# Date 2008-01-16 Time 03:14:41 PST -0800 (1200482081.64 s)
#phil __OFF__

Command line arguments: "../1159.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26656
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1159

-------------------------------------------------------------------------------
  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: (71.655, 47.1647, 85.9581, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99111
Completeness in resolution range: 0.954444
Completeness with d_max=infinity: 0.951569

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9911

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: (71.655, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99111
Completeness in resolution range: 0.954444
Completeness with d_max=infinity: 0.951569

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2611 [2152/2181]  1941   211   9.8%
  bin  2:  4.2611 -  3.3946 [2073/2089]  1863   210  10.1%
  bin  3:  3.3946 -  2.9691 [2032/2051]  1827   205  10.1%
  bin  4:  2.9691 -  2.6993 [2039/2069]  1838   201   9.9%
  bin  5:  2.6993 -  2.5068 [2022/2041]  1819   203  10.0%
  bin  6:  2.5068 -  2.3595 [1996/2021]  1790   206  10.3%
  bin  7:  2.3595 -  2.2418 [1986/2019]  1790   196   9.9%
  bin  8:  2.2418 -  2.1445 [1987/2018]  1793   194   9.8%
  bin  9:  2.1445 -  2.0621 [1985/2027]  1784   201  10.1%
  bin 10:  2.0621 -  1.9911 [1317/2008]  1185   132  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1159/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: 0.15 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:
        1.68 -     2.32: 5
        2.32 -     2.97: 1720
        2.97 -     3.61: 4492
        3.61 -     4.26: 9125
        4.26 -     4.90: 12694
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.680 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.105 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.174 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28031 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_1159/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1159/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 = 71.655 47.16465 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4450   r_free= 0.4359   ksol= 0.00   Bsol= 0.00   scale= 0.808    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.244713                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7529 0.99   1395  155 0.3743 0.3543      6.5469      6.4731|
|  2:  4.7529 -  3.7919 0.99   1350  146 0.3464 0.3664      6.6935      6.7084|
|  3:  3.7919 -  3.3182 0.99   1322  149 0.3916 0.3574      6.5837      6.6017|
|  4:  3.3182 -  3.0174 0.99   1321  152 0.4200 0.3955      6.4724      6.3904|
|  5:  3.0174 -  2.8026 0.99   1305  141 0.4624 0.4889      6.3308      6.3838|
|  6:  2.8026 -  2.6383 0.99   1292  145 0.4749 0.4724      6.2438      6.2148|
|  7:  2.6383 -  2.5068 0.99   1303  142 0.5012 0.4913      6.2417      6.2217|
|  8:  2.5068 -  2.3981 0.98   1270  146 0.4905 0.4733      6.1374      6.1284|
|  9:  2.3981 -  2.3061 0.98   1287  146 0.4846 0.5072      6.1095      6.1349|
| 10:  2.3061 -  2.2268 0.99   1271  137 0.4985 0.4817      6.0874      6.0618|
| 11:  2.2268 -  2.1573 0.99   1290  141 0.4932 0.4741      6.0265       6.013|
| 12:  2.1573 -  2.0958 0.97   1260  136 0.5083 0.5258      5.9701      6.0122|
| 13:  2.0958 -  2.0408 0.99   1270  143 0.5165 0.4993      5.8794      5.8256|
| 14:  2.0408 -  1.9911 0.53    694   80 0.5121 0.4172      5.8383      5.7181|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7529  1395   155  0.73  31.38   0.80     0.76      59910.85|
|  2:  4.7529 -  3.7919  1350   146  0.76  29.89   0.90     0.80      79896.12|
|  3:  3.7919 -  3.3182  1322   149  0.68  37.43   0.85     0.77      85743.31|
|  4:  3.3182 -  3.0174  1321   152  0.60  43.56   0.82     0.69      80343.32|
|  5:  3.0174 -  2.8026  1305   141  0.50  51.75   0.75     0.59      69857.50|
|  6:  2.8026 -  2.6383  1292   145  0.47  54.42   0.76     0.54      62661.34|
|  7:  2.6383 -  2.5068  1303   142  0.47  54.65   0.74     0.52      56352.97|
|  8:  2.5068 -  2.3981  1270   146  0.44  56.60   0.72     0.52      52005.18|
|  9:  2.3981 -  2.3061  1287   146  0.46  55.09   0.75     0.52      46149.80|
| 10:  2.3061 -  2.2268  1271   137  0.45  56.12   0.76     0.51      42655.11|
| 11:  2.2268 -  2.1573  1290   141  0.43  57.77   0.77     0.49      39681.19|
| 12:  2.1573 -  2.0958  1260   136  0.41  59.64   0.75     0.48      38752.95|
| 13:  2.0958 -  2.0408  1270   143  0.41  59.29   0.73     0.49      32304.99|
| 14:  2.0408 -  1.9911   694    80  0.50  52.08   0.72     0.54      23060.12|
|alpha:            min =        0.48 max =            0.80 mean =         0.59|
|beta:             min =    23060.12 max =        85743.31 mean =     56334.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           90.00 mean =        49.66|
|phase err.(test): min =        0.00 max =           89.86 mean =        49.59|
|-----------------------------------------------------------------------------|

============================== 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 = 10.117792             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.054   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.752169              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.875   (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:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1494 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2611 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3867 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5013 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6538 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7641 |
|-----------------------------------------------------------------------------|
|-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 |       54.160 |
| 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 |       1.635 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    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 = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4522   r_free= 0.4418   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.247415                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4373   r_free= 0.4237   ksol= 0.30   Bsol= 20.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.47,7.95,7.42,0.00,0.00,0.00); trace/3= 8.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.240436                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.108554              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.010   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.731461              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.279   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4373      final r-factor (work) = 0.3339          |
| start r-factor (free) = 0.4237      final r-factor (free) = 0.3654          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.6214 = 9.11 * 0.50 * 6.2493 + 1.00 * 54.1601                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.9247 = 9.11 * 0.50 * 6.1030 + 1.00 * 0.1297                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3339      final r-factor (work) = 0.2799          |
| start r-factor (free) = 0.3654      final r-factor (free) = 0.3226          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4785 = 0.73 * 1.00 * 6.1030 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3778 = 0.73 * 1.00 * 5.9686 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    56.00   10.45    None  None   None       |
|    all(noH): 2823   0      0.00    56.00   10.45    None  None   None       |
|    Sol.    : 438    0      0.00    56.00   26.27    None  None   None       |
|    Mac.    : 2385   0      0.00    54.15   7.55     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.600: 1207   |   5:    28.002 -  33.602:   95        |
|      1:     5.600 -  11.201:  742   |   6:    33.602 -  39.202:   74        |
|      2:    11.201 -  16.801:  329   |   7:    39.202 -  44.803:   48        |
|      3:    16.801 -  22.401:  166   |   8:    44.803 -  50.403:   26        |
|      4:    22.401 -  28.002:  122   |   9:    50.403 -  56.003:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2799 r_free = 0.3226             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2792 r_free = 0.3227             target_work(ml) = 5.919         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2792   r_free= 0.3227   ksol= 0.30   Bsol= 20.00   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.47,7.95,7.42,0.00,0.00,0.00); trace/3= 8.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.919464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2767   r_free= 0.3177   ksol= 0.33   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.19,4.79,5.04,0.00,0.00,0.00); trace/3= 5.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.920046                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.679481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.824   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.447843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.073  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2767      final r-factor (work) = 0.1852          |
| start r-factor (free) = 0.3177      final r-factor (free) = 0.2353          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0813 = 5.68 * 0.50 * 5.9694 + 1.00 * 0.1297                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4273 = 5.68 * 0.50 * 5.7585 + 1.00 * 0.0747                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1852      final r-factor (work) = 0.1653          |
| start r-factor (free) = 0.2353      final r-factor (free) = 0.2133          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5991 = 0.45 * 1.00 * 5.7585 + 1.00 * 0.0202                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5130 = 0.45 * 1.00 * 5.5135 + 1.00 * 0.0438                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.27   11.59    None  None   None       |
|    all(noH): 2823   0      0.00    71.27   11.59    None  None   None       |
|    Sol.    : 438    0      0.66    71.27   33.50    None  None   None       |
|    Mac.    : 2385   0      0.00    69.18   7.56     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 -   7.127: 1520   |   5:    35.636 -  42.764:   83        |
|      1:     7.127 -  14.255:  652   |   6:    42.764 -  49.891:   93        |
|      2:    14.255 -  21.382:  206   |   7:    49.891 -  57.018:   38        |
|      3:    21.382 -  28.509:   98   |   8:    57.018 -  64.145:   16        |
|      4:    28.509 -  35.636:  103   |   9:    64.145 -  71.273:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1653 r_free = 0.2133             target_work(ml) = 5.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1652 r_free = 0.2132             target_work(ml) = 5.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1652   r_free= 0.2132   ksol= 0.33   Bsol= 50.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.19,4.79,5.04,0.00,0.00,0.00); trace/3= 5.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.466158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1635   r_free= 0.2107   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.81,3.38,3.98,0.00,0.00,0.00); trace/3= 3.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.464964                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.305803              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.892  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.856145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.078   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1635      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.2107      final r-factor (free) = 0.1753          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2056 = 3.31 * 0.50 * 5.5242 + 1.00 * 0.0747                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9529 = 3.31 * 0.50 * 5.3716 + 1.00 * 0.0742                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1301      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1753      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6164 = 0.86 * 1.00 * 5.3716 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5028 = 0.86 * 1.00 * 5.2437 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.20   12.07    None  None   None       |
|    all(noH): 2823   0      0.00    80.20   12.07    None  None   None       |
|    Sol.    : 438    0      0.68    79.41   35.67    None  None   None       |
|    Mac.    : 2385   0      0.00    80.20   7.73     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 -   8.020: 1659   |   5:    40.098 -  48.118:   92        |
|      1:     8.020 -  16.039:  570   |   6:    48.118 -  56.137:   77        |
|      2:    16.039 -  24.059:  172   |   7:    56.137 -  64.157:   36        |
|      3:    24.059 -  32.078:  102   |   8:    64.157 -  72.176:   12        |
|      4:    32.078 -  40.098:   93   |   9:    72.176 -  80.196:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1705             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1235 r_free = 0.1704             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1704   ksol= 0.33   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.81,3.38,3.98,0.00,0.00,0.00); trace/3= 3.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.231684                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1700   ksol= 0.33   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,3.05,3.74,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.231836                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.583213              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.291  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.173774              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.453  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1237      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8488 = 2.58 * 0.50 * 5.2451 + 1.00 * 0.0742                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7996 = 2.58 * 0.50 * 5.2098 + 1.00 * 0.0706                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9186 = 0.17 * 1.00 * 5.2098 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9134 = 0.17 * 1.00 * 5.1981 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.39   11.70    None  None   None       |
|    all(noH): 2823   0      0.00    79.39   11.70    None  None   None       |
|    Sol.    : 438    0      1.21    78.74   33.91    None  None   None       |
|    Mac.    : 2385   0      0.00    79.39   7.62     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 -   7.939: 1683   |   5:    39.695 -  47.634:   86        |
|      1:     7.939 -  15.878:  570   |   6:    47.634 -  55.573:   66        |
|      2:    15.878 -  23.817:  162   |   7:    55.573 -  63.511:   29        |
|      3:    23.817 -  31.756:  106   |   8:    63.511 -  71.450:    8        |
|      4:    31.756 -  39.695:  104   |   9:    71.450 -  79.389:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1633             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1631             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1631   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,3.05,3.74,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.189767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1631   ksol= 0.32   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,2.97,3.70,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.189615                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.577456              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.532  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.555438              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.253  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1699 = 1.58 * 0.50 * 5.1973 + 1.00 * 0.0706                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1562 = 1.58 * 0.50 * 5.1931 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1186      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8946 = 0.56 * 1.00 * 5.1931 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8918 = 0.56 * 1.00 * 5.1848 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.19   11.83    None  None   None       |
|    all(noH): 2823   0      0.00    81.19   11.83    None  None   None       |
|    Sol.    : 438    0      1.25    79.48   34.40    None  None   None       |
|    Mac.    : 2385   0      0.00    81.19   7.69     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 -   8.120: 1676   |   5:    40.597 -  48.717:   86        |
|      1:     8.120 -  16.239:  569   |   6:    48.717 -  56.836:   64        |
|      2:    16.239 -  24.358:  161   |   7:    56.836 -  64.956:   26        |
|      3:    24.358 -  32.478:  115   |   8:    64.956 -  73.075:    6        |
|      4:    32.478 -  40.597:  112   |   9:    73.075 -  81.195:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1636             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1636             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1636   ksol= 0.32   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,2.97,3.70,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.189219                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7529 0.99   1395  155 0.1008 0.1318      5.3906      5.5304|
|  2:  4.7529 -  3.7919 0.99   1350  146 0.0898 0.1113      5.4627      5.6417|
|  3:  3.7919 -  3.3182 0.99   1322  149 0.1095 0.1573       5.499      5.8787|
|  4:  3.3182 -  3.0174 0.99   1321  152 0.1239 0.1595      5.4849      5.6193|
|  5:  3.0174 -  2.8026 0.99   1305  141 0.1408 0.1858      5.3813      5.5926|
|  6:  2.8026 -  2.6383 0.99   1292  145 0.1295 0.1946      5.2637      5.5214|
|  7:  2.6383 -  2.5068 0.99   1303  142 0.1324 0.1703      5.2278       5.408|
|  8:  2.5068 -  2.3981 0.98   1270  146 0.1256 0.1845      5.1115      5.3853|
|  9:  2.3981 -  2.3061 0.98   1287  146 0.1229 0.1868      5.0868      5.3737|
| 10:  2.3061 -  2.2268 0.99   1271  137 0.1185 0.1747      5.0011      5.2251|
| 11:  2.2268 -  2.1573 0.99   1290  141 0.1230 0.1871      4.9963      5.3321|
| 12:  2.1573 -  2.0958 0.97   1260  136 0.1140 0.1654      4.9084       5.117|
| 13:  2.0958 -  2.0408 0.99   1270  143 0.1260 0.1884      4.8481      5.1315|
| 14:  2.0408 -  1.9911 0.53    694   80 0.1089 0.1822      4.6964      4.9787|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7529  1395   155  0.94   8.78   0.97     0.95       7058.36|
|  2:  4.7529 -  3.7919  1350   146  0.95   8.13   1.00     0.99       9116.59|
|  3:  3.7919 -  3.3182  1322   149  0.93  11.78   1.02     1.01      10887.54|
|  4:  3.3182 -  3.0174  1321   152  0.92  13.99   1.00     0.97      10913.01|
|  5:  3.0174 -  2.8026  1305   141  0.89  17.19   0.99     0.97       9251.50|
|  6:  2.8026 -  2.6383  1292   145  0.89  16.82   0.98     0.95       7909.26|
|  7:  2.6383 -  2.5068  1303   142  0.90  16.25   0.98     0.95       6904.85|
|  8:  2.5068 -  2.3981  1270   146  0.90  16.47   0.98     0.96       5824.79|
|  9:  2.3981 -  2.3061  1287   146  0.90  16.29   1.00     0.97       5596.42|
| 10:  2.3061 -  2.2268  1271   137  0.90  16.12   0.99     0.95       4646.18|
| 11:  2.2268 -  2.1573  1290   141  0.89  17.11   0.99     0.95       4798.50|
| 12:  2.1573 -  2.0958  1260   136  0.91  15.48   1.00     0.98       4232.79|
| 13:  2.0958 -  2.0408  1270   143  0.89  17.62   0.99     0.98       3765.70|
| 14:  2.0408 -  1.9911   694    80  0.90  15.81   0.97     0.93       2749.92|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2749.92 max =        10913.01 mean =      6861.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.74|
|phase err.(test): min =        0.00 max =           89.48 mean =        14.11|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1636   ksol= 0.32   Bsol= 53.24   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.19,-0.28,0.47,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.189225                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1636   ksol= 0.32   Bsol= 53.24   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.19,-0.28,0.47,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.189225                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7529 0.99   1395  155 0.1008 0.1318      5.3906      5.5304|
|  2:  4.7529 -  3.7919 0.99   1350  146 0.0898 0.1113      5.4627      5.6417|
|  3:  3.7919 -  3.3182 0.99   1322  149 0.1095 0.1573      5.4989      5.8787|
|  4:  3.3182 -  3.0174 0.99   1321  152 0.1239 0.1595      5.4849      5.6193|
|  5:  3.0174 -  2.8026 0.99   1305  141 0.1408 0.1858      5.3814      5.5926|
|  6:  2.8026 -  2.6383 0.99   1292  145 0.1295 0.1945      5.2637      5.5213|
|  7:  2.6383 -  2.5068 0.99   1303  142 0.1324 0.1703      5.2277       5.408|
|  8:  2.5068 -  2.3981 0.98   1270  146 0.1256 0.1845      5.1115      5.3853|
|  9:  2.3981 -  2.3061 0.98   1287  146 0.1229 0.1868      5.0868      5.3736|
| 10:  2.3061 -  2.2268 0.99   1271  137 0.1185 0.1747      5.0011      5.2252|
| 11:  2.2268 -  2.1573 0.99   1290  141 0.1230 0.1872      4.9963      5.3322|
| 12:  2.1573 -  2.0958 0.97   1260  136 0.1140 0.1654      4.9086      5.1171|
| 13:  2.0958 -  2.0408 0.99   1270  143 0.1260 0.1884      4.8482      5.1316|
| 14:  2.0408 -  1.9911 0.53    694   80 0.1089 0.1822      4.6964      4.9786|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7529  1395   155  0.94   8.78   0.97     0.95       7057.95|
|  2:  4.7529 -  3.7919  1350   146  0.95   8.13   1.00     0.99       9115.79|
|  3:  3.7919 -  3.3182  1322   149  0.93  11.78   1.02     1.01      10886.44|
|  4:  3.3182 -  3.0174  1321   152  0.92  13.99   1.00     0.97      10913.21|
|  5:  3.0174 -  2.8026  1305   141  0.89  17.19   0.99     0.97       9251.16|
|  6:  2.8026 -  2.6383  1292   145  0.89  16.82   0.98     0.95       7908.92|
|  7:  2.6383 -  2.5068  1303   142  0.90  16.25   0.98     0.95       6904.02|
|  8:  2.5068 -  2.3981  1270   146  0.90  16.47   0.98     0.96       5823.91|
|  9:  2.3981 -  2.3061  1287   146  0.90  16.29   1.00     0.97       5595.76|
| 10:  2.3061 -  2.2268  1271   137  0.90  16.12   0.99     0.95       4646.41|
| 11:  2.2268 -  2.1573  1290   141  0.89  17.12   0.99     0.95       4799.44|
| 12:  2.1573 -  2.0958  1260   136  0.91  15.49   1.00     0.98       4234.25|
| 13:  2.0958 -  2.0408  1270   143  0.89  17.62   0.99     0.98       3766.24|
| 14:  2.0408 -  1.9911   694    80  0.90  15.81   0.97     0.93       2749.85|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2749.85 max =        10913.21 mean =      6861.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.74|
|phase err.(test): min =        0.00 max =           89.48 mean =        14.11|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.157)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.24    84.43   15.07    None  None   None       |
|    all(noH): 2823   0      3.24    84.43   15.07    None  None   None       |
|    Sol.    : 438    0      4.49    82.72   37.64    None  None   None       |
|    Mac.    : 2385   0      3.24    84.43   10.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.238 -  11.358: 1676   |   5:    43.835 -  51.955:   86        |
|      1:    11.358 -  19.477:  569   |   6:    51.955 -  60.074:   64        |
|      2:    19.477 -  27.596:  161   |   7:    60.074 -  68.194:   26        |
|      3:    27.596 -  35.716:  115   |   8:    68.194 -  76.313:    6        |
|      4:    35.716 -  43.835:  112   |   9:    76.313 -  84.433:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.349 - 4.618
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 331
   mapped sites are within: 0.707 - 4.618

peak=   10.290 closest distance to " CG2 VAL A 230 " =    1.409
peak=    7.532 closest distance to " CG2 VAL A 296 " =    1.143
peak=    6.088 closest distance to " O   HOH Z 111 " =    2.135
peak=    5.988 closest distance to " CG  LEU A   5 " =    1.231
peak=    5.754 closest distance to " CB  GLN A 223 " =    1.421
peak=    5.467 closest distance to " CD2 LEU A   5 " =    1.190
peak=    5.314 closest distance to " CG  LEU A 228 " =    1.209
peak=    4.894 closest distance to " CB  VAL A 230 " =    1.241
peak=    4.893 closest distance to " CB  SER A  63 " =    1.357
peak=    4.873 closest distance to " O   HOH Z 232 " =    2.293
peak=    4.853 closest distance to " CG  PRO A 213 " =    1.266
peak=    4.723 closest distance to " CG  PRO A 198 " =    1.259
peak=    4.525 closest distance to " CB  GLN A 183 " =    1.280
peak=    4.510 closest distance to " CG  PRO A 243 " =    1.159
peak=    4.472 closest distance to " O   HOH Z 298 " =    1.778
peak=    4.462 closest distance to " O   HOH Z 369 " =    2.074
peak=    4.445 closest distance to " CB  GLU A 128 " =    1.082
peak=    4.406 closest distance to " CB  ASN A 148 " =    1.334
peak=    4.393 closest distance to " O   PRO A 198 " =    1.597
peak=    4.330 closest distance to " CB  ARG A 275 " =    0.865
peak=    4.329 closest distance to " CD2 LEU A 228 " =    1.167
peak=    4.317 closest distance to " O   HOH Z 368 " =    2.256
peak=    4.304 closest distance to " O   HOH Z 126 " =    1.934
peak=    4.297 closest distance to " CB  TRP A 266 " =    0.951
peak=    4.283 closest distance to " NE2 GLN A  11 " =    1.138
peak=    4.268 closest distance to " O   HOH Z 272 " =    1.904
peak=    4.266 closest distance to " O   HOH Z 247 " =    1.411
peak=    4.250 closest distance to " CB  VAL A 296 " =    1.090
peak=    4.239 closest distance to " O   HOH Z 316 " =    3.109
peak=    4.222 closest distance to " O   HOH Z  78 " =    2.123
peak=    4.197 closest distance to " CZ  PHE A 218 " =    1.054
peak=    4.195 closest distance to " CB  SER A   3 " =    1.378
peak=    4.171 closest distance to " O   HOH Z 427 " =    3.155
peak=    4.157 closest distance to " O   HOH Z  54 " =    2.370
peak=    4.154 closest distance to " CB  ASP A 124 " =    0.763
peak=    4.147 closest distance to " O   HOH Z 236 " =    1.885
peak=    4.124 closest distance to " CB  SER A 216 " =    0.863
peak=    4.119 closest distance to " O   HOH Z 303 " =    2.094
peak=    4.104 closest distance to " CZ  PHE A 192 " =    0.980
peak=    4.093 closest distance to " CD  ARG A 159 " =    0.807
peak=    4.086 closest distance to " CA  TYR A  30 " =    0.954
peak=    4.079 closest distance to " CA  ALA A  51 " =    1.048
peak=    4.070 closest distance to " OD1 ASN A  69 " =    2.650
peak=    4.060 closest distance to " O   HOH Z 403 " =    1.753
peak=    4.060 closest distance to " NH1AARG A 145 " =    1.167
peak=    4.058 closest distance to " CB  GLU A 152 " =    1.128
peak=    4.028 closest distance to " O   HOH Z 263 " =    1.649
peak=    4.010 closest distance to " ND2 ASN A 187 " =    1.511
peak=    3.998 closest distance to " CB  VAL A 265 " =    1.271
peak=    3.993 closest distance to " O   HOH Z 112 " =    1.575
peak=    3.980 closest distance to " CB  PRO A  54 " =    0.781
peak=    3.978 closest distance to " ND2 ASN A 249 " =    1.893
peak=    3.975 closest distance to " CB  LEU A 228 " =    1.225
peak=    3.971 closest distance to " CB  ASP A 140 " =    0.866
peak=    3.971 closest distance to " NH2 ARG A 156 " =    1.126
peak=    3.969 closest distance to " O   HOH Z  88 " =    3.378
peak=    3.938 closest distance to " O   HOH Z 102 " =    1.275
peak=    3.921 closest distance to " CB  LEU A 143 " =    1.196
peak=    3.914 closest distance to " CG2 THR A 221 " =    1.030
peak=    3.911 closest distance to " CD1 LEU A 300 " =    1.189
peak=    3.890 closest distance to " CB  GLU A 277 " =    3.676
peak=    3.876 closest distance to " O   HOH Z  15 " =    2.106
peak=    3.856 closest distance to " O   HOH Z 234 " =    3.793
peak=    3.852 closest distance to " CG  GLN A  88 " =    1.040
peak=    3.847 closest distance to " CD ALYS A 290 " =    1.022
peak=    3.844 closest distance to " CB  SER A 212 " =    1.214
peak=    3.843 closest distance to " O   HOH Z 158 " =    2.962
peak=    3.842 closest distance to " CD  ARG A 269 " =    0.966
peak=    3.842 closest distance to " CB  ASN A  39 " =    0.898
peak=    3.824 closest distance to " CB  VAL A 202 " =    1.586
peak=    3.821 closest distance to " O   HOH Z 423 " =    1.668
peak=    3.821 closest distance to " OD2 ASP A 286 " =    2.875
peak=    3.820 closest distance to " CD  ARG A  66 " =    2.514
peak=    3.818 closest distance to " CA  THR A 264 " =    0.716
peak=    3.818 closest distance to " CA  SER A  87 " =    0.952
peak=    3.812 closest distance to " CB  ARG A  79 " =    1.485
peak=    3.807 closest distance to " CG1BVAL A  72 " =    1.632
peak=    3.802 closest distance to " O   HOH Z 411 " =    3.583
peak=    3.798 closest distance to " CD1 LEU A   5 " =    1.304
peak=    3.796 closest distance to " O   HOH Z 184 " =    1.509
peak=    3.793 closest distance to " O   TRP A 274 " =    1.847
peak=    3.793 closest distance to " O   HOH Z 280 " =    2.937
peak=    3.785 closest distance to " CG1 VAL A 153 " =    0.972
peak=    3.782 closest distance to " CB  ASN A 187 " =    1.111
peak=    3.772 closest distance to " O   HOH Z  63 " =    1.930
peak=    3.763 closest distance to " O   HOH Z 425 " =    1.389
peak=    3.760 closest distance to " O   HOH Z 437 " =    1.918
peak=    3.759 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.752 closest distance to " O   HOH Z 193 " =    2.108
peak=    3.751 closest distance to " CB  TRP A 179 " =    1.450
peak=    3.747 closest distance to " O   MET A 105 " =    1.840
peak=    3.744 closest distance to " CB  ARG A 190 " =    1.674
peak=    3.743 closest distance to " CG  MET A 185 " =    1.268
peak=    3.739 closest distance to " O   SER A  87 " =    2.306
peak=    3.735 closest distance to " CA  ALA A  21 " =    1.250
peak=    3.722 closest distance to " O   HOH Z 189 " =    2.862
peak=    3.712 closest distance to " NH1 ARG A  56 " =    0.977
peak=    3.712 closest distance to " O   HOH Z 261 " =    1.942
peak=    3.699 closest distance to " O   HOH Z  61 " =    1.624
peak=    3.690 closest distance to " CD  LYS A 166 " =    1.305
peak=    3.679 closest distance to " O   HOH Z 163 " =    1.606
peak=    3.669 closest distance to " CA  LYS A 117 " =    1.258
peak=    3.667 closest distance to " CB  ALA A   9 " =    1.591
peak=    3.663 closest distance to " O   HOH Z  97 " =    2.119
peak=    3.662 closest distance to " CA  ASN A 215 " =    1.236
peak=    3.661 closest distance to " O   ASP A 124 " =    1.059
peak=    3.656 closest distance to " CA  THR A 221 " =    0.890
peak=    3.655 closest distance to " CB  ALA A 248 " =    1.336
peak=    3.650 closest distance to " CA  ALA A 295 " =    1.126
peak=    3.648 closest distance to " O   HOH Z 295 " =    1.508
peak=    3.635 closest distance to " N   ASN A  39 " =    1.236
peak=    3.635 closest distance to " O   HOH Z 193 " =    1.691
peak=    3.633 closest distance to " CB AVAL A  41 " =    1.203
peak=    3.630 closest distance to " O   HOH Z 132 " =    2.665
peak=    3.628 closest distance to " O   HOH Z  80 " =    1.802
peak=    3.628 closest distance to " O   HOH Z 142 " =    1.573
peak=    3.624 closest distance to " O   HOH Z 383 " =    2.116
peak=    3.617 closest distance to " CA  MET A  40 " =    1.130
peak=    3.612 closest distance to " O   HOH Z 135 " =    1.893
peak=    3.608 closest distance to " O   HOH Z 203 " =    1.826
peak=    3.603 closest distance to " CG2 THR A 220 " =    0.974
peak=    3.602 closest distance to " CB  TRP A 150 " =    1.423
peak=    3.602 closest distance to " CG1 VAL A 296 " =    1.205
peak=    3.601 closest distance to " N   VAL A 126 " =    1.435
peak=    3.586 closest distance to " O   HOH Z 128 " =    2.156
peak=    3.584 closest distance to " O   HOH Z 346 " =    1.561
peak=    3.582 closest distance to " O   HOH Z  68 " =    1.592
peak=    3.577 closest distance to " CA  ASP A 140 " =    1.273
peak=    3.571 closest distance to " ND1 HIS A  81 " =    1.707
peak=    3.571 closest distance to " CD2 LEU A 255 " =    1.505
peak=    3.566 closest distance to " CE  LYS A  76 " =    0.846
peak=    3.556 closest distance to " O   HOH Z 126 " =    1.649
peak=    3.554 closest distance to " CB  ALA A 291 " =    1.340
peak=    3.551 closest distance to " O   HOH Z 133 " =    2.370
peak=    3.547 closest distance to " O   HOH Z  44 " =    2.080
peak=    3.541 closest distance to " N   SER A 135 " =    1.427
peak=    3.537 closest distance to " CB  MET A  40 " =    0.791
peak=    3.526 closest distance to " O   HOH Z  21 " =    1.689
peak=    3.522 closest distance to " CA  LEU A 282 " =    1.003
peak=    3.518 closest distance to " CA  ASP A 191 " =    0.738
peak=    3.516 closest distance to " O   HOH Z 344 " =    3.086
peak=    3.516 closest distance to " O   HOH Z 126 " =    1.572
peak=    3.509 closest distance to " O   HOH Z  43 " =    1.839
peak=    3.508 closest distance to " CA  VAL A  41 " =    0.866
peak=    3.502 closest distance to " O   HOH Z 134 " =    1.520
peak=    3.501 closest distance to " O   GLN A 278 " =    1.360
peak=    3.500 closest distance to " CB  ALA A 161 " =    0.948
peak=    3.494 closest distance to " O   HOH Z 171 " =    3.870
peak=    3.493 closest distance to " CB  ALA A 104 " =    0.816
peak=    3.492 closest distance to " O   HOH Z  20 " =    1.900
peak=    3.491 closest distance to " O   HOH Z 227 " =    1.601
peak=    3.488 closest distance to " CG2 VAL A 257 " =    0.917
peak=    3.484 closest distance to " CD1 TRP A 266 " =    1.117
peak=    3.483 closest distance to " NZ  LYS A 166 " =    3.217
peak=    3.483 closest distance to " CA  ARG A  36 " =    1.157
peak=    3.482 closest distance to " O   HOH Z  19 " =    2.525
peak=    3.480 closest distance to " CB  ILE A 120 " =    1.362
peak=    3.472 closest distance to " O   HOH Z 108 " =    2.515
peak=    3.467 closest distance to " O   HOH Z 281 " =    4.618
peak=    3.465 closest distance to " O   HOH Z 214 " =    2.057
peak=    3.464 closest distance to " CD1 LEU A  96 " =    0.707
peak=    3.464 closest distance to " CG BARG A 275 " =    1.482
peak=    3.461 closest distance to " OG BSER A 164 " =    2.208
peak=    3.460 closest distance to " NZ  LYS A 117 " =    3.256
peak=    3.460 closest distance to " CA  ARG A 195 " =    1.250
peak=    3.452 closest distance to " O   HOH Z 371 " =    3.285
peak=    3.449 closest distance to " ND1 HIS A  86 " =    1.693
peak=    3.447 closest distance to " OE1 GLN A  11 " =    1.862
peak=    3.444 closest distance to " CB  ALA A 137 " =    1.116
peak=    3.442 closest distance to " CB  PRO A 198 " =    0.993
peak=    3.441 closest distance to " CB  ASN A 142 " =    1.032
peak=    3.440 closest distance to " O   HOH Z 197 " =    2.883
peak=    3.438 closest distance to " CG1 ILE A 151 " =    1.074
peak=    3.435 closest distance to " O   HOH Z  68 " =    2.042
peak=    3.432 closest distance to " O   HOH Z 410 " =    1.396
peak=    3.430 closest distance to " CB  THR A  82 " =    1.369
peak=    3.429 closest distance to " O   HOH Z 145 " =    1.857
peak=    3.423 closest distance to " OG  SER A  22 " =    2.894
peak=    3.420 closest distance to " CB  THR A 157 " =    1.150
peak=    3.417 closest distance to " O   HOH Z 180 " =    2.071
peak=    3.415 closest distance to " CE1 TYR A 186 " =    1.291
peak=    3.414 closest distance to " CG1 ILE A  49 " =    1.514
peak=    3.413 closest distance to " O   HOH Z  57 " =    1.239
peak=    3.411 closest distance to " CB  ALA A 248 " =    1.098
peak=    3.410 closest distance to " O   HOH Z  10 " =    1.810
peak=    3.408 closest distance to " O   HOH Z 329 " =    3.834
peak=    3.407 closest distance to " O   ALA A 158 " =    1.422
peak=    3.403 closest distance to " O   HOH Z 183 " =    1.344
peak=    3.400 closest distance to " CB  LYS A 117 " =    1.155
peak=    3.399 closest distance to " C   SER A  32 " =    1.031
peak=    3.396 closest distance to " O   HOH Z 402 " =    1.488
peak=    3.392 closest distance to " CB  MET A  47 " =    1.061
peak=    3.392 closest distance to " CB  GLN A  88 " =    1.253
peak=    3.385 closest distance to " CB  ALA A 242 " =    0.846
peak=    3.382 closest distance to " O   HOH Z  97 " =    2.648
peak=    3.381 closest distance to " O   HOH Z 350 " =    1.640
peak=    3.379 closest distance to " O   HOH Z 245 " =    1.385
peak=    3.377 closest distance to " CB  ALA A  34 " =    0.820
peak=    3.376 closest distance to " O   HOH Z 133 " =    1.749
peak=    3.374 closest distance to " O   HOH Z 291 " =    1.611
peak=    3.370 closest distance to " CG  LEU A 167 " =    1.144
peak=    3.367 closest distance to " CD1 ILE A 106 " =    0.956
peak=    3.358 closest distance to " O   HOH Z 193 " =    1.910
peak=    3.355 closest distance to " N   PHE A 130 " =    1.270
peak=    3.349 closest distance to " O   HOH Z  62 " =    2.359
peak=    3.347 closest distance to " NH1 ARG A  14 " =    0.957
peak=    3.347 closest distance to " O   HOH Z 327 " =    2.266
peak=    3.339 closest distance to " OD1 ASN A 217 " =    1.633
peak=    3.337 closest distance to " CB  SER A 210 " =    0.872
peak=    3.333 closest distance to " ND2 ASN A 110 " =    1.674
peak=    3.333 closest distance to " O   HOH Z 313 " =    1.761
peak=    3.331 closest distance to " O   HOH Z 368 " =    3.546
peak=    3.330 closest distance to " NZ  LYS A  48 " =    1.517
peak=    3.325 closest distance to " O   HOH Z 345 " =    3.597
peak=    3.325 closest distance to " O   HOH Z  63 " =    1.256
peak=    3.319 closest distance to " O   HOH Z 290 " =    1.148
peak=    3.316 closest distance to " CB  ASN A 110 " =    1.301
peak=    3.315 closest distance to " CB  ALA A 114 " =    1.164
peak=    3.314 closest distance to " CB  HIS A 108 " =    0.826
peak=    3.313 closest distance to " CA  ALA A 291 " =    0.929
peak=    3.311 closest distance to " CB  SER A  62 " =    1.280
peak=    3.306 closest distance to " CB  VAL A 268 " =    0.843
peak=    3.303 closest distance to " CA  ALA A 158 " =    1.153
peak=    3.301 closest distance to " CA  GLY A 211 " =    1.271
peak=    3.299 closest distance to " CA  LYS A 290 " =    1.322
peak=    3.298 closest distance to " CB  LEU A 255 " =    0.825
peak=    3.298 closest distance to " O   HOH Z 313 " =    1.831
peak=    3.295 closest distance to " OG  SER A 206 " =    1.146
peak=    3.294 closest distance to " O   HOH Z 213 " =    1.776
peak=    3.288 closest distance to " O   HOH Z 172 " =    3.807
peak=    3.286 closest distance to " CA  ALA A 154 " =    1.212
peak=    3.285 closest distance to " CG  GLU A  37 " =    0.842
peak=    3.279 closest distance to " CZ  PHE A  38 " =    1.241
peak=    3.276 closest distance to " CG BARG A 102 " =    1.845
peak=    3.275 closest distance to " O   HOH Z 420 " =    1.979
peak=    3.275 closest distance to " O   HOH Z  48 " =    1.384
peak=    3.272 closest distance to " O   HOH Z  58 " =    1.559
peak=    3.266 closest distance to " CE1 HIS A 108 " =    1.200
peak=    3.264 closest distance to " O   HOH Z 302 " =    1.928
peak=    3.261 closest distance to " CD  ARG A 219 " =    1.086
peak=    3.261 closest distance to " O   HOH Z 298 " =    2.457
peak=    3.260 closest distance to " CA  ILE A 106 " =    0.820
peak=    3.258 closest distance to " CA  ALA A 299 " =    0.969
peak=    3.257 closest distance to " O   HOH Z 116 " =    1.806
peak=    3.254 closest distance to " O   HOH Z 185 " =    1.882
peak=    3.253 closest distance to " CG  PRO A 280 " =    0.712
peak=    3.250 closest distance to " CB  VAL A 250 " =    1.338
peak=    3.250 closest distance to " O   HOH Z 271 " =    2.040
peak=    3.250 closest distance to " O   HOH Z 273 " =    2.655
peak=    3.249 closest distance to " CB  ASN A 215 " =    1.161
peak=    3.249 closest distance to " CB  GLU A  46 " =    1.032
peak=    3.249 closest distance to " OG1 THR A 279 " =    1.555
peak=    3.249 closest distance to " CG  ARG A 138 " =    1.120
peak=    3.248 closest distance to " O   HOH Z 109 " =    2.617
peak=    3.248 closest distance to " O   HOH Z 250 " =    1.314
peak=    3.247 closest distance to " OG BSER A 212 " =    2.405
peak=    3.244 closest distance to " OH  TYR A 214 " =    1.227
peak=    3.241 closest distance to " OD1 ASP A 231 " =    1.908
peak=    3.240 closest distance to " NE2 HIS A 207 " =    1.382
peak=    3.238 closest distance to " CG2 ILE A 106 " =    0.893
peak=    3.235 closest distance to " O   HOH Z  49 " =    2.632
peak=    3.235 closest distance to " CD  ARG A  14 " =    1.222
peak=    3.233 closest distance to " CE2 TYR A 186 " =    0.904
peak=    3.232 closest distance to " O   HOH Z 147 " =    1.681
peak=    3.231 closest distance to " O   HOH Z 248 " =    1.846
peak=    3.230 closest distance to " O   HOH Z 305 " =    3.617
peak=    3.230 closest distance to " O   HOH Z 175 " =    3.573
peak=    3.227 closest distance to " N   GLN A 278 " =    0.987
peak=    3.226 closest distance to " O   HOH Z 286 " =    2.334
peak=    3.224 closest distance to " O   HOH Z 425 " =    1.976
peak=    3.223 closest distance to " O   HOH Z 128 " =    2.224
peak=    3.223 closest distance to " O   HOH Z 332 " =    1.541
peak=    3.217 closest distance to " CG1 VAL A 174 " =    1.150
peak=    3.215 closest distance to " O   HOH Z  48 " =    1.427
peak=    3.211 closest distance to " CG AARG A 275 " =    1.250
peak=    3.208 closest distance to " N   ASN A 127 " =    1.216
peak=    3.207 closest distance to " O   ALA A   1 " =    1.579
peak=    3.206 closest distance to " CG  MET A 185 " =    1.050
peak=    3.206 closest distance to " O   HOH Z   4 " =    1.825
peak=    3.203 closest distance to " CD1 LEU A 281 " =    1.145
peak=    3.202 closest distance to " O   HOH Z 201 " =    3.190
peak=    3.197 closest distance to " OG1 THR A 294 " =    1.727
peak=    3.194 closest distance to " O   HOH Z 104 " =    2.685
peak=    3.190 closest distance to " CD2 LEU A   5 " =    0.747
peak=    3.190 closest distance to " OG BSER A 134 " =    2.915
peak=    3.186 closest distance to " O   HOH Z 426 " =    1.512
peak=    3.182 closest distance to " CB  SER A 273 " =    0.861
peak=    3.182 closest distance to " O   HOH Z 353 " =    2.794
peak=    3.179 closest distance to " CB  ALA A 100 " =    1.313
peak=    3.173 closest distance to " O   HOH Z 130 " =    2.200
peak=    3.163 closest distance to " CA  GLU A 152 " =    0.848
peak=    3.163 closest distance to " O   HOH Z 391 " =    3.009
peak=    3.161 closest distance to " CB  PHE A  16 " =    1.133
peak=    3.160 closest distance to " N   TYR A  15 " =    0.824
peak=    3.160 closest distance to " CB  TYR A  30 " =    1.435
peak=    3.158 closest distance to " O   HOH Z 422 " =    2.636
peak=    3.152 closest distance to " CG  MET A 188 " =    0.955
peak=    3.149 closest distance to " N   ARG A 156 " =    1.422
peak=    3.146 closest distance to " CA  ASN A 217 " =    1.381
peak=    3.141 closest distance to " CG2 VAL A 197 " =    1.086
peak=    3.140 closest distance to " CB  GLN A  89 " =    1.118
peak=    3.137 closest distance to " CZ3 TRP A  85 " =    1.089
peak=    3.133 closest distance to " CE2 TYR A  30 " =    0.812
peak=    3.125 closest distance to " CB  ALA A  43 " =    0.899
peak=    3.120 closest distance to " CB  PRO A 243 " =    1.200
peak=    3.112 closest distance to " CA  TRP A  92 " =    0.941
peak=    3.108 closest distance to " C   GLN A  88 " =    1.552
peak=    3.108 closest distance to " NH2BARG A 145 " =    2.027
peak=    3.104 closest distance to " O   HOH Z 435 " =    1.997
peak=    3.089 closest distance to " CG2 ILE A 120 " =    1.283
peak=    3.089 closest distance to " CB  TYR A 116 " =    0.913
peak=    3.081 closest distance to " C   GLY A  80 " =    1.118
peak=    3.070 closest distance to " O   HOH Z 403 " =    1.379
peak=    3.070 closest distance to " O   HOH Z 128 " =    1.865
peak=    3.068 closest distance to " O   HOH Z 185 " =    2.296
peak=    3.066 closest distance to " O   THR A  31 " =    1.529
peak=    3.060 closest distance to " CD  LYS A 119 " =    1.582
peak=    3.059 closest distance to " CG  LEU A  25 " =    1.879
peak=    3.057 closest distance to " O   HOH Z  48 " =    1.436
peak=    3.055 closest distance to " O   HOH Z 156 " =    2.912
peak=    3.040 closest distance to " CA  ASN A 176 " =    1.145
peak=    3.026 closest distance to " O   HOH Z 392 " =    1.897
peak=    3.012 closest distance to " CB  ASP A 140 " =    0.713

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.634 - 5.532
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 194
   mapped sites are within: 0.781 - 5.532

peak=   -5.366 closest distance to " CG2 VAL A 230 " =    0.857
peak=   -4.303 closest distance to " CD  ARG A 156 " =    2.022
peak=   -4.098 closest distance to " O   HOH Z  52 " =    1.660
peak=   -4.074 closest distance to " O   HOH Z 290 " =    1.184
peak=   -4.046 closest distance to " O   HOH Z 266 " =    4.987
peak=   -3.998 closest distance to " CG  ASP A 231 " =    0.781
peak=   -3.975 closest distance to " O   HOH Z 231 " =    1.208
peak=   -3.973 closest distance to " O   ILE A 109 " =    2.628
peak=   -3.962 closest distance to " CG1 VAL A 296 " =    1.355
peak=   -3.942 closest distance to " CD  GLN A 223 " =    2.109
peak=   -3.938 closest distance to " CG  LEU A 101 " =    2.512
peak=   -3.918 closest distance to " CG2BVAL A  41 " =    2.570
peak=   -3.899 closest distance to " CE2 TYR A  30 " =    2.776
peak=   -3.879 closest distance to " C   ALA A 158 " =    1.294
peak=   -3.873 closest distance to " CD  ARG A  14 " =    3.244
peak=   -3.871 closest distance to " CA  SER A 271 " =    2.346
peak=   -3.868 closest distance to " CZ3 TRP A 179 " =    1.180
peak=   -3.866 closest distance to " CD  GLN A  58 " =    1.034
peak=   -3.862 closest distance to " NH2AARG A 275 " =    5.424
peak=   -3.860 closest distance to " O   HOH Z 231 " =    1.819
peak=   -3.836 closest distance to " CG2 VAL A 296 " =    1.499
peak=   -3.826 closest distance to " N   ALA A  43 " =    2.472
peak=   -3.809 closest distance to " CD2 LEU A 300 " =    2.822
peak=   -3.800 closest distance to " OG  SER A  97 " =    2.235
peak=   -3.778 closest distance to " CD1 LEU A 228 " =    2.425
peak=   -3.775 closest distance to " O   HOH Z  19 " =    2.289
peak=   -3.770 closest distance to " CB  PRO A 243 " =    2.662
peak=   -3.762 closest distance to " N   ALA A 226 " =    2.205
peak=   -3.755 closest distance to " O   HOH Z 166 " =    1.979
peak=   -3.751 closest distance to " CB  ALA A  43 " =    2.576
peak=   -3.745 closest distance to " CD2 LEU A 167 " =    1.745
peak=   -3.735 closest distance to " O   HOH Z 351 " =    1.513
peak=   -3.711 closest distance to " O   PRO A 163 " =    2.093
peak=   -3.705 closest distance to " O   HOH Z 394 " =    1.557
peak=   -3.703 closest distance to " O   HOH Z 196 " =    2.274
peak=   -3.701 closest distance to " CG1 VAL A 112 " =    3.045
peak=   -3.697 closest distance to " OG ASER A 134 " =    1.285
peak=   -3.675 closest distance to " CD2 TYR A 293 " =    2.067
peak=   -3.675 closest distance to " O   HOH Z 103 " =    1.909
peak=   -3.674 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.672 closest distance to " O   HOH Z  10 " =    1.557
peak=   -3.670 closest distance to " O   HOH Z 389 " =    1.880
peak=   -3.661 closest distance to " C   HIS A 108 " =    1.143
peak=   -3.661 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.660 closest distance to " NH2 ARG A  66 " =    1.947
peak=   -3.658 closest distance to " O   HOH Z 118 " =    3.000
peak=   -3.642 closest distance to " OD1 ASN A 148 " =    1.477
peak=   -3.638 closest distance to " SD BMET A  47 " =    0.897
peak=   -3.637 closest distance to " O   HOH Z  43 " =    1.657
peak=   -3.636 closest distance to " CG  ARG A 269 " =    2.348
peak=   -3.632 closest distance to " CB  PRO A 163 " =    2.569
peak=   -3.630 closest distance to " CG  TRP A 266 " =    1.821
peak=   -3.626 closest distance to " O   HOH Z  17 " =    1.515
peak=   -3.626 closest distance to " CA  GLY A 241 " =    3.057
peak=   -3.625 closest distance to " O   HOH Z 241 " =    1.175
peak=   -3.623 closest distance to " O   HOH Z 426 " =    1.699
peak=   -3.610 closest distance to " OE1 GLN A  88 " =    1.027
peak=   -3.605 closest distance to " OG  SER A  87 " =    1.571
peak=   -3.604 closest distance to " CG1 VAL A 250 " =    2.726
peak=   -3.592 closest distance to " O   HOH Z 353 " =    2.235
peak=   -3.588 closest distance to " O   HOH Z  13 " =    1.351
peak=   -3.585 closest distance to " CG1 VAL A 112 " =    2.657
peak=   -3.583 closest distance to " O   HOH Z  11 " =    1.923
peak=   -3.572 closest distance to " CD1 LEU A 101 " =    2.762
peak=   -3.570 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.561 closest distance to " O   GLY A  80 " =    2.592
peak=   -3.548 closest distance to " OG BSER A 134 " =    1.245
peak=   -3.547 closest distance to " O   HOH Z 184 " =    1.512
peak=   -3.545 closest distance to " O   HOH Z 275 " =    1.539
peak=   -3.537 closest distance to " O   HOH Z 283 " =    2.113
peak=   -3.533 closest distance to " CA  GLY A 241 " =    2.272
peak=   -3.525 closest distance to " O   HOH Z  38 " =    1.412
peak=   -3.524 closest distance to " CD  GLN A  88 " =    0.853
peak=   -3.524 closest distance to " CG1 VAL A 265 " =    2.440
peak=   -3.519 closest distance to " CG2 VAL A 112 " =    2.611
peak=   -3.513 closest distance to " O   GLY A 203 " =    2.410
peak=   -3.510 closest distance to " CD  LYS A 289 " =    2.573
peak=   -3.502 closest distance to " C   ASN A 285 " =    2.563
peak=   -3.502 closest distance to " O   HOH Z 350 " =    1.706
peak=   -3.497 closest distance to " O   HOH Z 185 " =    2.439
peak=   -3.488 closest distance to " CD  ARG A 139 " =    1.591
peak=   -3.484 closest distance to " O   HOH Z 388 " =    2.053
peak=   -3.480 closest distance to " CD1 PHE A  59 " =    1.905
peak=   -3.471 closest distance to " CA  GLY A 203 " =    2.429
peak=   -3.452 closest distance to " N   THR A 157 " =    1.544
peak=   -3.444 closest distance to " O   GLY A 211 " =    1.461
peak=   -3.440 closest distance to " ND2 ASN A  45 " =    1.074
peak=   -3.438 closest distance to " O   HOH Z 222 " =    1.453
peak=   -3.436 closest distance to " CB  ALA A 291 " =    2.231
peak=   -3.434 closest distance to " C   ASN A 187 " =    1.769
peak=   -3.433 closest distance to " CD1 LEU A   5 " =    2.584
peak=   -3.433 closest distance to " OG  SER A  26 " =    1.385
peak=   -3.428 closest distance to " O   HOH Z 407 " =    3.256
peak=   -3.412 closest distance to " CD  PRO A 213 " =    2.186
peak=   -3.410 closest distance to " OG BSER A 134 " =    1.869
peak=   -3.406 closest distance to " O   HOH Z 111 " =    2.234
peak=   -3.400 closest distance to " OXT GLY A 302 " =    2.968
peak=   -3.395 closest distance to " O   HOH Z 435 " =    2.832
peak=   -3.392 closest distance to " CB  PHE A 192 " =    1.830
peak=   -3.387 closest distance to " ND2 ASN A  45 " =    1.453
peak=   -3.386 closest distance to " ND2 ASN A  60 " =    1.429
peak=   -3.379 closest distance to " OG  SER A 206 " =    1.806
peak=   -3.377 closest distance to " O   HOH Z 128 " =    2.477
peak=   -3.376 closest distance to " NE2 GLN A  88 " =    2.224
peak=   -3.372 closest distance to " N   THR A  18 " =    1.339
peak=   -3.371 closest distance to " O   HOH Z 377 " =    1.927
peak=   -3.367 closest distance to " CB  TRP A  85 " =    2.447
peak=   -3.365 closest distance to " O   HOH Z  92 " =    1.693
peak=   -3.364 closest distance to " O   HOH Z 211 " =    1.587
peak=   -3.362 closest distance to " CG  ASP A  50 " =    2.363
peak=   -3.357 closest distance to " O   VAL A 189 " =    2.643
peak=   -3.352 closest distance to " O   GLY A 196 " =    1.217
peak=   -3.352 closest distance to " CB  PHE A 283 " =    3.004
peak=   -3.337 closest distance to " O   HOH Z 311 " =    3.849
peak=   -3.334 closest distance to " O   HOH Z  98 " =    2.064
peak=   -3.320 closest distance to " NE2 GLN A  88 " =    1.027
peak=   -3.319 closest distance to " C   ALA A   8 " =    1.571
peak=   -3.319 closest distance to " CE3 TRP A 150 " =    2.071
peak=   -3.316 closest distance to " O   HOH Z 166 " =    1.584
peak=   -3.315 closest distance to " CG  HIS A  86 " =    0.956
peak=   -3.313 closest distance to " CG1 VAL A 197 " =    2.346
peak=   -3.312 closest distance to " CG  GLU A 277 " =    1.179
peak=   -3.311 closest distance to " O   HOH Z 177 " =    1.629
peak=   -3.310 closest distance to " CE1 TYR A 169 " =    2.413
peak=   -3.307 closest distance to " CB  ASN A  39 " =    2.149
peak=   -3.307 closest distance to " C   LEU A 222 " =    0.814
peak=   -3.302 closest distance to " CH2 TRP A 177 " =    2.161
peak=   -3.295 closest distance to " OD2 ASP A 171 " =    1.831
peak=   -3.285 closest distance to " CE  MET A 105 " =    2.140
peak=   -3.283 closest distance to " OH  TYR A 169 " =    0.959
peak=   -3.281 closest distance to " O   HOH Z 165 " =    1.932
peak=   -3.279 closest distance to " CB  LEU A  83 " =    2.338
peak=   -3.277 closest distance to " O   HOH Z 292 " =    4.618
peak=   -3.276 closest distance to " CG2 ILE A  49 " =    2.828
peak=   -3.274 closest distance to " O   VAL A  67 " =    2.647
peak=   -3.264 closest distance to " CG  ARG A  66 " =    2.342
peak=   -3.263 closest distance to " O   HOH Z 243 " =    1.737
peak=   -3.259 closest distance to " O   HOH Z 191 " =    5.532
peak=   -3.258 closest distance to " CA  ASN A 127 " =    1.063
peak=   -3.251 closest distance to " OG  SER A  62 " =    1.717
peak=   -3.250 closest distance to " CD1 ILE A 151 " =    2.343
peak=   -3.246 closest distance to " N   SER A 212 " =    1.678
peak=   -3.237 closest distance to " ND2BASN A 224 " =    1.741
peak=   -3.236 closest distance to " O   HOH Z 417 " =    2.883
peak=   -3.231 closest distance to " CD1 ILE A 239 " =    2.110
peak=   -3.231 closest distance to " O   HOH Z  60 " =    2.112
peak=   -3.230 closest distance to " N   PHE A  59 " =    2.191
peak=   -3.227 closest distance to " CB  VAL A 230 " =    1.063
peak=   -3.226 closest distance to " N   GLN A  58 " =    1.897
peak=   -3.225 closest distance to " CE BMET A  47 " =    1.814
peak=   -3.224 closest distance to " ND2 ASN A 285 " =    2.242
peak=   -3.222 closest distance to " CA  GLY A 133 " =    2.259
peak=   -3.215 closest distance to " CG2 THR A 178 " =    2.227
peak=   -3.209 closest distance to " CB  ASP A 132 " =    2.279
peak=   -3.208 closest distance to " NH1 ARG A 195 " =    2.621
peak=   -3.191 closest distance to " O   HOH Z 396 " =    1.812
peak=   -3.185 closest distance to " O   HOH Z 308 " =    1.639
peak=   -3.185 closest distance to " O   HOH Z 234 " =    4.417
peak=   -3.185 closest distance to " CB  ALA A  10 " =    2.268
peak=   -3.184 closest distance to " CB  ALA A 291 " =    2.222
peak=   -3.179 closest distance to " O   HOH Z 174 " =    2.489
peak=   -3.177 closest distance to " NH2 ARG A  79 " =    1.981
peak=   -3.170 closest distance to " O   HOH Z 431 " =    1.661
peak=   -3.168 closest distance to " CZ  ARG A  66 " =    1.034
peak=   -3.167 closest distance to " NE2 GLN A 103 " =    1.785
peak=   -3.164 closest distance to " CA  SER A 135 " =    1.306
peak=   -3.162 closest distance to " O   HOH Z 189 " =    1.994
peak=   -3.156 closest distance to " O   HOH Z 252 " =    4.039
peak=   -3.154 closest distance to " CG  ARG A 259 " =    2.554
peak=   -3.150 closest distance to " CD2 LEU A 237 " =    2.855
peak=   -3.148 closest distance to " N   SER A 276 " =    1.317
peak=   -3.139 closest distance to " O   HOH Z 310 " =    1.990
peak=   -3.131 closest distance to " ND2 ASN A  60 " =    1.830
peak=   -3.129 closest distance to " C   MET A 188 " =    1.403
peak=   -3.124 closest distance to " NE2 GLN A 194 " =    1.857
peak=   -3.123 closest distance to " OD1 ASN A 187 " =    1.575
peak=   -3.123 closest distance to " CG1 VAL A 296 " =    1.284
peak=   -3.122 closest distance to " CD2 PHE A  61 " =    1.907
peak=   -3.117 closest distance to " CB  ALA A 248 " =    2.048
peak=   -3.116 closest distance to " CB  TYR A  15 " =    2.254
peak=   -3.110 closest distance to " O   HOH Z 423 " =    2.153
peak=   -3.108 closest distance to " CD2 PHE A  61 " =    2.412
peak=   -3.095 closest distance to " O   HOH Z 313 " =    1.139
peak=   -3.088 closest distance to " CE3 TRP A  70 " =    1.863
peak=   -3.087 closest distance to " OD1 ASP A 191 " =    1.500
peak=   -3.087 closest distance to " O   HOH Z 285 " =    1.514
peak=   -3.084 closest distance to " O   HOH Z 123 " =    2.483
peak=   -3.080 closest distance to " O   HOH Z 128 " =    4.212
peak=   -3.073 closest distance to " CD1 ILE A 199 " =    2.633
peak=   -3.053 closest distance to " O   HOH Z 106 " =    1.988
peak=   -3.037 closest distance to " CD  ARG A 195 " =    5.065
peak=   -3.025 closest distance to " C   ASP A 231 " =    2.655

================= 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    :  0.4450 0.4359   6.244713e+00   6.227356e+00
   1_bss:  0.4373 0.4237   6.240436e+00   6.218362e+00
   1_xyz:  0.3339 0.3654   6.058412e+00   6.120188e+00
   1_adp:  0.2799 0.3226   5.920190e+00   6.037934e+00
   1_occ:  0.2792 0.3227   5.919464e+00   6.039410e+00
   2_bss:  0.2767 0.3177   5.920046e+00   6.036714e+00
   2_xyz:  0.1852 0.2353   5.570093e+00   5.756353e+00
   2_adp:  0.1653 0.2133   5.466771e+00   5.664251e+00
   2_occ:  0.1652 0.2132   5.466158e+00   5.663955e+00
   3_bss:  0.1635 0.2107   5.464964e+00   5.662243e+00
   3_xyz:  0.1301 0.1753   5.267551e+00   5.492979e+00
   3_adp:  0.1235 0.1705   5.231988e+00   5.470317e+00
   3_occ:  0.1235 0.1704   5.231684e+00   5.470033e+00
   4_bss:  0.1237 0.1700   5.231836e+00   5.468552e+00
   4_xyz:  0.1171 0.1652   5.191788e+00   5.436052e+00
   4_adp:  0.1180 0.1633   5.190294e+00   5.424065e+00
   4_occ:  0.1179 0.1631   5.189767e+00   5.423502e+00
   5_bss:  0.1179 0.1631   5.189615e+00   5.423458e+00
   5_xyz:  0.1186 0.1630   5.192204e+00   5.422420e+00
   5_adp:  0.1170 0.1636   5.189096e+00   5.428332e+00
   5_occ:  0.1170 0.1636   5.189219e+00   5.428563e+00
   5_bss:  0.1170 0.1636   5.189225e+00   5.428564e+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:  0.300  20.000   9.468   7.955   7.417   0.000   0.000   0.000
   1_xyz:  0.300  20.000   9.468   7.955   7.417   0.000   0.000   0.000
   1_adp:  0.300  20.000   9.468   7.955   7.417   0.000   0.000   0.000
   1_occ:  0.300  20.000   9.468   7.955   7.417   0.000   0.000   0.000
   2_bss:  0.330  50.000   6.188   4.794   5.042   0.000   0.000   0.000
   2_xyz:  0.330  50.000   6.188   4.794   5.042   0.000   0.000   0.000
   2_adp:  0.330  50.000   6.188   4.794   5.042   0.000   0.000   0.000
   2_occ:  0.330  50.000   6.188   4.794   5.042   0.000   0.000   0.000
   3_bss:  0.327  50.000   3.806   3.382   3.982   0.000   0.000   0.000
   3_xyz:  0.327  50.000   3.806   3.382   3.982   0.000   0.000   0.000
   3_adp:  0.327  50.000   3.806   3.382   3.982   0.000   0.000   0.000
   3_occ:  0.327  50.000   3.806   3.382   3.982   0.000   0.000   0.000
   4_bss:  0.327  50.000   3.251   3.049   3.741   0.000   0.000   0.000
   4_xyz:  0.327  50.000   3.251   3.049   3.741   0.000   0.000   0.000
   4_adp:  0.327  50.000   3.251   3.049   3.741   0.000   0.000   0.000
   4_occ:  0.327  50.000   3.251   3.049   3.741   0.000   0.000   0.000
   5_bss:  0.322  50.000   3.060   2.969   3.699   0.000   0.000   0.000
   5_xyz:  0.322  50.000   3.060   2.969   3.699   0.000   0.000   0.000
   5_adp:  0.322  50.000   3.060   2.969   3.699   0.000   0.000   0.000
   5_occ:  0.322  50.000   3.060   2.969   3.699   0.000   0.000   0.000
   5_bss:  0.322  53.238  -0.191  -0.277   0.468   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.650 0.5262  0.5919    56335.578
   1_bss:  49.607 0.5247  0.7534    54121.727
   1_xyz:  41.005 0.6291  0.8800    38234.456
   1_adp:  34.453 0.7074  0.9741    29008.009
   1_occ:  34.528 0.7064  0.9725    29098.756
   2_bss:  34.346 0.7085  0.8802    28862.381
   2_xyz:  23.010 0.8315  0.9952    14088.661
   2_adp:  20.297 0.8590  1.0201    11540.845
   2_occ:  20.295 0.8590  1.0198    11537.498
   3_bss:  20.227 0.8598  0.9623    11491.935
   3_xyz:  16.163 0.8969  0.9805     7901.010
   3_adp:  15.639 0.9016  0.9820     7556.202
   3_occ:  15.632 0.9017  0.9819     7551.922
   4_bss:  15.607 0.9019  0.9682     7515.525
   4_xyz:  14.890 0.9080  0.9709     6973.943
   4_adp:  14.574 0.9108  0.9731     6823.187
   4_occ:  14.563 0.9109  0.9730     6816.354
   5_bss:  14.562 0.9109  0.9694     6814.714
   5_xyz:  14.501 0.9114  0.9687     6783.245
   5_adp:  14.670 0.9100  0.9666     6858.633
   5_occ:  14.680 0.9099  0.9665     6862.242
   5_bss:  14.680 0.9099  0.9663     6862.085
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4160e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4160e+01
   1_xyz:   1.611  0.012  0.105 18.030  0.006  4.112   1.2969e-01
   1_adp:   1.611  0.012  0.105 18.030  0.006  4.112   1.2969e-01
   1_occ:   1.611  0.012  0.105 18.030  0.006  4.112   1.2969e-01
   2_bss:   1.611  0.012  0.105 18.030  0.006  4.112   1.2969e-01
   2_xyz:   1.096  0.008  0.077 16.588  0.004  4.133   7.4686e-02
   2_adp:   1.096  0.008  0.077 16.588  0.004  4.133   7.4686e-02
   2_occ:   1.096  0.008  0.077 16.588  0.004  4.133   7.4686e-02
   3_bss:   1.096  0.008  0.077 16.588  0.004  4.133   7.4686e-02
   3_xyz:   1.096  0.009  0.085 16.260  0.004  4.117   7.4174e-02
   3_adp:   1.096  0.009  0.085 16.260  0.004  4.117   7.4174e-02
   3_occ:   1.096  0.009  0.085 16.260  0.004  4.117   7.4174e-02
   4_bss:   1.096  0.009  0.085 16.260  0.004  4.117   7.4174e-02
   4_xyz:   1.068  0.009  0.084 15.942  0.004  4.121   7.0646e-02
   4_adp:   1.068  0.009  0.084 15.942  0.004  4.121   7.0646e-02
   4_occ:   1.068  0.009  0.084 15.942  0.004  4.121   7.0646e-02
   5_bss:   1.068  0.009  0.084 15.942  0.004  4.121   7.0646e-02
   5_xyz:   0.975  0.007  0.077 15.611  0.003  4.122   6.0225e-02
   5_adp:   0.975  0.007  0.077 15.611  0.003  4.122   6.0225e-02
   5_occ:   0.975  0.007  0.077 15.611  0.003  4.122   6.0225e-02
   5_bss:   0.975  0.007  0.077 15.611  0.003  4.122   6.0225e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0227e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0227e+00
   1_xyz:  13.582  0.157  0.441 85.414  0.038  2.240   9.8053e-02
   1_adp:  13.582  0.157  0.441 85.414  0.038  2.240   9.8053e-02
   1_occ:  13.582  0.157  0.441 85.414  0.038  2.240   9.8053e-02
   2_bss:  13.582  0.157  0.441 85.414  0.038  2.240   9.8053e-02
   2_xyz:   7.268  0.065  0.249 87.520  0.041  2.259   5.2582e-02
   2_adp:   7.268  0.065  0.249 87.520  0.041  2.259   5.2582e-02
   2_occ:   7.268  0.065  0.249 87.520  0.041  2.259   5.2582e-02
   3_bss:   7.268  0.065  0.249 87.520  0.041  2.259   5.2582e-02
   3_xyz:   8.879  0.059  0.506 82.394  0.040  2.348   6.8082e-02
   3_adp:   8.879  0.059  0.506 82.394  0.040  2.348   6.8082e-02
   3_occ:   8.879  0.059  0.506 82.394  0.040  2.348   6.8082e-02
   4_bss:   8.879  0.059  0.506 82.394  0.040  2.348   6.8082e-02
   4_xyz:   8.022  0.042  0.557 83.694  0.040  2.348   4.7042e-02
   4_adp:   8.022  0.042  0.557 83.694  0.040  2.348   4.7042e-02
   4_occ:   8.022  0.042  0.557 83.694  0.040  2.348   4.7042e-02
   5_bss:   8.022  0.042  0.557 83.694  0.040  2.348   4.7042e-02
   5_xyz:   7.976  0.041  0.459 83.328  0.039  2.380   3.3960e-02
   5_adp:   7.976  0.041  0.459 83.328  0.039  2.380   3.3960e-02
   5_occ:   7.976  0.041  0.459 83.328  0.039  2.380   3.3960e-02
   5_bss:   7.976  0.041  0.459 83.328  0.039  2.380   3.3960e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  56.00   0.00  10.45  54.15   0.00   7.55  56.00   0.00  26.27
   1_occ:  56.00   0.00  10.45  54.15   0.00   7.55  56.00   0.00  26.27
   2_bss:  56.00   0.00  10.45  54.15   0.00   7.55  56.00   0.00  26.27
   2_xyz:  56.00   0.00  10.45  54.15   0.00   7.55  56.00   0.00  26.27
   2_adp:  71.27   0.00  11.59  69.18   0.00   7.56  71.27   0.66  33.50
   2_occ:  71.27   0.00  11.59  69.18   0.00   7.56  71.27   0.66  33.50
   3_bss:  71.27   0.00  11.59  69.18   0.00   7.56  71.27   0.66  33.50
   3_xyz:  71.27   0.00  11.59  69.18   0.00   7.56  71.27   0.66  33.50
   3_adp:  80.20   0.00  12.07  80.20   0.00   7.73  79.41   0.68  35.67
   3_occ:  80.20   0.00  12.07  80.20   0.00   7.73  79.41   0.68  35.67
   4_bss:  80.20   0.00  12.07  80.20   0.00   7.73  79.41   0.68  35.67
   4_xyz:  80.20   0.00  12.07  80.20   0.00   7.73  79.41   0.68  35.67
   4_adp:  79.39   0.00  11.70  79.39   0.00   7.62  78.74   1.21  33.91
   4_occ:  79.39   0.00  11.70  79.39   0.00   7.62  78.74   1.21  33.91
   5_bss:  79.39   0.00  11.70  79.39   0.00   7.62  78.74   1.21  33.91
   5_xyz:  79.39   0.00  11.70  79.39   0.00   7.62  78.74   1.21  33.91
   5_adp:  81.19   0.00  11.83  81.19   0.00   7.69  79.48   1.25  34.40
   5_occ:  81.19   0.00  11.83  81.19   0.00   7.69  79.48   1.25  34.40
   5_bss:  84.43   3.24  15.07  84.43   3.24  10.93  82.72   4.49  37.64
------------------------------------------------------------------------
 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:    1.194    0.018    0.410
   1_adp:    1.194    0.018    0.410
   1_occ:    1.194    0.018    0.410
   2_bss:    1.194    0.018    0.410
   2_xyz:    1.445    0.039    0.552
   2_adp:    1.445    0.039    0.552
   2_occ:    1.445    0.039    0.552
   3_bss:    1.445    0.039    0.552
   3_xyz:    1.430    0.040    0.594
   3_adp:    1.430    0.040    0.594
   3_occ:    1.430    0.040    0.594
   4_bss:    1.430    0.040    0.594
   4_xyz:    1.580    0.033    0.610
   4_adp:    1.580    0.033    0.610
   4_occ:    1.580    0.033    0.610
   5_bss:    1.580    0.033    0.610
   5_xyz:    1.649    0.028    0.616
   5_adp:    1.649    0.028    0.616
   5_occ:    1.649    0.028    0.616
   5_bss:    1.649    0.028    0.616
------------------------------------------------------------------------

CPU time actual refinement: 321.50


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1159/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_1159/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1159/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1159/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1159/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.34 
  Macro-tasks:
    bulk solvent and scale       = 41.16  
    individual site refinement   = 126.88 
    weights calculation          = 31.85  
    collect and process          = 6.60   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 206.60 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 96.80  
    alpha_beta                      = 8.43   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 106.47 
    fmodel                         = 7.22   
    r_factors                      = 0.29   
    phase_errors                   = 10.84  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 233.33 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.570 micro seconds
Total CPU time: 5.58 minutes
from_scatterers_fft:    641 calls, 96.46 s
gradients_fft:          585 calls, 93.49 s

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

# Date 2008-01-16 Time 03:20:15 PST -0800 (1200482415.78 s)
Start R-work = 0.4450, R-free = 0.4359 (no bulk solvent and anisotropic scale)
Final R-work = 0.1335, R-free = 0.1792 (no bulk solvent and anisotropic scale)

Start R-work = 0.4373, R-free = 0.4237
Final R-work = 0.1170, R-free = 0.1636