# Date 2008-01-16 Time 01:52:55 PST -0800 (1200477175.63 s)
#phil __OFF__

Command line arguments: "../612.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30952
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 612

-------------------------------------------------------------------------------
  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: (70.25, 45.7567, 87.2539, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (70.25, 45.7567, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 1.95343
Completeness in resolution range: 0.93361
Completeness with d_max=infinity: 0.930903

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0342
                             d_min =   1.9534

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: (70.25, 45.7567, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 1.95343
Completeness in resolution range: 0.93361
Completeness with d_max=infinity: 0.930903

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0346 -  4.1812 [2204/2230]  1983   221  10.0%
  bin  2:  4.1812 -  3.3306 [2124/2144]  1912   212  10.0%
  bin  3:  3.3306 -  2.9131 [2085/2104]  1879   206   9.9%
  bin  4:  2.9131 -  2.6483 [2068/2098]  1854   214  10.3%
  bin  5:  2.6483 -  2.4594 [2065/2084]  1868   197   9.5%
  bin  6:  2.4594 -  2.3149 [2055/2080]  1844   211  10.3%
  bin  7:  2.3149 -  2.1994 [2011/2039]  1806   205  10.2%
  bin  8:  2.1994 -  2.1039 [2068/2104]  1857   211  10.2%
  bin  9:  2.1039 -  2.0231 [2013/2055]  1823   190   9.4%
  bin 10:  2.0231 -  1.9534 [ 896/2044]   804    92  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_612/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:
        1.64 -     2.29: 30
        2.29 -     2.95: 1662
        2.95 -     3.60: 4559
        3.60 -     4.25: 9285
        4.25 -     4.90: 12970
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.642 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28501 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_612/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_612/model_refine_001.geo

CPU time processing inputs: 8.86


============================ 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 = 70.25 45.75675 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4958   r_free= 0.4874   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.300520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.6641 0.99   1427  157 0.4285 0.4228      6.6463      6.6818|
|  2:  4.6641 -  3.7205 0.99   1384  156 0.4298 0.3921      6.8517      6.7884|
|  3:  3.7205 -  3.2557 0.99   1353  148 0.4578 0.4130      6.6953      6.6498|
|  4:  3.2557 -  2.9605 0.99   1337  150 0.4850 0.4779      6.5546       6.516|
|  5:  2.9605 -  2.7497 0.99   1335  151 0.5314 0.5365      6.3778      6.4038|
|  6:  2.7497 -  2.5884 0.99   1326  145 0.5212 0.5494      6.2798      6.2179|
|  7:  2.5884 -  2.4594 0.99   1334  143 0.5229 0.5283       6.248      6.2005|
|  8:  2.4594 -  2.3527 0.98   1294  152 0.5451 0.4914      6.1806      6.1738|
|  9:  2.3527 -  2.2625 0.98   1313  144 0.5332 0.5615      6.1261      6.2224|
| 10:  2.2625 -  2.1846 1.00   1327  150 0.5387 0.5234      6.0924      6.0667|
| 11:  2.1846 -  2.1165 0.98   1306  139 0.5039 0.5255      6.0381      6.0224|
| 12:  2.1165 -  2.0562 0.98   1293  144 0.5272 0.5768      5.9394       5.984|
| 13:  2.0562 -  2.0022 0.95   1251  139 0.5617 0.5471      5.8897      5.8052|
| 14:  2.0022 -  1.9534 0.27    350   41 0.5395 0.4091      5.8669       5.838|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.6641  1427   157  0.64  39.41   0.78     0.70      91230.49|
|  2:  4.6641 -  3.7205  1384   156  0.68  37.28   0.85     0.76     119742.03|
|  3:  3.7205 -  3.2557  1353   148  0.56  46.74   0.84     0.70     123767.82|
|  4:  3.2557 -  2.9605  1337   150  0.47  54.61   0.77     0.56     112081.53|
|  5:  2.9605 -  2.7497  1335   151  0.35  63.80   0.72     0.44      92168.17|
|  6:  2.7497 -  2.5884  1326   145  0.31  66.54   0.71     0.38      80847.60|
|  7:  2.5884 -  2.4594  1334   143  0.26  70.19   0.75     0.32      73685.43|
|  8:  2.4594 -  2.3527  1294   152  0.24  71.97   0.71     0.29      66996.61|
|  9:  2.3527 -  2.2625  1313   144  0.24  72.00   0.73     0.30      62310.41|
| 10:  2.2625 -  2.1846  1327   150  0.27  69.59   0.74     0.34      53420.94|
| 11:  2.1846 -  2.1165  1306   139  0.29  68.56   0.78     0.36      51004.87|
| 12:  2.1165 -  2.0562  1293   144  0.26  70.49   0.75     0.34      45692.49|
| 13:  2.0562 -  2.0022  1251   139  0.24  71.98   0.71     0.33      40773.72|
| 14:  2.0022 -  1.9534   350    41  0.29  68.60   0.72     0.33      32858.64|
|alpha:            min =        0.29 max =            0.76 mean =         0.45|
|beta:             min =    32858.64 max =       123767.82 mean =     77672.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.59|
|phase err.(test): min =        0.00 max =           89.87 mean =        61.93|
|-----------------------------------------------------------------------------|

============================== 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 = 20.647247             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.459   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.736002              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.995   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      716 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1505 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2653 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3978 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5114 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6577 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7806 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.400 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.351 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.657)------------------------------------------|
|    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 = 11.657)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5001   r_free= 0.4868   ksol= 0.00   Bsol= 0.00   scale= 0.754    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.301657                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4870   r_free= 0.4757   ksol= 0.34   Bsol= 0.00   scale= 0.978    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.56,9.75,8.84,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.296228                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.189765             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.867   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.666346              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.015   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4870      final r-factor (work) = 0.4209          |
| start r-factor (free) = 0.4757      final r-factor (free) = 0.4438          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.3522 = 16.19 * 0.50 * 6.2944 + 1.00 * 53.3998                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.6732 = 16.19 * 0.50 * 6.2418 + 1.00 * 0.1462                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4209      final r-factor (work) = 0.3828          |
| start r-factor (free) = 0.4438      final r-factor (free) = 0.4475          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4155 = 1.67 * 1.00 * 6.2418 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3336 = 1.67 * 1.00 * 6.1893 + 1.00 * 0.0202                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.657)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.48   15.23    None  None   None       |
|    all(noH): 2823   0      0.00    78.48   15.23    None  None   None       |
|    Sol.    : 438    0      0.00    76.41   23.24    None  None   None       |
|    Mac.    : 2385   0      0.00    78.48   13.76    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 -   7.848:  887   |   5:    39.238 -  47.085:   81        |
|      1:     7.848 -  15.695:  848   |   6:    47.085 -  54.933:   37        |
|      2:    15.695 -  23.543:  523   |   7:    54.933 -  62.780:   18        |
|      3:    23.543 -  31.390:  271   |   8:    62.780 -  70.628:    7        |
|      4:    31.390 -  39.238:  144   |   9:    70.628 -  78.476:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3828 r_free = 0.4475             target_work(ml) = 6.185         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3827 r_free = 0.4471             target_work(ml) = 6.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3827   r_free= 0.4471   ksol= 0.34   Bsol= 0.00   scale= 1.114    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.56,9.75,8.84,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.184334                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3805   r_free= 0.4426   ksol= 0.36   Bsol= 39.47   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,5.64,4.91,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.185062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.814588             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.870  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.770319              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.468  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3805      final r-factor (work) = 0.3231          |
| start r-factor (free) = 0.4426      final r-factor (free) = 0.4047          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.2458 = 17.81 * 0.50 * 6.1859 + 1.00 * 0.1462                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.6274 = 17.81 * 0.50 * 6.1189 + 1.00 * 0.1246                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3231      final r-factor (work) = 0.3036          |
| start r-factor (free) = 0.4047      final r-factor (free) = 0.3904          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7338 = 0.77 * 1.00 * 6.1189 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6682 = 0.77 * 1.00 * 6.0443 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.657)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.66   14.43    None  None   None       |
|    all(noH): 2823   0      0.00    69.66   14.43    None  None   None       |
|    Sol.    : 438    0      0.00    69.66   26.76    None  None   None       |
|    Mac.    : 2385   0      0.00    66.12   12.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.967:  844   |   5:    34.833 -  41.799:  105        |
|      1:     6.967 -  13.933:  828   |   6:    41.799 -  48.765:   46        |
|      2:    13.933 -  20.900:  488   |   7:    48.765 -  55.732:   17        |
|      3:    20.900 -  27.866:  307   |   8:    55.732 -  62.698:   10        |
|      4:    27.866 -  34.833:  170   |   9:    62.698 -  69.665:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3036 r_free = 0.3904             target_work(ml) = 6.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3034 r_free = 0.3903             target_work(ml) = 6.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3034   r_free= 0.3903   ksol= 0.36   Bsol= 39.47   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,5.64,4.91,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.026858                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3032   r_free= 0.3872   ksol= 0.32   Bsol= 47.80   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.20,3.03,3.39,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.025758                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.620870              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.164  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.599768              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.539  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3032      final r-factor (work) = 0.2642          |
| start r-factor (free) = 0.3872      final r-factor (free) = 0.3365          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1112 = 5.62 * 0.50 * 6.0442 + 1.00 * 0.1244                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8616 = 5.62 * 0.50 * 5.9756 + 1.00 * 0.0674                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2642      final r-factor (work) = 0.2501          |
| start r-factor (free) = 0.3365      final r-factor (free) = 0.3281          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5962 = 0.60 * 1.00 * 5.9756 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5389 = 0.60 * 1.00 * 5.8796 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.657)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.99   14.98    None  None   None       |
|    all(noH): 2823   0      0.00    73.99   14.98    None  None   None       |
|    Sol.    : 438    0      0.00    73.99   31.68    None  None   None       |
|    Mac.    : 2385   0      0.00    70.78   11.91    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 -   7.399:  916   |   5:    36.993 -  44.392:  109        |
|      1:     7.399 -  14.797:  842   |   6:    44.392 -  51.790:   53        |
|      2:    14.797 -  22.196:  431   |   7:    51.790 -  59.189:   21        |
|      3:    22.196 -  29.594:  262   |   8:    59.189 -  66.588:   10        |
|      4:    29.594 -  36.993:  174   |   9:    66.588 -  73.986:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2501 r_free = 0.3281             target_work(ml) = 5.865         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2498 r_free = 0.3280             target_work(ml) = 5.865         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2498   r_free= 0.3280   ksol= 0.32   Bsol= 47.80   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.20,3.03,3.39,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.864523                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2492   r_free= 0.3273   ksol= 0.34   Bsol= 53.55   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.06,1.70,2.48,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.864246                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.802706              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.448  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.996841              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.043  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2492      final r-factor (work) = 0.1957          |
| start r-factor (free) = 0.3273      final r-factor (free) = 0.2594          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1232 = 5.80 * 0.50 * 5.8786 + 1.00 * 0.0674                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8132 = 5.80 * 0.50 * 5.7660 + 1.00 * 0.0840                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1957      final r-factor (work) = 0.1736          |
| start r-factor (free) = 0.2594      final r-factor (free) = 0.2334          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7602 = 1.00 * 1.00 * 5.7660 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5750 = 1.00 * 1.00 * 5.5784 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.657)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.30   15.44    None  None   None       |
|    all(noH): 2823   0      0.00    86.30   15.44    None  None   None       |
|    Sol.    : 438    0      2.98    85.50   40.51    None  None   None       |
|    Mac.    : 2385   0      0.00    86.30   10.84    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 -   8.630: 1268   |   5:    43.148 -  51.778:  107        |
|      1:     8.630 -  17.259:  812   |   6:    51.778 -  60.407:   80        |
|      2:    17.259 -  25.889:  229   |   7:    60.407 -  69.037:   38        |
|      3:    25.889 -  34.518:  142   |   8:    69.037 -  77.666:   11        |
|      4:    34.518 -  43.148:  129   |   9:    77.666 -  86.296:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1736 r_free = 0.2334             target_work(ml) = 5.529         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1734 r_free = 0.2331             target_work(ml) = 5.528         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1734   r_free= 0.2331   ksol= 0.34   Bsol= 53.55   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.06,1.70,2.48,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.528234                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1733   r_free= 0.2341   ksol= 0.33   Bsol= 53.55   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,0.64,2.24,0.00,0.00,0.00); trace/3= 1.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.527848                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.235641              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.057   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324028              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.711  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1733      final r-factor (work) = 0.1459          |
| start r-factor (free) = 0.2341      final r-factor (free) = 0.2050          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1094 = 3.24 * 0.50 * 5.5787 + 1.00 * 0.0840                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8964 = 3.24 * 0.50 * 5.4610 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1459      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.2050      final r-factor (free) = 0.1930          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7836 = 0.32 * 1.00 * 5.4610 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7538 = 0.32 * 1.00 * 5.3784 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.657)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.96   14.78    None  None   None       |
|    all(noH): 2823   0      0.00    86.96   14.78    None  None   None       |
|    Sol.    : 438    0      2.90    86.31   39.91    None  None   None       |
|    Mac.    : 2385   0      0.00    86.96   10.16    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 -   8.696: 1398   |   5:    43.482 -  52.178:  101        |
|      1:     8.696 -  17.393:  759   |   6:    52.178 -  60.875:   77        |
|      2:    17.393 -  26.089:  195   |   7:    60.875 -  69.571:   36        |
|      3:    26.089 -  34.786:  127   |   8:    69.571 -  78.268:   12        |
|      4:    34.786 -  43.482:  112   |   9:    78.268 -  86.964:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1399 r_free = 0.1930             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1397 r_free = 0.1928             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1928   ksol= 0.33   Bsol= 53.55   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,0.64,2.24,0.00,0.00,0.00); trace/3= 1.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.344681                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.6641 0.99   1427  157 0.1029 0.1439      5.4431      5.6697|
|  2:  4.6641 -  3.7205 0.99   1384  156 0.0986 0.1427      5.5834      5.8825|
|  3:  3.7205 -  3.2557 0.99   1353  148 0.1338 0.1772      5.6714      5.9341|
|  4:  3.2557 -  2.9605 0.99   1337  150 0.1595 0.2049      5.6696      5.8132|
|  5:  2.9605 -  2.7497 0.99   1335  151 0.1696 0.2260      5.5481      5.8118|
|  6:  2.7497 -  2.5884 0.99   1326  145 0.1551 0.2429      5.4047      5.6516|
|  7:  2.5884 -  2.4594 0.99   1334  143 0.1596 0.2015      5.3648      5.5135|
|  8:  2.4594 -  2.3527 0.98   1294  152 0.1562 0.2093      5.2976      5.5307|
|  9:  2.3527 -  2.2625 0.98   1313  144 0.1537 0.2198      5.2416      5.4999|
| 10:  2.2625 -  2.1846 1.00   1327  150 0.1403 0.2089      5.1377      5.3738|
| 11:  2.1846 -  2.1165 0.98   1306  139 0.1397 0.2252      5.1342      5.4892|
| 12:  2.1165 -  2.0562 0.98   1293  144 0.1518 0.2161       5.086      5.3607|
| 13:  2.0562 -  2.0022 0.95   1251  139 0.1437 0.1852      4.9643      5.1129|
| 14:  2.0022 -  1.9534 0.27    350   41 0.1374 0.1796      4.8611       5.031|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.6641  1427   157  0.93  10.64   0.97     0.95       8979.42|
|  2:  4.6641 -  3.7205  1384   156  0.94  10.25   1.03     1.02      12519.17|
|  3:  3.7205 -  3.2557  1353   148  0.90  15.49   1.04     1.04      15948.90|
|  4:  3.2557 -  2.9605  1337   150  0.88  18.63   1.02     0.99      16321.70|
|  5:  2.9605 -  2.7497  1335   151  0.86  20.56   1.01     0.97      13167.45|
|  6:  2.7497 -  2.5884  1326   145  0.85  21.11   0.99     0.93      10758.06|
|  7:  2.5884 -  2.4594  1334   143  0.86  20.38   1.00     0.96       9484.90|
|  8:  2.4594 -  2.3527  1294   152  0.85  21.25   1.01     0.97       8790.33|
|  9:  2.3527 -  2.2625  1313   144  0.86  20.38   1.00     0.94       7661.98|
| 10:  2.2625 -  2.1846  1327   150  0.86  20.27   1.01     0.96       6629.26|
| 11:  2.1846 -  2.1165  1306   139  0.86  20.65   1.01     0.94       6621.55|
| 12:  2.1165 -  2.0562  1293   144  0.86  20.87   1.01     1.00       6137.60|
| 13:  2.0562 -  2.0022  1251   139  0.86  21.05   1.00     0.97       4844.24|
| 14:  2.0022 -  1.9534   350    41  0.90  16.42   1.00     0.97       3414.80|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3414.80 max =        16321.70 mean =      9762.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.92 mean =        18.44|
|phase err.(test): min =        0.00 max =           88.91 mean =        17.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1401   r_free= 0.1922   ksol= 0.32   Bsol= 47.45   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,-0.55,1.05,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.343798                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1401   r_free= 0.1922   ksol= 0.32   Bsol= 47.45   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,-0.55,1.05,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.343798                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.6641 0.99   1427  157 0.1040 0.1400      5.4291      5.6492|
|  2:  4.6641 -  3.7205 0.99   1384  156 0.0990 0.1404       5.579      5.8767|
|  3:  3.7205 -  3.2557 0.99   1353  148 0.1338 0.1766      5.6704      5.9337|
|  4:  3.2557 -  2.9605 0.99   1337  150 0.1598 0.2048      5.6711      5.8147|
|  5:  2.9605 -  2.7497 0.99   1335  151 0.1695 0.2251      5.5488      5.8111|
|  6:  2.7497 -  2.5884 0.99   1326  145 0.1553 0.2430      5.4059      5.6546|
|  7:  2.5884 -  2.4594 0.99   1334  143 0.1597 0.2016      5.3669      5.5144|
|  8:  2.4594 -  2.3527 0.98   1294  152 0.1562 0.2100      5.2983      5.5323|
|  9:  2.3527 -  2.2625 0.98   1313  144 0.1538 0.2190      5.2423      5.4986|
| 10:  2.2625 -  2.1846 1.00   1327  150 0.1403 0.2092      5.1379      5.3751|
| 11:  2.1846 -  2.1165 0.98   1306  139 0.1397 0.2255      5.1348      5.4903|
| 12:  2.1165 -  2.0562 0.98   1293  144 0.1518 0.2165      5.0864      5.3622|
| 13:  2.0562 -  2.0022 0.95   1251  139 0.1438 0.1853      4.9653      5.1135|
| 14:  2.0022 -  1.9534 0.27    350   41 0.1376 0.1799      4.8616      5.0313|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.6641  1427   157  0.93  10.28   0.97     0.95       8396.24|
|  2:  4.6641 -  3.7205  1384   156  0.94  10.04   1.03     1.02      12139.46|
|  3:  3.7205 -  3.2557  1353   148  0.90  15.41   1.05     1.04      15862.30|
|  4:  3.2557 -  2.9605  1337   150  0.88  18.66   1.02     0.99      16355.98|
|  5:  2.9605 -  2.7497  1335   151  0.86  20.54   1.00     0.97      13153.61|
|  6:  2.7497 -  2.5884  1326   145  0.85  21.14   0.99     0.93      10788.44|
|  7:  2.5884 -  2.4594  1334   143  0.86  20.43   1.00     0.95       9534.42|
|  8:  2.4594 -  2.3527  1294   152  0.85  21.31   1.01     0.97       8823.66|
|  9:  2.3527 -  2.2625  1313   144  0.86  20.39   1.00     0.94       7674.42|
| 10:  2.2625 -  2.1846  1327   150  0.86  20.28   1.01     0.96       6633.25|
| 11:  2.1846 -  2.1165  1306   139  0.86  20.67   1.01     0.94       6633.60|
| 12:  2.1165 -  2.0562  1293   144  0.86  20.90   1.01     0.99       6149.71|
| 13:  2.0562 -  2.0022  1251   139  0.86  21.07   1.00     0.97       4857.80|
| 14:  2.0022 -  1.9534   350    41  0.90  16.44   1.00     0.97       3421.21|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3421.21 max =        16355.98 mean =      9692.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.89 mean =        18.40|
|phase err.(test): min =        0.00 max =           88.45 mean =        17.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.657)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.19    88.16   15.97    None  None   None       |
|    all(noH): 2823   0      1.19    88.16   15.97    None  None   None       |
|    Sol.    : 438    0      4.09    87.50   41.10    None  None   None       |
|    Mac.    : 2385   0      1.19    88.16   11.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.192 -   9.888: 1398   |   5:    44.674 -  53.370:  101        |
|      1:     9.888 -  18.584:  759   |   6:    53.370 -  62.066:   77        |
|      2:    18.584 -  27.281:  195   |   7:    62.066 -  70.763:   36        |
|      3:    27.281 -  35.977:  127   |   8:    70.763 -  79.459:   12        |
|      4:    35.977 -  44.674:  112   |   9:    79.459 -  88.156:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 347         
Filter by distance & map next to the model:
   mapped sites are within: 0.358 - 5.759
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 342 from: 347
   mapped sites are within: 0.754 - 5.759

peak=    8.138 closest distance to " O   HOH Z 390 " =    1.255
peak=    8.017 closest distance to " O   HOH Z 268 " =    1.312
peak=    7.953 closest distance to " CB  VAL A 230 " =    1.461
peak=    7.414 closest distance to " O   HOH Z 130 " =    2.344
peak=    6.592 closest distance to " CD2 LEU A   5 " =    1.508
peak=    6.200 closest distance to " CG  ARG A 138 " =    1.228
peak=    6.076 closest distance to " CG1 VAL A 296 " =    1.276
peak=    5.930 closest distance to " O   HOH Z 385 " =    1.672
peak=    5.828 closest distance to " O   HOH Z 375 " =    1.491
peak=    5.653 closest distance to " CD1AILE A 234 " =    1.054
peak=    5.409 closest distance to " NH1 ARG A 138 " =    0.977
peak=    5.388 closest distance to " O   PRO A 198 " =    1.455
peak=    5.385 closest distance to " O   HOH Z  65 " =    1.874
peak=    5.335 closest distance to " O   HOH Z 105 " =    1.205
peak=    5.322 closest distance to " O   HOH Z 124 " =    1.760
peak=    5.315 closest distance to " NE2 GLN A  11 " =    1.252
peak=    5.274 closest distance to " O   HOH Z 127 " =    1.343
peak=    5.200 closest distance to " O   HOH Z 222 " =    1.714
peak=    5.166 closest distance to " O   HOH Z 418 " =    1.511
peak=    5.136 closest distance to " O   HOH Z 245 " =    0.976
peak=    5.109 closest distance to " O   HOH Z 403 " =    1.560
peak=    5.102 closest distance to " O   HOH Z 139 " =    1.793
peak=    5.068 closest distance to " O   HOH Z 360 " =    1.206
peak=    5.046 closest distance to " O   HOH Z 350 " =    1.660
peak=    4.978 closest distance to " NZ BLYS A 290 " =    1.026
peak=    4.966 closest distance to " O   HOH Z  46 " =    1.285
peak=    4.889 closest distance to " O   HOH Z  66 " =    1.314
peak=    4.875 closest distance to " CB  PRO A  54 " =    1.252
peak=    4.852 closest distance to " O   HOH Z 415 " =    1.219
peak=    4.838 closest distance to " O   HOH Z  63 " =    1.646
peak=    4.822 closest distance to " O   HOH Z 417 " =    1.926
peak=    4.819 closest distance to " NH2 ARG A  56 " =    2.080
peak=    4.780 closest distance to " O   HOH Z 424 " =    1.620
peak=    4.771 closest distance to " O   HOH Z 225 " =    1.898
peak=    4.754 closest distance to " O   HOH Z   9 " =    2.060
peak=    4.739 closest distance to " O   HOH Z  24 " =    1.954
peak=    4.679 closest distance to " O   HOH Z 425 " =    1.664
peak=    4.665 closest distance to " O   HOH Z   7 " =    1.868
peak=    4.658 closest distance to " O   HOH Z  59 " =    1.752
peak=    4.608 closest distance to " O   HOH Z 427 " =    2.144
peak=    4.601 closest distance to " O   VAL A  72 " =    0.938
peak=    4.570 closest distance to " CG  PRO A  54 " =    1.499
peak=    4.556 closest distance to " O   HOH Z 410 " =    1.585
peak=    4.520 closest distance to " O   HOH Z 293 " =    1.473
peak=    4.503 closest distance to " CB  SER A   3 " =    1.497
peak=    4.494 closest distance to " CB  VAL A 230 " =    1.290
peak=    4.488 closest distance to " O   HOH Z  77 " =    1.212
peak=    4.483 closest distance to " CG2 ILE A 120 " =    1.031
peak=    4.473 closest distance to " O   HOH Z 142 " =    2.022
peak=    4.453 closest distance to " O   HOH Z 358 " =    1.368
peak=    4.438 closest distance to " O   HOH Z 209 " =    2.348
peak=    4.417 closest distance to " O   HOH Z 232 " =    2.204
peak=    4.411 closest distance to " O   HOH Z 257 " =    2.307
peak=    4.357 closest distance to " CB  ARG A 275 " =    1.122
peak=    4.356 closest distance to " O   HOH Z 428 " =    1.255
peak=    4.339 closest distance to " O   HOH Z 359 " =    1.290
peak=    4.301 closest distance to " CB  VAL A 296 " =    1.247
peak=    4.271 closest distance to " O  BHOH Z  74 " =    1.170
peak=    4.268 closest distance to " OG ASER A 258 " =    3.050
peak=    4.220 closest distance to " O   HOH Z 422 " =    1.034
peak=    4.220 closest distance to " O   HOH Z 126 " =    2.065
peak=    4.217 closest distance to " CB  ALA A 114 " =    1.170
peak=    4.213 closest distance to " O   HOH Z 414 " =    1.691
peak=    4.203 closest distance to " O   HOH Z 419 " =    2.164
peak=    4.190 closest distance to " O   HOH Z 426 " =    1.178
peak=    4.165 closest distance to " CA  ILE A 234 " =    1.072
peak=    4.161 closest distance to " CD  ARG A 138 " =    0.914
peak=    4.155 closest distance to " O   HOH Z 272 " =    1.860
peak=    4.154 closest distance to " O   HOH Z 369 " =    2.041
peak=    4.149 closest distance to " CG  LEU A 228 " =    1.134
peak=    4.133 closest distance to " CG  PRO A 243 " =    1.124
peak=    4.133 closest distance to " O   HOH Z 371 " =    3.051
peak=    4.133 closest distance to " CB  LYS A 290 " =    0.883
peak=    4.132 closest distance to " O   HOH Z 287 " =    1.767
peak=    4.108 closest distance to " O   HOH Z 146 " =    1.875
peak=    4.108 closest distance to " O   HOH Z 361 " =    1.697
peak=    4.101 closest distance to " O   HOH Z 112 " =    1.281
peak=    4.089 closest distance to " O   HOH Z  43 " =    1.482
peak=    4.089 closest distance to " O   HOH Z 400 " =    0.818
peak=    4.080 closest distance to " CG  LEU A   5 " =    1.174
peak=    4.057 closest distance to " CG  LEU A 167 " =    1.350
peak=    4.056 closest distance to " O   HOH Z 416 " =    1.321
peak=    4.033 closest distance to " CD2 LEU A 228 " =    1.320
peak=    4.014 closest distance to " CB  SER A 216 " =    1.043
peak=    4.010 closest distance to " CB  ASN A  39 " =    0.831
peak=    4.004 closest distance to " OE1 GLU A   2 " =    1.965
peak=    3.997 closest distance to " O   HOH Z 218 " =    2.317
peak=    3.993 closest distance to " CB  ASP A 124 " =    0.975
peak=    3.989 closest distance to " N   SER A  97 " =    0.875
peak=    3.979 closest distance to " O   HOH Z 133 " =    1.821
peak=    3.972 closest distance to " N   GLN A 278 " =    1.037
peak=    3.969 closest distance to " O   HOH Z 215 " =    1.558
peak=    3.957 closest distance to " O   HOH Z   1 " =    1.934
peak=    3.950 closest distance to " O   HOH Z 214 " =    1.315
peak=    3.911 closest distance to " CG2 VAL A 296 " =    0.986
peak=    3.905 closest distance to " O   HOH Z  78 " =    1.847
peak=    3.903 closest distance to " O   HOH Z 298 " =    1.972
peak=    3.900 closest distance to " CG2 ILE A 234 " =    0.929
peak=    3.899 closest distance to " O   HOH Z 233 " =    1.610
peak=    3.897 closest distance to " CG2 THR A 221 " =    1.164
peak=    3.882 closest distance to " OG  SER A 276 " =    0.954
peak=    3.873 closest distance to " O   HOH Z  27 " =    1.059
peak=    3.859 closest distance to " O   HOH Z 423 " =    1.906
peak=    3.858 closest distance to " O   HOH Z 123 " =    1.179
peak=    3.843 closest distance to " CB  SER A  63 " =    1.306
peak=    3.841 closest distance to " CE  MET A  93 " =    1.482
peak=    3.825 closest distance to " CB  ASN A 148 " =    1.437
peak=    3.821 closest distance to " CB  LEU A 300 " =    0.933
peak=    3.815 closest distance to " O   HOH Z 258 " =    1.232
peak=    3.811 closest distance to " O   HOH Z 125 " =    1.815
peak=    3.811 closest distance to " O   HOH Z 103 " =    0.992
peak=    3.795 closest distance to " CB  TRP A 266 " =    0.965
peak=    3.788 closest distance to " O   HOH Z  39 " =    1.599
peak=    3.787 closest distance to " CD1 LEU A   5 " =    1.291
peak=    3.776 closest distance to " O   HOH Z 153 " =    3.557
peak=    3.752 closest distance to " O   HOH Z 303 " =    2.029
peak=    3.748 closest distance to " CB  GLN A 183 " =    1.108
peak=    3.747 closest distance to " O   HOH Z 353 " =    2.119
peak=    3.745 closest distance to " O   HOH Z 423 " =    1.853
peak=    3.733 closest distance to " O   HOH Z 342 " =    1.058
peak=    3.732 closest distance to " CE3 TRP A 274 " =    1.387
peak=    3.731 closest distance to " CZ3 TRP A 266 " =    1.183
peak=    3.716 closest distance to " NH2AARG A 145 " =    1.094
peak=    3.714 closest distance to " NE1 TRP A 274 " =    1.085
peak=    3.712 closest distance to " CD  ARG A  66 " =    2.211
peak=    3.708 closest distance to " O   HOH Z  57 " =    1.294
peak=    3.708 closest distance to " O   HOH Z  30 " =    1.227
peak=    3.705 closest distance to " NH2AARG A 145 " =    2.313
peak=    3.693 closest distance to " O   HOH Z  91 " =    2.339
peak=    3.688 closest distance to " OD1 ASP A 200 " =    1.504
peak=    3.686 closest distance to " O   HOH Z  61 " =    1.940
peak=    3.683 closest distance to " O   HOH Z  49 " =    2.905
peak=    3.680 closest distance to " CA  ARG A 159 " =    1.187
peak=    3.679 closest distance to " CB  GLN A 223 " =    1.519
peak=    3.667 closest distance to " O   HOH Z  68 " =    2.073
peak=    3.667 closest distance to " CB  SER A 210 " =    1.021
peak=    3.665 closest distance to " N   ARG A 156 " =    1.353
peak=    3.664 closest distance to " O   HOH Z  57 " =    2.311
peak=    3.662 closest distance to " O   HOH Z 172 " =    1.716
peak=    3.662 closest distance to " O   HOH Z  49 " =    1.072
peak=    3.659 closest distance to " CB  SER A 276 " =    1.157
peak=    3.656 closest distance to " O   ILE A  20 " =    1.735
peak=    3.639 closest distance to " O   HOH Z 114 " =    2.080
peak=    3.639 closest distance to " CA  LEU A 222 " =    1.094
peak=    3.635 closest distance to " CZ AARG A 102 " =    1.985
peak=    3.633 closest distance to " N   CYS A 260 " =    1.055
peak=    3.633 closest distance to " O   HOH Z 371 " =    2.489
peak=    3.631 closest distance to " O   HOH Z  58 " =    2.083
peak=    3.623 closest distance to " CG1 ILE A  33 " =    1.403
peak=    3.619 closest distance to " O   HOH Z 158 " =    2.563
peak=    3.619 closest distance to " O   HOH Z 119 " =    1.526
peak=    3.607 closest distance to " CA  ASN A 127 " =    1.167
peak=    3.606 closest distance to " O   HOH Z 356 " =    1.920
peak=    3.603 closest distance to " CD2 LEU A 297 " =    0.943
peak=    3.601 closest distance to " O   HOH Z 422 " =    2.431
peak=    3.599 closest distance to " O   HOH Z 366 " =    2.939
peak=    3.595 closest distance to " O   HOH Z 430 " =    1.741
peak=    3.595 closest distance to " N   VAL A 296 " =    1.754
peak=    3.590 closest distance to " CA  ALA A 295 " =    0.846
peak=    3.584 closest distance to " O   HOH Z 193 " =    1.741
peak=    3.576 closest distance to " O   HOH Z 143 " =    1.547
peak=    3.575 closest distance to " O   HOH Z 405 " =    1.964
peak=    3.570 closest distance to " O   HOH Z  11 " =    1.296
peak=    3.566 closest distance to " O   HOH Z 427 " =    1.180
peak=    3.560 closest distance to " CB  GLU A 128 " =    0.948
peak=    3.559 closest distance to " ND2BASN A 224 " =    0.962
peak=    3.556 closest distance to " O   HOH Z 214 " =    1.972
peak=    3.550 closest distance to " C   GLN A  73 " =    1.029
peak=    3.545 closest distance to " O   HOH Z 236 " =    1.896
peak=    3.541 closest distance to " ND2 ASN A 110 " =    1.768
peak=    3.534 closest distance to " NH2 ARG A 269 " =    1.040
peak=    3.530 closest distance to " O   HOH Z 211 " =    1.345
peak=    3.525 closest distance to " CB  VAL A 296 " =    1.269
peak=    3.525 closest distance to " O   HOH Z 380 " =    2.250
peak=    3.523 closest distance to " CB  SER A  62 " =    1.046
peak=    3.505 closest distance to " N   TYR A  15 " =    0.992
peak=    3.491 closest distance to " O   HOH Z 392 " =    1.460
peak=    3.488 closest distance to " CG2AVAL A  72 " =    0.789
peak=    3.483 closest distance to " NE AARG A 275 " =    1.646
peak=    3.483 closest distance to " OE1 GLN A 240 " =    1.771
peak=    3.482 closest distance to " O   HOH Z   7 " =    3.308
peak=    3.479 closest distance to " O   HOH Z   6 " =    1.933
peak=    3.475 closest distance to " O   HOH Z  51 " =    2.068
peak=    3.474 closest distance to " OG  SER A  62 " =    3.094
peak=    3.471 closest distance to " O   HOH Z 159 " =    0.902
peak=    3.470 closest distance to " O   HOH Z 248 " =    1.970
peak=    3.467 closest distance to " O   HOH Z 352 " =    1.610
peak=    3.466 closest distance to " CD  GLN A  58 " =    5.759
peak=    3.466 closest distance to " CD  GLN A  77 " =    1.335
peak=    3.464 closest distance to " NZ  LYS A 117 " =    1.109
peak=    3.463 closest distance to " CD1 LEU A 228 " =    1.702
peak=    3.462 closest distance to " CB  ASN A 215 " =    1.613
peak=    3.457 closest distance to " CB  MET A  47 " =    1.265
peak=    3.456 closest distance to " C   VAL A 153 " =    1.070
peak=    3.447 closest distance to " O   ASN A 301 " =    2.032
peak=    3.446 closest distance to " N   GLU A   2 " =    1.349
peak=    3.445 closest distance to " CG1AVAL A 121 " =    0.833
peak=    3.442 closest distance to " O   ASN A 142 " =    1.098
peak=    3.442 closest distance to " CG  GLN A 278 " =    4.011
peak=    3.440 closest distance to " O   GLY A 302 " =    2.387
peak=    3.434 closest distance to " O   HOH Z  88 " =    3.512
peak=    3.432 closest distance to " O   HOH Z  40 " =    2.227
peak=    3.432 closest distance to " CA  ALA A  21 " =    0.991
peak=    3.431 closest distance to " CA  GLY A 136 " =    1.116
peak=    3.426 closest distance to " CG2 THR A 178 " =    1.251
peak=    3.424 closest distance to " CB  TRP A 179 " =    1.492
peak=    3.423 closest distance to " C   ASN A 209 " =    1.823
peak=    3.418 closest distance to " NE2 GLN A  73 " =    1.485
peak=    3.416 closest distance to " O   HOH Z 279 " =    2.514
peak=    3.416 closest distance to " CD  ARG A  56 " =    1.105
peak=    3.411 closest distance to " O   HOH Z 389 " =    1.536
peak=    3.411 closest distance to " CG  PRO A 198 " =    1.372
peak=    3.408 closest distance to " O   HOH Z 411 " =    3.102
peak=    3.398 closest distance to " CA  ARG A  36 " =    1.011
peak=    3.392 closest distance to " NH2AARG A 190 " =    1.808
peak=    3.388 closest distance to " CB  GLU A 277 " =    0.986
peak=    3.388 closest distance to " O   HOH Z  26 " =    1.667
peak=    3.385 closest distance to " O   HOH Z 425 " =    2.083
peak=    3.384 closest distance to " CB  ASN A 110 " =    0.936
peak=    3.383 closest distance to " NZ  LYS A 117 " =    3.363
peak=    3.381 closest distance to " CB  ASP A 140 " =    0.959
peak=    3.381 closest distance to " CA  ALA A  51 " =    1.054
peak=    3.379 closest distance to " CG2BVAL A  72 " =    1.293
peak=    3.371 closest distance to " O   HOH Z 238 " =    1.268
peak=    3.371 closest distance to " O   HOH Z 220 " =    1.365
peak=    3.369 closest distance to " NH1AARG A 275 " =    1.139
peak=    3.366 closest distance to " CG  GLN A 205 " =    1.063
peak=    3.363 closest distance to " CB  ASN A 187 " =    1.064
peak=    3.362 closest distance to " O   HOH Z 364 " =    1.289
peak=    3.361 closest distance to " CB  VAL A 202 " =    1.647
peak=    3.359 closest distance to " CG  LYS A  76 " =    1.789
peak=    3.356 closest distance to " CD2 LEU A 167 " =    1.257
peak=    3.355 closest distance to " CB  ALA A  43 " =    0.885
peak=    3.343 closest distance to " CG  ARG A 159 " =    0.754
peak=    3.342 closest distance to " CA  PHE A 283 " =    1.267
peak=    3.336 closest distance to " O   HOH Z 357 " =    1.264
peak=    3.335 closest distance to " CA  ASN A 284 " =    0.934
peak=    3.332 closest distance to " OG  SER A  26 " =    1.505
peak=    3.329 closest distance to " O   HOH Z 110 " =    1.692
peak=    3.327 closest distance to " O   HOH Z  88 " =    3.662
peak=    3.327 closest distance to " O   HOH Z 148 " =    1.752
peak=    3.325 closest distance to " NZ  LYS A 119 " =    2.689
peak=    3.322 closest distance to " O   HOH Z 331 " =    1.058
peak=    3.322 closest distance to " O   HOH Z  52 " =    1.032
peak=    3.320 closest distance to " CE  LYS A  48 " =    1.060
peak=    3.320 closest distance to " O   HOH Z 128 " =    1.945
peak=    3.319 closest distance to " N   VAL A 125 " =    1.522
peak=    3.317 closest distance to " O   HOH Z  44 " =    2.504
peak=    3.311 closest distance to " O   HOH Z 328 " =    1.533
peak=    3.310 closest distance to " O   HOH Z 158 " =    1.185
peak=    3.310 closest distance to " O   HOH Z  92 " =    1.254
peak=    3.306 closest distance to " CB  GLU A 277 " =    3.591
peak=    3.302 closest distance to " CA  ARG A 195 " =    1.234
peak=    3.292 closest distance to " O   HOH Z  21 " =    1.447
peak=    3.290 closest distance to " CE3 TRP A 150 " =    1.085
peak=    3.289 closest distance to " OE1 GLU A   2 " =    1.646
peak=    3.285 closest distance to " O   THR A 220 " =    1.852
peak=    3.282 closest distance to " CB  TRP A 150 " =    1.217
peak=    3.281 closest distance to " CA  LEU A 282 " =    1.115
peak=    3.281 closest distance to " CD1 ILE A  33 " =    1.841
peak=    3.277 closest distance to " O   HOH Z  15 " =    1.167
peak=    3.276 closest distance to " OG BSER A  99 " =    2.152
peak=    3.270 closest distance to " CE AMET A  47 " =    1.378
peak=    3.269 closest distance to " O   HOH Z 362 " =    1.690
peak=    3.268 closest distance to " ND2 ASN A 249 " =    0.836
peak=    3.266 closest distance to " O   HOH Z 353 " =    1.924
peak=    3.266 closest distance to " CB  VAL A 265 " =    1.409
peak=    3.265 closest distance to " CB  ARG A 138 " =    0.922
peak=    3.258 closest distance to " O   HOH Z 244 " =    1.521
peak=    3.255 closest distance to " O   HOH Z 145 " =    2.266
peak=    3.254 closest distance to " O   HOH Z   3 " =    1.495
peak=    3.252 closest distance to " O   HOH Z 389 " =    1.487
peak=    3.248 closest distance to " NH2BARG A 145 " =    1.794
peak=    3.248 closest distance to " CA  SER A  12 " =    1.710
peak=    3.247 closest distance to " O   HOH Z 303 " =    1.076
peak=    3.247 closest distance to " O   HOH Z  47 " =    1.644
peak=    3.243 closest distance to " O   HOH Z 384 " =    1.595
peak=    3.243 closest distance to " N   PHE A 130 " =    1.297
peak=    3.241 closest distance to " O   HOH Z 368 " =    1.851
peak=    3.240 closest distance to " O   ALA A 165 " =    1.354
peak=    3.236 closest distance to " O   HOH Z 412 " =    2.981
peak=    3.233 closest distance to " O   HOH Z 373 " =    1.494
peak=    3.231 closest distance to " O   HOH Z 434 " =    5.538
peak=    3.230 closest distance to " ND1 HIS A  81 " =    1.635
peak=    3.228 closest distance to " O   HOH Z 371 " =    1.922
peak=    3.225 closest distance to " CB  ASN A 142 " =    1.023
peak=    3.223 closest distance to " O   HOH Z 344 " =    3.025
peak=    3.220 closest distance to " O   HOH Z 280 " =    2.117
peak=    3.217 closest distance to " O   HOH Z 368 " =    0.968
peak=    3.209 closest distance to " CA  GLU A 152 " =    0.981
peak=    3.209 closest distance to " CB  ARG A  79 " =    0.837
peak=    3.209 closest distance to " NH2BARG A 190 " =    1.318
peak=    3.203 closest distance to " CA  ALA A 160 " =    1.149
peak=    3.200 closest distance to " OD2 ASP A  50 " =    1.061
peak=    3.200 closest distance to " CB  ARG A 156 " =    1.347
peak=    3.191 closest distance to " N   GLN A  11 " =    1.372
peak=    3.190 closest distance to " CD1 LEU A   5 " =    0.823
peak=    3.186 closest distance to " OD2 ASP A 286 " =    2.270
peak=    3.182 closest distance to " CD  LYS A 166 " =    1.347
peak=    3.181 closest distance to " O   HOH Z 207 " =    2.425
peak=    3.175 closest distance to " O   HOH Z 185 " =    1.827
peak=    3.171 closest distance to " N   ALA A   1 " =    1.425
peak=    3.170 closest distance to " O   HOH Z 240 " =    2.053
peak=    3.168 closest distance to " OD1 ASP A 298 " =    2.540
peak=    3.166 closest distance to " N   THR A 246 " =    1.361
peak=    3.159 closest distance to " O   HOH Z 379 " =    1.462
peak=    3.158 closest distance to " NH1AARG A 145 " =    1.102
peak=    3.156 closest distance to " CZ3 TRP A  92 " =    1.285
peak=    3.156 closest distance to " O   HOH Z 368 " =    3.033
peak=    3.153 closest distance to " N   TYR A 116 " =    1.522
peak=    3.153 closest distance to " O   HOH Z 286 " =    1.326
peak=    3.145 closest distance to " OG  SER A  22 " =    2.752
peak=    3.142 closest distance to " O   HOH Z 291 " =    1.954
peak=    3.141 closest distance to " CB  GLN A  73 " =    1.003
peak=    3.140 closest distance to " CG2AVAL A  72 " =    3.034
peak=    3.139 closest distance to " CA  TYR A  30 " =    1.105
peak=    3.137 closest distance to " CB  PRO A 213 " =    1.224
peak=    3.127 closest distance to " CB  SER A 212 " =    1.293
peak=    3.121 closest distance to " CE2 PHE A  16 " =    0.901
peak=    3.121 closest distance to " O   HOH Z 353 " =    1.703
peak=    3.116 closest distance to " N   LYS A  76 " =    1.395
peak=    3.111 closest distance to " CG1 ILE A 120 " =    1.531
peak=    3.110 closest distance to " CG2 THR A 246 " =    1.273
peak=    3.106 closest distance to " CB  GLU A 236 " =    1.368
peak=    3.106 closest distance to " O   HOH Z  11 " =    1.816
peak=    3.096 closest distance to " OG BSER A 258 " =    0.996
peak=    3.096 closest distance to " CD  ARG A  24 " =    1.032
peak=    3.093 closest distance to " CG  GLU A 277 " =    1.803
peak=    3.084 closest distance to " CG2 THR A 279 " =    1.000
peak=    3.084 closest distance to " CB  ALA A 114 " =    1.845
peak=    3.081 closest distance to " O   HOH Z 113 " =    1.802
peak=    3.078 closest distance to " CA  ALA A 299 " =    0.947
peak=    3.070 closest distance to " OD1 ASN A 217 " =    1.633
peak=    3.066 closest distance to " O   HOH Z  41 " =    2.451
peak=    3.057 closest distance to " N   GLN A  73 " =    1.029
peak=    3.054 closest distance to " CB  PHE A  16 " =    1.065
peak=    3.048 closest distance to " CG  GLN A  89 " =    1.577
peak=    3.041 closest distance to " O   HOH Z 357 " =    2.156
peak=    3.037 closest distance to " O   HOH Z  28 " =    1.465
peak=    3.032 closest distance to " O   HOH Z 143 " =    1.413
peak=    3.031 closest distance to " O   HOH Z 363 " =    1.432
peak=    3.026 closest distance to " O   HOH Z 323 " =    1.799

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.367 - 5.598
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 197
   mapped sites are within: 0.700 - 5.598

peak=   -5.097 closest distance to " CD  ARG A 138 " =    1.252
peak=   -5.018 closest distance to " CG2 VAL A 230 " =    0.806
peak=   -4.772 closest distance to " O   PRO A 198 " =    1.092
peak=   -4.342 closest distance to " OG BSER A 134 " =    1.618
peak=   -4.313 closest distance to " CG1 VAL A 296 " =    0.963
peak=   -4.191 closest distance to " NE1 TRP A 179 " =    1.100
peak=   -4.191 closest distance to " O   HOH Z  39 " =    0.892
peak=   -4.179 closest distance to " O   HOH Z 131 " =    3.734
peak=   -4.162 closest distance to " O   HOH Z 242 " =    1.543
peak=   -4.136 closest distance to " CD  ARG A  14 " =    2.918
peak=   -4.096 closest distance to " O   HOH Z 163 " =    1.836
peak=   -4.048 closest distance to " OE1 GLU A 277 " =    2.392
peak=   -4.033 closest distance to " CB  VAL A 230 " =    0.862
peak=   -4.026 closest distance to " O   HOH Z 385 " =    0.960
peak=   -4.008 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.960 closest distance to " O   HOH Z 377 " =    1.335
peak=   -3.921 closest distance to " O   ASP A 191 " =    1.849
peak=   -3.905 closest distance to " CB  PHE A 130 " =    1.130
peak=   -3.899 closest distance to " CA  GLY A 133 " =    2.109
peak=   -3.893 closest distance to " O   HOH Z 313 " =    0.857
peak=   -3.888 closest distance to " CD2 TYR A 293 " =    1.703
peak=   -3.872 closest distance to " N   VAL A  72 " =    2.101
peak=   -3.788 closest distance to " O   HOH Z 300 " =    1.026
peak=   -3.781 closest distance to " CB  ASP A  27 " =    2.452
peak=   -3.774 closest distance to " N   THR A 157 " =    1.677
peak=   -3.760 closest distance to " OG  SER A  97 " =    2.273
peak=   -3.751 closest distance to " O   ALA A  51 " =    1.274
peak=   -3.748 closest distance to " O   ALA A  84 " =    1.628
peak=   -3.743 closest distance to " C   VAL A  72 " =    0.875
peak=   -3.738 closest distance to " CB  ALA A 248 " =    2.091
peak=   -3.732 closest distance to " O   THR A 178 " =    0.852
peak=   -3.732 closest distance to " CB  GLN A  55 " =    1.223
peak=   -3.728 closest distance to " O   HOH Z  24 " =    1.034
peak=   -3.709 closest distance to " CE2 TYR A  30 " =    2.525
peak=   -3.707 closest distance to " O   HOH Z 298 " =    0.852
peak=   -3.706 closest distance to " O   HOH Z 275 " =    1.749
peak=   -3.702 closest distance to " CD2 LEU A   5 " =    0.906
peak=   -3.699 closest distance to " CB  TYR A  68 " =    1.291
peak=   -3.698 closest distance to " O   HOH Z 428 " =    1.715
peak=   -3.690 closest distance to " O   ALA A  10 " =    1.601
peak=   -3.661 closest distance to " CB  PRO A 243 " =    2.598
peak=   -3.654 closest distance to " O   HOH Z 390 " =    2.617
peak=   -3.650 closest distance to " O   HOH Z  28 " =    1.131
peak=   -3.646 closest distance to " O   ASN A 209 " =    2.232
peak=   -3.639 closest distance to " CZ2 TRP A 274 " =    0.921
peak=   -3.615 closest distance to " CD  LYS A 166 " =    2.582
peak=   -3.608 closest distance to " O   HOH Z 205 " =    1.330
peak=   -3.604 closest distance to " NE2 GLN A 223 " =    1.444
peak=   -3.597 closest distance to " CD1 LEU A 222 " =    2.441
peak=   -3.596 closest distance to " CG  PHE A  59 " =    1.784
peak=   -3.588 closest distance to " O   HOH Z 389 " =    2.458
peak=   -3.574 closest distance to " CG  ARG A 219 " =    2.307
peak=   -3.554 closest distance to " O   HOH Z 268 " =    0.810
peak=   -3.548 closest distance to " C   GLU A   2 " =    1.880
peak=   -3.543 closest distance to " O   HOH Z 238 " =    0.856
peak=   -3.543 closest distance to " NE2 GLN A  55 " =    0.837
peak=   -3.536 closest distance to " CA  GLY A 203 " =    2.543
peak=   -3.534 closest distance to " N   PRO A 163 " =    1.373
peak=   -3.532 closest distance to " OE1 GLU A  44 " =    1.099
peak=   -3.532 closest distance to " O   HOH Z 298 " =    2.609
peak=   -3.524 closest distance to " CG2AVAL A  41 " =    2.808
peak=   -3.515 closest distance to " O   HOH Z 359 " =    1.514
peak=   -3.514 closest distance to " O   SER A   3 " =    2.321
peak=   -3.512 closest distance to " CG2 ILE A 120 " =    1.272
peak=   -3.504 closest distance to " O   HOH Z 185 " =    2.135
peak=   -3.499 closest distance to " O   HOH Z  11 " =    1.961
peak=   -3.496 closest distance to " N   LEU A 282 " =    2.297
peak=   -3.485 closest distance to " O   HOH Z 286 " =    1.584
peak=   -3.484 closest distance to " O   HOH Z 111 " =    1.294
peak=   -3.476 closest distance to " O   GLN A  11 " =    1.617
peak=   -3.472 closest distance to " CG  ASP A  50 " =    1.115
peak=   -3.470 closest distance to " O   HOH Z 222 " =    4.562
peak=   -3.464 closest distance to " CD2 TYR A 116 " =    2.157
peak=   -3.453 closest distance to " CA  GLY A  57 " =    2.209
peak=   -3.450 closest distance to " O   HOH Z 352 " =    1.578
peak=   -3.448 closest distance to " O   HOH Z 331 " =    1.052
peak=   -3.446 closest distance to " O   HOH Z 189 " =    3.397
peak=   -3.444 closest distance to " O   HOH Z 415 " =    0.883
peak=   -3.443 closest distance to " CD1 ILE A 239 " =    2.454
peak=   -3.442 closest distance to " O   HOH Z 364 " =    0.928
peak=   -3.437 closest distance to " CG  PRO A 163 " =    2.514
peak=   -3.434 closest distance to " CB  ALA A 114 " =    2.461
peak=   -3.433 closest distance to " CA  GLY A  98 " =    1.726
peak=   -3.430 closest distance to " O   ILE A  49 " =    1.603
peak=   -3.425 closest distance to " O   HOH Z 414 " =    1.700
peak=   -3.423 closest distance to " CD1 TRP A 274 " =    1.039
peak=   -3.417 closest distance to " O   HOH Z 350 " =    2.470
peak=   -3.412 closest distance to " O   HOH Z 351 " =    1.603
peak=   -3.410 closest distance to " CG2 ILE A 120 " =    0.939
peak=   -3.407 closest distance to " CB  ALA A  43 " =    2.391
peak=   -3.404 closest distance to " OD2 ASP A 272 " =    1.422
peak=   -3.402 closest distance to " O   HOH Z 159 " =    1.509
peak=   -3.390 closest distance to " O   HOH Z  76 " =    1.070
peak=   -3.388 closest distance to " O   HOH Z 186 " =    1.401
peak=   -3.371 closest distance to " O   TRP A 179 " =    1.673
peak=   -3.368 closest distance to " CA  GLY A  35 " =    1.958
peak=   -3.367 closest distance to " O   HOH Z 268 " =    0.937
peak=   -3.366 closest distance to " CG  GLU A 277 " =    1.158
peak=   -3.364 closest distance to " CG  TRP A 266 " =    1.958
peak=   -3.360 closest distance to " CB  ASN A  45 " =    2.022
peak=   -3.353 closest distance to " O   HOH Z  53 " =    1.731
peak=   -3.349 closest distance to " O   ARG A 145 " =    1.370
peak=   -3.345 closest distance to " O   HOH Z 102 " =    1.723
peak=   -3.343 closest distance to " CB  ALA A  10 " =    2.109
peak=   -3.343 closest distance to " O   HOH Z 211 " =    1.068
peak=   -3.340 closest distance to " OG BSER A 210 " =    2.365
peak=   -3.340 closest distance to " CB  ALA A   9 " =    2.452
peak=   -3.339 closest distance to " O   LYS A  76 " =    1.254
peak=   -3.333 closest distance to " C   ASN A 285 " =    2.002
peak=   -3.329 closest distance to " O   HOH Z 266 " =    4.931
peak=   -3.325 closest distance to " CG  ASN A 284 " =    1.301
peak=   -3.324 closest distance to " OE2 GLU A 152 " =    1.133
peak=   -3.322 closest distance to " NH2AARG A 275 " =    5.346
peak=   -3.316 closest distance to " O   HOH Z 308 " =    1.474
peak=   -3.316 closest distance to " CD  GLN A  58 " =    0.888
peak=   -3.315 closest distance to " OG  SER A 271 " =    0.944
peak=   -3.314 closest distance to " O   HOH Z 128 " =    2.462
peak=   -3.312 closest distance to " C   PHE A 155 " =    0.700
peak=   -3.307 closest distance to " O   SER A  22 " =    2.667
peak=   -3.296 closest distance to " O   HOH Z  95 " =    1.513
peak=   -3.292 closest distance to " CD  GLN A  77 " =    1.111
peak=   -3.292 closest distance to " CD2 LEU A 237 " =    2.344
peak=   -3.291 closest distance to " O   HOH Z  60 " =    1.632
peak=   -3.291 closest distance to " O   HOH Z 136 " =    2.887
peak=   -3.290 closest distance to " O   HOH Z 189 " =    1.250
peak=   -3.287 closest distance to " O   SER A 273 " =    1.565
peak=   -3.287 closest distance to " C   ARG A  79 " =    2.583
peak=   -3.285 closest distance to " CA  GLY A  57 " =    2.093
peak=   -3.274 closest distance to " O   HOH Z 387 " =    1.173
peak=   -3.271 closest distance to " O   HOH Z 428 " =    2.394
peak=   -3.269 closest distance to " O   GLY A 203 " =    2.572
peak=   -3.264 closest distance to " O   HOH Z 422 " =    3.589
peak=   -3.264 closest distance to " CD  ARG A 139 " =    1.724
peak=   -3.262 closest distance to " OD2 ASP A 171 " =    2.213
peak=   -3.250 closest distance to " O   HOH Z 353 " =    1.160
peak=   -3.246 closest distance to " CB  ASN A  39 " =    2.343
peak=   -3.240 closest distance to " O   HOH Z 359 " =    3.361
peak=   -3.240 closest distance to " CB  ALA A 291 " =    2.140
peak=   -3.240 closest distance to " O   HOH Z 231 " =    1.929
peak=   -3.238 closest distance to " N   HIS A 115 " =    2.187
peak=   -3.233 closest distance to " CB  ASN A 301 " =    1.822
peak=   -3.231 closest distance to " CG1 ILE A 234 " =    1.567
peak=   -3.227 closest distance to " O   HOH Z 435 " =    2.267
peak=   -3.225 closest distance to " O   HOH Z 414 " =    1.828
peak=   -3.225 closest distance to " CG BLYS A 290 " =    0.914
peak=   -3.224 closest distance to " CD1 ILE A  33 " =    2.229
peak=   -3.224 closest distance to " OG  SER A 245 " =    1.523
peak=   -3.220 closest distance to " O   HOH Z 412 " =    5.598
peak=   -3.216 closest distance to " CG  LEU A 228 " =    0.882
peak=   -3.215 closest distance to " CG  MET A  40 " =    2.232
peak=   -3.208 closest distance to " O   VAL A  67 " =    2.590
peak=   -3.199 closest distance to " C   HIS A 108 " =    1.273
peak=   -3.192 closest distance to " OG ASER A 134 " =    0.881
peak=   -3.191 closest distance to " O   PRO A 163 " =    1.849
peak=   -3.188 closest distance to " O   HOH Z 111 " =    1.559
peak=   -3.183 closest distance to " O   HOH Z 207 " =    2.037
peak=   -3.183 closest distance to " O   HOH Z 174 " =    2.974
peak=   -3.180 closest distance to " N   ALA A   1 " =    1.067
peak=   -3.180 closest distance to " N   ALA A  43 " =    2.782
peak=   -3.180 closest distance to " NE2 GLN A 194 " =    1.930
peak=   -3.173 closest distance to " O   VAL A  72 " =    0.959
peak=   -3.169 closest distance to " O   GLY A  17 " =    1.240
peak=   -3.166 closest distance to " CE1 PHE A  59 " =    1.514
peak=   -3.165 closest distance to " CG  PRO A 243 " =    1.695
peak=   -3.158 closest distance to " O   HOH Z 111 " =    1.554
peak=   -3.157 closest distance to " CD1 PHE A  59 " =    2.112
peak=   -3.155 closest distance to " CB  SER A 273 " =    2.364
peak=   -3.151 closest distance to " O   HOH Z 274 " =    3.360
peak=   -3.151 closest distance to " O   HOH Z  52 " =    0.903
peak=   -3.145 closest distance to " NE1 TRP A 177 " =    1.776
peak=   -3.145 closest distance to " O   HOH Z 241 " =    1.127
peak=   -3.142 closest distance to " C   ILE A 239 " =    1.832
peak=   -3.139 closest distance to " O   HOH Z  22 " =    2.724
peak=   -3.138 closest distance to " O   HOH Z 140 " =    1.465
peak=   -3.135 closest distance to " O   HOH Z  52 " =    2.063
peak=   -3.134 closest distance to " O   HOH Z  54 " =    1.459
peak=   -3.133 closest distance to " O   HOH Z 162 " =    2.760
peak=   -3.126 closest distance to " CB  ASP A  50 " =    2.221
peak=   -3.126 closest distance to " O   HOH Z 201 " =    1.564
peak=   -3.123 closest distance to " NE2 GLN A  11 " =    1.343
peak=   -3.119 closest distance to " O   HOH Z  65 " =    1.135
peak=   -3.119 closest distance to " CG2 THR A  31 " =    2.352
peak=   -3.110 closest distance to " O   CYS A 260 " =    1.228
peak=   -3.107 closest distance to " CG  GLN A  88 " =    0.973
peak=   -3.084 closest distance to " O   PHE A 218 " =    1.674
peak=   -3.081 closest distance to " O   HOH Z 434 " =    4.631
peak=   -3.077 closest distance to " C   ARG A 269 " =    1.384
peak=   -3.075 closest distance to " O   PHE A 155 " =    1.912
peak=   -3.075 closest distance to " CG  ASP A 231 " =    0.754
peak=   -3.073 closest distance to " O   HOH Z  67 " =    3.010
peak=   -3.070 closest distance to " CB  LYS A 289 " =    2.978
peak=   -3.066 closest distance to " N   VAL A 189 " =    1.716
peak=   -3.043 closest distance to " CG  ARG A 138 " =    0.737

================= 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    :  0.4958 0.4874   6.300520e+00   6.286058e+00
   1_bss:  0.4870 0.4757   6.296228e+00   6.279600e+00
   1_xyz:  0.4209 0.4438   6.226962e+00   6.254044e+00
   1_adp:  0.3828 0.4475   6.184567e+00   6.253826e+00
   1_occ:  0.3827 0.4471   6.184334e+00   6.254378e+00
   2_bss:  0.3805 0.4426   6.185062e+00   6.252984e+00
   2_xyz:  0.3231 0.4047   6.060653e+00   6.189205e+00
   2_adp:  0.3036 0.3904   6.026982e+00   6.166532e+00
   2_occ:  0.3034 0.3903   6.026858e+00   6.166708e+00
   3_bss:  0.3032 0.3872   6.025758e+00   6.164649e+00
   3_xyz:  0.2642 0.3365   5.899869e+00   6.061704e+00
   3_adp:  0.2501 0.3281   5.865112e+00   6.038923e+00
   3_occ:  0.2498 0.3280   5.864523e+00   6.038648e+00
   4_bss:  0.2492 0.3273   5.864246e+00   6.038140e+00
   4_xyz:  0.1957 0.2594   5.634397e+00   5.839119e+00
   4_adp:  0.1736 0.2334   5.529296e+00   5.754495e+00
   4_occ:  0.1734 0.2331   5.528234e+00   5.753394e+00
   5_bss:  0.1733 0.2341   5.527848e+00   5.753108e+00
   5_xyz:  0.1459 0.2050   5.391928e+00   5.639016e+00
   5_adp:  0.1399 0.1930   5.345794e+00   5.582673e+00
   5_occ:  0.1397 0.1928   5.344681e+00   5.581489e+00
   5_bss:  0.1401 0.1922   5.343798e+00   5.580080e+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:  0.342   0.000   6.556   9.751   8.839   0.000   0.000   0.000
   1_xyz:  0.342   0.000   6.556   9.751   8.839   0.000   0.000   0.000
   1_adp:  0.342   0.000   6.556   9.751   8.839   0.000   0.000   0.000
   1_occ:  0.342   0.000   6.556   9.751   8.839   0.000   0.000   0.000
   2_bss:  0.359  39.471   3.282   5.643   4.913   0.000   0.000   0.000
   2_xyz:  0.359  39.471   3.282   5.643   4.913   0.000   0.000   0.000
   2_adp:  0.359  39.471   3.282   5.643   4.913   0.000   0.000   0.000
   2_occ:  0.359  39.471   3.282   5.643   4.913   0.000   0.000   0.000
   3_bss:  0.324  47.795   2.202   3.031   3.393   0.000   0.000   0.000
   3_xyz:  0.324  47.795   2.202   3.031   3.393   0.000   0.000   0.000
   3_adp:  0.324  47.795   2.202   3.031   3.393   0.000   0.000   0.000
   3_occ:  0.324  47.795   2.202   3.031   3.393   0.000   0.000   0.000
   4_bss:  0.338  53.550   1.060   1.704   2.480   0.000   0.000   0.000
   4_xyz:  0.338  53.550   1.060   1.704   2.480   0.000   0.000   0.000
   4_adp:  0.338  53.550   1.060   1.704   2.480   0.000   0.000   0.000
   4_occ:  0.338  53.550   1.060   1.704   2.480   0.000   0.000   0.000
   5_bss:  0.330  53.550   0.699   0.637   2.238   0.000   0.000   0.000
   5_xyz:  0.330  53.550   0.699   0.637   2.238   0.000   0.000   0.000
   5_adp:  0.330  53.550   0.699   0.637   2.238   0.000   0.000   0.000
   5_occ:  0.330  53.550   0.699   0.637   2.238   0.000   0.000   0.000
   5_bss:  0.318  47.448  -0.492  -0.555   1.047   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.627 0.3726  0.4499    77672.474
   1_bss:  61.200 0.3772  0.5767    75919.248
   1_xyz:  54.810 0.4588  0.6869    64758.739
   1_adp:  54.750 0.4591  0.7493    64673.835
   1_occ:  54.846 0.4579  0.7467    64914.039
   2_bss:  54.265 0.4654  0.6745    64178.218
   2_xyz:  46.241 0.5657  0.8194    48949.887
   2_adp:  43.538 0.5995  0.8613    45120.449
   2_occ:  43.558 0.5992  0.8607    45111.328
   3_bss:  43.277 0.6024  0.8133    44507.148
   3_xyz:  35.531 0.6946  0.9160    31644.269
   3_adp:  33.904 0.7138  0.9366    29572.956
   3_occ:  33.908 0.7137  0.9362    29549.785
   4_bss:  33.855 0.7144  0.9002    29521.351
   4_xyz:  25.885 0.8013  0.9718    17280.887
   4_adp:  22.936 0.8322  0.9784    14122.780
   4_occ:  22.894 0.8326  0.9785    14072.712
   5_bss:  22.876 0.8328  0.9592    14069.317
   5_xyz:  19.886 0.8622  0.9738    10892.671
   5_adp:  18.373 0.8772  0.9720     9805.340
   5_occ:  18.351 0.8774  0.9717     9762.418
   5_bss:  18.314 0.8776  0.9712     9692.896
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3400e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3400e+01
   1_xyz:   1.700  0.013  0.106 18.465  0.006  4.104   1.4624e-01
   1_adp:   1.700  0.013  0.106 18.465  0.006  4.104   1.4624e-01
   1_occ:   1.700  0.013  0.106 18.465  0.006  4.104   1.4624e-01
   2_bss:   1.700  0.013  0.106 18.465  0.006  4.104   1.4624e-01
   2_xyz:   1.415  0.011  0.094 17.098  0.006  4.103   1.2455e-01
   2_adp:   1.415  0.011  0.094 17.098  0.006  4.103   1.2455e-01
   2_occ:   1.415  0.011  0.094 17.098  0.006  4.103   1.2455e-01
   3_bss:   1.415  0.011  0.094 17.098  0.006  4.103   1.2455e-01
   3_xyz:   1.018  0.007  0.075 15.818  0.004  4.115   6.7447e-02
   3_adp:   1.018  0.007  0.075 15.818  0.004  4.115   6.7447e-02
   3_occ:   1.018  0.007  0.075 15.818  0.004  4.115   6.7447e-02
   4_bss:   1.018  0.007  0.075 15.818  0.004  4.115   6.7447e-02
   4_xyz:   1.158  0.009  0.085 15.889  0.005  4.107   8.4019e-02
   4_adp:   1.158  0.009  0.085 15.889  0.005  4.107   8.4019e-02
   4_occ:   1.158  0.009  0.085 15.889  0.005  4.107   8.4019e-02
   5_bss:   1.158  0.009  0.085 15.889  0.005  4.107   8.4019e-02
   5_xyz:   0.987  0.007  0.072 15.567  0.004  4.107   6.1566e-02
   5_adp:   0.987  0.007  0.072 15.567  0.004  4.107   6.1566e-02
   5_occ:   0.987  0.007  0.072 15.567  0.004  4.107   6.1566e-02
   5_bss:   0.987  0.007  0.072 15.567  0.004  4.107   6.1566e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9187e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9187e+00
   1_xyz:  13.060  0.190  0.407 87.633  0.032  2.101   9.8224e-02
   1_adp:  13.060  0.190  0.407 87.633  0.032  2.101   9.8224e-02
   1_occ:  13.060  0.190  0.407 87.633  0.032  2.101   9.8224e-02
   2_bss:  13.060  0.190  0.407 87.633  0.032  2.101   9.8224e-02
   2_xyz:   9.797  0.125  0.325 84.136  0.043  1.897   8.3926e-02
   2_adp:   9.797  0.125  0.325 84.136  0.043  1.897   8.3926e-02
   2_occ:   9.797  0.125  0.325 84.136  0.043  1.897   8.3926e-02
   3_bss:   9.797  0.125  0.325 84.136  0.043  1.897   8.3926e-02
   3_xyz:   7.350  0.046  0.281 81.811  0.032  2.255   6.6309e-02
   3_adp:   7.350  0.046  0.281 81.811  0.032  2.255   6.6309e-02
   3_occ:   7.350  0.046  0.281 81.811  0.032  2.255   6.6309e-02
   4_bss:   7.350  0.046  0.281 81.811  0.032  2.255   6.6309e-02
   4_xyz:   7.365  0.058  0.274 79.540  0.036  2.224   1.1372e-01
   4_adp:   7.365  0.058  0.274 79.540  0.036  2.224   1.1372e-01
   4_occ:   7.365  0.058  0.274 79.540  0.036  2.224   1.1372e-01
   5_bss:   7.365  0.058  0.274 79.540  0.036  2.224   1.1372e-01
   5_xyz:   6.641  0.045  0.278 80.333  0.033  2.347   3.8794e-02
   5_adp:   6.641  0.045  0.278 80.333  0.033  2.347   3.8794e-02
   5_occ:   6.641  0.045  0.278 80.333  0.033  2.347   3.8794e-02
   5_bss:   6.641  0.045  0.278 80.333  0.033  2.347   3.8794e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  78.48   0.00  15.23  78.48   0.00  13.76  76.41   0.00  23.24
   1_occ:  78.48   0.00  15.23  78.48   0.00  13.76  76.41   0.00  23.24
   2_bss:  78.48   0.00  15.23  78.48   0.00  13.76  76.41   0.00  23.24
   2_xyz:  78.48   0.00  15.23  78.48   0.00  13.76  76.41   0.00  23.24
   2_adp:  69.66   0.00  14.43  66.12   0.00  12.17  69.66   0.00  26.76
   2_occ:  69.66   0.00  14.43  66.12   0.00  12.17  69.66   0.00  26.76
   3_bss:  69.66   0.00  14.43  66.12   0.00  12.17  69.66   0.00  26.76
   3_xyz:  69.66   0.00  14.43  66.12   0.00  12.17  69.66   0.00  26.76
   3_adp:  73.99   0.00  14.98  70.78   0.00  11.91  73.99   0.00  31.68
   3_occ:  73.99   0.00  14.98  70.78   0.00  11.91  73.99   0.00  31.68
   4_bss:  73.99   0.00  14.98  70.78   0.00  11.91  73.99   0.00  31.68
   4_xyz:  73.99   0.00  14.98  70.78   0.00  11.91  73.99   0.00  31.68
   4_adp:  86.30   0.00  15.44  86.30   0.00  10.84  85.50   2.98  40.51
   4_occ:  86.30   0.00  15.44  86.30   0.00  10.84  85.50   2.98  40.51
   5_bss:  86.30   0.00  15.44  86.30   0.00  10.84  85.50   2.98  40.51
   5_xyz:  86.30   0.00  15.44  86.30   0.00  10.84  85.50   2.98  40.51
   5_adp:  86.96   0.00  14.78  86.96   0.00  10.16  86.31   2.90  39.91
   5_occ:  86.96   0.00  14.78  86.96   0.00  10.16  86.31   2.90  39.91
   5_bss:  88.16   1.19  15.97  88.16   1.19  11.35  87.50   4.09  41.10
------------------------------------------------------------------------
 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:    1.290    0.015    0.410
   1_adp:    1.290    0.015    0.410
   1_occ:    1.290    0.015    0.410
   2_bss:    1.290    0.015    0.410
   2_xyz:    1.578    0.042    0.603
   2_adp:    1.578    0.042    0.603
   2_occ:    1.578    0.042    0.603
   3_bss:    1.578    0.042    0.603
   3_xyz:    1.561    0.038    0.672
   3_adp:    1.561    0.038    0.672
   3_occ:    1.561    0.038    0.672
   4_bss:    1.561    0.038    0.672
   4_xyz:    1.877    0.046    0.821
   4_adp:    1.877    0.046    0.821
   4_occ:    1.877    0.046    0.821
   5_bss:    1.877    0.046    0.821
   5_xyz:    1.979    0.049    0.859
   5_adp:    1.979    0.049    0.859
   5_occ:    1.979    0.049    0.859
   5_bss:    1.979    0.049    0.859
------------------------------------------------------------------------

CPU time actual refinement: 337.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_612/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_612/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_612/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_612/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_612/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.44 
  Macro-tasks:
    bulk solvent and scale       = 44.47  
    individual site refinement   = 136.12 
    weights calculation          = 32.89  
    collect and process          = 6.53   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 220.13 
  Micro-tasks:
    mask                            = 2.77   
    f_calc                          = 104.34 
    alpha_beta                      = 8.63   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 108.89 
    fmodel                         = 7.55   
    r_factors                      = 0.20   
    phase_errors                   = 10.72  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 244.56 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.808 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    626 calls, 103.84 s
gradients_fft:          572 calls,  97.91 s

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

# Date 2008-01-16 Time 01:58:46 PST -0800 (1200477526.54 s)
Start R-work = 0.4958, R-free = 0.4874 (no bulk solvent and anisotropic scale)
Final R-work = 0.1557, R-free = 0.2072 (no bulk solvent and anisotropic scale)

Start R-work = 0.4870, R-free = 0.4757
Final R-work = 0.1401, R-free = 0.1922