# Date 2008-01-16 Time 02:03:44 PST -0800 (1200477824.37 s)
#phil __OFF__

Command line arguments: "../676.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9570
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 676

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.1647, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2.00044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   2.0004

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2.00044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2795 [2093/2118]  1884   209  10.0%
  bin  2:  4.2795 -  3.4099 [2024/2042]  1822   202  10.0%
  bin  3:  3.4099 -  2.9828 [1983/2002]  1784   199  10.0%
  bin  4:  2.9828 -  2.7118 [1956/1986]  1761   195  10.0%
  bin  5:  2.7118 -  2.5184 [1960/1979]  1764   196  10.0%
  bin  6:  2.5184 -  2.3705 [1949/1974]  1751   198  10.2%
  bin  7:  2.3705 -  2.2522 [1944/1972]  1755   189   9.7%
  bin  8:  2.2522 -  2.1545 [1941/1977]  1744   197  10.1%
  bin  9:  2.1545 -  2.0718 [1902/1944]  1711   191  10.0%
  bin 10:  2.0718 -  2.0004 [1837/1961]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_676/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: 7
        2.42 -     3.04: 2202
        3.04 -     3.66: 4619
        3.66 -     4.28: 9035
        4.28 -     4.90: 12349
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.209 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28207 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_676/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_676/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.16465 86.39 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: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4096   r_free= 0.3947   ksol= 0.00   Bsol= 0.00   scale= 0.834    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.192834                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7727 0.99   1370  153 0.3494 0.3263      6.4897      6.4167|
|  2:  4.7727 -  3.8087 0.99   1303  145 0.2979 0.3074      6.5607      6.6042|
|  3:  3.8087 -  3.3333 0.99   1280  142 0.3425 0.3268      6.5063      6.4994|
|  4:  3.3333 -  3.0313 0.99   1281  140 0.3855 0.3349      6.4124      6.2865|
|  5:  3.0313 -  2.8155 0.99   1257  142 0.4151 0.4218       6.272       6.303|
|  6:  2.8155 -  2.6505 0.99   1273  140 0.4262 0.4679      6.2019      6.2122|
|  7:  2.6505 -  2.5184 0.99   1251  139 0.4601 0.4360      6.1917      6.0938|
|  8:  2.5184 -  2.4092 0.98   1254  140 0.4559 0.4234      6.1313      6.1146|
|  9:  2.4092 -  2.3168 0.98   1240  140 0.4611 0.4614      6.0755      6.0527|
| 10:  2.3168 -  2.2372 0.99   1236  137 0.4765 0.4531      6.0981      6.0314|
| 11:  2.2372 -  2.1674 0.98   1254  137 0.4683 0.3994      6.0076      5.9484|
| 12:  2.1674 -  2.1056 0.97   1236  138 0.4753 0.4453      5.9639       5.982|
| 13:  2.1056 -  2.0503 1.00   1229  134 0.4808 0.5215      5.8729      5.9235|
| 14:  2.0503 -  2.0004 0.91   1166  132 0.4844 0.4425       5.824      5.7045|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7727  1370   153  0.75  29.75   0.82     0.77      53740.94|
|  2:  4.7727 -  3.8087  1303   145  0.80  26.01   0.93     0.84      62807.86|
|  3:  3.8087 -  3.3333  1280   142  0.75  30.63   0.89     0.82      63234.32|
|  4:  3.3333 -  3.0313  1281   140  0.70  35.06   0.85     0.75      55653.46|
|  5:  3.0313 -  2.8155  1257   142  0.61  42.83   0.79     0.67      52097.73|
|  6:  2.8155 -  2.6505  1273   140  0.59  45.13   0.78     0.64      48708.86|
|  7:  2.6505 -  2.5184  1251   139  0.56  46.98   0.76     0.62      45977.74|
|  8:  2.5184 -  2.4092  1254   140  0.57  46.97   0.79     0.63      40870.74|
|  9:  2.4092 -  2.3168  1240   140  0.59  45.38   0.76     0.64      34914.47|
| 10:  2.3168 -  2.2372  1236   137  0.60  44.59   0.77     0.66      31299.66|
| 11:  2.2372 -  2.1674  1254   137  0.58  46.24   0.79     0.65      29798.14|
| 12:  2.1674 -  2.1056  1236   138  0.53  50.21   0.79     0.61      31132.79|
| 13:  2.1056 -  2.0503  1229   134  0.49  52.95   0.77     0.56      28300.88|
| 14:  2.0503 -  2.0004  1166   132  0.52  50.57   0.75     0.56      22261.47|
|alpha:            min =        0.56 max =            0.84 mean =         0.68|
|beta:             min =    22261.47 max =        63234.32 mean =     43251.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           90.00 mean =        42.15|
|phase err.(test): min =        0.00 max =           89.87 mean =        42.25|
|-----------------------------------------------------------------------------|

============================== 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 = 6.231262              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.124   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.488832              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.578   (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:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      680 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1496 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2610 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3921 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5035 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6588 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7694 |
|-----------------------------------------------------------------------------|
|-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 |       53.886 |
| 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 |       1.647 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    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 = 11.978)------------------------------------------|
|    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: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4186   r_free= 0.4001   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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: 6.203003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4015   r_free= 0.3813   ksol= 0.34   Bsol= 21.77   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.25,8.68,8.21,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.190442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.876292              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.132   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.485318              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.674   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4015      final r-factor (work) = 0.2832          |
| start r-factor (free) = 0.3813      final r-factor (free) = 0.3039          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.1540 = 5.88 * 0.50 * 6.2177 + 1.00 * 53.8856                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7052 = 5.88 * 0.50 * 5.9897 + 1.00 * 0.1064                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2832      final r-factor (work) = 0.2073          |
| start r-factor (free) = 0.3039      final r-factor (free) = 0.2344          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9217 = 0.49 * 1.00 * 5.9897 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8031 = 0.49 * 1.00 * 5.7546 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    47.97   9.52     None  None   None       |
|    all(noH): 2823   0      0.00    47.97   9.52     None  None   None       |
|    Sol.    : 438    0      0.00    47.97   25.68    None  None   None       |
|    Mac.    : 2385   0      0.00    43.47   6.56     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   4.797: 1168   |   5:    23.983 -  28.780:  109        |
|      1:     4.797 -   9.593:  783   |   6:    28.780 -  33.576:   95        |
|      2:     9.593 -  14.390:  285   |   7:    33.576 -  38.373:   94        |
|      3:    14.390 -  19.187:  151   |   8:    38.373 -  43.170:   33        |
|      4:    19.187 -  23.983:   96   |   9:    43.170 -  47.966:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2073 r_free = 0.2344             target_work(ml) = 5.633         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2066 r_free = 0.2344             target_work(ml) = 5.631         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2066   r_free= 0.2344   ksol= 0.34   Bsol= 21.77   scale= 1.080   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.25,8.68,8.21,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.631221                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2014   r_free= 0.2295   ksol= 0.34   Bsol= 41.53   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.03,5.14,5.41,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.628985                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.216380              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.616   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.420  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2014      final r-factor (work) = 0.1463          |
| start r-factor (free) = 0.2295      final r-factor (free) = 0.1784          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5040 = 2.22 * 0.50 * 5.7734 + 1.00 * 0.1060                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1144 = 2.22 * 0.50 * 5.4647 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1463      final r-factor (work) = 0.1363          |
| start r-factor (free) = 0.1784      final r-factor (free) = 0.1704          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3100 = 0.24 * 1.00 * 5.4647 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2990 = 0.24 * 1.00 * 5.3013 + 1.00 * 0.0449                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.59   10.02    None  None   None       |
|    all(noH): 2823   0      0.00    79.59   10.02    None  None   None       |
|    Sol.    : 438    0      0.90    49.11   28.62    None  None   None       |
|    Mac.    : 2385   0      0.00    79.59   6.60     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.959: 1770   |   5:    39.794 -  47.753:   65        |
|      1:     7.959 -  15.918:  509   |   6:    47.753 -  55.712:    4        |
|      2:    15.918 -  23.877:  167   |   7:    55.712 -  63.671:    0        |
|      3:    23.877 -  31.835:  133   |   8:    63.671 -  71.630:    0        |
|      4:    31.835 -  39.794:  174   |   9:    71.630 -  79.588:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1363 r_free = 0.1704             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1362 r_free = 0.1706             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1362   r_free= 0.1706   ksol= 0.34   Bsol= 41.53   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.03,5.14,5.41,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.279905                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1359   r_free= 0.1704   ksol= 0.33   Bsol= 41.53   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,4.11,4.80,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280056                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.486627              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.229  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.701783              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.050   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1359      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1704      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6535 = 2.49 * 0.50 * 5.3043 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5503 = 2.49 * 0.50 * 5.2152 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1186      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6763 = 0.70 * 1.00 * 5.2152 + 1.00 * 0.0164                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6314 = 0.70 * 1.00 * 5.1568 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.13   10.86    None  None   None       |
|    all(noH): 2823   0      0.00    70.13   10.86    None  None   None       |
|    Sol.    : 438    0      0.00    66.03   32.81    None  None   None       |
|    Mac.    : 2385   0      0.00    70.13   6.83     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 -   7.013: 1658   |   5:    35.067 -  42.080:   74        |
|      1:     7.013 -  14.027:  546   |   6:    42.080 -  49.094:   83        |
|      2:    14.027 -  21.040:  166   |   7:    49.094 -  56.107:   55        |
|      3:    21.040 -  28.054:  106   |   8:    56.107 -  63.120:   18        |
|      4:    28.054 -  35.067:  110   |   9:    63.120 -  70.134:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1549             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1548             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1548   ksol= 0.33   Bsol= 41.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,4.11,4.80,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1549   ksol= 0.32   Bsol= 41.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,4.11,4.80,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147808                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.390718              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.980  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.204804              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.629  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6517 = 1.39 * 0.50 * 5.1563 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6372 = 1.39 * 0.50 * 5.1538 + 1.00 * 0.0535                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1149      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0680 = 0.20 * 1.00 * 5.1538 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0690 = 0.20 * 1.00 * 5.1647 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.86   10.47    None  None   None       |
|    all(noH): 2823   0      0.00    69.86   10.47    None  None   None       |
|    Sol.    : 438    0      0.66    62.14   31.03    None  None   None       |
|    Mac.    : 2385   0      0.00    69.86   6.69     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.986: 1678   |   5:    34.929 -  41.915:   87        |
|      1:     6.986 -  13.972:  540   |   6:    41.915 -  48.901:   70        |
|      2:    13.972 -  20.958:  163   |   7:    48.901 -  55.887:   39        |
|      3:    20.958 -  27.943:  108   |   8:    55.887 -  62.872:   12        |
|      4:    27.943 -  34.929:  121   |   9:    62.872 -  69.858:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1560             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1160 r_free = 0.1561             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1561   ksol= 0.32   Bsol= 41.53   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,4.11,4.80,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161916                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1561   ksol= 0.32   Bsol= 41.53   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.33,3.94,4.77,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161771                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.771051              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.291  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.443337              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.671   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6267 = 1.77 * 0.50 * 5.1641 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6201 = 1.77 * 0.50 * 5.1502 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2944 = 0.44 * 1.00 * 5.1502 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3145 = 0.44 * 1.00 * 5.1413 + 1.00 * 0.0352                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.58   10.58    None  None   None       |
|    all(noH): 2823   0      0.00    70.58   10.58    None  None   None       |
|    Sol.    : 438    0      0.46    62.62   31.51    None  None   None       |
|    Mac.    : 2385   0      0.00    70.58   6.73     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 -   7.058: 1684   |   5:    35.289 -  42.347:   89        |
|      1:     7.058 -  14.116:  526   |   6:    42.347 -  49.405:   69        |
|      2:    14.116 -  21.174:  164   |   7:    49.405 -  56.463:   42        |
|      3:    21.174 -  28.231:  111   |   8:    56.463 -  63.521:   12        |
|      4:    28.231 -  35.289:  120   |   9:    63.521 -  70.578:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1126 r_free = 0.1555             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1125 r_free = 0.1556             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1556   ksol= 0.32   Bsol= 41.53   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.33,3.94,4.77,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144609                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7727 0.99   1370  153 0.1021 0.1281      5.3979      5.5093|
|  2:  4.7727 -  3.8087 0.99   1303  145 0.0875 0.1116      5.4488      5.6391|
|  3:  3.8087 -  3.3333 0.99   1280  142 0.1057 0.1486      5.4797      5.8549|
|  4:  3.3333 -  3.0313 0.99   1281  140 0.1211 0.1471      5.4525      5.5803|
|  5:  3.0313 -  2.8155 0.99   1257  142 0.1306 0.1718      5.3323       5.529|
|  6:  2.8155 -  2.6505 0.99   1273  140 0.1219 0.1784      5.2151      5.4613|
|  7:  2.6505 -  2.5184 0.99   1251  139 0.1268 0.1672      5.1745      5.3835|
|  8:  2.5184 -  2.4092 0.98   1254  140 0.1169 0.1761      5.0879      5.3924|
|  9:  2.4092 -  2.3168 0.98   1240  140 0.1187 0.1711      5.0493      5.2615|
| 10:  2.3168 -  2.2372 0.99   1236  137 0.1128 0.1792      4.9817      5.2631|
| 11:  2.2372 -  2.1674 0.98   1254  137 0.1130 0.1636      4.9307      5.2076|
| 12:  2.1674 -  2.1056 0.97   1236  138 0.1127 0.1709       4.885      5.2188|
| 13:  2.1056 -  2.0503 1.00   1229  134 0.1144 0.1654      4.8064      5.0592|
| 14:  2.0503 -  2.0004 0.91   1166  132 0.1092 0.1789      4.6866      4.9612|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7727  1370   153  0.94   9.03   0.98     0.96       7203.73|
|  2:  4.7727 -  3.8087  1303   145  0.95   7.90   1.01     1.00       8944.48|
|  3:  3.8087 -  3.3333  1280   142  0.94  10.78   1.02     1.01      10216.62|
|  4:  3.3333 -  3.0313  1281   140  0.92  13.08   1.00     0.98      10025.05|
|  5:  3.0313 -  2.8155  1257   142  0.90  15.51   0.99     0.95       8227.88|
|  6:  2.8155 -  2.6505  1273   140  0.90  15.60   0.98     0.95       6994.94|
|  7:  2.6505 -  2.5184  1251   139  0.91  15.52   0.98     0.95       6171.52|
|  8:  2.5184 -  2.4092  1254   140  0.91  14.73   0.99     0.96       5390.57|
|  9:  2.4092 -  2.3168  1240   140  0.91  15.65   1.00     0.98       5169.95|
| 10:  2.3168 -  2.2372  1236   137  0.90  15.50   1.00     0.96       4474.71|
| 11:  2.2372 -  2.1674  1254   137  0.90  15.83   0.99     0.96       4286.70|
| 12:  2.1674 -  2.1056  1236   138  0.91  14.89   1.01     0.99       3886.59|
| 13:  2.1056 -  2.0503  1229   134  0.91  15.45   1.00     0.99       3376.14|
| 14:  2.0503 -  2.0004  1166   132  0.91  14.78   0.97     0.94       2581.37|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2581.37 max =        10216.62 mean =      6264.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.87 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.68 mean =        13.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1556   ksol= 0.32   Bsol= 45.61   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,-0.11,0.76,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144582                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1556   ksol= 0.32   Bsol= 45.61   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,-0.11,0.76,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144582                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7727 0.99   1370  153 0.1021 0.1282      5.3982      5.5097|
|  2:  4.7727 -  3.8087 0.99   1303  145 0.0875 0.1116       5.449      5.6392|
|  3:  3.8087 -  3.3333 0.99   1280  142 0.1057 0.1487      5.4799      5.8552|
|  4:  3.3333 -  3.0313 0.99   1281  140 0.1211 0.1471      5.4525      5.5803|
|  5:  3.0313 -  2.8155 0.99   1257  142 0.1306 0.1717      5.3321      5.5287|
|  6:  2.8155 -  2.6505 0.99   1273  140 0.1219 0.1783      5.2149      5.4609|
|  7:  2.6505 -  2.5184 0.99   1251  139 0.1268 0.1674      5.1745      5.3838|
|  8:  2.5184 -  2.4092 0.98   1254  140 0.1169 0.1761      5.0879      5.3925|
|  9:  2.4092 -  2.3168 0.98   1240  140 0.1187 0.1710      5.0492      5.2614|
| 10:  2.3168 -  2.2372 0.99   1236  137 0.1128 0.1792      4.9817      5.2633|
| 11:  2.2372 -  2.1674 0.98   1254  137 0.1130 0.1637      4.9306      5.2075|
| 12:  2.1674 -  2.1056 0.97   1236  138 0.1127 0.1708      4.8849      5.2186|
| 13:  2.1056 -  2.0503 1.00   1229  134 0.1144 0.1654      4.8062      5.0593|
| 14:  2.0503 -  2.0004 0.91   1166  132 0.1092 0.1788      4.6863      4.9606|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7727  1370   153  0.94   9.04   0.98     0.96       7210.22|
|  2:  4.7727 -  3.8087  1303   145  0.95   7.91   1.01     1.00       8950.65|
|  3:  3.8087 -  3.3333  1280   142  0.94  10.78   1.02     1.01      10222.35|
|  4:  3.3333 -  3.0313  1281   140  0.92  13.08   1.00     0.98      10023.83|
|  5:  3.0313 -  2.8155  1257   142  0.90  15.51   0.99     0.96       8223.24|
|  6:  2.8155 -  2.6505  1273   140  0.90  15.59   0.98     0.96       6992.08|
|  7:  2.6505 -  2.5184  1251   139  0.91  15.52   0.98     0.96       6171.36|
|  8:  2.5184 -  2.4092  1254   140  0.91  14.73   0.99     0.96       5389.73|
|  9:  2.4092 -  2.3168  1240   140  0.91  15.66   1.01     0.98       5171.19|
| 10:  2.3168 -  2.2372  1236   137  0.90  15.50   1.00     0.96       4473.55|
| 11:  2.2372 -  2.1674  1254   137  0.90  15.83   1.00     0.96       4286.68|
| 12:  2.1674 -  2.1056  1236   138  0.91  14.89   1.01     0.99       3885.58|
| 13:  2.1056 -  2.0503  1229   134  0.91  15.43   1.00     0.99       3373.95|
| 14:  2.0503 -  2.0004  1166   132  0.91  14.77   0.98     0.94       2578.40|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2578.40 max =        10222.35 mean =      6265.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.87 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.68 mean =        13.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.08    74.66   14.65    None  None   None       |
|    all(noH): 2823   0      4.08    74.66   14.65    None  None   None       |
|    Sol.    : 438    0      4.54    66.70   35.59    None  None   None       |
|    Mac.    : 2385   0      4.08    74.66   10.81    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:     4.077 -  11.135: 1684   |   5:    39.367 -  46.424:   89        |
|      1:    11.135 -  18.193:  526   |   6:    46.424 -  53.482:   69        |
|      2:    18.193 -  25.251:  164   |   7:    53.482 -  60.540:   42        |
|      3:    25.251 -  32.309:  111   |   8:    60.540 -  67.598:   12        |
|      4:    32.309 -  39.367:  120   |   9:    67.598 -  74.656:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.280 - 3.928
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 302
   mapped sites are within: 0.704 - 3.928

peak=   10.574 closest distance to " CG2 VAL A 230 " =    1.416
peak=    7.292 closest distance to " CG2 VAL A 296 " =    1.148
peak=    6.069 closest distance to " CG  LEU A   5 " =    1.261
peak=    5.640 closest distance to " CG  LEU A 228 " =    1.202
peak=    5.585 closest distance to " CD2 LEU A   5 " =    1.172
peak=    5.475 closest distance to " CB  GLN A 223 " =    1.422
peak=    5.435 closest distance to " CG  PRO A  54 " =    1.323
peak=    5.417 closest distance to " NH2 ARG A  56 " =    2.227
peak=    5.076 closest distance to " CB  VAL A 296 " =    1.095
peak=    5.033 closest distance to " CB  PRO A  54 " =    0.971
peak=    4.959 closest distance to " CB  SER A  63 " =    1.262
peak=    4.937 closest distance to " CB  ARG A 275 " =    0.919
peak=    4.936 closest distance to " CB  VAL A 230 " =    1.175
peak=    4.915 closest distance to " O   HOH Z 232 " =    2.364
peak=    4.787 closest distance to " O   HOH Z 126 " =    1.914
peak=    4.766 closest distance to " CB  GLN A 183 " =    1.301
peak=    4.665 closest distance to " O   HOH Z 209 " =    2.270
peak=    4.638 closest distance to " CG  PRO A 213 " =    1.248
peak=    4.560 closest distance to " NE2 GLN A  11 " =    1.112
peak=    4.536 closest distance to " CG  PRO A 198 " =    1.220
peak=    4.507 closest distance to " CB  GLU A 152 " =    1.169
peak=    4.468 closest distance to " O   HOH Z 142 " =    1.652
peak=    4.451 closest distance to " CG  PRO A 243 " =    1.119
peak=    4.372 closest distance to " O   HOH Z 272 " =    1.908
peak=    4.362 closest distance to " O   HOH Z 402 " =    1.510
peak=    4.353 closest distance to " CB  ASN A 148 " =    1.429
peak=    4.350 closest distance to " C   PRO A 198 " =    1.482
peak=    4.301 closest distance to " O   HOH Z 427 " =    3.055
peak=    4.275 closest distance to " O   HOH Z  43 " =    2.106
peak=    4.258 closest distance to " O   HOH Z  61 " =    1.682
peak=    4.254 closest distance to " O   HOH Z 298 " =    1.812
peak=    4.251 closest distance to " O   HOH Z 316 " =    3.081
peak=    4.222 closest distance to " O   HOH Z 303 " =    2.085
peak=    4.205 closest distance to " O   SER A  87 " =    2.242
peak=    4.200 closest distance to " O   HOH Z 423 " =    1.781
peak=    4.193 closest distance to " CZ  PHE A 218 " =    1.085
peak=    4.190 closest distance to " O   HOH Z 236 " =    1.834
peak=    4.182 closest distance to " O   HOH Z 346 " =    1.572
peak=    4.148 closest distance to " O   HOH Z 234 " =    3.664
peak=    4.126 closest distance to " CB  GLU A 128 " =    1.021
peak=    4.120 closest distance to " O   HOH Z 368 " =    2.151
peak=    4.106 closest distance to " ND2 ASN A 187 " =    1.517
peak=    4.096 closest distance to " CB  SER A   3 " =    1.252
peak=    4.096 closest distance to " O   HOH Z 369 " =    2.219
peak=    4.067 closest distance to " O   HOH Z 248 " =    1.651
peak=    4.051 closest distance to " CD2 LEU A 228 " =    1.088
peak=    4.047 closest distance to " CB  ASN A  39 " =    0.895
peak=    4.025 closest distance to " O   HOH Z 280 " =    2.957
peak=    4.015 closest distance to " CB  ARG A 190 " =    1.629
peak=    4.015 closest distance to " OD1 ASN A  69 " =    2.615
peak=    4.003 closest distance to " O   HOH Z 189 " =    2.705
peak=    4.002 closest distance to " O   HOH Z  78 " =    1.672
peak=    3.992 closest distance to " O   HOH Z 265 " =    2.398
peak=    3.991 closest distance to " CB  GLU A 277 " =    3.605
peak=    3.990 closest distance to " CA  TYR A  30 " =    0.938
peak=    3.987 closest distance to " CB  VAL A 265 " =    1.299
peak=    3.955 closest distance to " CG1BVAL A  72 " =    1.714
peak=    3.940 closest distance to " O   HOH Z 403 " =    1.698
peak=    3.928 closest distance to " CB  ASP A 124 " =    0.704
peak=    3.926 closest distance to " CB  TRP A 266 " =    0.944
peak=    3.918 closest distance to " O   HOH Z  97 " =    2.010
peak=    3.918 closest distance to " O   HOH Z 193 " =    1.759
peak=    3.885 closest distance to " O   HOH Z 158 " =    3.157
peak=    3.882 closest distance to " CB  ARG A  79 " =    1.421
peak=    3.881 closest distance to " O   HOH Z 250 " =    1.354
peak=    3.852 closest distance to " O   HOH Z 203 " =    1.714
peak=    3.844 closest distance to " O   HOH Z  15 " =    2.085
peak=    3.809 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.805 closest distance to " CB  ALA A   9 " =    1.593
peak=    3.804 closest distance to " CB  ARG A 139 " =    0.893
peak=    3.793 closest distance to " O   HOH Z  40 " =    1.645
peak=    3.783 closest distance to " O   HOH Z 197 " =    3.028
peak=    3.778 closest distance to " CB  ASN A 142 " =    1.138
peak=    3.778 closest distance to " CA  ASN A 215 " =    1.211
peak=    3.748 closest distance to " O   HOH Z 411 " =    3.716
peak=    3.747 closest distance to " CB  ASP A 140 " =    0.931
peak=    3.741 closest distance to " O   HOH Z  48 " =    1.658
peak=    3.736 closest distance to " O   HOH Z 389 " =    1.868
peak=    3.734 closest distance to " O   HOH Z  97 " =    2.459
peak=    3.729 closest distance to " CG1 ILE A  49 " =    1.491
peak=    3.727 closest distance to " NH2 ARG A 156 " =    1.119
peak=    3.719 closest distance to " CG1 VAL A 153 " =    0.982
peak=    3.713 closest distance to " CB  GLU A  46 " =    1.000
peak=    3.712 closest distance to " CB BVAL A  41 " =    1.052
peak=    3.707 closest distance to " O   HOH Z 263 " =    1.645
peak=    3.702 closest distance to " O   HOH Z 126 " =    2.156
peak=    3.697 closest distance to " CA  ALA A  51 " =    0.973
peak=    3.693 closest distance to " CB  SER A  26 " =    1.722
peak=    3.689 closest distance to " CD  ARG A 269 " =    0.948
peak=    3.689 closest distance to " CD  LYS A 166 " =    1.317
peak=    3.686 closest distance to " CG2 VAL A 257 " =    0.888
peak=    3.680 closest distance to " CB  VAL A 202 " =    1.543
peak=    3.667 closest distance to " CA  ALA A  21 " =    1.117
peak=    3.666 closest distance to " CB  ALA A 248 " =    1.431
peak=    3.652 closest distance to " O   HOH Z 371 " =    3.099
peak=    3.649 closest distance to " O   HOH Z 147 " =    1.775
peak=    3.643 closest distance to " CB  ALA A 291 " =    1.362
peak=    3.638 closest distance to " O   HOH Z 172 " =    3.705
peak=    3.638 closest distance to " O   HOH Z 214 " =    2.259
peak=    3.638 closest distance to " O   TRP A 274 " =    1.858
peak=    3.631 closest distance to " N   ASN A  39 " =    1.166
peak=    3.620 closest distance to " O   HOH Z 273 " =    2.708
peak=    3.616 closest distance to " O   HOH Z 344 " =    3.056
peak=    3.613 closest distance to " CD BLYS A 290 " =    1.077
peak=    3.607 closest distance to " CA  VAL A  41 " =    0.805
peak=    3.597 closest distance to " CA  ARG A  36 " =    1.041
peak=    3.595 closest distance to " O   HOH Z 261 " =    1.945
peak=    3.593 closest distance to " CB  THR A  31 " =    1.587
peak=    3.587 closest distance to " O   HOH Z  66 " =    2.228
peak=    3.574 closest distance to " CA  THR A 264 " =    0.759
peak=    3.569 closest distance to " O   HOH Z  80 " =    1.687
peak=    3.565 closest distance to " O   ASP A 124 " =    1.114
peak=    3.562 closest distance to " O   HOH Z 425 " =    2.041
peak=    3.560 closest distance to " CB  ALA A 104 " =    0.705
peak=    3.555 closest distance to " CA  THR A 221 " =    0.930
peak=    3.553 closest distance to " CA  PHE A 283 " =    1.190
peak=    3.551 closest distance to " CD  ARG A 159 " =    0.729
peak=    3.551 closest distance to " O   HOH Z 112 " =    1.658
peak=    3.547 closest distance to " CG  MET A 185 " =    1.176
peak=    3.547 closest distance to " CD2 TRP A 179 " =    1.371
peak=    3.544 closest distance to " CB  LEU A 143 " =    1.151
peak=    3.544 closest distance to " CB  HIS A 108 " =    0.778
peak=    3.542 closest distance to " NH1AARG A 145 " =    1.141
peak=    3.540 closest distance to " O   HOH Z 245 " =    1.369
peak=    3.536 closest distance to " O   HOH Z  21 " =    1.712
peak=    3.533 closest distance to " O   HOH Z 435 " =    2.018
peak=    3.529 closest distance to " CG  ARG A  66 " =    2.767
peak=    3.525 closest distance to " CG  GLN A  77 " =    2.164
peak=    3.519 closest distance to " CB  ALA A 295 " =    1.140
peak=    3.517 closest distance to " O   MET A 105 " =    1.843
peak=    3.514 closest distance to " CE1 TYR A 186 " =    1.341
peak=    3.508 closest distance to " O   HOH Z  19 " =    2.206
peak=    3.506 closest distance to " OG BSER A 164 " =    2.221
peak=    3.503 closest distance to " N   VAL A 126 " =    1.438
peak=    3.499 closest distance to " O   HOH Z 404 " =    2.318
peak=    3.496 closest distance to " CG2 ILE A  20 " =    1.432
peak=    3.491 closest distance to " O   HOH Z 128 " =    2.183
peak=    3.488 closest distance to " O   HOH Z 417 " =    3.175
peak=    3.484 closest distance to " O   HOH Z  88 " =    3.024
peak=    3.480 closest distance to " CD1 LEU A 300 " =    1.268
peak=    3.476 closest distance to " O   HOH Z 128 " =    2.093
peak=    3.474 closest distance to " O   HOH Z 407 " =    2.508
peak=    3.464 closest distance to " CE  LYS A  76 " =    0.893
peak=    3.453 closest distance to " O   HOH Z 130 " =    2.238
peak=    3.452 closest distance to " O   HOH Z 383 " =    1.945
peak=    3.450 closest distance to " O   HOH Z 145 " =    2.208
peak=    3.449 closest distance to " O   HOH Z 422 " =    2.660
peak=    3.447 closest distance to " O   HOH Z 261 " =    1.624
peak=    3.440 closest distance to " OD2 ASP A 286 " =    2.828
peak=    3.436 closest distance to " N   SER A 135 " =    1.392
peak=    3.435 closest distance to " CA  ARG A 195 " =    1.194
peak=    3.435 closest distance to " CG2 ILE A 120 " =    1.229
peak=    3.434 closest distance to " NH1BARG A 190 " =    2.050
peak=    3.434 closest distance to " NE2 GLN A  77 " =    3.250
peak=    3.430 closest distance to " CA  ALA A 158 " =    1.244
peak=    3.427 closest distance to " O   HOH Z 193 " =    1.947
peak=    3.422 closest distance to " CB  TRP A 150 " =    1.436
peak=    3.418 closest distance to " O   HOH Z 313 " =    1.790
peak=    3.416 closest distance to " O   HOH Z 403 " =    1.395
peak=    3.415 closest distance to " O   HOH Z 285 " =    3.056
peak=    3.408 closest distance to " CB  THR A 157 " =    1.202
peak=    3.408 closest distance to " CB  ASN A 110 " =    1.110
peak=    3.408 closest distance to " O   HOH Z 148 " =    3.247
peak=    3.407 closest distance to " CD1 ILE A 106 " =    1.024
peak=    3.406 closest distance to " CG1 VAL A 296 " =    1.210
peak=    3.406 closest distance to " CB  LEU A 228 " =    1.282
peak=    3.403 closest distance to " O   HOH Z  54 " =    1.542
peak=    3.403 closest distance to " CB  GLN A 278 " =    0.885
peak=    3.399 closest distance to " O   HOH Z 227 " =    1.674
peak=    3.397 closest distance to " N   PHE A 130 " =    1.268
peak=    3.395 closest distance to " CA  ILE A 106 " =    0.741
peak=    3.389 closest distance to " O   HOH Z  59 " =    2.210
peak=    3.389 closest distance to " NZ  LYS A 117 " =    3.159
peak=    3.386 closest distance to " O   HOH Z 426 " =    1.550
peak=    3.385 closest distance to " CB  GLN A  89 " =    1.128
peak=    3.383 closest distance to " CA  LYS A 117 " =    1.267
peak=    3.378 closest distance to " CG  MET A 185 " =    1.063
peak=    3.374 closest distance to " N   ARG A 156 " =    1.407
peak=    3.372 closest distance to " CG2 THR A 221 " =    1.089
peak=    3.369 closest distance to " CB  ARG A  79 " =    0.896
peak=    3.367 closest distance to " O   HOH Z 329 " =    3.928
peak=    3.365 closest distance to " O   HOH Z 291 " =    1.568
peak=    3.363 closest distance to " CD1 ILE A  33 " =    1.653
peak=    3.351 closest distance to " CA  SER A  87 " =    1.061
peak=    3.350 closest distance to " CA  ASP A 191 " =    1.008
peak=    3.349 closest distance to " O   HOH Z 251 " =    1.498
peak=    3.341 closest distance to " O   HOH Z 305 " =    3.673
peak=    3.339 closest distance to " O   GLN A 278 " =    1.315
peak=    3.339 closest distance to " CB  SER A 212 " =    1.250
peak=    3.339 closest distance to " CA  GLY A 211 " =    1.315
peak=    3.330 closest distance to " N   ASP A 162 " =    1.348
peak=    3.330 closest distance to " O   HOH Z 421 " =    1.728
peak=    3.328 closest distance to " O   HOH Z 193 " =    1.599
peak=    3.327 closest distance to " CB  MET A  40 " =    0.812
peak=    3.325 closest distance to " O   HOH Z 102 " =    1.294
peak=    3.322 closest distance to " CG  GLN A  58 " =    2.854
peak=    3.320 closest distance to " O   HOH Z 250 " =    1.359
peak=    3.315 closest distance to " O   HOH Z 166 " =    3.726
peak=    3.312 closest distance to " ND1 HIS A  81 " =    1.680
peak=    3.306 closest distance to " CB  ALA A 114 " =    1.244
peak=    3.296 closest distance to " OG1 THR A 294 " =    2.386
peak=    3.295 closest distance to " O   HOH Z 247 " =    1.371
peak=    3.294 closest distance to " CA  ASP A 140 " =    1.237
peak=    3.293 closest distance to " O   HOH Z  90 " =    2.295
peak=    3.291 closest distance to " CB  GLN A 205 " =    1.129
peak=    3.290 closest distance to " CG  LEU A 167 " =    1.173
peak=    3.290 closest distance to " OG  SER A  22 " =    2.730
peak=    3.290 closest distance to " CB  MET A  47 " =    1.105
peak=    3.285 closest distance to " CA  ALA A 291 " =    0.928
peak=    3.285 closest distance to " CD  LYS A 119 " =    1.793
peak=    3.283 closest distance to " O   HOH Z 437 " =    1.962
peak=    3.282 closest distance to " CE1 HIS A 108 " =    1.136
peak=    3.276 closest distance to " O   HOH Z 132 " =    2.688
peak=    3.276 closest distance to " CB  PRO A 198 " =    1.081
peak=    3.274 closest distance to " CZ  PHE A 192 " =    0.938
peak=    3.273 closest distance to " CA  LEU A 282 " =    1.061
peak=    3.273 closest distance to " N   ARG A 190 " =    1.030
peak=    3.264 closest distance to " OG1 THR A 294 " =    1.701
peak=    3.263 closest distance to " O   HOH Z 365 " =    3.013
peak=    3.261 closest distance to " O   HOH Z 359 " =    3.799
peak=    3.259 closest distance to " O   HOH Z  10 " =    1.711
peak=    3.258 closest distance to " CG2 THR A 220 " =    0.863
peak=    3.255 closest distance to " O   HOH Z 313 " =    1.716
peak=    3.255 closest distance to " CG1 ILE A  33 " =    1.299
peak=    3.252 closest distance to " NZ  LYS A  48 " =    1.319
peak=    3.250 closest distance to " O   HOH Z 368 " =    3.531
peak=    3.246 closest distance to " CB  SER A 216 " =    0.767
peak=    3.238 closest distance to " CA  ASP A 162 " =    1.013
peak=    3.237 closest distance to " CA  MET A 105 " =    0.952
peak=    3.236 closest distance to " CG  GLN A  88 " =    1.049
peak=    3.236 closest distance to " OE2 GLU A   2 " =    1.802
peak=    3.229 closest distance to " ND2 ASN A 110 " =    1.582
peak=    3.229 closest distance to " CA  ALA A 233 " =    1.346
peak=    3.228 closest distance to " CB  ASN A 224 " =    1.037
peak=    3.228 closest distance to " CB  ILE A 120 " =    1.305
peak=    3.225 closest distance to " CG2 ILE A 234 " =    2.089
peak=    3.225 closest distance to " CB  LEU A 255 " =    0.825
peak=    3.217 closest distance to " CZ3 TRP A  85 " =    0.961
peak=    3.208 closest distance to " NH2 ARG A  79 " =    1.323
peak=    3.208 closest distance to " O   HOH Z 425 " =    1.325
peak=    3.207 closest distance to " O   HOH Z  50 " =    2.113
peak=    3.206 closest distance to " CD2 LEU A 297 " =    0.897
peak=    3.203 closest distance to " CA  TYR A 116 " =    1.430
peak=    3.199 closest distance to " OG  SER A 245 " =    1.596
peak=    3.195 closest distance to " O   HOH Z 290 " =    1.105
peak=    3.194 closest distance to " O   HOH Z 185 " =    1.788
peak=    3.188 closest distance to " CG2AVAL A 121 " =    2.315
peak=    3.187 closest distance to " CA  SER A 146 " =    1.716
peak=    3.186 closest distance to " CG2 VAL A 197 " =    1.025
peak=    3.185 closest distance to " CB  ALA A 248 " =    1.021
peak=    3.176 closest distance to " CG  LEU A 281 " =    1.076
peak=    3.175 closest distance to " CB  ASN A 215 " =    1.194
peak=    3.175 closest distance to " OG BSER A 134 " =    2.917
peak=    3.173 closest distance to " O   HOH Z 135 " =    1.823
peak=    3.163 closest distance to " O   HOH Z  49 " =    2.580
peak=    3.162 closest distance to " O   HOH Z  66 " =    2.316
peak=    3.160 closest distance to " CA  GLN A 194 " =    1.246
peak=    3.159 closest distance to " CB  VAL A 268 " =    0.808
peak=    3.159 closest distance to " N   ASN A 127 " =    1.203
peak=    3.157 closest distance to " O   ALA A 158 " =    1.343
peak=    3.154 closest distance to " O   HOH Z 293 " =    1.711
peak=    3.149 closest distance to " N   SER A  12 " =    1.593
peak=    3.148 closest distance to " CA  VAL A 126 " =    0.868
peak=    3.148 closest distance to " O   HOH Z 133 " =    1.571
peak=    3.147 closest distance to " NZ  LYS A  76 " =    1.525
peak=    3.146 closest distance to " CB  LYS A 290 " =    0.930
peak=    3.141 closest distance to " NE2 HIS A 207 " =    1.280
peak=    3.141 closest distance to " O   HOH Z 123 " =    2.187
peak=    3.139 closest distance to " CD1 LEU A 228 " =    1.926
peak=    3.138 closest distance to " CB  LYS A 117 " =    1.176
peak=    3.138 closest distance to " O   HOH Z 302 " =    2.006
peak=    3.129 closest distance to " O   HOH Z 180 " =    2.109
peak=    3.125 closest distance to " CB  PRO A 243 " =    1.558
peak=    3.124 closest distance to " CZ2 TRP A 274 " =    1.546
peak=    3.122 closest distance to " O   HOH Z 423 " =    3.117
peak=    3.121 closest distance to " O   ALA A   1 " =    1.762
peak=    3.121 closest distance to " CG2 VAL A 202 " =    1.124
peak=    3.117 closest distance to " O   HOH Z 409 " =    3.464
peak=    3.116 closest distance to " CA  LYS A 290 " =    1.183
peak=    3.115 closest distance to " O   HOH Z  47 " =    1.710
peak=    3.115 closest distance to " O   HOH Z 124 " =    1.258
peak=    3.111 closest distance to " CG BARG A 275 " =    1.403
peak=    3.108 closest distance to " CB  ILE A  20 " =    1.423
peak=    3.099 closest distance to " O   HOH Z 345 " =    3.259
peak=    3.098 closest distance to " O   HOH Z 353 " =    2.711
peak=    3.085 closest distance to " CB  GLN A 103 " =    0.912
peak=    3.083 closest distance to " O   HOH Z 141 " =    1.568
peak=    3.076 closest distance to " O   HOH Z 406 " =    1.529
peak=    3.073 closest distance to " O   HOH Z 327 " =    1.760
peak=    3.069 closest distance to " CD  ARG A  66 " =    2.631
peak=    3.069 closest distance to " O   SER A 164 " =    1.107
peak=    3.065 closest distance to " O   HOH Z 336 " =    1.760
peak=    3.053 closest distance to " CB  ALA A 100 " =    1.234
peak=    3.046 closest distance to " CD2 LEU A   5 " =    0.759

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.544 - 5.442
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 198
   mapped sites are within: 0.742 - 5.442

peak=   -5.649 closest distance to " CG2 VAL A 230 " =    0.742
peak=   -4.559 closest distance to " CD  ARG A 156 " =    2.019
peak=   -4.457 closest distance to " CG2BVAL A  41 " =    2.553
peak=   -4.390 closest distance to " SG  CYS A 254 " =    3.307
peak=   -4.322 closest distance to " CB  PRO A 243 " =    2.651
peak=   -4.297 closest distance to " O   HOH Z 290 " =    1.097
peak=   -4.257 closest distance to " CD  GLN A  58 " =    1.036
peak=   -4.246 closest distance to " O   HOH Z 266 " =    5.099
peak=   -4.196 closest distance to " C   HIS A 108 " =    1.191
peak=   -4.103 closest distance to " OG BSER A 134 " =    1.171
peak=   -4.048 closest distance to " O   HOH Z 114 " =    3.140
peak=   -4.038 closest distance to " O   HOH Z 351 " =    1.498
peak=   -4.036 closest distance to " CB  PHE A 192 " =    1.950
peak=   -4.013 closest distance to " CG2 VAL A 296 " =    1.200
peak=   -4.006 closest distance to " O   ILE A 109 " =    2.622
peak=   -3.989 closest distance to " CG  ASP A 231 " =    0.796
peak=   -3.986 closest distance to " CZ3 TRP A 179 " =    1.234
peak=   -3.980 closest distance to " O   HOH Z 166 " =    1.970
peak=   -3.970 closest distance to " CA  VAL A  67 " =    2.764
peak=   -3.958 closest distance to " CE2 TYR A  30 " =    2.778
peak=   -3.947 closest distance to " OG  SER A  97 " =    2.288
peak=   -3.920 closest distance to " O   HOH Z 231 " =    1.980
peak=   -3.905 closest distance to " CG  GLN A 223 " =    2.044
peak=   -3.895 closest distance to " O   HOH Z 196 " =    2.139
peak=   -3.868 closest distance to " CD1 ILE A 199 " =    2.548
peak=   -3.863 closest distance to " OXT GLY A 302 " =    2.849
peak=   -3.828 closest distance to " N   ALA A 226 " =    2.072
peak=   -3.796 closest distance to " CD1 LEU A 101 " =    2.463
peak=   -3.779 closest distance to " O   HOH Z 389 " =    1.918
peak=   -3.751 closest distance to " O   HOH Z 185 " =    2.388
peak=   -3.749 closest distance to " N   GLN A  58 " =    1.809
peak=   -3.733 closest distance to " N   ALA A  43 " =    2.548
peak=   -3.732 closest distance to " O   PRO A 163 " =    2.129
peak=   -3.699 closest distance to " CB  ALA A 291 " =    2.290
peak=   -3.695 closest distance to " O   HOH Z  52 " =    1.560
peak=   -3.687 closest distance to " NH2AARG A 275 " =    5.142
peak=   -3.679 closest distance to " CD1 LEU A 101 " =    2.728
peak=   -3.677 closest distance to " OD1 ASN A 187 " =    1.703
peak=   -3.672 closest distance to " NE2 GLN A  88 " =    1.993
peak=   -3.668 closest distance to " ND2 ASN A  45 " =    1.386
peak=   -3.665 closest distance to " O   HOH Z  37 " =    1.892
peak=   -3.662 closest distance to " ND2 ASN A 187 " =    1.547
peak=   -3.661 closest distance to " CA  ASP A 298 " =    1.048
peak=   -3.661 closest distance to " O   HOH Z 394 " =    1.563
peak=   -3.649 closest distance to " CG  ARG A 269 " =    2.336
peak=   -3.644 closest distance to " O   HOH Z 435 " =    2.770
peak=   -3.644 closest distance to " CE2 PHE A 218 " =    2.594
peak=   -3.629 closest distance to " C   MET A 188 " =    1.417
peak=   -3.621 closest distance to " CG1 VAL A 112 " =    2.797
peak=   -3.618 closest distance to " C   ALA A 158 " =    1.292
peak=   -3.616 closest distance to " CB  ALA A 248 " =    2.155
peak=   -3.613 closest distance to " ND2 ASN A  45 " =    1.091
peak=   -3.579 closest distance to " CB  PRO A 163 " =    2.559
peak=   -3.567 closest distance to " NH2 ARG A  79 " =    1.979
peak=   -3.554 closest distance to " O   PRO A 198 " =    1.223
peak=   -3.546 closest distance to " CG1 VAL A 112 " =    2.637
peak=   -3.538 closest distance to " O   HOH Z 426 " =    1.710
peak=   -3.532 closest distance to " CD2 LEU A 237 " =    2.745
peak=   -3.523 closest distance to " O   SER A 271 " =    2.103
peak=   -3.522 closest distance to " CG  GLU A 277 " =    1.150
peak=   -3.521 closest distance to " O   HOH Z 407 " =    3.045
peak=   -3.520 closest distance to " OD1 ASN A 148 " =    1.466
peak=   -3.517 closest distance to " CB  ASP A 171 " =    2.238
peak=   -3.515 closest distance to " O   HOH Z  11 " =    1.886
peak=   -3.514 closest distance to " CA  GLY A 241 " =    3.065
peak=   -3.508 closest distance to " O   HOH Z  10 " =    1.492
peak=   -3.507 closest distance to " CB  ALA A  43 " =    2.500
peak=   -3.501 closest distance to " CB  ALA A 291 " =    2.197
peak=   -3.499 closest distance to " CG2 ILE A 263 " =    2.373
peak=   -3.496 closest distance to " CG  TRP A 266 " =    1.911
peak=   -3.494 closest distance to " O   HOH Z 211 " =    1.651
peak=   -3.493 closest distance to " O   VAL A 189 " =    2.611
peak=   -3.483 closest distance to " CE3 TRP A 150 " =    2.132
peak=   -3.482 closest distance to " N   THR A 157 " =    1.513
peak=   -3.481 closest distance to " CD  ARG A 139 " =    1.624
peak=   -3.479 closest distance to " CB  ASP A 132 " =    2.342
peak=   -3.474 closest distance to " CB  ALA A 248 " =    2.351
peak=   -3.474 closest distance to " CE  MET A 105 " =    2.108
peak=   -3.472 closest distance to " N   MET A 105 " =    2.660
peak=   -3.464 closest distance to " CD1 PHE A  59 " =    1.892
peak=   -3.456 closest distance to " O   HOH Z 166 " =    1.582
peak=   -3.453 closest distance to " CZ  TYR A 169 " =    1.715
peak=   -3.449 closest distance to " O   GLY A 196 " =    1.094
peak=   -3.432 closest distance to " CE BMET A  47 " =    1.753
peak=   -3.429 closest distance to " O   HOH Z 102 " =    1.636
peak=   -3.425 closest distance to " NE2 GLN A 194 " =    1.793
peak=   -3.425 closest distance to " O   HOH Z  44 " =    2.172
peak=   -3.412 closest distance to " CD1 LEU A  25 " =    2.473
peak=   -3.410 closest distance to " N   THR A 235 " =    1.334
peak=   -3.409 closest distance to " O   HOH Z 292 " =    4.539
peak=   -3.405 closest distance to " CD2 LEU A 300 " =    2.710
peak=   -3.404 closest distance to " O   HOH Z  60 " =    2.003
peak=   -3.398 closest distance to " O   HOH Z  13 " =    1.501
peak=   -3.396 closest distance to " CG1 VAL A 230 " =    1.905
peak=   -3.393 closest distance to " NE2 GLN A  88 " =    0.953
peak=   -3.390 closest distance to " O   HOH Z 295 " =    1.607
peak=   -3.388 closest distance to " N   ASP A 171 " =    2.347
peak=   -3.385 closest distance to " C   ASP A 231 " =    2.534
peak=   -3.380 closest distance to " O   HOH Z 353 " =    2.071
peak=   -3.378 closest distance to " O   HOH Z 123 " =    2.446
peak=   -3.370 closest distance to " C   ILE A 239 " =    2.110
peak=   -3.369 closest distance to " N   VAL A 230 " =    1.094
peak=   -3.369 closest distance to " CG1 VAL A 296 " =    1.274
peak=   -3.365 closest distance to " CD  LYS A 289 " =    2.556
peak=   -3.362 closest distance to " N   SER A 212 " =    2.017
peak=   -3.355 closest distance to " O   HOH Z 369 " =    2.271
peak=   -3.355 closest distance to " NE2 GLN A 103 " =    1.748
peak=   -3.348 closest distance to " NZ  LYS A 119 " =    3.512
peak=   -3.344 closest distance to " OG  SER A  62 " =    1.657
peak=   -3.343 closest distance to " OD2 ASP A  50 " =    2.327
peak=   -3.329 closest distance to " CB  ASN A  69 " =    1.170
peak=   -3.322 closest distance to " O   HOH Z 311 " =    3.759
peak=   -3.311 closest distance to " C   LEU A 143 " =    1.011
peak=   -3.306 closest distance to " C   ASN A 187 " =    1.940
peak=   -3.299 closest distance to " NH2 ARG A  79 " =    1.576
peak=   -3.299 closest distance to " OG  SER A 206 " =    1.695
peak=   -3.297 closest distance to " O   HOH Z 191 " =    5.442
peak=   -3.296 closest distance to " O   HOH Z  47 " =    1.589
peak=   -3.290 closest distance to " O   HOH Z 262 " =    2.839
peak=   -3.283 closest distance to " O   HOH Z 175 " =    4.331
peak=   -3.282 closest distance to " O   HOH Z  38 " =    1.605
peak=   -3.282 closest distance to " O   HOH Z  43 " =    1.694
peak=   -3.278 closest distance to " CG2 ILE A  20 " =    2.937
peak=   -3.267 closest distance to " OG ASER A 134 " =    1.260
peak=   -3.263 closest distance to " O   SER A  95 " =    1.708
peak=   -3.260 closest distance to " O   HOH Z 313 " =    1.125
peak=   -3.259 closest distance to " O   HOH Z 134 " =    2.796
peak=   -3.255 closest distance to " O   HOH Z 234 " =    4.157
peak=   -3.255 closest distance to " CD2 LEU A 167 " =    1.786
peak=   -3.254 closest distance to " C   SER A 206 " =    1.523
peak=   -3.249 closest distance to " CB  ASP A 132 " =    2.395
peak=   -3.247 closest distance to " O   HOH Z 136 " =    2.226
peak=   -3.245 closest distance to " CD2 TYR A 293 " =    2.145
peak=   -3.242 closest distance to " O   HOH Z 165 " =    1.851
peak=   -3.235 closest distance to " O   GLY A  75 " =    1.871
peak=   -3.234 closest distance to " O   PRO A 198 " =    1.316
peak=   -3.233 closest distance to " CB  ASN A  39 " =    2.249
peak=   -3.232 closest distance to " CD  PRO A 243 " =    2.101
peak=   -3.232 closest distance to " O   HOH Z 283 " =    2.241
peak=   -3.229 closest distance to " O   VAL A 125 " =    2.326
peak=   -3.227 closest distance to " CG  LEU A 228 " =    1.008
peak=   -3.223 closest distance to " N   ASN A  60 " =    1.313
peak=   -3.221 closest distance to " CD  GLN A 223 " =    1.173
peak=   -3.217 closest distance to " O   HOH Z 222 " =    1.519
peak=   -3.216 closest distance to " CG  GLU A  53 " =    1.589
peak=   -3.214 closest distance to " O   HOH Z 128 " =    2.588
peak=   -3.207 closest distance to " N   SER A   3 " =    2.011
peak=   -3.204 closest distance to " O   HOH Z 377 " =    1.782
peak=   -3.197 closest distance to " OG  SER A  87 " =    1.466
peak=   -3.191 closest distance to " O   HOH Z 372 " =    2.364
peak=   -3.187 closest distance to " O   HOH Z 174 " =    2.388
peak=   -3.187 closest distance to " CA  GLY A  98 " =    1.913
peak=   -3.187 closest distance to " N   SER A 276 " =    1.331
peak=   -3.185 closest distance to " O   HOH Z 113 " =    2.399
peak=   -3.185 closest distance to " CA  GLY A 203 " =    2.386
peak=   -3.184 closest distance to " NH2 ARG A  66 " =    1.856
peak=   -3.182 closest distance to " NE2 GLN A  58 " =    2.783
peak=   -3.181 closest distance to " C   ASP A 270 " =    1.205
peak=   -3.178 closest distance to " OXT GLY A 302 " =    3.445
peak=   -3.177 closest distance to " N   HIS A 115 " =    2.105
peak=   -3.174 closest distance to " CD1 LEU A 228 " =    2.234
peak=   -3.171 closest distance to " O   LEU A 167 " =    1.450
peak=   -3.167 closest distance to " O   HOH Z 423 " =    2.052
peak=   -3.167 closest distance to " O   ALA A  10 " =    1.767
peak=   -3.165 closest distance to " CG1 VAL A 197 " =    2.245
peak=   -3.162 closest distance to " CD  PRO A 213 " =    2.168
peak=   -3.160 closest distance to " O   SER A  22 " =    2.259
peak=   -3.160 closest distance to " O   HOH Z 384 " =    3.389
peak=   -3.159 closest distance to " O   HOH Z 431 " =    1.928
peak=   -3.158 closest distance to " NE2 GLN A 278 " =    1.961
peak=   -3.157 closest distance to " CG1 VAL A 112 " =    2.915
peak=   -3.156 closest distance to " O   ALA A 161 " =    1.707
peak=   -3.154 closest distance to " O   HOH Z 339 " =    1.763
peak=   -3.150 closest distance to " NH1 ARG A  36 " =    2.056
peak=   -3.149 closest distance to " O   MET A  40 " =    2.673
peak=   -3.147 closest distance to " O   HOH Z 241 " =    1.282
peak=   -3.144 closest distance to " O   HOH Z 198 " =    2.265
peak=   -3.141 closest distance to " CB  GLN A  11 " =    1.754
peak=   -3.140 closest distance to " O   HOH Z  19 " =    2.282
peak=   -3.139 closest distance to " CG1 VAL A  67 " =    3.029
peak=   -3.128 closest distance to " O   HOH Z 313 " =    1.607
peak=   -3.128 closest distance to " OG  SER A  26 " =    1.199
peak=   -3.125 closest distance to " OG BSER A 134 " =    1.779
peak=   -3.106 closest distance to " CD1 LEU A   5 " =    2.548
peak=   -3.095 closest distance to " O   HOH Z   6 " =    1.697
peak=   -3.083 closest distance to " O   HOH Z 350 " =    1.932
peak=   -3.075 closest distance to " O   SER A 276 " =    1.703
peak=   -3.065 closest distance to " CG  PRO A 163 " =    2.601
peak=   -3.063 closest distance to " CA  GLY A 133 " =    1.990
peak=   -3.062 closest distance to " O   HOH Z 193 " =    1.941
peak=   -3.062 closest distance to " O   HOH Z 298 " =    2.617
peak=   -3.054 closest distance to " O   HOH Z 139 " =    3.116
peak=   -3.043 closest distance to " O   HOH Z 389 " =    4.819
peak=   -3.040 closest distance to " ND2 ASN A  60 " =    1.395
peak=   -3.030 closest distance to " CD  GLN A  88 " =    0.792

================= 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    :  0.4096 0.3947   6.192834e+00   6.161856e+00
   1_bss:  0.4015 0.3813   6.190442e+00   6.143753e+00
   1_xyz:  0.2832 0.3039   5.921481e+00   5.973069e+00
   1_adp:  0.2073 0.2344   5.632820e+00   5.752079e+00
   1_occ:  0.2066 0.2344   5.631221e+00   5.753239e+00
   2_bss:  0.2014 0.2295   5.628985e+00   5.745836e+00
   2_xyz:  0.1463 0.1784   5.341265e+00   5.515147e+00
   2_adp:  0.1363 0.1704   5.279808e+00   5.465709e+00
   2_occ:  0.1362 0.1706   5.279905e+00   5.466491e+00
   3_bss:  0.1359 0.1704   5.280056e+00   5.466064e+00
   3_xyz:  0.1186 0.1576   5.176012e+00   5.399031e+00
   3_adp:  0.1139 0.1549   5.148536e+00   5.382147e+00
   3_occ:  0.1138 0.1548   5.148191e+00   5.381928e+00
   4_bss:  0.1138 0.1549   5.147808e+00   5.381589e+00
   4_xyz:  0.1149 0.1564   5.159141e+00   5.391857e+00
   4_adp:  0.1160 0.1560   5.161773e+00   5.387856e+00
   4_occ:  0.1160 0.1561   5.161916e+00   5.388268e+00
   5_bss:  0.1160 0.1561   5.161771e+00   5.388175e+00
   5_xyz:  0.1133 0.1551   5.145407e+00   5.380387e+00
   5_adp:  0.1126 0.1555   5.145170e+00   5.385803e+00
   5_occ:  0.1125 0.1556   5.144609e+00   5.385532e+00
   5_bss:  0.1124 0.1556   5.144582e+00   5.385528e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.342  21.773   7.252   8.683   8.211   0.000   0.000   0.000
   1_xyz:  0.342  21.773   7.252   8.683   8.211   0.000   0.000   0.000
   1_adp:  0.342  21.773   7.252   8.683   8.211   0.000   0.000   0.000
   1_occ:  0.342  21.773   7.252   8.683   8.211   0.000   0.000   0.000
   2_bss:  0.336  41.534   4.035   5.138   5.412   0.000   0.000   0.000
   2_xyz:  0.336  41.534   4.035   5.138   5.412   0.000   0.000   0.000
   2_adp:  0.336  41.534   4.035   5.138   5.412   0.000   0.000   0.000
   2_occ:  0.336  41.534   4.035   5.138   5.412   0.000   0.000   0.000
   3_bss:  0.328  41.534   3.367   4.115   4.800   0.000   0.000   0.000
   3_xyz:  0.328  41.534   3.367   4.115   4.800   0.000   0.000   0.000
   3_adp:  0.328  41.534   3.367   4.115   4.800   0.000   0.000   0.000
   3_occ:  0.328  41.534   3.367   4.115   4.800   0.000   0.000   0.000
   4_bss:  0.319  41.534   3.367   4.115   4.800   0.000   0.000   0.000
   4_xyz:  0.319  41.534   3.367   4.115   4.800   0.000   0.000   0.000
   4_adp:  0.319  41.534   3.367   4.115   4.800   0.000   0.000   0.000
   4_occ:  0.319  41.534   3.367   4.115   4.800   0.000   0.000   0.000
   5_bss:  0.320  41.534   3.334   3.944   4.766   0.000   0.000   0.000
   5_xyz:  0.320  41.534   3.334   3.944   4.766   0.000   0.000   0.000
   5_adp:  0.320  41.534   3.334   3.944   4.766   0.000   0.000   0.000
   5_occ:  0.320  41.534   3.334   3.944   4.766   0.000   0.000   0.000
   5_bss:  0.320  45.611  -0.650  -0.109   0.759   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.164 0.6193  0.6751    43250.844
   1_bss:  41.368 0.6269  0.8707    40403.468
   1_xyz:  32.010 0.7347  0.9911    24710.653
   1_adp:  22.530 0.8380  1.0704    13790.807
   1_occ:  22.551 0.8378  1.0697    13810.018
   2_bss:  22.336 0.8398  0.9542    13546.586
   2_xyz:  16.720 0.8921  0.9909     8196.602
   2_adp:  15.613 0.9019  0.9985     7469.809
   2_occ:  15.628 0.9018  0.9982     7481.489
   3_bss:  15.622 0.9018  0.9698     7482.440
   3_xyz:  14.143 0.9139  0.9750     6463.917
   3_adp:  13.800 0.9168  0.9755     6229.315
   3_occ:  13.790 0.9168  0.9755     6227.536
   4_bss:  13.782 0.9169  0.9754     6219.327
   4_xyz:  13.907 0.9162  0.9740     6350.238
   4_adp:  13.785 0.9173  0.9742     6308.138
   4_occ:  13.793 0.9172  0.9741     6315.087
   5_bss:  13.790 0.9172  0.9714     6313.579
   5_xyz:  13.649 0.9182  0.9721     6215.069
   5_adp:  13.776 0.9172  0.9698     6267.163
   5_occ:  13.766 0.9173  0.9697     6264.620
   5_bss:  13.765 0.9173  0.9719     6264.883
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3886e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3886e+01
   1_xyz:   1.429  0.010  0.098 17.701  0.006  4.124   1.0644e-01
   1_adp:   1.429  0.010  0.098 17.701  0.006  4.124   1.0644e-01
   1_occ:   1.429  0.010  0.098 17.701  0.006  4.124   1.0644e-01
   2_bss:   1.429  0.010  0.098 17.701  0.006  4.124   1.0644e-01
   2_xyz:   0.964  0.006  0.073 15.951  0.003  4.126   5.8550e-02
   2_adp:   0.964  0.006  0.073 15.951  0.003  4.126   5.8550e-02
   2_occ:   0.964  0.006  0.073 15.951  0.003  4.126   5.8550e-02
   3_bss:   0.964  0.006  0.073 15.951  0.003  4.126   5.8550e-02
   3_xyz:   1.052  0.008  0.087 15.722  0.004  4.134   6.6181e-02
   3_adp:   1.052  0.008  0.087 15.722  0.004  4.134   6.6181e-02
   3_occ:   1.052  0.008  0.087 15.722  0.004  4.134   6.6181e-02
   4_bss:   1.052  0.008  0.087 15.722  0.004  4.134   6.6181e-02
   4_xyz:   0.913  0.006  0.075 15.278  0.003  4.134   5.3450e-02
   4_adp:   0.913  0.006  0.075 15.278  0.003  4.134   5.3450e-02
   4_occ:   0.913  0.006  0.075 15.278  0.003  4.134   5.3450e-02
   5_bss:   0.913  0.006  0.075 15.278  0.003  4.134   5.3450e-02
   5_xyz:   0.982  0.007  0.081 15.326  0.003  4.123   5.9400e-02
   5_adp:   0.982  0.007  0.081 15.326  0.003  4.123   5.9400e-02
   5_occ:   0.982  0.007  0.081 15.326  0.003  4.123   5.9400e-02
   5_bss:   0.982  0.007  0.081 15.326  0.003  4.123   5.9400e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9870e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9870e+00
   1_xyz:  11.407  0.122  0.394 87.266  0.038  2.272   7.9051e-02
   1_adp:  11.407  0.122  0.394 87.266  0.038  2.272   7.9051e-02
   1_occ:  11.407  0.122  0.394 87.266  0.038  2.272   7.9051e-02
   2_bss:  11.407  0.122  0.394 87.266  0.038  2.272   7.9051e-02
   2_xyz:   7.083  0.053  0.385 82.136  0.032  2.348   4.0723e-02
   2_adp:   7.083  0.053  0.385 82.136  0.032  2.348   4.0723e-02
   2_occ:   7.083  0.053  0.385 82.136  0.032  2.348   4.0723e-02
   3_bss:   7.083  0.053  0.385 82.136  0.032  2.348   4.0723e-02
   3_xyz:   7.034  0.046  0.645 83.670  0.038  2.343   4.4176e-02
   3_adp:   7.034  0.046  0.645 83.670  0.038  2.343   4.4176e-02
   3_occ:   7.034  0.046  0.645 83.670  0.038  2.343   4.4176e-02
   4_bss:   7.034  0.046  0.645 83.670  0.038  2.343   4.4176e-02
   4_xyz:   6.820  0.041  0.470 82.226  0.038  2.405   4.1833e-02
   4_adp:   6.820  0.041  0.470 82.226  0.038  2.405   4.1833e-02
   4_occ:   6.820  0.041  0.470 82.226  0.038  2.405   4.1833e-02
   5_bss:   6.820  0.041  0.470 82.226  0.038  2.405   4.1833e-02
   5_xyz:   6.798  0.042  0.551 83.110  0.037  2.358   3.5321e-02
   5_adp:   6.798  0.042  0.551 83.110  0.037  2.358   3.5321e-02
   5_occ:   6.798  0.042  0.551 83.110  0.037  2.358   3.5321e-02
   5_bss:   6.798  0.042  0.551 83.110  0.037  2.358   3.5321e-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:  47.97   0.00   9.52  43.47   0.00   6.56  47.97   0.00  25.68
   1_occ:  47.97   0.00   9.52  43.47   0.00   6.56  47.97   0.00  25.68
   2_bss:  47.97   0.00   9.52  43.47   0.00   6.56  47.97   0.00  25.68
   2_xyz:  47.97   0.00   9.52  43.47   0.00   6.56  47.97   0.00  25.68
   2_adp:  79.59   0.00  10.02  79.59   0.00   6.60  49.11   0.90  28.62
   2_occ:  79.59   0.00  10.02  79.59   0.00   6.60  49.11   0.90  28.62
   3_bss:  79.59   0.00  10.02  79.59   0.00   6.60  49.11   0.90  28.62
   3_xyz:  79.59   0.00  10.02  79.59   0.00   6.60  49.11   0.90  28.62
   3_adp:  70.13   0.00  10.86  70.13   0.00   6.83  66.03   0.00  32.81
   3_occ:  70.13   0.00  10.86  70.13   0.00   6.83  66.03   0.00  32.81
   4_bss:  70.13   0.00  10.86  70.13   0.00   6.83  66.03   0.00  32.81
   4_xyz:  70.13   0.00  10.86  70.13   0.00   6.83  66.03   0.00  32.81
   4_adp:  69.86   0.00  10.47  69.86   0.00   6.69  62.14   0.66  31.03
   4_occ:  69.86   0.00  10.47  69.86   0.00   6.69  62.14   0.66  31.03
   5_bss:  69.86   0.00  10.47  69.86   0.00   6.69  62.14   0.66  31.03
   5_xyz:  69.86   0.00  10.47  69.86   0.00   6.69  62.14   0.66  31.03
   5_adp:  70.58   0.00  10.58  70.58   0.00   6.73  62.62   0.46  31.51
   5_occ:  70.58   0.00  10.58  70.58   0.00   6.73  62.62   0.46  31.51
   5_bss:  74.66   4.08  14.65  74.66   4.08  10.81  66.70   4.54  35.59
------------------------------------------------------------------------
 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:    1.161    0.016    0.397
   1_adp:    1.161    0.016    0.397
   1_occ:    1.161    0.016    0.397
   2_bss:    1.161    0.016    0.397
   2_xyz:    1.470    0.009    0.467
   2_adp:    1.470    0.009    0.467
   2_occ:    1.470    0.009    0.467
   3_bss:    1.470    0.009    0.467
   3_xyz:    1.402    0.017    0.492
   3_adp:    1.402    0.017    0.492
   3_occ:    1.402    0.017    0.492
   4_bss:    1.402    0.017    0.492
   4_xyz:    1.540    0.025    0.498
   4_adp:    1.540    0.025    0.498
   4_occ:    1.540    0.025    0.498
   5_bss:    1.540    0.025    0.498
   5_xyz:    1.530    0.038    0.503
   5_adp:    1.530    0.038    0.503
   5_occ:    1.530    0.038    0.503
   5_bss:    1.530    0.038    0.503
------------------------------------------------------------------------

CPU time actual refinement: 331.14


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_676/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_676/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_676/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_676/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_676/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.98 
  Macro-tasks:
    bulk solvent and scale       = 40.68  
    individual site refinement   = 143.39 
    weights calculation          = 32.13  
    collect and process          = 6.47   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 222.78 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 100.63 
    alpha_beta                      = 8.07   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 113.65 
    fmodel                         = 7.22   
    r_factors                      = 0.23   
    phase_errors                   = 10.81  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 243.22 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.525 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    668 calls, 100.28 s
gradients_fft:          612 calls,  98.89 s

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

# Date 2008-01-16 Time 02:09:28 PST -0800 (1200478168.15 s)
Start R-work = 0.4096, R-free = 0.3947 (no bulk solvent and anisotropic scale)
Final R-work = 0.1301, R-free = 0.1714 (no bulk solvent and anisotropic scale)

Start R-work = 0.4015, R-free = 0.3813
Final R-work = 0.1124, R-free = 0.1556