =    0.967
peak=   -3.574 closest distance to " O   HOH Z 298 " =    1.054
peak=   -3.572 closest distance to " N   LEU A 281 " =    1.931
peak=   -3.571 closest distance to " O   ALA A 165 " =    1.059
peak=   -3.552 closest distance to " C   SER A 288 " =    0.917
peak=   -3.548 closest distance to " O   SER A  22 " =    2.331
peak=   -3.543 closest distance to " CA  VAL A  67 " =    2.839
peak=   -3.543 closest distance to " N   MET A 188 " =    1.832
peak=   -3.541 closest distance to " O   HOH Z 424 " =    0.760
peak=   -3.541 closest distance to " O   HOH Z 231 " =    1.649
peak=   -3.526 closest distance to " O   HOH Z 131 " =    3.828
peak=   -3.520 closest distance to " OE1 GLU A 277 " =    2.072
peak=   -3.509 closest distance to " O   HOH Z 205 " =    1.172
peak=   -3.496 closest distance to " O   HOH Z 407 " =    3.272
peak=   -3.492 closest distance to " OG  SER A   3 " =    1.014
peak=   -3.490 closest distance to " O   PRO A 163 " =    1.722
peak=   -3.488 closest distance to " O   HOH Z 245 " =    1.420
peak=   -3.487 closest distance to " O   HOH Z  88 " =    2.246
peak=   -3.485 closest distance to " C   SER A  63 " =    1.042
peak=   -3.467 closest distance to " CA  GLY A  23 " =    1.940
peak=   -3.461 closest distance to " O   HOH Z 244 " =    1.509
peak=   -3.460 closest distance to " O   HOH Z  19 " =    1.867
peak=   -3.459 closest distance to " O   HOH Z 377 " =    1.101
peak=   -3.447 closest distance to " CD  GLU A 152 " =    2.607
peak=   -3.444 closest distance to " NZ  LYS A 117 " =    0.846
peak=   -3.442 closest distance to " CD2 LEU A 228 " =    0.768
peak=   -3.435 closest distance to " CE BMET A  47 " =    1.653
peak=   -3.429 closest distance to " O   HOH Z 266 " =    4.590
peak=   -3.422 closest distance to " O   HOH Z 415 " =    1.035
peak=   -3.420 closest distance to " O   HOH Z 264 " =    1.389
peak=   -3.414 closest distance to " O   HOH Z 150 " =    3.014
peak=   -3.414 closest distance to " CD  ARG A 219 " =    2.519
peak=   -3.406 closest distance to " C   ILE A 239 " =    1.975
peak=   -3.405 closest distance to " C   ASP A 231 " =    2.377
peak=   -3.401 closest distance to " CG2 THR A  52 " =    2.905
peak=   -3.400 closest distance to " N   THR A 235 " =    0.982
peak=   -3.397 closest distance to " O   HOH Z 219 " =    3.333
peak=   -3.395 closest distance to " O   SER A 245 " =    1.526
peak=   -3.394 closest distance to " CG  ASN A  60 " =    1.070
peak=   -3.392 closest distance to " O   HOH Z 385 " =    0.711
peak=   -3.392 closest distance to " OE1 GLN A 223 " =    2.312
peak=   -3.385 closest distance to " N   PHE A  59 " =    1.129
peak=   -3.380 closest distance to " O   HOH Z 431 " =    1.149
peak=   -3.377 closest distance to " CA  TYR A  68 " =    2.752
peak=   -3.376 closest distance to " NE2 GLN A  77 " =    2.106
peak=   -3.372 closest distance to " O   HOH Z 404 " =    1.337
peak=   -3.371 closest distance to " O   ALA A 161 " =    1.646
peak=   -3.366 closest distance to " O   SER A  22 " =    1.285
peak=   -3.363 closest distance to " CG  GLN A  88 " =    0.844
peak=   -3.359 closest distance to " O   HOH Z 235 " =    1.055
peak=   -3.356 closest distance to " O   HOH Z 193 " =    1.291
peak=   -3.350 closest distance to " O   ALA A  51 " =    1.274
peak=   -3.346 closest distance to " O   HOH Z 234 " =    3.072
peak=   -3.346 closest distance to " O   GLY A 118 " =    1.384
peak=   -3.344 closest distance to " CE3 TRP A 274 " =    2.530
peak=   -3.341 closest distance to " CZ3 TRP A 274 " =    1.879
peak=   -3.341 closest distance to " CA  ILE A 106 " =    2.141
peak=   -3.337 closest distance to " O   LYS A 119 " =    0.854
peak=   -3.332 closest distance to " CD  PRO A 213 " =    2.125
peak=   -3.331 closest distance to " CG  PRO A 163 " =    2.606
peak=   -3.328 closest distance to " N   LYS A 166 " =    1.719
peak=   -3.322 closest distance to " CD1 LEU A  96 " =    2.328
peak=   -3.314 closest distance to " C   THR A 251 " =    1.839
peak=   -3.311 closest distance to " CA  SER A 245 " =    2.254
peak=   -3.302 closest distance to " O   PRO A 198 " =    0.908
peak=   -3.301 closest distance to " O   HOH Z 419 " =    0.798
peak=   -3.293 closest distance to " O   HOH Z 426 " =    1.902
peak=   -3.291 closest distance to " O   HOH Z 313 " =    1.796
peak=   -3.290 closest distance to " O   SER A 146 " =    1.009
peak=   -3.289 closest distance to " CG  ARG A 139 " =    1.141
peak=   -3.289 closest distance to " N   SER A 276 " =    0.949
peak=   -3.287 closest distance to " O   VAL A 197 " =    1.270
peak=   -3.287 closest distance to " O   HOH Z 143 " =    0.832
peak=   -3.285 closest distance to " CG  LYS A  76 " =    2.721
peak=   -3.283 closest distance to " O   HOH Z  63 " =    1.095
peak=   -3.273 closest distance to " C   ASN A  60 " =    1.264
peak=   -3.272 closest distance to " CE2 TYR A 116 " =    2.975
peak=   -3.269 closest distance to " CD  LYS A 166 " =    1.054
peak=   -3.268 closest distance to " O   HOH Z 260 " =    0.726
peak=   -3.266 closest distance to " O   HOH Z  39 " =    1.070
peak=   -3.265 closest distance to " OE2 GLU A   2 " =    0.909
peak=   -3.262 closest distance to " CB  ASP A  27 " =    2.436
peak=   -3.252 closest distance to " O   ASP A 200 " =    0.905
peak=   -3.251 closest distance to " O   HOH Z 354 " =    2.493
peak=   -3.245 closest distance to " CG  ARG A 138 " =    0.864
peak=   -3.245 closest distance to " O   HOH Z  65 " =    0.726
peak=   -3.243 closest distance to " O   GLU A 152 " =    1.700
peak=   -3.242 closest distance to " NE  ARG A 269 " =    1.337
peak=   -3.237 closest distance to " ND2 ASN A  45 " =    1.629
peak=   -3.237 closest distance to " OG1 THR A 279 " =    0.928
peak=   -3.237 closest distance to " OD2 ASP A  50 " =    1.303
peak=   -3.234 closest distance to " CA  SER A  63 " =    1.499
peak=   -3.224 closest distance to " O   GLN A  73 " =    1.548
peak=   -3.223 closest distance to " OG BSER A 134 " =    1.328
peak=   -3.219 closest distance to " CG  HIS A 108 " =    0.972
peak=   -3.213 closest distance to " O   GLY A  57 " =    1.668
peak=   -3.212 closest distance to " O   HOH Z 365 " =    1.108
peak=   -3.211 closest distance to " O   HOH Z 331 " =    0.883
peak=   -3.210 closest distance to " O   GLY A 136 " =    1.993
peak=   -3.209 closest distance to " O   HOH Z 220 " =    1.049
peak=   -3.206 closest distance to " O   HOH Z 280 " =    0.832
peak=   -3.203 closest distance to " CB  ALA A 248 " =    2.105
peak=   -3.198 closest distance to " O   VAL A 174 " =    2.499
peak=   -3.197 closest distance to " CG  GLN A  73 " =    1.479
peak=   -3.197 closest distance to " CD1 ILE A 151 " =    2.446
peak=   -3.194 closest distance to " O   GLU A  44 " =    1.802
peak=   -3.193 closest distance to " O   HOH Z 359 " =    2.143
peak=   -3.189 closest distance to " O   HOH Z 387 " =    1.824
peak=   -3.189 closest distance to " CD2 LEU A 237 " =    2.413
peak=   -3.188 closest distance to " CD  PRO A 198 " =    1.316
peak=   -3.186 closest distance to " O   HOH Z 275 " =    1.630
peak=   -3.184 closest distance to " O   HOH Z 220 " =    1.629
peak=   -3.184 closest distance to " CD2 TYR A 293 " =    2.151
peak=   -3.177 closest distance to " OD1 ASP A 200 " =    1.216
peak=   -3.176 closest distance to " CD2 LEU A 237 " =    2.548
peak=   -3.176 closest distance to " N   GLN A  88 " =    1.570
peak=   -3.175 closest distance to " O   HOH Z 279 " =    1.206
peak=   -3.170 closest distance to " CD  ARG A 156 " =    1.826
peak=   -3.167 closest distance to " O   LYS A  76 " =    1.723
peak=   -3.166 closest distance to " ND2 ASN A 127 " =    1.440
peak=   -3.163 closest distance to " OD1 ASN A 301 " =    2.133
peak=   -3.155 closest distance to " CB  ALA A 248 " =    1.789
peak=   -3.153 closest distance to " C   VAL A 265 " =    0.906
peak=   -3.151 closest distance to " CD1 LEU A 255 " =    2.780
peak=   -3.150 closest distance to " SD BMET A  47 " =    2.673
peak=   -3.149 closest distance to " O   HOH Z 390 " =    2.642
peak=   -3.140 closest distance to " CG  LEU A 228 " =    1.199
peak=   -3.134 closest distance to " O   HOH Z  61 " =    0.885
peak=   -3.133 closest distance to " O   HOH Z 188 " =    4.610
peak=   -3.133 closest distance to " O   HOH Z 100 " =    1.324
peak=   -3.128 closest distance to " O   HOH Z  90 " =    2.396
peak=   -3.119 closest distance to " O   HOH Z 416 " =    0.809
peak=   -3.118 closest distance to " C   TYR A  30 " =    1.006
peak=   -3.116 closest distance to " O   ASN A 301 " =    1.393
peak=   -3.114 closest distance to " O   TRP A 179 " =    1.765
peak=   -3.106 closest distance to " O   HOH Z 366 " =    1.010
peak=   -3.102 closest distance to " O   HOH Z 189 " =    2.015
peak=   -3.100 closest distance to " O   HOH Z 300 " =    1.084
peak=   -3.099 closest distance to " CB  ARG A  66 " =    1.780
peak=   -3.095 closest distance to " CG BARG A 275 " =    0.787
peak=   -3.087 closest distance to " O   GLN A  77 " =    1.757
peak=   -3.083 closest distance to " O   HOH Z  69 " =    1.680
peak=   -3.078 closest distance to " SD  MET A 113 " =    0.738
peak=   -3.078 closest distance to " O   HOH Z  13 " =    1.108
peak=   -3.065 closest distance to " O   VAL A 189 " =    2.112
peak=   -3.065 closest distance to " CD  GLU A 277 " =    0.992
peak=   -3.021 closest distance to " CG  ASP A  50 " =    2.192

================= 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    :  0.5191 0.5209   6.309412e+00   6.305124e+00
   1_bss:  0.5117 0.5092   6.304795e+00   6.297032e+00
   1_xyz:  0.4587 0.4824   6.255186e+00   6.276671e+00
   1_adp:  0.4195 0.4802   6.221794e+00   6.274795e+00
   1_occ:  0.4190 0.4815   6.221443e+00   6.275109e+00
   2_bss:  0.4184 0.4801   6.222718e+00   6.274855e+00
   2_xyz:  0.3709 0.4443   6.135829e+00   6.232305e+00
   2_adp:  0.3547 0.4350   6.111787e+00   6.218138e+00
   2_occ:  0.3543 0.4352   6.111765e+00   6.218287e+00
   3_bss:  0.3538 0.4347   6.111082e+00   6.218116e+00
   3_xyz:  0.2911 0.3622   5.957991e+00   6.105595e+00
   3_adp:  0.2612 0.3470   5.890462e+00   6.074330e+00
   3_occ:  0.2610 0.3471   5.890142e+00   6.074304e+00
   4_bss:  0.2604 0.3460   5.887807e+00   6.071422e+00
   4_xyz:  0.2170 0.2925   5.733599e+00   5.941947e+00
   4_adp:  0.2071 0.2678   5.673744e+00   5.855761e+00
   4_occ:  0.2066 0.2671   5.671578e+00   5.852629e+00
   5_bss:  0.2063 0.2658   5.669781e+00   5.850169e+00
   5_xyz:  0.1593 0.2054   5.426374e+00   5.629724e+00
   5_adp:  0.1462 0.1954   5.355043e+00   5.580666e+00
   5_occ:  0.1459 0.1948   5.353464e+00   5.578175e+00
   5_bss:  0.1455 0.1946   5.352139e+00   5.577157e+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:  0.417  20.000   5.508   8.151   7.835   0.000   0.000   0.000
   1_xyz:  0.417  20.000   5.508   8.151   7.835   0.000   0.000   0.000
   1_adp:  0.417  20.000   5.508   8.151   7.835   0.000   0.000   0.000
   1_occ:  0.417  20.000   5.508   8.151   7.835   0.000   0.000   0.000
   2_bss:  0.398  50.000   3.361   5.122   5.789   0.000   0.000   0.000
   2_xyz:  0.398  50.000   3.361   5.122   5.789   0.000   0.000   0.000
   2_adp:  0.398  50.000   3.361   5.122   5.789   0.000   0.000   0.000
   2_occ:  0.398  50.000   3.361   5.122   5.789   0.000   0.000   0.000
   3_bss:  0.338  50.000   2.137   3.231   3.818   0.000   0.000   0.000
   3_xyz:  0.338  50.000   2.137   3.231   3.818   0.000   0.000   0.000
   3_adp:  0.338  50.000   2.137   3.231   3.818   0.000   0.000   0.000
   3_occ:  0.338  50.000   2.137   3.231   3.818   0.000   0.000   0.000
   4_bss:  0.334  49.079   1.613   1.710   2.720   0.000   0.000   0.000
   4_xyz:  0.334  49.079   1.613   1.710   2.720   0.000   0.000   0.000
   4_adp:  0.334  49.079   1.613   1.710   2.720   0.000   0.000   0.000
   4_occ:  0.334  49.079   1.613   1.710   2.720   0.000   0.000   0.000
   5_bss:  0.325  37.885   0.740   1.193   1.892   0.000   0.000   0.000
   5_xyz:  0.325  37.885   0.740   1.193   1.892   0.000   0.000   0.000
   5_adp:  0.325  37.885   0.740   1.193   1.892   0.000   0.000   0.000
   5_occ:  0.325  37.885   0.740   1.193   1.892   0.000   0.000   0.000
   5_bss:  0.325  38.460  -0.414  -0.203   0.618   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.297 0.2994  0.3663    87418.384
   1_bss:  66.845 0.3042  0.4537    84649.019
   1_xyz:  61.121 0.3779  0.5551    74234.189
   1_adp:  60.639 0.3839  0.6175    73753.992
   1_occ:  60.779 0.3820  0.6129    73992.203
   2_bss:  60.511 0.3854  0.5721    73599.104
   2_xyz:  52.056 0.4933  0.7379    58760.371
   2_adp:  48.852 0.5344  0.8102    55108.658
   2_occ:  48.854 0.5344  0.8100    55129.678
   3_bss:  48.739 0.5356  0.7635    54901.062
   3_xyz:  38.999 0.6543  0.9161    36801.434
   3_adp:  36.249 0.6869  0.9291    32658.204
   3_occ:  36.248 0.6869  0.9290    32638.909
   4_bss:  36.096 0.6885  0.8953    32264.776
   4_xyz:  29.820 0.7596  0.9657    22503.898
   4_adp:  25.928 0.8029  0.9971    18532.976
   4_occ:  25.833 0.8039  0.9978    18399.924
   5_bss:  25.752 0.8046  0.9700    18198.749
   5_xyz:  19.347 0.8686  1.0110    10874.345
   5_adp:  17.987 0.8815  1.0135     9863.683
   5_occ:  17.938 0.8819  1.0135     9793.422
   5_bss:  17.906 0.8821  0.9871     9744.550
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2430e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2430e+01
   1_xyz:   1.858  0.015  0.114 18.544  0.007  4.102   1.7096e-01
   1_adp:   1.858  0.015  0.114 18.544  0.007  4.102   1.7096e-01
   1_occ:   1.858  0.015  0.114 18.544  0.007  4.102   1.7096e-01
   2_bss:   1.858  0.015  0.114 18.544  0.007  4.102   1.7096e-01
   2_xyz:   1.314  0.010  0.084 17.153  0.006  4.101   1.1945e-01
   2_adp:   1.314  0.010  0.084 17.153  0.006  4.101   1.1945e-01
   2_occ:   1.314  0.010  0.084 17.153  0.006  4.101   1.1945e-01
   3_bss:   1.314  0.010  0.084 17.153  0.006  4.101   1.1945e-01
   3_xyz:   1.327  0.010  0.089 16.916  0.005  4.099   1.0098e-01
   3_adp:   1.327  0.010  0.089 16.916  0.005  4.099   1.0098e-01
   3_occ:   1.327  0.010  0.089 16.916  0.005  4.099   1.0098e-01
   4_bss:   1.327  0.010  0.089 16.916  0.005  4.099   1.0098e-01
   4_xyz:   1.011  0.007  0.070 15.888  0.003  4.104   6.7713e-02
   4_adp:   1.011  0.007  0.070 15.888  0.003  4.104   6.7713e-02
   4_occ:   1.011  0.007  0.070 15.888  0.003  4.104   6.7713e-02
   5_bss:   1.011  0.007  0.070 15.888  0.003  4.104   6.7713e-02
   5_xyz:   1.061  0.008  0.070 15.853  0.004  4.103   7.1586e-02
   5_adp:   1.061  0.008  0.070 15.853  0.004  4.103   7.1586e-02
   5_occ:   1.061  0.008  0.070 15.853  0.004  4.103   7.1586e-02
   5_bss:   1.061  0.008  0.070 15.853  0.004  4.103   7.1586e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.542   6.7865e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.542   6.7865e+00
   1_xyz:  14.808  0.208  0.499 85.594  0.064  2.009   1.1043e-01
   1_adp:  14.808  0.208  0.499 85.594  0.064  2.009   1.1043e-01
   1_occ:  14.808  0.208  0.499 85.594  0.064  2.009   1.1043e-01
   2_bss:  14.808  0.208  0.499 85.594  0.064  2.009   1.1043e-01
   2_xyz:   7.873  0.102  0.319 76.712  0.047  2.099   2.0822e-01
   2_adp:   7.873  0.102  0.319 76.712  0.047  2.099   2.0822e-01
   2_occ:   7.873  0.102  0.319 76.712  0.047  2.099   2.0822e-01
   3_bss:   7.873  0.102  0.319 76.712  0.047  2.099   2.0822e-01
   3_xyz:   8.697  0.077  0.356 70.687  0.048  2.170   8.5263e-02
   3_adp:   8.697  0.077  0.356 70.687  0.048  2.170   8.5263e-02
   3_occ:   8.697  0.077  0.356 70.687  0.048  2.170   8.5263e-02
   4_bss:   8.697  0.077  0.356 70.687  0.048  2.170   8.5263e-02
   4_xyz:   7.806  0.048  0.303 85.329  0.015  2.264   5.5741e-02
   4_adp:   7.806  0.048  0.303 85.329  0.015  2.264   5.5741e-02
   4_occ:   7.806  0.048  0.303 85.329  0.015  2.264   5.5741e-02
   5_bss:   7.806  0.048  0.303 85.329  0.015  2.264   5.5741e-02
   5_xyz:   6.945  0.048  0.259 81.867  0.025  2.345   1.1674e-01
   5_adp:   6.945  0.048  0.259 81.867  0.025  2.345   1.1674e-01
   5_occ:   6.945  0.048  0.259 81.867  0.025  2.345   1.1674e-01
   5_bss:   6.945  0.048  0.259 81.867  0.025  2.345   1.1674e-01
------------------------------------------------------------------------
           |-----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:  89.96   0.00  16.60  80.99   0.00  15.60  89.96   0.00  22.02
   1_occ:  89.96   0.00  16.60  80.99   0.00  15.60  89.96   0.00  22.02
   2_bss:  89.96   0.00  16.60  80.99   0.00  15.60  89.96   0.00  22.02
   2_xyz:  89.96   0.00  16.60  80.99   0.00  15.60  89.96   0.00  22.02
   2_adp: 102.84   0.00  15.66  91.97   0.00  14.00 102.84   0.00  24.70
   2_occ: 102.84   0.00  15.66  91.97   0.00  14.00 102.84   0.00  24.70
   3_bss: 102.84   0.00  15.66  91.97   0.00  14.00 102.84   0.00  24.70
   3_xyz: 102.84   0.00  15.66  91.97   0.00  14.00 102.84   0.00  24.70
   3_adp: 112.56   0.00  17.24 112.56   0.00  13.50 109.90   0.29  37.59
   3_occ: 112.56   0.00  17.24 112.56   0.00  13.50 109.90   0.29  37.59
   4_bss: 112.56   0.00  17.24 112.56   0.00  13.50 109.90   0.29  37.59
   4_xyz: 112.56   0.00  17.24 112.56   0.00  13.50 109.90   0.29  37.59
   4_adp: 105.79   0.00  14.72 105.07   0.00  10.85 105.79   2.29  35.79
   4_occ: 105.79   0.00  14.72 105.07   0.00  10.85 105.79   2.29  35.79
   5_bss: 105.79   0.00  14.72 105.07   0.00  10.85 105.79   2.29  35.79
   5_xyz: 105.79   0.00  14.72 105.07   0.00  10.85 105.79   2.29  35.79
   5_adp: 104.04   0.00  14.90 103.99   0.00  10.37 104.04   3.87  39.54
   5_occ: 104.04   0.00  14.90 103.99   0.00  10.37 104.04   3.87  39.54
   5_bss: 104.62   0.58  15.48 104.57   0.58  10.95 104.62   4.44  40.12
------------------------------------------------------------------------
 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:    1.302    0.028    0.426
   1_adp:    1.302    0.028    0.426
   1_occ:    1.302    0.028    0.426
   2_bss:    1.302    0.028    0.426
   2_xyz:    1.771    0.024    0.591
   2_adp:    1.771    0.024    0.591
   2_occ:    1.771    0.024    0.591
   3_bss:    1.771    0.024    0.591
   3_xyz:    1.734    0.028    0.734
   3_adp:    1.734    0.028    0.734
   3_occ:    1.734    0.028    0.734
   4_bss:    1.734    0.028    0.734
   4_xyz:    1.730    0.039    0.829
   4_adp:    1.730    0.039    0.829
   4_occ:    1.730    0.039    0.829
   5_bss:    1.730    0.039    0.829
   5_xyz:    1.940    0.053    0.921
   5_adp:    1.940    0.053    0.921
   5_occ:    1.940    0.053    0.921
   5_bss:    1.940    0.053    0.921
------------------------------------------------------------------------

CPU time actual refinement: 343.88


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_253/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_253/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_253/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_253/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_253/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.72 
  Macro-tasks:
    bulk solvent and scale       = 41.03  
    individual site refinement   = 139.61 
    weights calculation          = 31.74  
    collect and process          = 6.28   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 218.77 
  Micro-tasks:
    mask                            = 3.00   
    f_calc                          = 109.13 
    alpha_beta                      = 8.00   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 117.29 
    fmodel                         = 7.23   
    r_factors                      = 0.25   
    phase_errors                   = 9.72   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 256.05 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.892 micro seconds
Total CPU time: 5.96 minutes
from_scatterers_fft:    646 calls, 108.68 s
gradients_fft:          591 calls, 104.77 s

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

# Date 2008-01-16 Time 01:09:09 PST -0800 (1200474549.85 s)
Start R-work = 0.5191, R-free = 0.5209 (no bulk solvent and anisotropic scale)
Final R-work = 0.1605, R-free = 0.2092 (no bulk solvent and anisotropic scale)

Start R-work = 0.5117, R-free = 0.5092
Final R-work = 0.1455, R-free = 0.1946