# Date 2008-01-16 Time 01:45:07 PST -0800 (1200476707.21 s)
#phil __OFF__

Command line arguments: "../545.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16853
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 545

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.93, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99058
Completeness in resolution range: 0.972497
Completeness with d_max=infinity: 0.969417

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9592
                             d_min =   1.9906

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99058
Completeness in resolution range: 0.972497
Completeness with d_max=infinity: 0.969417

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9596 -  4.2587 [2117/2141]  1903   214  10.1%
  bin  2:  4.2587 -  3.3932 [2037/2056]  1836   201   9.9%
  bin  3:  3.3932 -  2.9681 [2007/2026]  1808   199   9.9%
  bin  4:  2.9681 -  2.6985 [1983/2013]  1778   205  10.3%
  bin  5:  2.6985 -  2.5060 [1981/2000]  1786   195   9.8%
  bin  6:  2.5060 -  2.3589 [1964/1989]  1769   195   9.9%
  bin  7:  2.3589 -  2.2411 [1953/1981]  1758   195  10.0%
  bin  8:  2.2411 -  2.1439 [1946/1982]  1751   195  10.0%
  bin  9:  2.1439 -  2.0615 [1929/1971]  1735   194  10.1%
  bin 10:  2.0615 -  1.9906 [1672/1984]  1506   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_545/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2206
        3.04 -     3.66: 4634
        3.66 -     4.28: 9075
        4.28 -     4.90: 12326
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.096 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.240 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28247 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_545/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_545/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.93 86.82195 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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4095   r_free= 0.3968   ksol= 0.00   Bsol= 0.00   scale= 0.835    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.193722                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1380  153 0.3479 0.3212      6.4894      6.4223|
|  2:  4.7496 -  3.7901 0.99   1312  149 0.2962 0.3075       6.554      6.6022|
|  3:  3.7901 -  3.3169 0.99   1305  145 0.3452 0.3209      6.4951      6.4713|
|  4:  3.3169 -  3.0164 0.99   1290  136 0.3832 0.3649      6.4033      6.3235|
|  5:  3.0164 -  2.8017 0.99   1268  144 0.4193 0.4426      6.2737      6.3171|
|  6:  2.8017 -  2.6374 0.99   1276  145 0.4304 0.4951      6.2072      6.1776|
|  7:  2.6374 -  2.5060 0.99   1280  142 0.4501 0.4568       6.176      6.1336|
|  8:  2.5060 -  2.3974 0.98   1261  136 0.4630 0.4305      6.1299      6.1113|
|  9:  2.3974 -  2.3054 0.98   1253  143 0.4604 0.4560      6.0649      6.0602|
| 10:  2.3054 -  2.2261 0.99   1261  136 0.4810 0.4305      6.1035      5.9788|
| 11:  2.2261 -  2.1567 0.98   1263  142 0.4742 0.3850      6.0136      5.9309|
| 12:  2.1567 -  2.0953 0.97   1228  139 0.4787 0.4524      5.9514      5.9841|
| 13:  2.0953 -  2.0402 1.00   1263  137 0.4726 0.4727      5.8686      5.8466|
| 14:  2.0402 -  1.9906 0.78    990  112 0.4799 0.4412      5.8413      5.7119|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7496  1380   153  0.75  29.63   0.82     0.77      53892.08|
|  2:  4.7496 -  3.7901  1312   149  0.80  26.03   0.93     0.84      62632.26|
|  3:  3.7901 -  3.3169  1305   145  0.75  30.97   0.89     0.82      63762.30|
|  4:  3.3169 -  3.0164  1290   136  0.69  35.88   0.84     0.74      57625.49|
|  5:  3.0164 -  2.8017  1268   144  0.60  44.03   0.79     0.66      54741.57|
|  6:  2.8017 -  2.6374  1276   145  0.57  46.67   0.77     0.62      51283.75|
|  7:  2.6374 -  2.5060  1280   142  0.54  49.22   0.77     0.61      48736.76|
|  8:  2.5060 -  2.3974  1261   136  0.54  48.67   0.78     0.61      42387.01|
|  9:  2.3974 -  2.3054  1253   143  0.58  46.01   0.76     0.64      36135.26|
| 10:  2.3054 -  2.2261  1261   136  0.59  44.87   0.79     0.67      31006.01|
| 11:  2.2261 -  2.1567  1263   142  0.59  45.38   0.78     0.67      29352.62|
| 12:  2.1567 -  2.0953  1228   139  0.54  49.19   0.80     0.64      29444.71|
| 13:  2.0953 -  2.0402  1263   137  0.53  49.93   0.78     0.60      26079.19|
| 14:  2.0402 -  1.9906   990   112  0.58  46.29   0.75     0.60      19546.40|
|alpha:            min =        0.60 max =            0.84 mean =         0.68|
|beta:             min =    19546.40 max =        63762.30 mean =     43940.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.96 mean =        42.11|
|phase err.(test): min =        0.00 max =           89.92 mean =        42.38|
|-----------------------------------------------------------------------------|

============================== 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 = 5.926966              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.365   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.466296              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.453   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1498 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2621 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3944 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5049 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6570 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7757 |
|-----------------------------------------------------------------------------|
|-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 |       53.731 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.686 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    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 = 11.898)------------------------------------------|
|    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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4197   r_free= 0.4017   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.203187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4023   r_free= 0.3840   ksol= 0.35   Bsol= 20.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.33,8.17,8.85,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.188624                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.554617              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.434   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.452724              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.214   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4023      final r-factor (work) = 0.2845          |
| start r-factor (free) = 0.3840      final r-factor (free) = 0.3009          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.0022 = 5.55 * 0.50 * 6.2186 + 1.00 * 53.7313                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7543 = 5.55 * 0.50 * 5.9946 + 1.00 * 0.1053                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2845      final r-factor (work) = 0.2057          |
| start r-factor (free) = 0.3009      final r-factor (free) = 0.2329          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7287 = 0.45 * 1.00 * 5.9946 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6092 = 0.45 * 1.00 * 5.7408 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    56.41   10.12    None  None   None       |
|    all(noH): 2823   0      0.00    56.41   10.12    None  None   None       |
|    Sol.    : 438    0      0.00    53.44   27.62    None  None   None       |
|    Mac.    : 2385   0      0.00    56.41   6.91     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 -   5.641: 1316   |   5:    28.203 -  33.843:  107        |
|      1:     5.641 -  11.281:  741   |   6:    33.843 -  39.484:   94        |
|      2:    11.281 -  16.922:  252   |   7:    39.484 -  45.124:   54        |
|      3:    16.922 -  22.562:  137   |   8:    45.124 -  50.765:   21        |
|      4:    22.562 -  28.203:   94   |   9:    50.765 -  56.405:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2057 r_free = 0.2329             target_work(ml) = 5.618         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2050 r_free = 0.2331             target_work(ml) = 5.616         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2050   r_free= 0.2331   ksol= 0.35   Bsol= 20.00   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.33,8.17,8.85,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.615951                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1985   r_free= 0.2269   ksol= 0.34   Bsol= 39.90   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,4.37,5.59,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.612929                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.603601              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.962   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.226439              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.561  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1985      final r-factor (work) = 0.1397          |
| start r-factor (free) = 0.2269      final r-factor (free) = 0.1733          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6113 = 2.60 * 0.50 * 5.7662 + 1.00 * 0.1049                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1425 = 2.60 * 0.50 * 5.4396 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1397      final r-factor (work) = 0.1298          |
| start r-factor (free) = 0.1733      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2417 = 0.23 * 1.00 * 5.4396 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2007 = 0.23 * 1.00 * 5.2603 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    58.94   10.43    None  None   None       |
|    all(noH): 2823   0      0.00    58.94   10.43    None  None   None       |
|    Sol.    : 438    0      0.92    55.55   30.10    None  None   None       |
|    Mac.    : 2385   0      0.00    58.94   6.82     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:     0.000 -   5.894: 1435   |   5:    29.469 -  35.363:  106        |
|      1:     5.894 -  11.788:  658   |   6:    35.363 -  41.257:  107        |
|      2:    11.788 -  17.681:  220   |   7:    41.257 -  47.150:   63        |
|      3:    17.681 -  23.575:  102   |   8:    47.150 -  53.044:   25        |
|      4:    23.575 -  29.469:  102   |   9:    53.044 -  58.938:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1298 r_free = 0.1659             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1297 r_free = 0.1658             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1297   r_free= 0.1658   ksol= 0.34   Bsol= 39.90   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,4.37,5.59,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.238121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1663   ksol= 0.33   Bsol= 44.18   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,3.78,4.95,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.238448                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.344547              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.468  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.831648              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.991  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1296      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1663      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8613 = 3.34 * 0.50 * 5.2623 + 1.00 * 0.0613                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7335 = 3.34 * 0.50 * 5.1777 + 1.00 * 0.0750                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3154 = 0.83 * 1.00 * 5.1777 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2835 = 0.83 * 1.00 * 5.1323 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.44   10.97    None  None   None       |
|    all(noH): 2823   0      0.00    70.44   10.97    None  None   None       |
|    Sol.    : 438    0      0.26    65.05   32.92    None  None   None       |
|    Mac.    : 2385   0      0.00    70.44   6.94     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 -   7.044: 1635   |   5:    35.219 -  42.263:   86        |
|      1:     7.044 -  14.088:  568   |   6:    42.263 -  49.306:   75        |
|      2:    14.088 -  21.131:  167   |   7:    49.306 -  56.350:   60        |
|      3:    21.131 -  28.175:   97   |   8:    56.350 -  63.394:   14        |
|      4:    28.175 -  35.219:  115   |   9:    63.394 -  70.438:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1103 r_free = 0.1548             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1548             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1548   ksol= 0.33   Bsol= 44.18   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,3.78,4.95,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130135                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1548   ksol= 0.32   Bsol= 44.18   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,3.78,4.95,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129840                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.934728              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.526  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.508378              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.956   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0397 = 1.93 * 0.50 * 5.1320 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0285 = 1.93 * 0.50 * 5.1358 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6256 = 0.51 * 1.00 * 5.1358 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6407 = 0.51 * 1.00 * 5.1384 + 1.00 * 0.0285                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.50   10.95    None  None   None       |
|    all(noH): 2823   0      0.00    71.50   10.95    None  None   None       |
|    Sol.    : 438    0      0.50    65.30   32.81    None  None   None       |
|    Mac.    : 2385   0      0.00    71.50   6.93     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 -   7.151: 1661   |   5:    35.752 -  42.903:   90        |
|      1:     7.151 -  14.301:  542   |   6:    42.903 -  50.053:   76        |
|      2:    14.301 -  21.451:  169   |   7:    50.053 -  57.204:   50        |
|      3:    21.451 -  28.602:  107   |   8:    57.204 -  64.354:   15        |
|      4:    28.602 -  35.752:  107   |   9:    64.354 -  71.505:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1553             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1554             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1554   ksol= 0.32   Bsol= 44.18   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,3.78,4.95,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138774                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1554   ksol= 0.32   Bsol= 44.18   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,3.77,4.93,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138725                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.210526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 166.255  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.655750              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.787   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3079 = 3.21 * 0.50 * 5.1379 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3013 = 3.21 * 0.50 * 5.1243 + 1.00 * 0.0756                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5198 = 1.66 * 1.00 * 5.1243 + 1.00 * 0.0353                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4881 = 1.66 * 1.00 * 5.1181 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.64   11.10    None  None   None       |
|    all(noH): 2823   0      0.00    80.64   11.10    None  None   None       |
|    Sol.    : 438    0      0.30    71.80   33.64    None  None   None       |
|    Mac.    : 2385   0      0.00    80.64   6.96     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.064: 1770   |   5:    40.320 -  48.384:   87        |
|      1:     8.064 -  16.128:  489   |   6:    48.384 -  56.448:   63        |
|      2:    16.128 -  24.192:  148   |   7:    56.448 -  64.512:   28        |
|      3:    24.192 -  32.256:  112   |   8:    64.512 -  72.576:   12        |
|      4:    32.256 -  40.320:  111   |   9:    72.576 -  80.640:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1557             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1073 r_free = 0.1557             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1557   ksol= 0.32   Bsol= 44.18   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,3.77,4.93,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121971                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1380  153 0.0985 0.1282      5.3777        5.52|
|  2:  4.7496 -  3.7901 0.99   1312  149 0.0822 0.1120      5.4192      5.6455|
|  3:  3.7901 -  3.3169 0.99   1305  145 0.1017 0.1490      5.4514      5.8335|
|  4:  3.3169 -  3.0164 0.99   1290  136 0.1146 0.1487      5.4133      5.5519|
|  5:  3.0164 -  2.8017 0.99   1268  144 0.1256 0.1677      5.2986      5.5306|
|  6:  2.8017 -  2.6374 0.99   1276  145 0.1132 0.1851      5.1802      5.4681|
|  7:  2.6374 -  2.5060 0.99   1280  142 0.1200 0.1627       5.143      5.3376|
|  8:  2.5060 -  2.3974 0.98   1261  136 0.1122 0.1694      5.0606      5.3614|
|  9:  2.3974 -  2.3054 0.98   1253  143 0.1131 0.1859      5.0238      5.3116|
| 10:  2.3054 -  2.2261 0.99   1261  136 0.1074 0.1689      4.9523      5.2023|
| 11:  2.2261 -  2.1567 0.98   1263  142 0.1082 0.1709      4.9295      5.2264|
| 12:  2.1567 -  2.0953 0.97   1228  139 0.1100 0.1653      4.8657      5.2138|
| 13:  2.0953 -  2.0402 1.00   1263  137 0.1076 0.1653       4.778      5.0266|
| 14:  2.0402 -  1.9906 0.78    990  112 0.1000 0.1797      4.6501      4.9755|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7496  1380   153  0.94   9.15   0.98     0.96       7278.08|
|  2:  4.7496 -  3.7901  1312   149  0.95   7.79   1.02     1.00       8969.55|
|  3:  3.7901 -  3.3169  1305   145  0.94  10.86   1.03     1.02      10033.49|
|  4:  3.3169 -  3.0164  1290   136  0.93  12.81   1.01     0.99       9647.67|
|  5:  3.0164 -  2.8017  1268   144  0.90  15.38   1.00     0.97       7977.62|
|  6:  2.8017 -  2.6374  1276   145  0.90  15.52   0.98     0.95       6853.95|
|  7:  2.6374 -  2.5060  1280   142  0.91  15.41   0.98     0.95       6053.00|
|  8:  2.5060 -  2.3974  1261   136  0.91  14.60   0.99     0.97       5238.47|
|  9:  2.3974 -  2.3054  1253   143  0.91  15.48   1.01     0.98       5092.90|
| 10:  2.3054 -  2.2261  1261   136  0.90  15.85   1.00     0.95       4410.38|
| 11:  2.2261 -  2.1567  1263   142  0.90  15.94   1.00     0.97       4452.20|
| 12:  2.1567 -  2.0953  1228   139  0.91  15.37   1.01     1.00       3894.76|
| 13:  2.0953 -  2.0402  1263   137  0.91  15.38   1.00     0.98       3294.48|
| 14:  2.0402 -  1.9906   990   112  0.92  14.31   0.98     0.94       2526.03|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2526.03 max =        10033.49 mean =      6215.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.44 mean =        13.31|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1557   ksol= 0.32   Bsol= 48.28   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.23,0.96,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121949                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1557   ksol= 0.32   Bsol= 48.28   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.23,0.96,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121949                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1380  153 0.0985 0.1284      5.3775      5.5199|
|  2:  4.7496 -  3.7901 0.99   1312  149 0.0822 0.1120      5.4196      5.6458|
|  3:  3.7901 -  3.3169 0.99   1305  145 0.1018 0.1490      5.4516      5.8337|
|  4:  3.3169 -  3.0164 0.99   1290  136 0.1146 0.1487      5.4132      5.5518|
|  5:  3.0164 -  2.8017 0.99   1268  144 0.1256 0.1676      5.2984      5.5303|
|  6:  2.8017 -  2.6374 0.99   1276  145 0.1132 0.1851      5.1801      5.4678|
|  7:  2.6374 -  2.5060 0.99   1280  142 0.1200 0.1627       5.143      5.3377|
|  8:  2.5060 -  2.3974 0.98   1261  136 0.1122 0.1694      5.0607      5.3614|
|  9:  2.3974 -  2.3054 0.98   1253  143 0.1131 0.1858      5.0238      5.3115|
| 10:  2.3054 -  2.2261 0.99   1261  136 0.1074 0.1689      4.9523      5.2025|
| 11:  2.2261 -  2.1567 0.98   1263  142 0.1082 0.1709      4.9294      5.2262|
| 12:  2.1567 -  2.0953 0.97   1228  139 0.1100 0.1652      4.8656      5.2136|
| 13:  2.0953 -  2.0402 1.00   1263  137 0.1076 0.1652      4.7779      5.0266|
| 14:  2.0402 -  1.9906 0.78    990  112 0.1000 0.1796        4.65      4.9751|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7496  1380   153  0.94   9.16   0.98     0.96       7273.96|
|  2:  4.7496 -  3.7901  1312   149  0.95   7.79   1.02     1.00       8973.16|
|  3:  3.7901 -  3.3169  1305   145  0.94  10.87   1.03     1.02      10038.84|
|  4:  3.3169 -  3.0164  1290   136  0.93  12.81   1.01     1.00       9645.29|
|  5:  3.0164 -  2.8017  1268   144  0.90  15.37   1.00     0.97       7973.78|
|  6:  2.8017 -  2.6374  1276   145  0.90  15.52   0.99     0.96       6851.33|
|  7:  2.6374 -  2.5060  1280   142  0.91  15.41   0.99     0.96       6052.48|
|  8:  2.5060 -  2.3974  1261   136  0.91  14.60   1.00     0.97       5238.10|
|  9:  2.3974 -  2.3054  1253   143  0.91  15.48   1.01     0.98       5093.82|
| 10:  2.3054 -  2.2261  1261   136  0.90  15.85   1.00     0.96       4409.85|
| 11:  2.2261 -  2.1567  1263   142  0.90  15.94   1.00     0.97       4452.06|
| 12:  2.1567 -  2.0953  1228   139  0.91  15.37   1.02     1.00       3894.08|
| 13:  2.0953 -  2.0402  1263   137  0.91  15.38   1.00     0.98       3293.37|
| 14:  2.0402 -  1.9906   990   112  0.92  14.30   0.99     0.95       2524.63|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2524.63 max =        10038.84 mean =      6214.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.44 mean =        13.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.898)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.10    84.74   15.19    None  None   None       |
|    all(noH): 2823   0      4.10    84.74   15.19    None  None   None       |
|    Sol.    : 438    0      4.40    75.90   37.73    None  None   None       |
|    Mac.    : 2385   0      4.10    84.74   11.05    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:     4.096 -  12.160: 1770   |   5:    44.417 -  52.481:   87        |
|      1:    12.160 -  20.225:  489   |   6:    52.481 -  60.545:   63        |
|      2:    20.225 -  28.289:  148   |   7:    60.545 -  68.609:   28        |
|      3:    28.289 -  36.353:  112   |   8:    68.609 -  76.673:   12        |
|      4:    36.353 -  44.417:  111   |   9:    76.673 -  84.737:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.231 - 4.788
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 301
   mapped sites are within: 0.729 - 4.788

peak=   10.166 closest distance to " CG2 VAL A 230 " =    1.260
peak=    6.560 closest distance to " CG  LEU A   5 " =    1.166
peak=    6.002 closest distance to " CG2 VAL A 296 " =    1.057
peak=    5.978 closest distance to " CG  LEU A 228 " =    1.139
peak=    5.891 closest distance to " CB  VAL A 296 " =    1.061
peak=    5.599 closest distance to " NH2 ARG A  56 " =    2.235
peak=    5.460 closest distance to " CB  VAL A 230 " =    1.183
peak=    5.421 closest distance to " CG  PRO A  54 " =    1.235
peak=    5.403 closest distance to " NE2 GLN A  11 " =    1.135
peak=    5.130 closest distance to " CB  GLN A 223 " =    1.480
peak=    5.121 closest distance to " O   HOH Z 142 " =    1.717
peak=    5.116 closest distance to " CD2 LEU A   5 " =    1.137
peak=    5.021 closest distance to " CB  GLN A 183 " =    1.296
peak=    4.923 closest distance to " CB  ARG A 275 " =    0.924
peak=    4.904 closest distance to " O   HOH Z 232 " =    2.384
peak=    4.748 closest distance to " CB  SER A  63 " =    1.221
peak=    4.651 closest distance to " O   HOH Z 126 " =    1.924
peak=    4.614 closest distance to " O   HOH Z 209 " =    2.291
peak=    4.530 closest distance to " O   HOH Z  61 " =    1.696
peak=    4.527 closest distance to " O   HOH Z 427 " =    2.962
peak=    4.508 closest distance to " O   HOH Z 346 " =    1.624
peak=    4.505 closest distance to " CB  PRO A  54 " =    0.928
peak=    4.477 closest distance to " O   HOH Z  43 " =    1.972
peak=    4.415 closest distance to " CB  ARG A  79 " =    1.440
peak=    4.411 closest distance to " C   PRO A 198 " =    1.463
peak=    4.391 closest distance to " O   SER A  87 " =    2.257
peak=    4.377 closest distance to " O   HOH Z  15 " =    2.150
peak=    4.324 closest distance to " CB  GLU A 152 " =    1.209
peak=    4.324 closest distance to " O   HOH Z 423 " =    1.838
peak=    4.301 closest distance to " O   HOH Z 193 " =    1.732
peak=    4.276 closest distance to " CA  TYR A  30 " =    0.961
peak=    4.269 closest distance to " O   HOH Z 272 " =    1.859
peak=    4.226 closest distance to " O   HOH Z 316 " =    3.059
peak=    4.223 closest distance to " OD1 ASN A  69 " =    2.598
peak=    4.223 closest distance to " CG  PRO A 213 " =    1.168
peak=    4.193 closest distance to " O   HOH Z 236 " =    2.013
peak=    4.191 closest distance to " O   HOH Z 158 " =    3.157
peak=    4.185 closest distance to " O   HOH Z 369 " =    2.358
peak=    4.178 closest distance to " O   HOH Z  78 " =    1.692
peak=    4.136 closest distance to " O   HOH Z 265 " =    2.316
peak=    4.106 closest distance to " O   HOH Z 298 " =    1.809
peak=    4.101 closest distance to " CB  ASN A 148 " =    1.374
peak=    4.093 closest distance to " CZ  PHE A 218 " =    1.158
peak=    4.091 closest distance to " O   HOH Z 248 " =    1.594
peak=    4.087 closest distance to " O   HOH Z 403 " =    1.678
peak=    4.079 closest distance to " O   HOH Z 368 " =    2.219
peak=    4.067 closest distance to " O   HOH Z 303 " =    2.064
peak=    4.057 closest distance to " ND2 ASN A 187 " =    1.484
peak=    4.043 closest distance to " CB  ARG A 190 " =    1.647
peak=    3.997 closest distance to " O   HOH Z 234 " =    3.587
peak=    3.995 closest distance to " CB  VAL A 265 " =    1.328
peak=    3.994 closest distance to " O   HOH Z 371 " =    3.063
peak=    3.985 closest distance to " O   HOH Z 203 " =    1.578
peak=    3.976 closest distance to " O   HOH Z 280 " =    2.955
peak=    3.966 closest distance to " CB  GLU A 277 " =    3.592
peak=    3.965 closest distance to " CB  ASP A 140 " =    1.113
peak=    3.921 closest distance to " O   HOH Z 189 " =    2.802
peak=    3.919 closest distance to " O   HOH Z 147 " =    1.778
peak=    3.917 closest distance to " O   HOH Z 402 " =    1.385
peak=    3.908 closest distance to " O   HOH Z 126 " =    2.069
peak=    3.908 closest distance to " OG BSER A 164 " =    2.192
peak=    3.906 closest distance to " CB  TRP A 179 " =    1.354
peak=    3.903 closest distance to " O   HOH Z 411 " =    3.783
peak=    3.884 closest distance to " O   HOH Z 250 " =    1.352
peak=    3.878 closest distance to " O   HOH Z  59 " =    2.076
peak=    3.859 closest distance to " CB  TRP A 266 " =    1.008
peak=    3.851 closest distance to " CB  ALA A   9 " =    1.603
peak=    3.844 closest distance to " O   HOH Z 193 " =    1.980
peak=    3.843 closest distance to " CG  PRO A 243 " =    1.094
peak=    3.834 closest distance to " CG1 ILE A  49 " =    1.489
peak=    3.830 closest distance to " CD2 TRP A 179 " =    1.394
peak=    3.823 closest distance to " CB  SER A   3 " =    1.251
peak=    3.812 closest distance to " CG1BVAL A  72 " =    1.604
peak=    3.808 closest distance to " CB  GLU A 128 " =    1.014
peak=    3.806 closest distance to " O   HOH Z 392 " =    3.088
peak=    3.802 closest distance to " O   HOH Z  97 " =    2.458
peak=    3.799 closest distance to " O   HOH Z 425 " =    2.134
peak=    3.797 closest distance to " CB  VAL A 202 " =    1.559
peak=    3.782 closest distance to " NZ  LYS A 117 " =    3.208
peak=    3.777 closest distance to " O   HOH Z  97 " =    1.973
peak=    3.762 closest distance to " CG  ARG A  66 " =    2.696
peak=    3.741 closest distance to " CD2 LEU A 228 " =    1.099
peak=    3.724 closest distance to " O   HOH Z 313 " =    1.810
peak=    3.723 closest distance to " O   HOH Z 389 " =    1.857
peak=    3.706 closest distance to " O   HOH Z 145 " =    2.197
peak=    3.703 closest distance to " O   HOH Z  19 " =    2.356
peak=    3.702 closest distance to " O   HOH Z 245 " =    1.371
peak=    3.686 closest distance to " O   HOH Z 261 " =    1.901
peak=    3.681 closest distance to " O   HOH Z 325 " =    2.181
peak=    3.681 closest distance to " CA  ALA A  21 " =    1.169
peak=    3.677 closest distance to " CG  MET A 185 " =    1.233
peak=    3.676 closest distance to " O   HOH Z 112 " =    1.695
peak=    3.673 closest distance to " CB  THR A  31 " =    1.625
peak=    3.673 closest distance to " CB  ASN A 142 " =    1.122
peak=    3.670 closest distance to " O   HOH Z 261 " =    1.732
peak=    3.664 closest distance to " O   HOH Z 417 " =    3.323
peak=    3.654 closest distance to " CE1 TYR A 186 " =    1.316
peak=    3.650 closest distance to " CB  ASN A  39 " =    0.921
peak=    3.645 closest distance to " CA  PHE A 283 " =    1.240
peak=    3.641 closest distance to " CB  ARG A 139 " =    0.938
peak=    3.637 closest distance to " CB AVAL A  41 " =    1.090
peak=    3.615 closest distance to " O   HOH Z 214 " =    2.208
peak=    3.610 closest distance to " CG  PRO A 198 " =    1.160
peak=    3.608 closest distance to " O   HOH Z 422 " =    2.589
peak=    3.583 closest distance to " O   HOH Z 145 " =    3.834
peak=    3.583 closest distance to " CA  ALA A 158 " =    1.301
peak=    3.578 closest distance to " O   HOH Z 172 " =    3.540
peak=    3.577 closest distance to " CA  ARG A 195 " =    1.208
peak=    3.575 closest distance to " CA  ASN A 215 " =    1.144
peak=    3.564 closest distance to " O   HOH Z   1 " =    1.949
peak=    3.558 closest distance to " CB  ASN A 148 " =    1.923
peak=    3.554 closest distance to " O   HOH Z 407 " =    2.416
peak=    3.553 closest distance to " CA  ALA A  51 " =    0.914
peak=    3.542 closest distance to " CA  TYR A  30 " =    1.044
peak=    3.539 closest distance to " O   HOH Z 128 " =    2.118
peak=    3.538 closest distance to " O   HOH Z 435 " =    1.934
peak=    3.537 closest distance to " N   ASN A  39 " =    1.281
peak=    3.537 closest distance to " CA  ALA A 291 " =    0.856
peak=    3.526 closest distance to " CA  ARG A  36 " =    1.008
peak=    3.522 closest distance to " N   PHE A 130 " =    1.258
peak=    3.520 closest distance to " CD BLYS A 290 " =    1.108
peak=    3.517 closest distance to " NE2 GLN A  77 " =    3.170
peak=    3.512 closest distance to " O   HOH Z 187 " =    2.273
peak=    3.504 closest distance to " CD1 LEU A 300 " =    1.278
peak=    3.503 closest distance to " O   HOH Z 299 " =    4.219
peak=    3.497 closest distance to " CG2 THR A 221 " =    1.256
peak=    3.497 closest distance to " CB  ASN A 110 " =    1.120
peak=    3.495 closest distance to " O   HOH Z 251 " =    1.517
peak=    3.492 closest distance to " O   HOH Z 273 " =    2.804
peak=    3.492 closest distance to " O   HOH Z 368 " =    3.562
peak=    3.480 closest distance to " O   HOH Z 126 " =    1.568
peak=    3.480 closest distance to " O   HOH Z 285 " =    2.806
peak=    3.470 closest distance to " CA  LYS A 117 " =    1.249
peak=    3.470 closest distance to " CG2 ILE A  20 " =    1.430
peak=    3.470 closest distance to " CG2 VAL A 257 " =    0.817
peak=    3.463 closest distance to " O   HOH Z 345 " =    3.323
peak=    3.461 closest distance to " CB  THR A 157 " =    1.145
peak=    3.459 closest distance to " OG1 THR A 294 " =    2.410
peak=    3.449 closest distance to " CG  MET A 185 " =    1.060
peak=    3.442 closest distance to " O   HOH Z 180 " =    2.109
peak=    3.440 closest distance to " O   HOH Z 193 " =    1.646
peak=    3.438 closest distance to " O   HOH Z  80 " =    1.624
peak=    3.437 closest distance to " NZ  LYS A  48 " =    1.255
peak=    3.430 closest distance to " O   HOH Z 322 " =    2.015
peak=    3.421 closest distance to " O   HOH Z  40 " =    1.690
peak=    3.420 closest distance to " CG1 VAL A 153 " =    0.954
peak=    3.420 closest distance to " O   HOH Z 344 " =    3.003
peak=    3.417 closest distance to " O   GLN A 278 " =    1.270
peak=    3.415 closest distance to " OD2 ASP A 286 " =    2.786
peak=    3.415 closest distance to " NH1AARG A 145 " =    1.148
peak=    3.413 closest distance to " CB  LEU A 228 " =    1.314
peak=    3.410 closest distance to " CB  LEU A 143 " =    1.181
peak=    3.410 closest distance to " CB  GLN A  88 " =    1.181
peak=    3.409 closest distance to " CB  HIS A 108 " =    0.831
peak=    3.407 closest distance to " N   ASP A 162 " =    1.241
peak=    3.404 closest distance to " O   HOH Z 426 " =    1.591
peak=    3.399 closest distance to " CA  SER A 146 " =    1.775
peak=    3.399 closest distance to " O   HOH Z 359 " =    3.760
peak=    3.396 closest distance to " CE  LYS A  76 " =    0.879
peak=    3.395 closest distance to " O   MET A 105 " =    1.861
peak=    3.391 closest distance to " CB  SER A  26 " =    1.756
peak=    3.390 closest distance to " O   ASP A 124 " =    1.135
peak=    3.390 closest distance to " CG  LEU A 167 " =    1.257
peak=    3.388 closest distance to " NH2 ARG A 156 " =    1.106
peak=    3.385 closest distance to " CD  LYS A 119 " =    1.531
peak=    3.383 closest distance to " CD  LYS A 166 " =    1.315
peak=    3.369 closest distance to " O   HOH Z 148 " =    3.349
peak=    3.365 closest distance to " O   HOH Z 403 " =    1.388
peak=    3.362 closest distance to " O   HOH Z  88 " =    3.002
peak=    3.360 closest distance to " CD2 LEU A 297 " =    0.945
peak=    3.357 closest distance to " O   HOH Z 128 " =    2.172
peak=    3.356 closest distance to " O   HOH Z 305 " =    3.651
peak=    3.355 closest distance to " O   HOH Z  66 " =    2.201
peak=    3.352 closest distance to " O  BHOH Z 338 " =    2.430
peak=    3.352 closest distance to " O   HOH Z 175 " =    2.122
peak=    3.349 closest distance to " CB  GLN A  89 " =    1.263
peak=    3.347 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.346 closest distance to " O   HOH Z 291 " =    1.542
peak=    3.345 closest distance to " O   HOH Z  10 " =    1.769
peak=    3.341 closest distance to " CD1 LEU A 228 " =    1.956
peak=    3.341 closest distance to " O   HOH Z 302 " =    1.994
peak=    3.340 closest distance to " CB  SER A 212 " =    1.129
peak=    3.335 closest distance to " CB  TRP A 150 " =    1.365
peak=    3.327 closest distance to " CG2 ILE A 120 " =    1.229
peak=    3.322 closest distance to " CB  GLU A  46 " =    1.062
peak=    3.319 closest distance to " O   HOH Z 337 " =    3.546
peak=    3.317 closest distance to " O   HOH Z 130 " =    2.258
peak=    3.315 closest distance to " CA  TYR A 116 " =    1.381
peak=    3.315 closest distance to " CG1 VAL A 296 " =    1.211
peak=    3.313 closest distance to " O   ARG A  56 " =    2.849
peak=    3.309 closest distance to " O   HOH Z 286 " =    2.390
peak=    3.304 closest distance to " OG  SER A  22 " =    2.740
peak=    3.304 closest distance to " CG BARG A 275 " =    1.347
peak=    3.303 closest distance to " O   HOH Z  48 " =    1.591
peak=    3.302 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.302 closest distance to " O   HOH Z 406 " =    1.489
peak=    3.300 closest distance to " N   SER A 135 " =    1.344
peak=    3.297 closest distance to " O   HOH Z 282 " =    1.964
peak=    3.290 closest distance to " CB  ALA A 291 " =    1.400
peak=    3.289 closest distance to " CB  ASN A 224 " =    1.015
peak=    3.285 closest distance to " CE  LYS A  48 " =    1.100
peak=    3.279 closest distance to " CA  THR A 264 " =    0.754
peak=    3.279 closest distance to " O   HOH Z 365 " =    2.973
peak=    3.278 closest distance to " CA  GLY A 267 " =    0.729
peak=    3.276 closest distance to " O   HOH Z 171 " =    2.194
peak=    3.274 closest distance to " N   VAL A 126 " =    1.402
peak=    3.274 closest distance to " CB  ILE A  20 " =    1.514
peak=    3.273 closest distance to " O   HOH Z  85 " =    2.098
peak=    3.272 closest distance to " O   HOH Z 421 " =    1.736
peak=    3.271 closest distance to " O   HOH Z  35 " =    2.474
peak=    3.271 closest distance to " CA  ALA A 233 " =    1.301
peak=    3.270 closest distance to " O   HOH Z 353 " =    2.696
peak=    3.267 closest distance to " O   HOH Z  44 " =    1.656
peak=    3.265 closest distance to " CG1 ILE A  33 " =    1.243
peak=    3.264 closest distance to " O   TRP A 274 " =    1.860
peak=    3.264 closest distance to " O   HOH Z 133 " =    2.427
peak=    3.262 closest distance to " CA  ASP A 162 " =    1.050
peak=    3.259 closest distance to " O   HOH Z   9 " =    2.052
peak=    3.259 closest distance to " CB  VAL A 268 " =    0.809
peak=    3.258 closest distance to " ND1 HIS A  81 " =    1.738
peak=    3.258 closest distance to " CA  VAL A  41 " =    0.794
peak=    3.254 closest distance to " OE1 GLU A   2 " =    2.056
peak=    3.253 closest distance to " O   HOH Z 250 " =    1.363
peak=    3.251 closest distance to " O   HOH Z 425 " =    1.290
peak=    3.248 closest distance to " NZ  LYS A  76 " =    1.538
peak=    3.247 closest distance to " O   HOH Z  21 " =    1.708
peak=    3.246 closest distance to " N   ASN A 127 " =    1.277
peak=    3.243 closest distance to " O   HOH Z 185 " =    1.785
peak=    3.243 closest distance to " O   HOH Z 298 " =    2.671
peak=    3.242 closest distance to " CD1 ILE A  33 " =    1.673
peak=    3.241 closest distance to " CG  GLN A  88 " =    1.071
peak=    3.240 closest distance to " CA  MET A 105 " =    0.967
peak=    3.233 closest distance to " O   HOH Z 329 " =    4.057
peak=    3.232 closest distance to " O   HOH Z 213 " =    1.711
peak=    3.228 closest distance to " O   HOH Z 234 " =    1.837
peak=    3.227 closest distance to " CA  THR A 221 " =    0.982
peak=    3.227 closest distance to " O   HOH Z  85 " =    1.245
peak=    3.212 closest distance to " OE2 GLU A  53 " =    1.964
peak=    3.210 closest distance to " O   HOH Z 132 " =    2.636
peak=    3.207 closest distance to " O   HOH Z 263 " =    1.651
peak=    3.207 closest distance to " O   HOH Z 313 " =    1.583
peak=    3.204 closest distance to " CB  THR A  52 " =    1.042
peak=    3.203 closest distance to " CG AARG A 275 " =    1.126
peak=    3.202 closest distance to " O   HOH Z  40 " =    2.367
peak=    3.195 closest distance to " O   HOH Z 409 " =    3.302
peak=    3.195 closest distance to " CZ3 TRP A  85 " =    0.921
peak=    3.194 closest distance to " O   HOH Z   1 " =    4.773
peak=    3.188 closest distance to " O   HOH Z 423 " =    3.021
peak=    3.187 closest distance to " O   SER A 164 " =    1.118
peak=    3.182 closest distance to " CG2 THR A 294 " =    1.704
peak=    3.181 closest distance to " O   HOH Z 189 " =    2.681
peak=    3.178 closest distance to " CB  GLN A 205 " =    1.135
peak=    3.176 closest distance to " CB  LYS A 117 " =    1.186
peak=    3.176 closest distance to " CB  ALA A 248 " =    1.023
peak=    3.167 closest distance to " CA  ALA A  84 " =    1.379
peak=    3.165 closest distance to " OG BSER A 134 " =    3.128
peak=    3.164 closest distance to " O   HOH Z 359 " =    1.297
peak=    3.160 closest distance to " CD2 HIS A  81 " =    0.855
peak=    3.156 closest distance to " NE2 HIS A 207 " =    1.371
peak=    3.154 closest distance to " CB  ALA A 248 " =    1.534
peak=    3.154 closest distance to " CA  ASN A 176 " =    1.144
peak=    3.151 closest distance to " O   HOH Z 109 " =    2.536
peak=    3.142 closest distance to " O   HOH Z 128 " =    1.923
peak=    3.139 closest distance to " CB  ALA A 295 " =    1.284
peak=    3.135 closest distance to " ND2 ASN A 110 " =    1.577
peak=    3.135 closest distance to " O   HOH Z 227 " =    2.126
peak=    3.132 closest distance to " CD1 ILE A 106 " =    1.020
peak=    3.131 closest distance to " CG  GLN A  77 " =    2.196
peak=    3.128 closest distance to " CA  LEU A 282 " =    1.090
peak=    3.127 closest distance to " CA  GLY A 211 " =    1.322
peak=    3.124 closest distance to " O   ALA A 158 " =    1.342
peak=    3.120 closest distance to " CB  MET A  47 " =    1.125
peak=    3.116 closest distance to " O   HOH Z 371 " =    3.280
peak=    3.116 closest distance to " O   HOH Z  88 " =    2.556
peak=    3.114 closest distance to " O   HOH Z 336 " =    1.732
peak=    3.109 closest distance to " O   HOH Z 116 " =    1.725
peak=    3.103 closest distance to " CA  ILE A 106 " =    0.733
peak=    3.103 closest distance to " O   HOH Z 357 " =    1.856
peak=    3.089 closest distance to " CB  GLN A 278 " =    0.865
peak=    3.088 closest distance to " O   HOH Z 222 " =    2.513
peak=    3.087 closest distance to " CB  LYS A 290 " =    1.134
peak=    3.087 closest distance to " CB  ALA A   1 " =    4.788
peak=    3.083 closest distance to " CB  LEU A 255 " =    0.785
peak=    3.083 closest distance to " O   HOH Z 141 " =    1.578
peak=    3.078 closest distance to " CD1 PHE A 204 " =    1.376
peak=    3.074 closest distance to " OE2 GLU A   2 " =    1.792
peak=    3.069 closest distance to " CB  TYR A 116 " =    0.841
peak=    3.054 closest distance to " CA  ASN A 127 " =    1.016
peak=    3.042 closest distance to " O   HOH Z 218 " =    2.482
peak=    3.033 closest distance to " CB  SER A 216 " =    0.796
peak=    3.030 closest distance to " CA  ARG A 102 " =    1.129
peak=    3.013 closest distance to " O   HOH Z 391 " =    2.934

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.803 - 5.494
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.803 - 5.494

peak=   -5.456 closest distance to " CG2 VAL A 230 " =    0.803
peak=   -4.628 closest distance to " SG  CYS A 254 " =    3.344
peak=   -4.594 closest distance to " CD  ARG A 156 " =    2.028
peak=   -4.581 closest distance to " CB  PRO A 243 " =    2.658
peak=   -4.434 closest distance to " OG BSER A 134 " =    1.243
peak=   -4.432 closest distance to " O   HOH Z 266 " =    5.201
peak=   -4.307 closest distance to " C   HIS A 108 " =    1.188
peak=   -4.290 closest distance to " CD  GLN A  58 " =    1.102
peak=   -4.233 closest distance to " CG  GLN A 223 " =    2.084
peak=   -4.117 closest distance to " CG2BVAL A  41 " =    2.649
peak=   -4.115 closest distance to " CB  PHE A 192 " =    1.926
peak=   -4.061 closest distance to " O   PRO A 163 " =    2.133
peak=   -4.056 closest distance to " O   HOH Z 114 " =    3.097
peak=   -4.043 closest distance to " O   VAL A  67 " =    2.838
peak=   -4.016 closest distance to " O   HOH Z 231 " =    2.102
peak=   -3.994 closest distance to " OXT GLY A 302 " =    2.785
peak=   -3.992 closest distance to " CD1 ILE A 199 " =    2.481
peak=   -3.965 closest distance to " CB  ALA A 161 " =    2.589
peak=   -3.962 closest distance to " CG2 VAL A 296 " =    1.226
peak=   -3.947 closest distance to " CG1 VAL A 112 " =    2.744
peak=   -3.867 closest distance to " O   HOH Z 196 " =    2.163
peak=   -3.858 closest distance to " O   HOH Z 351 " =    1.524
peak=   -3.840 closest distance to " O   HOH Z 166 " =    1.922
peak=   -3.826 closest distance to " NE2 GLN A  88 " =    1.866
peak=   -3.817 closest distance to " N   ALA A  43 " =    2.609
peak=   -3.811 closest distance to " CE  MET A 105 " =    2.331
peak=   -3.806 closest distance to " CB  ALA A 291 " =    2.315
peak=   -3.804 closest distance to " O   HOH Z 389 " =    1.951
peak=   -3.770 closest distance to " CA  ASP A 298 " =    1.050
peak=   -3.759 closest distance to " ND2 ASN A  45 " =    1.197
peak=   -3.745 closest distance to " CB  ALA A 248 " =    2.315
peak=   -3.738 closest distance to " CB  ALA A  43 " =    2.463
peak=   -3.730 closest distance to " C   ILE A 239 " =    2.199
peak=   -3.728 closest distance to " ND2 ASN A 187 " =    1.502
peak=   -3.726 closest distance to " O   HOH Z  44 " =    2.262
peak=   -3.709 closest distance to " O   HOH Z 290 " =    1.273
peak=   -3.708 closest distance to " CB  ASP A 171 " =    2.249
peak=   -3.695 closest distance to " O   HOH Z 435 " =    2.773
peak=   -3.694 closest distance to " OD1 ASN A 187 " =    1.624
peak=   -3.692 closest distance to " CE2 TYR A  30 " =    2.717
peak=   -3.677 closest distance to " CZ3 TRP A 179 " =    1.197
peak=   -3.677 closest distance to " CG1 VAL A 250 " =    2.729
peak=   -3.652 closest distance to " N   ALA A 248 " =    1.753
peak=   -3.651 closest distance to " O   HOH Z 166 " =    1.539
peak=   -3.647 closest distance to " CD1 LEU A 101 " =    2.343
peak=   -3.645 closest distance to " CB  PRO A 163 " =    2.503
peak=   -3.629 closest distance to " O   HOH Z 185 " =    2.439
peak=   -3.622 closest distance to " O   HOH Z 394 " =    1.536
peak=   -3.619 closest distance to " O   HOH Z 211 " =    1.580
peak=   -3.609 closest distance to " CE2 PHE A 218 " =    2.517
peak=   -3.606 closest distance to " CB  ASP A 132 " =    2.374
peak=   -3.599 closest distance to " CB  ASP A 132 " =    2.317
peak=   -3.595 closest distance to " O   HOH Z 429 " =    2.035
peak=   -3.591 closest distance to " N   THR A 157 " =    1.471
peak=   -3.590 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -3.576 closest distance to " O   HOH Z  11 " =    1.812
peak=   -3.571 closest distance to " NH2AARG A 275 " =    5.126
peak=   -3.569 closest distance to " OG  SER A  97 " =    2.275
peak=   -3.568 closest distance to " O   HOH Z 198 " =    2.173
peak=   -3.561 closest distance to " CZ  PHE A  59 " =    1.529
peak=   -3.532 closest distance to " N   ALA A 226 " =    2.058
peak=   -3.528 closest distance to " ND2 ASN A  45 " =    1.656
peak=   -3.518 closest distance to " CE BMET A  47 " =    1.521
peak=   -3.512 closest distance to " O   PRO A 198 " =    1.251
peak=   -3.510 closest distance to " N   THR A 235 " =    1.339
peak=   -3.508 closest distance to " O   HOH Z 407 " =    3.007
peak=   -3.508 closest distance to " N   GLN A  58 " =    1.617
peak=   -3.499 closest distance to " OD1 ASN A 148 " =    1.482
peak=   -3.498 closest distance to " CG  TRP A 266 " =    1.862
peak=   -3.498 closest distance to " CD  LYS A 289 " =    2.432
peak=   -3.495 closest distance to " CB  ALA A 291 " =    2.157
peak=   -3.495 closest distance to " O   VAL A 189 " =    2.609
peak=   -3.481 closest distance to " O   HOH Z 139 " =    3.129
peak=   -3.478 closest distance to " O   PHE A 218 " =    1.673
peak=   -3.474 closest distance to " O   HOH Z 103 " =    1.797
peak=   -3.463 closest distance to " O   HOH Z 295 " =    1.600
peak=   -3.460 closest distance to " CA  GLY A 241 " =    3.109
peak=   -3.451 closest distance to " CG  ASP A 231 " =    0.807
peak=   -3.444 closest distance to " O   HOH Z 102 " =    1.587
peak=   -3.443 closest distance to " O   HOH Z  52 " =    1.460
peak=   -3.440 closest distance to " NH2 ARG A  79 " =    1.992
peak=   -3.437 closest distance to " N   SER A 276 " =    1.344
peak=   -3.431 closest distance to " O   HOH Z  13 " =    1.723
peak=   -3.431 closest distance to " CZ  TYR A 169 " =    1.704
peak=   -3.428 closest distance to " N   HIS A 115 " =    2.093
peak=   -3.427 closest distance to " C   ASN A 187 " =    1.872
peak=   -3.422 closest distance to " CD  ARG A 139 " =    1.620
peak=   -3.421 closest distance to " O   HOH Z 313 " =    1.647
peak=   -3.402 closest distance to " CE3 TRP A 150 " =    2.125
peak=   -3.397 closest distance to " CG2 ILE A 263 " =    2.279
peak=   -3.386 closest distance to " CG1 VAL A 230 " =    1.854
peak=   -3.378 closest distance to " CG1 VAL A 197 " =    2.247
peak=   -3.373 closest distance to " ND2 ASN A 249 " =    2.347
peak=   -3.371 closest distance to " O   HOH Z 353 " =    2.136
peak=   -3.368 closest distance to " N   ASP A 171 " =    2.264
peak=   -3.363 closest distance to " O   MET A  40 " =    2.767
peak=   -3.362 closest distance to " O   HOH Z 369 " =    2.233
peak=   -3.351 closest distance to " O   HOH Z  73 " =    2.197
peak=   -3.349 closest distance to " O   HOH Z  88 " =    4.507
peak=   -3.342 closest distance to " O   HOH Z 243 " =    1.927
peak=   -3.340 closest distance to " CD1 LEU A 101 " =    2.688
peak=   -3.339 closest distance to " CB  GLN A  11 " =    1.903
peak=   -3.336 closest distance to " CD1 PHE A  59 " =    1.973
peak=   -3.334 closest distance to " NE2 GLN A 278 " =    1.896
peak=   -3.333 closest distance to " C   PHE A  59 " =    1.355
peak=   -3.333 closest distance to " CD2 LEU A 167 " =    1.766
peak=   -3.329 closest distance to " O   HOH Z 134 " =    3.112
peak=   -3.323 closest distance to " OG  SER A  62 " =    1.630
peak=   -3.321 closest distance to " C   MET A 188 " =    1.452
peak=   -3.319 closest distance to " O   SER A 271 " =    2.115
peak=   -3.318 closest distance to " CD2 LEU A 300 " =    2.667
peak=   -3.314 closest distance to " C   LEU A 143 " =    1.011
peak=   -3.313 closest distance to " CB  ASN A  39 " =    2.313
peak=   -3.312 closest distance to " C   ASP A 231 " =    2.422
peak=   -3.312 closest distance to " CD1 LEU A 228 " =    2.120
peak=   -3.309 closest distance to " O   HOH Z  43 " =    1.760
peak=   -3.306 closest distance to " O   HOH Z 313 " =    1.135
peak=   -3.302 closest distance to " CA  GLY A 203 " =    2.413
peak=   -3.302 closest distance to " NE2 GLN A 194 " =    1.766
peak=   -3.297 closest distance to " O   HOH Z 262 " =    2.848
peak=   -3.295 closest distance to " O   HOH Z 191 " =    5.494
peak=   -3.294 closest distance to " O   HOH Z 253 " =    3.833
peak=   -3.286 closest distance to " CB  VAL A 230 " =    1.007
peak=   -3.283 closest distance to " O   ALA A  10 " =    1.752
peak=   -3.282 closest distance to " O   HOH Z 123 " =    2.409
peak=   -3.281 closest distance to " CD2 TYR A 247 " =    2.311
peak=   -3.279 closest distance to " O   HOH Z   6 " =    1.627
peak=   -3.279 closest distance to " CD2 TYR A 293 " =    2.052
peak=   -3.276 closest distance to " C   ALA A 158 " =    1.270
peak=   -3.266 closest distance to " NZ  LYS A 119 " =    3.557
peak=   -3.264 closest distance to " CG  ARG A 269 " =    2.312
peak=   -3.260 closest distance to " O   HOH Z 311 " =    3.788
peak=   -3.260 closest distance to " OD2 ASP A  50 " =    2.278
peak=   -3.259 closest distance to " CB  VAL A 296 " =    1.045
peak=   -3.259 closest distance to " O   HOH Z 367 " =    2.594
peak=   -3.259 closest distance to " OG ASER A 134 " =    1.240
peak=   -3.257 closest distance to " O   HOH Z 411 " =    3.872
peak=   -3.257 closest distance to " O   HOH Z  38 " =    1.631
peak=   -3.253 closest distance to " CA  ASN A 127 " =    1.277
peak=   -3.252 closest distance to " CG  GLU A 277 " =    1.184
peak=   -3.248 closest distance to " O   HOH Z 136 " =    2.263
peak=   -3.247 closest distance to " OG  SER A  26 " =    1.217
peak=   -3.241 closest distance to " O   HOH Z 174 " =    2.416
peak=   -3.238 closest distance to " CA  GLY A 133 " =    1.975
peak=   -3.237 closest distance to " CG  PHE A 283 " =    2.641
peak=   -3.233 closest distance to " CG1 VAL A  67 " =    3.025
peak=   -3.232 closest distance to " O   SER A 276 " =    1.624
peak=   -3.231 closest distance to " O   HOH Z 426 " =    1.714
peak=   -3.230 closest distance to " CA  PRO A 243 " =    2.257
peak=   -3.229 closest distance to " O   ALA A 161 " =    1.752
peak=   -3.228 closest distance to " CG  PRO A 163 " =    2.647
peak=   -3.228 closest distance to " O   PRO A 198 " =    1.363
peak=   -3.224 closest distance to " CB  TYR A  15 " =    2.229
peak=   -3.218 closest distance to " CB  ASN A  69 " =    1.156
peak=   -3.215 closest distance to " CA  GLY A  98 " =    1.906
peak=   -3.215 closest distance to " OG BSER A 134 " =    1.720
peak=   -3.212 closest distance to " O   SER A 210 " =    1.867
peak=   -3.210 closest distance to " CA  GLY A 133 " =    2.297
peak=   -3.206 closest distance to " O   ALA A  51 " =    1.327
peak=   -3.204 closest distance to " O   SER A  95 " =    1.571
peak=   -3.203 closest distance to " CG  LEU A 228 " =    1.042
peak=   -3.199 closest distance to " O   HOH Z 265 " =    1.560
peak=   -3.196 closest distance to " CD  PRO A 213 " =    2.191
peak=   -3.196 closest distance to " O   GLY A 196 " =    1.164
peak=   -3.195 closest distance to " O   HOH Z 350 " =    1.851
peak=   -3.193 closest distance to " CG1 VAL A 296 " =    1.346
peak=   -3.191 closest distance to " O   SER A 135 " =    1.453
peak=   -3.184 closest distance to " O   HOH Z  10 " =    1.415
peak=   -3.184 closest distance to " CB  ASN A 252 " =    1.793
peak=   -3.180 closest distance to " O   HOH Z 339 " =    1.764
peak=   -3.178 closest distance to " OD2 ASP A 191 " =    1.424
peak=   -3.177 closest distance to " N   GLN A  77 " =    1.683
peak=   -3.176 closest distance to " O   SER A  22 " =    2.266
peak=   -3.173 closest distance to " CB  LEU A  83 " =    2.342
peak=   -3.173 closest distance to " O   HOH Z 385 " =    2.146
peak=   -3.161 closest distance to " O   HOH Z 165 " =    1.922
peak=   -3.161 closest distance to " O   HOH Z 175 " =    4.266
peak=   -3.158 closest distance to " O   HOH Z 281 " =    2.717
peak=   -3.152 closest distance to " O   LYS A 117 " =    1.691
peak=   -3.137 closest distance to " O   GLY A  75 " =    1.848
peak=   -3.132 closest distance to " O   HOH Z 200 " =    4.527
peak=   -3.131 closest distance to " OE2 GLU A 152 " =    1.299
peak=   -3.122 closest distance to " O   HOH Z 193 " =    1.635
peak=   -3.116 closest distance to " O   GLN A 240 " =    2.346
peak=   -3.113 closest distance to " ND2 ASN A  60 " =    1.379
peak=   -3.107 closest distance to " CZ2 TRP A 274 " =    0.956
peak=   -3.102 closest distance to " O   HOH Z 389 " =    4.939
peak=   -3.097 closest distance to " ND2 ASN A 252 " =    1.887
peak=   -3.085 closest distance to " O   GLN A 240 " =    2.131
peak=   -3.081 closest distance to " CE1 HIS A  81 " =    1.423
peak=   -3.066 closest distance to " CA  SER A  62 " =    2.610
peak=   -3.059 closest distance to " CE1 TYR A 247 " =    2.707
peak=   -3.054 closest distance to " O   HOH Z 216 " =    1.718

================= 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    :  0.4095 0.3968   6.193722e+00   6.159574e+00
   1_bss:  0.4023 0.3840   6.188624e+00   6.141257e+00
   1_xyz:  0.2845 0.3009   5.920716e+00   5.961483e+00
   1_adp:  0.2057 0.2329   5.618086e+00   5.738040e+00
   1_occ:  0.2050 0.2331   5.615951e+00   5.738444e+00
   2_bss:  0.1985 0.2269   5.612929e+00   5.732162e+00
   2_xyz:  0.1397 0.1733   5.299027e+00   5.478249e+00
   2_adp:  0.1298 0.1659   5.238276e+00   5.431398e+00
   2_occ:  0.1297 0.1658   5.238121e+00   5.431637e+00
   3_bss:  0.1296 0.1663   5.238448e+00   5.431489e+00
   3_xyz:  0.1139 0.1559   5.147299e+00   5.380855e+00
   3_adp:  0.1103 0.1548   5.130030e+00   5.374966e+00
   3_occ:  0.1103 0.1548   5.130135e+00   5.375260e+00
   4_bss:  0.1103 0.1548   5.129840e+00   5.374983e+00
   4_xyz:  0.1114 0.1555   5.138918e+00   5.381591e+00
   4_adp:  0.1115 0.1553   5.139346e+00   5.382139e+00
   4_occ:  0.1114 0.1554   5.138774e+00   5.381911e+00
   5_bss:  0.1114 0.1554   5.138725e+00   5.381887e+00
   5_xyz:  0.1078 0.1548   5.120682e+00   5.376921e+00
   5_adp:  0.1073 0.1557   5.122115e+00   5.381946e+00
   5_occ:  0.1073 0.1557   5.121971e+00   5.381771e+00
   5_bss:  0.1072 0.1557   5.121949e+00   5.381715e+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:  0.349  20.002   7.328   8.172   8.852   0.000   0.000   0.000
   1_xyz:  0.349  20.002   7.328   8.172   8.852   0.000   0.000   0.000
   1_adp:  0.349  20.002   7.328   8.172   8.852   0.000   0.000   0.000
   1_occ:  0.349  20.002   7.328   8.172   8.852   0.000   0.000   0.000
   2_bss:  0.337  39.898   3.785   4.368   5.589   0.000   0.000   0.000
   2_xyz:  0.337  39.898   3.785   4.368   5.589   0.000   0.000   0.000
   2_adp:  0.337  39.898   3.785   4.368   5.589   0.000   0.000   0.000
   2_occ:  0.337  39.898   3.785   4.368   5.589   0.000   0.000   0.000
   3_bss:  0.331  44.182   3.198   3.780   4.947   0.000   0.000   0.000
   3_xyz:  0.331  44.182   3.198   3.780   4.947   0.000   0.000   0.000
   3_adp:  0.331  44.182   3.198   3.780   4.947   0.000   0.000   0.000
   3_occ:  0.331  44.182   3.198   3.780   4.947   0.000   0.000   0.000
   4_bss:  0.325  44.182   3.198   3.780   4.947   0.000   0.000   0.000
   4_xyz:  0.325  44.182   3.198   3.780   4.947   0.000   0.000   0.000
   4_adp:  0.325  44.182   3.198   3.780   4.947   0.000   0.000   0.000
   4_occ:  0.325  44.182   3.198   3.780   4.947   0.000   0.000   0.000
   5_bss:  0.324  44.182   3.222   3.766   4.934   0.000   0.000   0.000
   5_xyz:  0.324  44.182   3.222   3.766   4.934   0.000   0.000   0.000
   5_adp:  0.324  44.182   3.222   3.766   4.934   0.000   0.000   0.000
   5_occ:  0.324  44.182   3.222   3.766   4.934   0.000   0.000   0.000
   5_bss:  0.322  48.279  -0.737  -0.225   0.962  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.133 0.6197  0.6808    43940.057
   1_bss:  41.854 0.6210  0.8726    41278.806
   1_xyz:  31.356 0.7421  1.0059    23834.496
   1_adp:  22.235 0.8407  1.0850    13415.787
   1_occ:  22.217 0.8409  1.0845    13409.005
   2_bss:  21.996 0.8430  0.9556    13163.860
   2_xyz:  16.020 0.8979  0.9939     7622.292
   2_adp:  14.906 0.9076  1.0010     6990.525
   2_occ:  14.915 0.9075  1.0008     6987.519
   3_bss:  14.910 0.9076  0.9780     6989.240
   3_xyz:  13.813 0.9165  0.9811     6245.490
   3_adp:  13.685 0.9177  0.9793     6143.017
   3_occ:  13.690 0.9176  0.9792     6144.762
   4_bss:  13.684 0.9176  0.9792     6138.401
   4_xyz:  13.734 0.9175  0.9782     6225.788
   4_adp:  13.744 0.9174  0.9760     6223.361
   4_occ:  13.739 0.9174  0.9759     6221.833
   5_bss:  13.737 0.9174  0.9759     6221.499
   5_xyz:  13.644 0.9181  0.9770     6175.060
   5_adp:  13.737 0.9174  0.9740     6217.431
   5_occ:  13.735 0.9174  0.9739     6214.902
   5_bss:  13.735 0.9174  0.9783     6214.355
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3731e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3731e+01
   1_xyz:   1.422  0.010  0.098 17.705  0.006  4.122   1.0531e-01
   1_adp:   1.422  0.010  0.098 17.705  0.006  4.122   1.0531e-01
   1_occ:   1.422  0.010  0.098 17.705  0.006  4.122   1.0531e-01
   2_bss:   1.422  0.010  0.098 17.705  0.006  4.122   1.0531e-01
   2_xyz:   0.994  0.007  0.076 15.914  0.004  4.124   6.1248e-02
   2_adp:   0.994  0.007  0.076 15.914  0.004  4.124   6.1248e-02
   2_occ:   0.994  0.007  0.076 15.914  0.004  4.124   6.1248e-02
   3_bss:   0.994  0.007  0.076 15.914  0.004  4.124   6.1248e-02
   3_xyz:   1.108  0.009  0.093 15.844  0.004  4.122   7.4965e-02
   3_adp:   1.108  0.009  0.093 15.844  0.004  4.122   7.4965e-02
   3_occ:   1.108  0.009  0.093 15.844  0.004  4.122   7.4965e-02
   4_bss:   1.108  0.009  0.093 15.844  0.004  4.122   7.4965e-02
   4_xyz:   0.981  0.007  0.081 15.493  0.004  4.118   6.0243e-02
   4_adp:   0.981  0.007  0.081 15.493  0.004  4.118   6.0243e-02
   4_occ:   0.981  0.007  0.081 15.493  0.004  4.118   6.0243e-02
   5_bss:   0.981  0.007  0.081 15.493  0.004  4.118   6.0243e-02
   5_xyz:   1.116  0.010  0.094 15.723  0.004  4.120   7.5555e-02
   5_adp:   1.116  0.010  0.094 15.723  0.004  4.120   7.5555e-02
   5_occ:   1.116  0.010  0.094 15.723  0.004  4.120   7.5555e-02
   5_bss:   1.116  0.010  0.094 15.723  0.004  4.120   7.5555e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9667e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9667e+00
   1_xyz:  11.127  0.121  0.422 88.288  0.034  2.245   7.6510e-02
   1_adp:  11.127  0.121  0.422 88.288  0.034  2.245   7.6510e-02
   1_occ:  11.127  0.121  0.422 88.288  0.034  2.245   7.6510e-02
   2_bss:  11.127  0.121  0.422 88.288  0.034  2.245   7.6510e-02
   2_xyz:   6.529  0.053  0.438 84.340  0.034  2.273   4.4702e-02
   2_adp:   6.529  0.053  0.438 84.340  0.034  2.273   4.4702e-02
   2_occ:   6.529  0.053  0.438 84.340  0.034  2.273   4.4702e-02
   3_bss:   6.529  0.053  0.438 84.340  0.034  2.273   4.4702e-02
   3_xyz:   6.974  0.051  0.676 83.797  0.038  2.303   6.1960e-02
   3_adp:   6.974  0.051  0.676 83.797  0.038  2.303   6.1960e-02
   3_occ:   6.974  0.051  0.676 83.797  0.038  2.303   6.1960e-02
   4_bss:   6.974  0.051  0.676 83.797  0.038  2.303   6.1960e-02
   4_xyz:   6.494  0.047  0.546 82.900  0.038  2.367   3.9451e-02
   4_adp:   6.494  0.047  0.546 82.900  0.038  2.367   3.9451e-02
   4_occ:   6.494  0.047  0.546 82.900  0.038  2.367   3.9451e-02
   5_bss:   6.494  0.047  0.546 82.900  0.038  2.367   3.9451e-02
   5_xyz:   7.091  0.054  0.707 83.044  0.040  2.274   5.8640e-02
   5_adp:   7.091  0.054  0.707 83.044  0.040  2.274   5.8640e-02
   5_occ:   7.091  0.054  0.707 83.044  0.040  2.274   5.8640e-02
   5_bss:   7.091  0.054  0.707 83.044  0.040  2.274   5.8640e-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:  56.41   0.00  10.12  56.41   0.00   6.91  53.44   0.00  27.62
   1_occ:  56.41   0.00  10.12  56.41   0.00   6.91  53.44   0.00  27.62
   2_bss:  56.41   0.00  10.12  56.41   0.00   6.91  53.44   0.00  27.62
   2_xyz:  56.41   0.00  10.12  56.41   0.00   6.91  53.44   0.00  27.62
   2_adp:  58.94   0.00  10.43  58.94   0.00   6.82  55.55   0.92  30.10
   2_occ:  58.94   0.00  10.43  58.94   0.00   6.82  55.55   0.92  30.10
   3_bss:  58.94   0.00  10.43  58.94   0.00   6.82  55.55   0.92  30.10
   3_xyz:  58.94   0.00  10.43  58.94   0.00   6.82  55.55   0.92  30.10
   3_adp:  70.44   0.00  10.97  70.44   0.00   6.94  65.05   0.26  32.92
   3_occ:  70.44   0.00  10.97  70.44   0.00   6.94  65.05   0.26  32.92
   4_bss:  70.44   0.00  10.97  70.44   0.00   6.94  65.05   0.26  32.92
   4_xyz:  70.44   0.00  10.97  70.44   0.00   6.94  65.05   0.26  32.92
   4_adp:  71.50   0.00  10.95  71.50   0.00   6.93  65.30   0.50  32.81
   4_occ:  71.50   0.00  10.95  71.50   0.00   6.93  65.30   0.50  32.81
   5_bss:  71.50   0.00  10.95  71.50   0.00   6.93  65.30   0.50  32.81
   5_xyz:  71.50   0.00  10.95  71.50   0.00   6.93  65.30   0.50  32.81
   5_adp:  80.64   0.00  11.10  80.64   0.00   6.96  71.80   0.30  33.64
   5_occ:  80.64   0.00  11.10  80.64   0.00   6.96  71.80   0.30  33.64
   5_bss:  84.74   4.10  15.19  84.74   4.10  11.05  75.90   4.40  37.73
------------------------------------------------------------------------
 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:    1.175    0.018    0.395
   1_adp:    1.175    0.018    0.395
   1_occ:    1.175    0.018    0.395
   2_bss:    1.175    0.018    0.395
   2_xyz:    1.401    0.015    0.465
   2_adp:    1.401    0.015    0.465
   2_occ:    1.401    0.015    0.465
   3_bss:    1.401    0.015    0.465
   3_xyz:    1.297    0.029    0.490
   3_adp:    1.297    0.029    0.490
   3_occ:    1.297    0.029    0.490
   4_bss:    1.297    0.029    0.490
   4_xyz:    1.409    0.031    0.493
   4_adp:    1.409    0.031    0.493
   4_occ:    1.409    0.031    0.493
   5_bss:    1.409    0.031    0.493
   5_xyz:    1.434    0.022    0.497
   5_adp:    1.434    0.022    0.497
   5_occ:    1.434    0.022    0.497
   5_bss:    1.434    0.022    0.497
------------------------------------------------------------------------

CPU time actual refinement: 326.48


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_545/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_545/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_545/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_545/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_545/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.32 
  Macro-tasks:
    bulk solvent and scale       = 41.62  
    individual site refinement   = 128.10 
    weights calculation          = 33.11  
    collect and process          = 6.66   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 209.63 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 99.27  
    alpha_beta                      = 8.23   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 108.78 
    fmodel                         = 7.51   
    r_factors                      = 0.24   
    phase_errors                   = 11.04  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 237.64 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.636 micro seconds
Total CPU time: 5.66 minutes
from_scatterers_fft:    644 calls, 98.88 s
gradients_fft:          588 calls, 95.93 s

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

# Date 2008-01-16 Time 01:50:46 PST -0800 (1200477046.83 s)
Start R-work = 0.4095, R-free = 0.3968 (no bulk solvent and anisotropic scale)
Final R-work = 0.1253, R-free = 0.1716 (no bulk solvent and anisotropic scale)

Start R-work = 0.4023, R-free = 0.3840
Final R-work = 0.1072, R-free = 0.1557