# Date 2008-01-16 Time 02:27:23 PST -0800 (1200479243.89 s)
#phil __OFF__

Command line arguments: "../840.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26048
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 840

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 48.1033, 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: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99136
Completeness in resolution range: 0.950507
Completeness with d_max=infinity: 0.947564

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9914

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99136
Completeness in resolution range: 0.950507
Completeness with d_max=infinity: 0.947564

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2607 [2166/2194]  1949   217  10.0%
  bin  2:  4.2607 -  3.3947 [2074/2097]  1865   209  10.1%
  bin  3:  3.3947 -  2.9693 [2045/2070]  1841   204  10.0%
  bin  4:  2.9693 -  2.6996 [2045/2061]  1843   202   9.9%
  bin  5:  2.6996 -  2.5070 [2017/2054]  1812   205  10.2%
  bin  6:  2.5070 -  2.3598 [2001/2035]  1812   189   9.4%
  bin  7:  2.3598 -  2.2420 [1989/2026]  1788   201  10.1%
  bin  8:  2.2420 -  2.1447 [1991/2033]  1785   206  10.3%
  bin  9:  2.1447 -  2.0624 [1988/2023]  1796   192   9.7%
  bin 10:  2.0624 -  1.9914 [1273/2016]  1139   134  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_840/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 9
        2.26 -     2.92: 1461
        2.92 -     3.58: 4422
        3.58 -     4.24: 9089
        4.24 -     4.90: 13010
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.599 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.687 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.734 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 277 " - " O   HOH Z 343 "  1.860 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27986 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_840/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_840/model_refine_001.geo

CPU time processing inputs: 7.70


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 48.10325 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 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4904   r_free= 0.4754   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.294578                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7520 0.99   1401  158 0.4082 0.4142      6.6196      6.6208|
|  2:  4.7520 -  3.7918 0.99   1361  145 0.4214 0.4558      6.8446      6.8852|
|  3:  3.7918 -  3.3184 0.99   1320  154 0.4584 0.4033      6.7101      6.6385|
|  4:  3.3184 -  3.0176 0.99   1328  144 0.4854 0.4345      6.5481      6.4686|
|  5:  3.0176 -  2.8028 0.98   1298  145 0.5307 0.5195      6.3945      6.4211|
|  6:  2.8028 -  2.6385 0.99   1304  145 0.5191 0.4824      6.2914      6.1715|
|  7:  2.6385 -  2.5070 0.99   1298  146 0.5028 0.4632      6.2499      6.1858|
|  8:  2.5070 -  2.3983 0.99   1298  145 0.5206 0.5194       6.175      6.1768|
|  9:  2.3983 -  2.3063 0.99   1283  136 0.5264 0.5276      6.1247      6.1531|
| 10:  2.3063 -  2.2270 0.98   1278  146 0.5319 0.5259      6.1094      6.1083|
| 11:  2.2270 -  2.1576 0.98   1275  142 0.5308 0.5269      6.0423      6.0384|
| 12:  2.1576 -  2.0961 0.99   1268  142 0.5304 0.5026      5.9726      6.0034|
| 13:  2.0961 -  2.0410 0.96   1276  138 0.5296 0.5161      5.8759      5.8691|
| 14:  2.0410 -  1.9914 0.50    642   73 0.5554 0.5184      5.8541      5.7357|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7520  1401   158  0.65  38.72   0.78     0.68      88101.50|
|  2:  4.7520 -  3.7918  1361   145  0.67  37.66   0.87     0.72     114896.47|
|  3:  3.7918 -  3.3184  1320   154  0.58  45.06   0.80     0.68     117785.78|
|  4:  3.3184 -  3.0176  1328   144  0.50  51.54   0.78     0.59     100157.68|
|  5:  3.0176 -  2.8028  1298   145  0.44  56.92   0.72     0.52      80576.40|
|  6:  2.8028 -  2.6385  1304   145  0.43  57.49   0.72     0.49      66308.49|
|  7:  2.6385 -  2.5070  1298   146  0.43  57.54   0.73     0.48      60440.28|
|  8:  2.5070 -  2.3983  1298   145  0.37  62.34   0.72     0.43      58552.81|
|  9:  2.3983 -  2.3063  1283   136  0.31  67.06   0.71     0.37      58175.36|
| 10:  2.3063 -  2.2270  1278   146  0.28  68.98   0.73     0.33      54252.01|
| 11:  2.2270 -  2.1576  1275   142  0.28  69.38   0.75     0.34      49992.24|
| 12:  2.1576 -  2.0961  1268   142  0.29  68.68   0.74     0.36      45534.24|
| 13:  2.0961 -  2.0410  1276   138  0.27  70.15   0.71     0.33      39457.37|
| 14:  2.0410 -  1.9914   642    73  0.24  72.26   0.72     0.27      32835.67|
|alpha:            min =        0.27 max =            0.72 mean =         0.48|
|beta:             min =    32835.67 max =       117785.78 mean =     70940.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.96 mean =        58.06|
|phase err.(test): min =        0.00 max =           89.98 mean =        58.14|
|-----------------------------------------------------------------------------|

============================== 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 = 15.437344             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.739   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.341415              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.429   (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 |  1.177 -  1.549:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.549 -  1.921:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.921 -  2.294:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.294 -  2.666:      664 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.666 -  3.038:     1451 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.038 -  3.411:     2545 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.411 -  3.783:     3898 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.783 -  4.155:     5066 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.155 -  4.528:     6479 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.528 -  4.900:     7711 |
|-----------------------------------------------------------------------------|
|-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 |       54.223 |
| 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  1.177 |       1.896 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    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 = 12.168)------------------------------------------|
|    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 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4957   r_free= 0.4833   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.295539                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4829   r_free= 0.4695   ksol= 0.30   Bsol= 20.00   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.22,12.57,6.96,0.00,0.00,0.00); trace/3= 8.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.288876                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.067942             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.182   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.243655              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.536   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4829      final r-factor (work) = 0.4146          |
| start r-factor (free) = 0.4695      final r-factor (free) = 0.4261          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 101.6331 = 15.07 * 0.50 * 6.2929 + 1.00 * 54.2225                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.0267 = 15.07 * 0.50 * 6.2229 + 1.00 * 0.1437                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4146      final r-factor (work) = 0.3713          |
| start r-factor (free) = 0.4261      final r-factor (free) = 0.4095          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7538 = 1.24 * 1.00 * 6.2229 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6780 = 1.24 * 1.00 * 6.1588 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.69   13.43    None  None   None       |
|    all(noH): 2823   0      0.00    73.69   13.43    None  None   None       |
|    Sol.    : 438    0      0.00    73.69   24.22    None  None   None       |
|    Mac.    : 2385   0      0.00    58.83   11.45    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 -   7.369: 1027   |   5:    36.845 -  44.214:   66        |
|      1:     7.369 -  14.738:  788   |   6:    44.214 -  51.583:   38        |
|      2:    14.738 -  22.107:  481   |   7:    51.583 -  58.951:   17        |
|      3:    22.107 -  29.476:  256   |   8:    58.951 -  66.320:    5        |
|      4:    29.476 -  36.845:  143   |   9:    66.320 -  73.689:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3713 r_free = 0.4095             target_work(ml) = 6.144         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3710 r_free = 0.4088             target_work(ml) = 6.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3710   r_free= 0.4088   ksol= 0.30   Bsol= 20.00   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.22,12.57,6.96,0.00,0.00,0.00); trace/3= 8.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.142867                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3684   r_free= 0.4040   ksol= 0.30   Bsol= 31.65   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.76,7.82,3.94,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.144446                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.491888              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.214  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.579100              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.404  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3684      final r-factor (work) = 0.3134          |
| start r-factor (free) = 0.4040      final r-factor (free) = 0.3780          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.2759 = 8.49 * 0.50 * 6.1547 + 1.00 * 0.1432                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8354 = 8.49 * 0.50 * 6.0620 + 1.00 * 0.0963                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3134      final r-factor (work) = 0.3033          |
| start r-factor (free) = 0.3780      final r-factor (free) = 0.3720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5446 = 0.58 * 1.00 * 6.0620 + 1.00 * 0.0340                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5406 = 0.58 * 1.00 * 6.0236 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.39   13.01    None  None   None       |
|    all(noH): 2823   0      0.00    74.39   13.01    None  None   None       |
|    Sol.    : 438    0      0.00    74.39   25.57    None  None   None       |
|    Mac.    : 2385   0      0.00    60.15   10.70    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 -   7.439: 1130   |   5:    37.193 -  44.632:   65        |
|      1:     7.439 -  14.877:  754   |   6:    44.632 -  52.070:   30        |
|      2:    14.877 -  22.316:  433   |   7:    52.070 -  59.509:   17        |
|      3:    22.316 -  29.754:  256   |   8:    59.509 -  66.947:    5        |
|      4:    29.754 -  37.193:  130   |   9:    66.947 -  74.386:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3033 r_free = 0.3720             target_work(ml) = 6.019         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3030 r_free = 0.3722             target_work(ml) = 6.019         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3030   r_free= 0.3722   ksol= 0.30   Bsol= 31.65   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.76,7.82,3.94,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.018650                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3035   r_free= 0.3724   ksol= 0.29   Bsol= 31.65   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.53,6.06,3.39,0.00,0.00,0.00); trace/3= 3.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.020579                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.715260              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.644  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.892299              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.085   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3035      final r-factor (work) = 0.2583          |
| start r-factor (free) = 0.3724      final r-factor (free) = 0.3122          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3108 = 5.72 * 0.50 * 6.0241 + 1.00 * 0.0963                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0880 = 5.72 * 0.50 * 5.9517 + 1.00 * 0.0803                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2583      final r-factor (work) = 0.2376          |
| start r-factor (free) = 0.3122      final r-factor (free) = 0.3030          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.2328 = 2.89 * 1.00 * 5.9517 + 1.00 * 0.0187                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.8785 = 2.89 * 1.00 * 5.8271 + 1.00 * 0.0247                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.10   15.57    None  None   None       |
|    all(noH): 2823   0      0.00    98.10   15.57    None  None   None       |
|    Sol.    : 438    0      0.59    98.10   36.78    None  None   None       |
|    Mac.    : 2385   0      0.00    96.66   11.67    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 -   9.810: 1451   |   5:    49.050 -  58.860:   81        |
|      1:     9.810 -  19.620:  625   |   6:    58.860 -  68.670:   59        |
|      2:    19.620 -  29.430:  287   |   7:    68.670 -  78.479:   25        |
|      3:    29.430 -  39.240:  148   |   8:    78.479 -  88.289:   11        |
|      4:    39.240 -  49.050:  128   |   9:    88.289 -  98.099:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2376 r_free = 0.3030             target_work(ml) = 5.821         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2375 r_free = 0.3029             target_work(ml) = 5.821         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2375   r_free= 0.3029   ksol= 0.29   Bsol= 31.65   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.53,6.06,3.39,0.00,0.00,0.00); trace/3= 3.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.820539                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2371   r_free= 0.3033   ksol= 0.32   Bsol= 57.64   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.07,4.63,3.00,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.820327                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.442260              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.446  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.635783              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.756  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2371      final r-factor (work) = 0.2019          |
| start r-factor (free) = 0.3033      final r-factor (free) = 0.2631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1076 = 3.44 * 0.50 * 5.8260 + 1.00 * 0.0803                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9592 = 3.44 * 0.50 * 5.7490 + 1.00 * 0.0644                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2019      final r-factor (work) = 0.1910          |
| start r-factor (free) = 0.2631      final r-factor (free) = 0.2434          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6801 = 0.64 * 1.00 * 5.7490 + 1.00 * 0.0250                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6069 = 0.64 * 1.00 * 5.6487 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.41   14.44    None  None   None       |
|    all(noH): 2823   0      0.00    97.41   14.44    None  None   None       |
|    Sol.    : 438    0      0.00    94.38   37.59    None  None   None       |
|    Mac.    : 2385   0      0.00    97.41   10.19    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 -   9.741: 1576   |   5:    48.704 -  58.445:   79        |
|      1:     9.741 -  19.482:  619   |   6:    58.445 -  68.186:   43        |
|      2:    19.482 -  29.223:  201   |   7:    68.186 -  77.927:   20        |
|      3:    29.223 -  38.963:  147   |   8:    77.927 -  87.667:    8        |
|      4:    38.963 -  48.704:  119   |   9:    87.667 -  97.408:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1910 r_free = 0.2434             target_work(ml) = 5.616         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1909 r_free = 0.2436             target_work(ml) = 5.616         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1909   r_free= 0.2436   ksol= 0.32   Bsol= 57.64   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.07,4.63,3.00,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.615904                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1912   r_free= 0.2435   ksol= 0.32   Bsol= 57.64   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,3.69,2.87,0.00,0.00,0.00); trace/3= 2.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.617831                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.542986              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.424  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.647819              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.021  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1912      final r-factor (work) = 0.1514          |
| start r-factor (free) = 0.2435      final r-factor (free) = 0.1995          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8967 = 4.54 * 0.50 * 5.6493 + 1.00 * 0.0644                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6100 = 4.54 * 0.50 * 5.5160 + 1.00 * 0.0805                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1514      final r-factor (work) = 0.1394          |
| start r-factor (free) = 0.1995      final r-factor (free) = 0.1887          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5888 = 0.65 * 1.00 * 5.5160 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4898 = 0.65 * 1.00 * 5.3648 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.54   14.21    None  None   None       |
|    all(noH): 2823   0      0.00    98.54   14.21    None  None   None       |
|    Sol.    : 438    0      1.78    98.54   39.96    None  None   None       |
|    Mac.    : 2385   0      0.00    98.10   9.48     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 -   9.854: 1668   |   5:    49.271 -  59.126:   89        |
|      1:     9.854 -  19.709:  590   |   6:    59.126 -  68.980:   49        |
|      2:    19.709 -  29.563:  164   |   7:    68.980 -  78.834:   21        |
|      3:    29.563 -  39.417:  117   |   8:    78.834 -  88.688:   11        |
|      4:    39.417 -  49.271:  107   |   9:    88.688 -  98.542:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1394 r_free = 0.1887             target_work(ml) = 5.335         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1394 r_free = 0.1888             target_work(ml) = 5.335         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1888   ksol= 0.32   Bsol= 57.64   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,3.69,2.87,0.00,0.00,0.00); trace/3= 2.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.335126                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7520 0.99   1401  158 0.1018 0.1399      5.4382      5.6246|
|  2:  4.7520 -  3.7918 0.99   1361  145 0.0974 0.1247      5.5583      5.7557|
|  3:  3.7918 -  3.3184 0.99   1320  154 0.1290 0.1851      5.6546      5.9907|
|  4:  3.3184 -  3.0176 0.99   1328  144 0.1522 0.1990      5.6324      5.8212|
|  5:  3.0176 -  2.8028 0.98   1298  145 0.1668 0.1904       5.523      5.6399|
|  6:  2.8028 -  2.6385 0.99   1304  145 0.1548 0.2281       5.396      5.5988|
|  7:  2.6385 -  2.5070 0.99   1298  146 0.1545 0.2050      5.3386      5.5699|
|  8:  2.5070 -  2.3983 0.99   1298  145 0.1546 0.1963      5.2721      5.4735|
|  9:  2.3983 -  2.3063 0.99   1283  136 0.1592 0.2147       5.239      5.4936|
| 10:  2.3063 -  2.2270 0.98   1278  146 0.1553 0.2376      5.2177      5.4635|
| 11:  2.2270 -  2.1576 0.98   1275  142 0.1523 0.2243      5.1595      5.4524|
| 12:  2.1576 -  2.0961 0.99   1268  142 0.1430 0.1958      5.0841      5.2864|
| 13:  2.0961 -  2.0410 0.96   1276  138 0.1543 0.2211      5.0089      5.2893|
| 14:  2.0410 -  1.9914 0.50    642   73 0.1412 0.1857      4.9011      5.0928|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7520  1401   158  0.93  10.64   0.97     0.94       8805.44|
|  2:  4.7520 -  3.7918  1361   145  0.94  10.26   1.02     1.00      11921.37|
|  3:  3.7918 -  3.3184  1320   154  0.91  14.57   1.03     1.02      14927.52|
|  4:  3.3184 -  3.0176  1328   144  0.89  17.24   1.02     0.99      14352.46|
|  5:  3.0176 -  2.8028  1298   145  0.87  19.62   1.02     1.01      11948.95|
|  6:  2.8028 -  2.6385  1304   145  0.87  19.33   1.00     0.96       9741.18|
|  7:  2.6385 -  2.5070  1298   146  0.88  18.88   1.00     0.97       8470.47|
|  8:  2.5070 -  2.3983  1298   145  0.87  19.19   1.02     0.99       7784.14|
|  9:  2.3983 -  2.3063  1283   136  0.87  19.87   1.02     0.97       7329.08|
| 10:  2.3063 -  2.2270  1278   146  0.86  20.96   1.01     0.97       7366.83|
| 11:  2.2270 -  2.1576  1275   142  0.85  21.21   1.00     0.94       6692.12|
| 12:  2.1576 -  2.0961  1268   142  0.87  19.94   1.02     1.00       6076.04|
| 13:  2.0961 -  2.0410  1276   138  0.86  20.83   1.01     1.01       5094.20|
| 14:  2.0410 -  1.9914   642    73  0.86  20.13   0.99     0.96       4170.55|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     4170.55 max =        14927.52 mean =      9124.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.91 mean =        17.88|
|phase err.(test): min =        0.00 max =           89.25 mean =        17.01|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1396   r_free= 0.1887   ksol= 0.33   Bsol= 63.84   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.55,0.28,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.335747                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1396   r_free= 0.1887   ksol= 0.33   Bsol= 63.84   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.55,0.28,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.335747                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7520 0.99   1401  158 0.1043 0.1399      5.4509      5.6191|
|  2:  4.7520 -  3.7918 0.99   1361  145 0.0984 0.1248      5.5615       5.753|
|  3:  3.7918 -  3.3184 0.99   1320  154 0.1295 0.1857      5.6578      5.9917|
|  4:  3.3184 -  3.0176 0.99   1328  144 0.1517 0.1998      5.6302      5.8224|
|  5:  3.0176 -  2.8028 0.98   1298  145 0.1666 0.1888      5.5213      5.6347|
|  6:  2.8028 -  2.6385 0.99   1304  145 0.1543 0.2262      5.3941      5.5954|
|  7:  2.6385 -  2.5070 0.99   1298  146 0.1544 0.2064      5.3377      5.5701|
|  8:  2.5070 -  2.3983 0.99   1298  145 0.1541 0.1961       5.271      5.4718|
|  9:  2.3983 -  2.3063 0.99   1283  136 0.1586 0.2150      5.2369      5.4924|
| 10:  2.3063 -  2.2270 0.98   1278  146 0.1551 0.2380      5.2166      5.4643|
| 11:  2.2270 -  2.1576 0.98   1275  142 0.1518 0.2244      5.1581      5.4519|
| 12:  2.1576 -  2.0961 0.99   1268  142 0.1431 0.1960      5.0841      5.2885|
| 13:  2.0961 -  2.0410 0.96   1276  138 0.1545 0.2204      5.0098      5.2902|
| 14:  2.0410 -  1.9914 0.50    642   73 0.1410 0.1841      4.8998      5.0884|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7520  1401   158  0.93  10.55   0.96     0.93       8619.38|
|  2:  4.7520 -  3.7918  1361   145  0.94  10.18   1.01     0.99      11813.16|
|  3:  3.7918 -  3.3184  1320   154  0.91  14.56   1.02     1.01      14982.72|
|  4:  3.3184 -  3.0176  1328   144  0.89  17.22   1.01     0.98      14265.29|
|  5:  3.0176 -  2.8028  1298   145  0.87  19.57   1.01     0.99      11879.81|
|  6:  2.8028 -  2.6385  1304   145  0.87  19.23   0.98     0.95       9691.37|
|  7:  2.6385 -  2.5070  1298   146  0.88  18.86   0.98     0.95       8463.91|
|  8:  2.5070 -  2.3983  1298   145  0.87  19.19   1.00     0.97       7791.82|
|  9:  2.3983 -  2.3063  1283   136  0.87  19.85   0.99     0.95       7321.65|
| 10:  2.3063 -  2.2270  1278   146  0.86  20.94   0.99     0.95       7353.16|
| 11:  2.2270 -  2.1576  1275   142  0.85  21.17   0.98     0.92       6674.36|
| 12:  2.1576 -  2.0961  1268   142  0.87  19.95   0.99     0.98       6090.48|
| 13:  2.0961 -  2.0410  1276   138  0.86  20.81   0.98     0.98       5090.00|
| 14:  2.0410 -  1.9914   642    73  0.86  20.11   0.97     0.93       4153.07|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     4153.07 max =        14982.72 mean =      9087.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.86 mean =        17.84|
|phase err.(test): min =        0.00 max =           89.63 mean =        16.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.30    100.84  16.51    None  None   None       |
|    all(noH): 2823   0      2.30    100.84  16.51    None  None   None       |
|    Sol.    : 438    0      4.07    100.84  42.26    None  None   None       |
|    Mac.    : 2385   0      2.30    100.40  11.78    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:     2.298 -  12.152: 1668   |   5:    51.569 -  61.423:   89        |
|      1:    12.152 -  22.006:  590   |   6:    61.423 -  71.278:   49        |
|      2:    22.006 -  31.861:  164   |   7:    71.278 -  81.132:   21        |
|      3:    31.861 -  41.715:  117   |   8:    81.132 -  90.986:   11        |
|      4:    41.715 -  51.569:  107   |   9:    90.986 - 100.840:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.742 - 5.095
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 326 from: 328
   mapped sites are within: 0.742 - 5.095

peak=    7.433 closest distance to " O   HOH Z  57 " =    1.212
peak=    7.247 closest distance to " O   HOH Z 120 " =    1.642
peak=    6.783 closest distance to " CG2 VAL A 230 " =    1.178
peak=    6.633 closest distance to " CG  LEU A   5 " =    1.351
peak=    6.374 closest distance to " OD1 ASN A 301 " =    1.115
peak=    6.153 closest distance to " CG1 ILE A 234 " =    1.419
peak=    6.094 closest distance to " O   HOH Z 426 " =    1.236
peak=    6.025 closest distance to " CG2 VAL A 296 " =    1.146
peak=    5.586 closest distance to " O   HOH Z 210 " =    1.678
peak=    5.501 closest distance to " O   GLN A  11 " =    0.992
peak=    5.279 closest distance to " O   HOH Z 422 " =    1.277
peak=    5.220 closest distance to " CG  GLN A  77 " =    0.935
peak=    5.091 closest distance to " CG  ARG A 138 " =    1.131
peak=    5.038 closest distance to " O   HOH Z 111 " =    2.132
peak=    5.020 closest distance to " O   HOH Z 159 " =    1.235
peak=    5.006 closest distance to " CB  SER A  63 " =    1.286
peak=    4.994 closest distance to " O   HOH Z  54 " =    1.215
peak=    4.940 closest distance to " CB  ARG A 275 " =    0.937
peak=    4.934 closest distance to " N   ASP A 298 " =    0.936
peak=    4.895 closest distance to " CB  VAL A 296 " =    1.104
peak=    4.707 closest distance to " O   HOH Z 246 " =    1.554
peak=    4.699 closest distance to " O   HOH Z 124 " =    1.472
peak=    4.627 closest distance to " O   HOH Z 128 " =    1.674
peak=    4.619 closest distance to " CB  VAL A 230 " =    1.218
peak=    4.520 closest distance to " CB  ASN A 285 " =    0.972
peak=    4.470 closest distance to " CG  PRO A  54 " =    1.207
peak=    4.469 closest distance to " CD  GLN A  73 " =    1.036
peak=    4.453 closest distance to " O   HOH Z 102 " =    1.503
peak=    4.439 closest distance to " O   HOH Z 425 " =    1.638
peak=    4.427 closest distance to " OE1 GLN A  11 " =    2.132
peak=    4.389 closest distance to " CD  ARG A  36 " =    1.266
peak=    4.388 closest distance to " NE  ARG A  36 " =    1.230
peak=    4.372 closest distance to " O   ASP A 298 " =    0.831
peak=    4.371 closest distance to " O  BHOH Z 338 " =    1.110
peak=    4.368 closest distance to " O   HOH Z  20 " =    2.042
peak=    4.365 closest distance to " OD2 ASP A 298 " =    0.948
peak=    4.337 closest distance to " CD  LYS A 166 " =    1.746
peak=    4.305 closest distance to " O   HOH Z 126 " =    1.651
peak=    4.303 closest distance to " O   HOH Z  80 " =    2.306
peak=    4.278 closest distance to " O   HOH Z 412 " =    3.211
peak=    4.275 closest distance to " O   HOH Z 433 " =    2.290
peak=    4.243 closest distance to " CD2 LEU A 228 " =    1.242
peak=    4.223 closest distance to " CD  LYS A 289 " =    1.102
peak=    4.206 closest distance to " OE1 GLU A   2 " =    1.568
peak=    4.197 closest distance to " CG  LEU A 228 " =    1.399
peak=    4.196 closest distance to " NH1 ARG A 138 " =    0.987
peak=    4.186 closest distance to " O   HOH Z 234 " =    3.455
peak=    4.131 closest distance to " NZ  LYS A  76 " =    1.077
peak=    4.124 closest distance to " CB  ARG A  66 " =    1.315
peak=    4.118 closest distance to " CG  PRO A 280 " =    0.959
peak=    4.116 closest distance to " O   HOH Z 403 " =    1.885
peak=    4.113 closest distance to " N   SER A 164 " =    1.016
peak=    4.103 closest distance to " O   HOH Z 134 " =    2.457
peak=    4.103 closest distance to " O   HOH Z 154 " =    1.507
peak=    4.098 closest distance to " CB  GLN A  73 " =    1.185
peak=    4.097 closest distance to " O   HOH Z 209 " =    2.265
peak=    4.094 closest distance to " NE2 HIS A 115 " =    1.110
peak=    4.091 closest distance to " O   HOH Z 416 " =    1.372
peak=    4.039 closest distance to " CA  TYR A  30 " =    0.969
peak=    4.033 closest distance to " O   HOH Z  88 " =    3.553
peak=    4.022 closest distance to " CB  TRP A 179 " =    1.402
peak=    4.012 closest distance to " O   HOH Z 395 " =    1.528
peak=    4.002 closest distance to " NE2 GLN A  11 " =    1.037
peak=    3.998 closest distance to " O   HOH Z 209 " =    2.173
peak=    3.978 closest distance to " CB  GLN A 183 " =    1.259
peak=    3.977 closest distance to " O   HOH Z  47 " =    1.819
peak=    3.974 closest distance to " O   HOH Z 389 " =    2.145
peak=    3.969 closest distance to " CB  GLN A  88 " =    1.230
peak=    3.948 closest distance to " O   HOH Z 261 " =    2.046
peak=    3.947 closest distance to " CD2 TRP A 179 " =    2.523
peak=    3.944 closest distance to " O   HOH Z 431 " =    1.847
peak=    3.941 closest distance to " O   HOH Z 418 " =    1.786
peak=    3.939 closest distance to " CA  ARG A 195 " =    1.139
peak=    3.910 closest distance to " O   HOH Z 370 " =    1.156
peak=    3.896 closest distance to " O   HOH Z 214 " =    1.359
peak=    3.894 closest distance to " O   HOH Z 388 " =    1.102
peak=    3.860 closest distance to " N   GLY A  75 " =    1.022
peak=    3.860 closest distance to " O   HOH Z 404 " =    1.271
peak=    3.859 closest distance to " O   HOH Z 369 " =    1.797
peak=    3.859 closest distance to " O   HOH Z 394 " =    1.891
peak=    3.852 closest distance to " O   LYS A 289 " =    1.103
peak=    3.851 closest distance to " ND2 ASN A 301 " =    1.038
peak=    3.843 closest distance to " O   HOH Z  15 " =    2.304
peak=    3.835 closest distance to " CB BVAL A  41 " =    1.279
peak=    3.834 closest distance to " O   HOH Z  48 " =    2.036
peak=    3.829 closest distance to " CE1 HIS A 108 " =    1.119
peak=    3.813 closest distance to " CE  LYS A 119 " =    1.424
peak=    3.810 closest distance to " O   HOH Z  44 " =    1.785
peak=    3.809 closest distance to " O   HOH Z  49 " =    1.310
peak=    3.789 closest distance to " CD  ARG A 269 " =    0.933
peak=    3.785 closest distance to " NH2 ARG A 156 " =    1.292
peak=    3.774 closest distance to " O   HOH Z  52 " =    1.377
peak=    3.759 closest distance to " O   HOH Z 133 " =    1.722
peak=    3.759 closest distance to " CG2 VAL A 296 " =    1.689
peak=    3.754 closest distance to " CG  PRO A 213 " =    1.332
peak=    3.753 closest distance to " O   HOH Z 193 " =    1.320
peak=    3.749 closest distance to " O   HOH Z  43 " =    2.041
peak=    3.747 closest distance to " NH1 ARG A  36 " =    1.334
peak=    3.745 closest distance to " C   VAL A 265 " =    1.038
peak=    3.738 closest distance to " OE1 GLN A  88 " =    0.852
peak=    3.736 closest distance to " CD1 LEU A 222 " =    0.934
peak=    3.717 closest distance to " CB  SER A  26 " =    0.924
peak=    3.712 closest distance to " CB  ARG A 275 " =    1.498
peak=    3.710 closest distance to " CB  ASN A 187 " =    1.130
peak=    3.709 closest distance to " O   HOH Z 155 " =    1.677
peak=    3.707 closest distance to " CB  TYR A  30 " =    0.969
peak=    3.703 closest distance to " O   HOH Z 279 " =    1.242
peak=    3.687 closest distance to " CG1BVAL A 121 " =    1.438
peak=    3.683 closest distance to " O   HOH Z 245 " =    1.451
peak=    3.682 closest distance to " CB  SER A  62 " =    0.957
peak=    3.679 closest distance to " CG1 ILE A 120 " =    1.142
peak=    3.674 closest distance to " CB  SER A 141 " =    0.987
peak=    3.664 closest distance to " CB  LEU A 255 " =    1.174
peak=    3.660 closest distance to " O   HOH Z 146 " =    1.693
peak=    3.658 closest distance to " O   HOH Z 132 " =    2.602
peak=    3.657 closest distance to " O   ALA A 165 " =    1.294
peak=    3.655 closest distance to " CA  SER A  12 " =    1.342
peak=    3.655 closest distance to " O   HOH Z  63 " =    1.959
peak=    3.653 closest distance to " C   ALA A 299 " =    0.853
peak=    3.652 closest distance to " CA  ALA A   1 " =    1.533
peak=    3.647 closest distance to " CD ALYS A 290 " =    1.126
peak=    3.632 closest distance to " O   HOH Z 174 " =    1.385
peak=    3.630 closest distance to " N   ALA A 256 " =    1.114
peak=    3.629 closest distance to " O   HOH Z 377 " =    1.466
peak=    3.626 closest distance to " CZ  PHE A 218 " =    1.151
peak=    3.621 closest distance to " CG1 ILE A  33 " =    1.264
peak=    3.621 closest distance to " O   HOH Z 418 " =    3.021
peak=    3.619 closest distance to " O   HOH Z 142 " =    1.502
peak=    3.616 closest distance to " CD2 TRP A 179 " =    1.175
peak=    3.613 closest distance to " CB  ALA A 299 " =    1.025
peak=    3.610 closest distance to " O   HOH Z   7 " =    0.798
peak=    3.609 closest distance to " O   HOH Z 332 " =    1.675
peak=    3.603 closest distance to " O   HOH Z 419 " =    2.438
peak=    3.596 closest distance to " CA  ALA A  21 " =    1.411
peak=    3.595 closest distance to " O   HOH Z 350 " =    1.273
peak=    3.591 closest distance to " N   TYR A  15 " =    0.851
peak=    3.589 closest distance to " CG2 VAL A  78 " =    1.004
peak=    3.575 closest distance to " O   HOH Z  40 " =    2.374
peak=    3.568 closest distance to " O   GLY A  23 " =    2.483
peak=    3.565 closest distance to " O   GLU A   2 " =    1.231
peak=    3.563 closest distance to " O   HOH Z 156 " =    3.165
peak=    3.555 closest distance to " CA  SER A  87 " =    0.839
peak=    3.553 closest distance to " O   HOH Z  68 " =    2.010
peak=    3.552 closest distance to " OG  SER A 245 " =    1.486
peak=    3.551 closest distance to " O   HOH Z  57 " =    2.124
peak=    3.550 closest distance to " O   HOH Z   4 " =    1.513
peak=    3.547 closest distance to " OG  SER A  62 " =    2.923
peak=    3.542 closest distance to " O   ASP A 124 " =    1.535
peak=    3.540 closest distance to " O   HOH Z 359 " =    2.010
peak=    3.539 closest distance to " CA  THR A 294 " =    1.785
peak=    3.539 closest distance to " CB  MET A  40 " =    0.742
peak=    3.536 closest distance to " CD  LYS A 289 " =    1.019
peak=    3.535 closest distance to " O   HOH Z  95 " =    1.640
peak=    3.532 closest distance to " O   HOH Z 271 " =    2.142
peak=    3.529 closest distance to " N   VAL A 121 " =    0.842
peak=    3.528 closest distance to " O   HOH Z 273 " =    3.009
peak=    3.528 closest distance to " O   HOH Z 130 " =    1.142
peak=    3.528 closest distance to " CA  THR A 246 " =    1.095
peak=    3.525 closest distance to " O   HOH Z 280 " =    2.993
peak=    3.524 closest distance to " CB  GLU A   2 " =    1.231
peak=    3.523 closest distance to " CB  SER A 273 " =    0.837
peak=    3.518 closest distance to " CD2 LEU A 297 " =    1.050
peak=    3.514 closest distance to " CB  PRO A  54 " =    0.844
peak=    3.511 closest distance to " CG AARG A 275 " =    1.175
peak=    3.510 closest distance to " CB  TRP A 266 " =    1.047
peak=    3.499 closest distance to " OE1 GLN A 223 " =    2.067
peak=    3.499 closest distance to " CA  ALA A 248 " =    1.141
peak=    3.496 closest distance to " OE1 GLN A  73 " =    1.396
peak=    3.494 closest distance to " O   HOH Z 139 " =    1.075
peak=    3.485 closest distance to " CG  PRO A 198 " =    1.386
peak=    3.476 closest distance to " OG  SER A  62 " =    3.415
peak=    3.474 closest distance to " N   ASN A  39 " =    1.264
peak=    3.471 closest distance to " O   HOH Z 387 " =    2.634
peak=    3.471 closest distance to " O   HOH Z  37 " =    1.106
peak=    3.468 closest distance to " O   HOH Z 435 " =    1.867
peak=    3.467 closest distance to " O   HOH Z 417 " =    1.432
peak=    3.466 closest distance to " O   HOH Z 146 " =    1.554
peak=    3.464 closest distance to " CB  PRO A 243 " =    1.176
peak=    3.460 closest distance to " CG1 VAL A 153 " =    1.091
peak=    3.454 closest distance to " O   HOH Z 426 " =    3.437
peak=    3.451 closest distance to " O   HOH Z 272 " =    1.328
peak=    3.446 closest distance to " O   ASN A 301 " =    1.451
peak=    3.446 closest distance to " O   HOH Z 154 " =    2.264
peak=    3.445 closest distance to " CA  GLY A  23 " =    0.915
peak=    3.442 closest distance to " O   HOH Z 257 " =    2.463
peak=    3.438 closest distance to " O   HOH Z 162 " =    1.788
peak=    3.436 closest distance to " ND2 ASN A 284 " =    0.999
peak=    3.432 closest distance to " CB  ALA A 100 " =    1.517
peak=    3.432 closest distance to " O   HOH Z   5 " =    1.756
peak=    3.431 closest distance to " CA  GLN A  11 " =    1.022
peak=    3.431 closest distance to " CB  GLN A  58 " =    1.093
peak=    3.431 closest distance to " O   HOH Z 272 " =    2.121
peak=    3.430 closest distance to " CB  PRO A 198 " =    0.996
peak=    3.425 closest distance to " O   HOH Z  97 " =    1.930
peak=    3.425 closest distance to " CB  THR A  31 " =    1.411
peak=    3.424 closest distance to " CG2 THR A 221 " =    1.198
peak=    3.423 closest distance to " CB  MET A 105 " =    1.289
peak=    3.420 closest distance to " ND1 HIS A  81 " =    1.474
peak=    3.417 closest distance to " O   VAL A  72 " =    1.086
peak=    3.417 closest distance to " O   HOH Z 126 " =    2.462
peak=    3.417 closest distance to " CB  ALA A  34 " =    1.043
peak=    3.416 closest distance to " O   HOH Z 149 " =    2.049
peak=    3.413 closest distance to " CB  VAL A 202 " =    1.364
peak=    3.413 closest distance to " O   HOH Z 149 " =    1.391
peak=    3.409 closest distance to " CB  GLU A 277 " =    1.010
peak=    3.409 closest distance to " CB  GLN A 223 " =    1.357
peak=    3.403 closest distance to " O   HOH Z  28 " =    1.575
peak=    3.396 closest distance to " O   HOH Z 277 " =    2.703
peak=    3.392 closest distance to " CD  PRO A  54 " =    0.996
peak=    3.390 closest distance to " O   HOH Z 256 " =    2.298
peak=    3.387 closest distance to " NE  ARG A  24 " =    1.093
peak=    3.386 closest distance to " O   HOH Z 265 " =    1.884
peak=    3.384 closest distance to " O   HOH Z 428 " =    3.978
peak=    3.381 closest distance to " O   HOH Z  99 " =    2.901
peak=    3.378 closest distance to " O   SER A  87 " =    2.458
peak=    3.377 closest distance to " O   HOH Z 368 " =    3.164
peak=    3.376 closest distance to " O   HOH Z 248 " =    1.883
peak=    3.373 closest distance to " OD1 ASP A 298 " =    0.942
peak=    3.372 closest distance to " CG  GLU A 277 " =    3.388
peak=    3.371 closest distance to " O   HOH Z 203 " =    1.835
peak=    3.367 closest distance to " O   HOH Z 393 " =    3.505
peak=    3.367 closest distance to " CG  MET A 185 " =    1.345
peak=    3.364 closest distance to " O   HOH Z 133 " =    2.187
peak=    3.363 closest distance to " O   HOH Z 189 " =    3.654
peak=    3.362 closest distance to " CB  GLU A 175 " =    1.274
peak=    3.362 closest distance to " O   HOH Z 236 " =    1.646
peak=    3.355 closest distance to " O   HOH Z 162 " =    1.470
peak=    3.354 closest distance to " CB  PHE A  16 " =    1.161
peak=    3.352 closest distance to " CG2 THR A 251 " =    1.308
peak=    3.349 closest distance to " CG  GLU A  37 " =    0.950
peak=    3.348 closest distance to " CA  VAL A  41 " =    0.842
peak=    3.348 closest distance to " NH1BARG A 145 " =    1.364
peak=    3.339 closest distance to " O   PRO A 198 " =    1.606
peak=    3.335 closest distance to " CD1 LEU A 101 " =    1.410
peak=    3.334 closest distance to " N   TYR A 247 " =    1.298
peak=    3.334 closest distance to " CD1 TRP A 274 " =    1.023
peak=    3.332 closest distance to " CB  ARG A 190 " =    1.787
peak=    3.325 closest distance to " O   HOH Z 130 " =    2.874
peak=    3.321 closest distance to " CA  ALA A  51 " =    1.110
peak=    3.320 closest distance to " OG ASER A 134 " =    1.416
peak=    3.320 closest distance to " NH1AARG A 145 " =    1.101
peak=    3.316 closest distance to " OG BSER A 258 " =    2.700
peak=    3.315 closest distance to " CA  GLU A 277 " =    0.916
peak=    3.311 closest distance to " CA  ARG A 139 " =    1.360
peak=    3.309 closest distance to " O   HOH Z 380 " =    2.135
peak=    3.308 closest distance to " O   HOH Z 238 " =    3.122
peak=    3.303 closest distance to " CG  PRO A 243 " =    1.218
peak=    3.300 closest distance to " CG2 THR A 220 " =    0.930
peak=    3.298 closest distance to " CG  LEU A 167 " =    1.078
peak=    3.296 closest distance to " CB  MET A  47 " =    1.148
peak=    3.293 closest distance to " O   HOH Z 294 " =    1.761
peak=    3.292 closest distance to " O   HOH Z 403 " =    1.496
peak=    3.290 closest distance to " O   HOH Z 177 " =    1.416
peak=    3.290 closest distance to " CB  PHE A 283 " =    0.863
peak=    3.289 closest distance to " O   HOH Z 334 " =    1.521
peak=    3.283 closest distance to " O   HOH Z 227 " =    1.675
peak=    3.282 closest distance to " O   HOH Z 232 " =    2.276
peak=    3.281 closest distance to " O   HOH Z 316 " =    3.053
peak=    3.276 closest distance to " O   HOH Z  61 " =    1.353
peak=    3.273 closest distance to " O   HOH Z 424 " =    3.107
peak=    3.269 closest distance to " O   HOH Z 427 " =    3.270
peak=    3.261 closest distance to " OD2 ASP A 171 " =    1.406
peak=    3.258 closest distance to " CB  ILE A 199 " =    1.061
peak=    3.257 closest distance to " CA  GLY A 196 " =    0.870
peak=    3.252 closest distance to " O   HOH Z 193 " =    1.307
peak=    3.252 closest distance to " NE1 TRP A  92 " =    1.334
peak=    3.247 closest distance to " O   HOH Z 394 " =    4.256
peak=    3.243 closest distance to " CE3 TRP A 274 " =    3.647
peak=    3.241 closest distance to " O   HOH Z 128 " =    2.078
peak=    3.241 closest distance to " O   HOH Z 185 " =    1.878
peak=    3.240 closest distance to " CA  GLN A 183 " =    1.824
peak=    3.237 closest distance to " NH1 ARG A  14 " =    1.200
peak=    3.235 closest distance to " CD2 HIS A  81 " =    1.456
peak=    3.231 closest distance to " CA  HIS A 115 " =    0.951
peak=    3.230 closest distance to " O   HOH Z 139 " =    4.736
peak=    3.227 closest distance to " CE1 PHE A 208 " =    1.116
peak=    3.226 closest distance to " O   HOH Z 191 " =    1.541
peak=    3.222 closest distance to " CD  ARG A  24 " =    1.315
peak=    3.220 closest distance to " O   GLY A  91 " =    1.164
peak=    3.220 closest distance to " O   ALA A 158 " =    1.106
peak=    3.219 closest distance to " CB  ALA A  71 " =    1.119
peak=    3.216 closest distance to " O   HOH Z 269 " =    3.391
peak=    3.211 closest distance to " N   GLU A   2 " =    0.906
peak=    3.210 closest distance to " O   HOH Z 189 " =    3.007
peak=    3.200 closest distance to " O   HOH Z  85 " =    2.008
peak=    3.199 closest distance to " O   HOH Z  22 " =    2.448
peak=    3.197 closest distance to " O   HOH Z 289 " =    1.584
peak=    3.190 closest distance to " CB  SER A  28 " =    1.186
peak=    3.187 closest distance to " CA  ALA A 100 " =    1.195
peak=    3.186 closest distance to " ND2 ASN A  45 " =    1.546
peak=    3.185 closest distance to " CA  ASN A 217 " =    1.308
peak=    3.183 closest distance to " NH1 ARG A 269 " =    0.839
peak=    3.183 closest distance to " ND1 HIS A  81 " =    1.412
peak=    3.178 closest distance to " O   HOH Z 176 " =    1.605
peak=    3.171 closest distance to " O   HOH Z 415 " =    1.751
peak=    3.170 closest distance to " OG1 THR A 279 " =    1.571
peak=    3.159 closest distance to " OG  SER A  62 " =    3.834
peak=    3.159 closest distance to " OG1 THR A 294 " =    1.516
peak=    3.157 closest distance to " CG2AVAL A 121 " =    1.873
peak=    3.157 closest distance to " O   HOH Z 336 " =    1.653
peak=    3.143 closest distance to " O   HOH Z  66 " =    1.666
peak=    3.142 closest distance to " O   HOH Z  59 " =    1.937
peak=    3.142 closest distance to " C   PRO A  54 " =    0.823
peak=    3.139 closest distance to " CB  VAL A 265 " =    1.315
peak=    3.136 closest distance to " NH1BARG A 145 " =    2.040
peak=    3.132 closest distance to " O   HOH Z 222 " =    2.867
peak=    3.131 closest distance to " CD1 TYR A 169 " =    0.975
peak=    3.130 closest distance to " O   HOH Z 359 " =    1.241
peak=    3.129 closest distance to " CG2 THR A 279 " =    4.483
peak=    3.123 closest distance to " CA  ALA A 160 " =    1.012
peak=    3.117 closest distance to " CB  ALA A 256 " =    1.172
peak=    3.115 closest distance to " O   THR A 178 " =    2.839
peak=    3.114 closest distance to " O   HOH Z 183 " =    1.863
peak=    3.098 closest distance to " NH2AARG A 275 " =    3.801
peak=    3.093 closest distance to " N   THR A  42 " =    1.285
peak=    3.090 closest distance to " O   HOH Z 423 " =    1.799
peak=    3.077 closest distance to " O   HOH Z 172 " =    5.095
peak=    3.074 closest distance to " CB  ASN A 148 " =    1.270
peak=    3.073 closest distance to " N   GLN A 278 " =    1.305
peak=    3.070 closest distance to " CG2 THR A  29 " =    1.600
peak=    3.052 closest distance to " CA  GLU A 128 " =    1.470
peak=    3.048 closest distance to " C   ILE A 106 " =    1.774
peak=    3.043 closest distance to " CA  ASP A 124 " =    0.832
peak=    3.038 closest distance to " CG  GLN A  11 " =    1.056
peak=    3.036 closest distance to " CA  ASP A 132 " =    1.166
peak=    3.019 closest distance to " N   GLU A  44 " =    1.423

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 228         
Filter by distance & map next to the model:
   mapped sites are within: 0.677 - 5.649
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 226 from: 228
   mapped sites are within: 0.781 - 5.649

peak=   -4.844 closest distance to " OD1 ASN A 301 " =    0.792
peak=   -4.834 closest distance to " CG2 VAL A 230 " =    0.973
peak=   -4.684 closest distance to " NH2 ARG A  36 " =    0.998
peak=   -4.554 closest distance to " O   HOH Z 166 " =    1.604
peak=   -4.334 closest distance to " O   GLN A  11 " =    0.880
peak=   -4.325 closest distance to " CA  ASP A 298 " =    1.021
peak=   -4.282 closest distance to " O   HOH Z  52 " =    2.060
peak=   -4.244 closest distance to " O   HOH Z 151 " =    1.001
peak=   -4.244 closest distance to " NH2 ARG A  66 " =    1.107
peak=   -4.230 closest distance to " CG  GLU A   2 " =    1.391
peak=   -4.196 closest distance to " C   ASN A 285 " =    2.370
peak=   -4.172 closest distance to " CG  PRO A 243 " =    1.675
peak=   -4.169 closest distance to " CG2BVAL A  41 " =    2.323
peak=   -4.141 closest distance to " O   HOH Z  37 " =    1.246
peak=   -4.137 closest distance to " CA  SER A 276 " =    1.447
peak=   -4.107 closest distance to " O   ASP A 298 " =    1.225
peak=   -4.095 closest distance to " CA  ASN A 127 " =    0.989
peak=   -4.076 closest distance to " O   HOH Z  13 " =    1.509
peak=   -4.064 closest distance to " CG  ARG A 138 " =    0.975
peak=   -4.053 closest distance to " O   HOH Z 411 " =    5.118
peak=   -4.023 closest distance to " CD1 PHE A  59 " =    1.806
peak=   -3.969 closest distance to " CD  ARG A  14 " =    3.256
peak=   -3.959 closest distance to " CA  SER A 164 " =    1.940
peak=   -3.956 closest distance to " O   HOH Z   7 " =    1.486
peak=   -3.946 closest distance to " CB  ALA A 291 " =    2.461
peak=   -3.928 closest distance to " O   ILE A 109 " =    2.645
peak=   -3.926 closest distance to " OXT GLY A 302 " =    2.885
peak=   -3.926 closest distance to " O   HOH Z 414 " =    2.038
peak=   -3.910 closest distance to " CD  GLN A 223 " =    1.519
peak=   -3.885 closest distance to " O   HOH Z 418 " =    1.338
peak=   -3.880 closest distance to " O   SER A  95 " =    1.877
peak=   -3.856 closest distance to " O   HOH Z   5 " =    1.729
peak=   -3.840 closest distance to " O   SER A  32 " =    1.163
peak=   -3.828 closest distance to " OD1 ASN A 148 " =    1.521
peak=   -3.815 closest distance to " CG  ASP A 231 " =    0.832
peak=   -3.811 closest distance to " O   HOH Z 388 " =    1.625
peak=   -3.797 closest distance to " CD2 LEU A 237 " =    2.501
peak=   -3.795 closest distance to " O   HOH Z 400 " =    0.863
peak=   -3.791 closest distance to " ND2 ASN A  39 " =    1.211
peak=   -3.779 closest distance to " O   HOH Z 184 " =    0.971
peak=   -3.775 closest distance to " O   VAL A 121 " =    0.911
peak=   -3.758 closest distance to " CA  TYR A  68 " =    2.792
peak=   -3.752 closest distance to " CG2 ILE A  49 " =    2.623
peak=   -3.751 closest distance to " O   HOH Z 426 " =    0.938
peak=   -3.747 closest distance to " O   HOH Z 196 " =    2.395
peak=   -3.730 closest distance to " CD2 PHE A  59 " =    2.412
peak=   -3.724 closest distance to " O   HOH Z  46 " =    0.807
peak=   -3.712 closest distance to " ND2 ASN A  60 " =    1.534
peak=   -3.689 closest distance to " O   HOH Z 351 " =    1.663
peak=   -3.685 closest distance to " N   ARG A 275 " =    0.989
peak=   -3.678 closest distance to " CG2 THR A 182 " =    2.339
peak=   -3.671 closest distance to " O   HOH Z 369 " =    2.348
peak=   -3.671 closest distance to " ND2 ASN A  60 " =    1.650
peak=   -3.661 closest distance to " O   HOH Z  60 " =    1.493
peak=   -3.656 closest distance to " O   HOH Z  56 " =    1.483
peak=   -3.656 closest distance to " O   HOH Z 401 " =    1.405
peak=   -3.655 closest distance to " CG1 VAL A 112 " =    2.414
peak=   -3.655 closest distance to " SG BCYS A 201 " =    1.154
peak=   -3.651 closest distance to " CB  LEU A 167 " =    2.009
peak=   -3.647 closest distance to " CA  GLY A 203 " =    2.319
peak=   -3.638 closest distance to " CD1 LEU A 228 " =    2.444
peak=   -3.628 closest distance to " O   HOH Z 422 " =    0.971
peak=   -3.622 closest distance to " O   HOH Z 407 " =    1.616
peak=   -3.620 closest distance to " NE2 GLN A  88 " =    0.935
peak=   -3.616 closest distance to " CD  GLN A  58 " =    1.156
peak=   -3.606 closest distance to " O   HOH Z 119 " =    2.035
peak=   -3.580 closest distance to " CD2 HIS A 115 " =    1.006
peak=   -3.579 closest distance to " CG1 VAL A 296 " =    1.230
peak=   -3.573 closest distance to " CE  MET A 105 " =    2.216
peak=   -3.568 closest distance to " O   HOH Z  39 " =    1.900
peak=   -3.562 closest distance to " O   HOH Z 109 " =    3.486
peak=   -3.561 closest distance to " CD  GLN A  77 " =    0.865
peak=   -3.553 closest distance to " O   HOH Z 407 " =    1.585
peak=   -3.543 closest distance to " CG  ARG A 269 " =    2.415
peak=   -3.542 closest distance to " O   HOH Z 120 " =    0.954
peak=   -3.541 closest distance to " N   THR A 264 " =    1.471
peak=   -3.540 closest distance to " O   HOH Z 290 " =    1.037
peak=   -3.537 closest distance to " CE3 TRP A  70 " =    1.574
peak=   -3.529 closest distance to " CB  SER A 146 " =    2.109
peak=   -3.506 closest distance to " N   SER A   3 " =    2.593
peak=   -3.495 closest distance to " O   HOH Z 109 " =    3.407
peak=   -3.490 closest distance to " O   HOH Z  15 " =    1.590
peak=   -3.486 closest distance to " N   GLU A   2 " =    1.215
peak=   -3.484 closest distance to " N   GLN A  58 " =    1.680
peak=   -3.482 closest distance to " O   HOH Z 402 " =    1.204
peak=   -3.469 closest distance to " CE3 TRP A 150 " =    2.266
peak=   -3.460 closest distance to " C   GLY A 133 " =    1.241
peak=   -3.457 closest distance to " O   PRO A 198 " =    1.305
peak=   -3.456 closest distance to " O   HOH Z  54 " =    1.555
peak=   -3.454 closest distance to " NE2 GLN A  58 " =    3.902
peak=   -3.438 closest distance to " O   HOH Z 423 " =    1.131
peak=   -3.437 closest distance to " O   HOH Z 222 " =    1.338
peak=   -3.430 closest distance to " O   HOH Z 105 " =    3.197
peak=   -3.428 closest distance to " OD2 ASP A 298 " =    0.825
peak=   -3.418 closest distance to " CE2 TRP A  85 " =    1.133
peak=   -3.418 closest distance to " NZ  LYS A  76 " =    1.943
peak=   -3.416 closest distance to " O   SER A 135 " =    2.085
peak=   -3.408 closest distance to " CD  LYS A 289 " =    2.411
peak=   -3.407 closest distance to " O   HOH Z 258 " =    1.936
peak=   -3.407 closest distance to " CA  VAL A 197 " =    1.018
peak=   -3.406 closest distance to " O   HOH Z 132 " =    1.390
peak=   -3.404 closest distance to " CG  ARG A 259 " =    2.478
peak=   -3.390 closest distance to " O   HOH Z 111 " =    1.237
peak=   -3.384 closest distance to " OE2 GLU A 277 " =    2.797
peak=   -3.383 closest distance to " O   HOH Z 200 " =    1.374
peak=   -3.383 closest distance to " CD1 LEU A   5 " =    1.427
peak=   -3.380 closest distance to " CD2 LEU A 237 " =    2.280
peak=   -3.380 closest distance to " CA  ALA A 137 " =    2.661
peak=   -3.379 closest distance to " O   HOH Z 108 " =    2.219
peak=   -3.379 closest distance to " O   HOH Z 384 " =    1.858
peak=   -3.367 closest distance to " CB  ALA A  10 " =    1.957
peak=   -3.366 closest distance to " O   HOH Z 269 " =    3.708
peak=   -3.353 closest distance to " O   HOH Z 430 " =    1.217
peak=   -3.352 closest distance to " O   HOH Z 166 " =    1.285
peak=   -3.351 closest distance to " O   HOH Z 252 " =    1.025
peak=   -3.348 closest distance to " OG1 THR A  82 " =    1.734
peak=   -3.347 closest distance to " CD1 ILE A 151 " =    2.294
peak=   -3.340 closest distance to " CB  TRP A 266 " =    2.145
peak=   -3.338 closest distance to " O   HOH Z 423 " =    2.797
peak=   -3.331 closest distance to " N   ALA A 226 " =    2.203
peak=   -3.329 closest distance to " CG2 THR A 235 " =    2.470
peak=   -3.328 closest distance to " O   HOH Z  81 " =    1.134
peak=   -3.327 closest distance to " O   HOH Z 394 " =    1.932
peak=   -3.325 closest distance to " OD1 ASP A 298 " =    2.347
peak=   -3.325 closest distance to " CD1 TRP A 179 " =    1.099
peak=   -3.324 closest distance to " CA  SER A 288 " =    1.102
peak=   -3.324 closest distance to " NE2 GLN A 103 " =    1.953
peak=   -3.323 closest distance to " NH2BARG A 145 " =    2.373
peak=   -3.320 closest distance to " O   HOH Z 131 " =    0.809
peak=   -3.318 closest distance to " NH1 ARG A 195 " =    0.999
peak=   -3.315 closest distance to " O   HOH Z 435 " =    2.732
peak=   -3.314 closest distance to " O   HOH Z 263 " =    3.333
peak=   -3.301 closest distance to " OD1 ASN A  69 " =    1.766
peak=   -3.300 closest distance to " O   GLY A  23 " =    1.170
peak=   -3.298 closest distance to " NE  ARG A  24 " =    1.065
peak=   -3.298 closest distance to " CD2 TYR A 293 " =    1.659
peak=   -3.297 closest distance to " O   HOH Z 185 " =    2.409
peak=   -3.296 closest distance to " O   HOH Z 323 " =    1.199
peak=   -3.287 closest distance to " OG  SER A  97 " =    2.312
peak=   -3.282 closest distance to " O   LEU A 300 " =    2.418
peak=   -3.281 closest distance to " O   HOH Z 174 " =    1.856
peak=   -3.275 closest distance to " O   HOH Z  50 " =    1.025
peak=   -3.273 closest distance to " CD1 LEU A 222 " =    2.624
peak=   -3.269 closest distance to " CB  ALA A  43 " =    2.743
peak=   -3.268 closest distance to " O   HOH Z  53 " =    1.549
peak=   -3.268 closest distance to " O   HOH Z 126 " =    1.958
peak=   -3.267 closest distance to " CG  ARG A 219 " =    2.286
peak=   -3.265 closest distance to " CG  GLN A 103 " =    2.362
peak=   -3.265 closest distance to " O   HOH Z 210 " =    1.010
peak=   -3.262 closest distance to " O   GLY A  80 " =    2.302
peak=   -3.262 closest distance to " O   HOH Z 275 " =    1.784
peak=   -3.260 closest distance to " CG  ASP A  50 " =    2.198
peak=   -3.258 closest distance to " O   HOH Z 219 " =    4.764
peak=   -3.254 closest distance to " N   ASP A 272 " =    1.210
peak=   -3.253 closest distance to " CA  GLU A 277 " =    1.101
peak=   -3.252 closest distance to " O   HOH Z 250 " =    1.624
peak=   -3.250 closest distance to " O   GLU A  53 " =    2.724
peak=   -3.248 closest distance to " CG2 THR A 178 " =    1.928
peak=   -3.246 closest distance to " CG1 VAL A 197 " =    2.519
peak=   -3.246 closest distance to " OG  SER A  26 " =    1.385
peak=   -3.234 closest distance to " O   HOH Z 139 " =    4.256
peak=   -3.233 closest distance to " OG  SER A  87 " =    1.685
peak=   -3.225 closest distance to " CG2 THR A 251 " =    1.578
peak=   -3.220 closest distance to " O   HOH Z 435 " =    1.406
peak=   -3.219 closest distance to " NE1 TRP A 150 " =    2.231
peak=   -3.216 closest distance to " CG  PRO A 163 " =    1.879
peak=   -3.215 closest distance to " O   HOH Z 265 " =    1.646
peak=   -3.215 closest distance to " CE3 TRP A 179 " =    2.326
peak=   -3.214 closest distance to " CD2 LEU A 237 " =    2.133
peak=   -3.207 closest distance to " O   HOH Z 396 " =    1.525
peak=   -3.205 closest distance to " O   HOH Z 127 " =    1.530
peak=   -3.204 closest distance to " O   HOH Z  93 " =    2.088
peak=   -3.202 closest distance to " OD2 ASP A 171 " =    1.864
peak=   -3.197 closest distance to " O   HOH Z 432 " =    1.145
peak=   -3.197 closest distance to " N   VAL A  72 " =    1.056
peak=   -3.194 closest distance to " CG2 VAL A 296 " =    1.136
peak=   -3.194 closest distance to " C   VAL A 265 " =    0.990
peak=   -3.192 closest distance to " NE2 GLN A 194 " =    2.497
peak=   -3.189 closest distance to " OE1 GLN A  88 " =    1.198
peak=   -3.188 closest distance to " CB  ALA A 291 " =    2.442
peak=   -3.187 closest distance to " O   HOH Z  29 " =    1.321
peak=   -3.177 closest distance to " CD  PRO A 243 " =    1.662
peak=   -3.175 closest distance to " O   HOH Z  64 " =    1.825
peak=   -3.172 closest distance to " ND2 ASN A  45 " =    1.267
peak=   -3.171 closest distance to " O   HOH Z  38 " =    1.299
peak=   -3.170 closest distance to " O   HOH Z 103 " =    2.000
peak=   -3.168 closest distance to " O   TRP A  92 " =    2.047
peak=   -3.168 closest distance to " O  BHOH Z  74 " =    1.700
peak=   -3.165 closest distance to " O   HOH Z 134 " =    1.890
peak=   -3.155 closest distance to " O   HOH Z 171 " =    2.591
peak=   -3.150 closest distance to " O   HOH Z 272 " =    1.149
peak=   -3.150 closest distance to " CG  GLN A  73 " =    0.872
peak=   -3.146 closest distance to " CD2 TYR A  30 " =    2.662
peak=   -3.134 closest distance to " CD2 LEU A 255 " =    1.779
peak=   -3.132 closest distance to " CD  GLU A 128 " =    1.905
peak=   -3.131 closest distance to " NE1 TRP A 266 " =    1.927
peak=   -3.129 closest distance to " O   HOH Z 234 " =    4.021
peak=   -3.126 closest distance to " CB  ALA A 114 " =    2.573
peak=   -3.122 closest distance to " O   HOH Z  19 " =    2.233
peak=   -3.122 closest distance to " CE  LYS A 119 " =    1.895
peak=   -3.119 closest distance to " O   HOH Z 126 " =    1.885
peak=   -3.117 closest distance to " CG2 THR A 279 " =    5.649
peak=   -3.114 closest distance to " OH  TYR A 293 " =    1.458
peak=   -3.107 closest distance to " N   ASP A 286 " =    1.242
peak=   -3.103 closest distance to " O   HOH Z  90 " =    1.693
peak=   -3.101 closest distance to " O   TYR A  15 " =    1.682
peak=   -3.099 closest distance to " N   THR A 178 " =    2.074
peak=   -3.097 closest distance to " O   VAL A 174 " =    1.810
peak=   -3.096 closest distance to " O   HOH Z  58 " =    0.958
peak=   -3.094 closest distance to " O   SER A   3 " =    1.070
peak=   -3.089 closest distance to " CG2 THR A   4 " =    1.967
peak=   -3.089 closest distance to " OD1 ASP A 149 " =    1.019
peak=   -3.085 closest distance to " O   HOH Z 193 " =    1.837
peak=   -3.082 closest distance to " OXT GLY A 302 " =    4.019
peak=   -3.078 closest distance to " CA  ASN A 110 " =    1.007
peak=   -3.075 closest distance to " OH  TYR A 169 " =    0.874
peak=   -3.073 closest distance to " NE2 GLN A 278 " =    2.498
peak=   -3.072 closest distance to " OD1AASN A 224 " =    1.898
peak=   -3.066 closest distance to " O   HOH Z 368 " =    2.018
peak=   -3.065 closest distance to " OG BSER A 134 " =    1.555
peak=   -3.060 closest distance to " C   ASN A  74 " =    1.981
peak=   -3.051 closest distance to " CB  ALA A  19 " =    2.460
peak=   -3.047 closest distance to " OE2 GLU A  53 " =    1.295
peak=   -3.032 closest distance to " O   HOH Z   5 " =    1.555
peak=   -3.030 closest distance to " CD  GLN A  73 " =    0.781
peak=   -3.016 closest distance to " CB  ALA A  64 " =    2.390

================= 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    :  0.4904 0.4754   6.294578e+00   6.273674e+00
   1_bss:  0.4829 0.4695   6.288876e+00   6.268018e+00
   1_xyz:  0.4146 0.4261   6.209862e+00   6.222308e+00
   1_adp:  0.3713 0.4095   6.143638e+00   6.201944e+00
   1_occ:  0.3710 0.4088   6.142867e+00   6.201631e+00
   2_bss:  0.3684 0.4040   6.144446e+00   6.200914e+00
   2_xyz:  0.3134 0.3780   6.034282e+00   6.148648e+00
   2_adp:  0.3033 0.3720   6.019020e+00   6.139260e+00
   2_occ:  0.3030 0.3722   6.018650e+00   6.139389e+00
   3_bss:  0.3035 0.3724   6.020579e+00   6.140268e+00
   3_xyz:  0.2583 0.3122   5.866144e+00   6.007199e+00
   3_adp:  0.2376 0.3030   5.820870e+00   5.990150e+00
   3_occ:  0.2375 0.3029   5.820539e+00   5.990044e+00
   4_bss:  0.2371 0.3033   5.820327e+00   5.989287e+00
   4_xyz:  0.2019 0.2631   5.669150e+00   5.865719e+00
   4_adp:  0.1910 0.2434   5.615938e+00   5.802792e+00
   4_occ:  0.1909 0.2436   5.615904e+00   5.803100e+00
   5_bss:  0.1912 0.2435   5.617831e+00   5.803528e+00
   5_xyz:  0.1514 0.1995   5.399523e+00   5.616372e+00
   5_adp:  0.1394 0.1887   5.335195e+00   5.559785e+00
   5_occ:  0.1394 0.1888   5.335126e+00   5.559970e+00
   5_bss:  0.1396 0.1887   5.335747e+00   5.558741e+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   6.224  12.568   6.960   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.224  12.568   6.960   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.224  12.568   6.960   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.224  12.568   6.960   0.000   0.000   0.000
   2_bss:  0.302  31.650   2.756   7.816   3.935   0.000   0.000   0.000
   2_xyz:  0.302  31.650   2.756   7.816   3.935   0.000   0.000   0.000
   2_adp:  0.302  31.650   2.756   7.816   3.935   0.000   0.000   0.000
   2_occ:  0.302  31.650   2.756   7.816   3.935   0.000   0.000   0.000
   3_bss:  0.293  31.650   2.530   6.057   3.391   0.000   0.000   0.000
   3_xyz:  0.293  31.650   2.530   6.057   3.391   0.000   0.000   0.000
   3_adp:  0.293  31.650   2.530   6.057   3.391   0.000   0.000   0.000
   3_occ:  0.293  31.650   2.530   6.057   3.391   0.000   0.000   0.000
   4_bss:  0.318  57.643   2.071   4.630   3.003   0.000   0.000   0.000
   4_xyz:  0.318  57.643   2.071   4.630   3.003   0.000   0.000   0.000
   4_adp:  0.318  57.643   2.071   4.630   3.003   0.000   0.000   0.000
   4_occ:  0.318  57.643   2.071   4.630   3.003   0.000   0.000   0.000
   5_bss:  0.316  57.643   1.824   3.685   2.873   0.000   0.000   0.000
   5_xyz:  0.316  57.643   1.824   3.685   2.873   0.000   0.000   0.000
   5_adp:  0.316  57.643   1.824   3.685   2.873   0.000   0.000   0.000
   5_occ:  0.316  57.643   1.824   3.685   2.873   0.000   0.000   0.000
   5_bss:  0.328  63.842  -0.829   0.551   0.278   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.065 0.4192  0.4813    70941.399
   1_bss:  58.179 0.4162  0.6081    69080.967
   1_xyz:  50.172 0.5178  0.7435    55092.813
   1_adp:  46.584 0.5628  0.8560    49392.550
   1_occ:  46.564 0.5630  0.8556    49292.109
   2_bss:  46.247 0.5669  0.7596    48917.984
   2_xyz:  42.330 0.6143  0.8216    41669.725
   2_adp:  41.409 0.6256  0.8280    40322.573
   2_occ:  41.393 0.6258  0.8275    40316.802
   3_bss:  41.312 0.6269  0.8067    40321.389
   3_xyz:  33.032 0.7237  0.9106    26768.069
   3_adp:  32.272 0.7322  0.9135    25591.118
   3_occ:  32.267 0.7322  0.9131    25565.332
   4_bss:  32.176 0.7333  0.8915    25481.681
   4_xyz:  27.072 0.7890  0.9405    18489.181
   4_adp:  24.457 0.8174  0.9535    15874.291
   4_occ:  24.462 0.8174  0.9536    15889.534
   5_bss:  24.452 0.8176  0.9396    15918.510
   5_xyz:  19.243 0.8685  0.9776    10151.285
   5_adp:  17.792 0.8824  0.9816     9116.641
   5_occ:  17.792 0.8824  0.9816     9125.420
   5_bss:  17.755 0.8827  0.9650     9088.483
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4223e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4223e+01
   1_xyz:   1.699  0.013  0.107 18.126  0.007  4.124   1.4368e-01
   1_adp:   1.699  0.013  0.107 18.126  0.007  4.124   1.4368e-01
   1_occ:   1.699  0.013  0.107 18.126  0.007  4.124   1.4368e-01
   2_bss:   1.699  0.013  0.107 18.126  0.007  4.124   1.4368e-01
   2_xyz:   1.286  0.009  0.084 16.898  0.005  4.110   9.6300e-02
   2_adp:   1.286  0.009  0.084 16.898  0.005  4.110   9.6300e-02
   2_occ:   1.286  0.009  0.084 16.898  0.005  4.110   9.6300e-02
   3_bss:   1.286  0.009  0.084 16.898  0.005  4.110   9.6300e-02
   3_xyz:   1.201  0.009  0.087 15.358  0.005  4.111   8.0260e-02
   3_adp:   1.201  0.009  0.087 15.358  0.005  4.111   8.0260e-02
   3_occ:   1.201  0.009  0.087 15.358  0.005  4.111   8.0260e-02
   4_bss:   1.201  0.009  0.087 15.358  0.005  4.111   8.0260e-02
   4_xyz:   1.022  0.007  0.071 15.191  0.004  4.122   6.4443e-02
   4_adp:   1.022  0.007  0.071 15.191  0.004  4.122   6.4443e-02
   4_occ:   1.022  0.007  0.071 15.191  0.004  4.122   6.4443e-02
   5_bss:   1.022  0.007  0.071 15.191  0.004  4.122   6.4443e-02
   5_xyz:   1.173  0.009  0.088 15.584  0.004  4.115   8.0493e-02
   5_adp:   1.173  0.009  0.088 15.584  0.004  4.115   8.0493e-02
   5_occ:   1.173  0.009  0.088 15.584  0.004  4.115   8.0493e-02
   5_bss:   1.173  0.009  0.088 15.584  0.004  4.115   8.0493e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.177   7.0288e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.177   7.0288e+00
   1_xyz:  14.962  0.116  0.505 87.636  0.042  2.227   1.0191e-01
   1_adp:  14.962  0.116  0.505 87.636  0.042  2.227   1.0191e-01
   1_occ:  14.962  0.116  0.505 87.636  0.042  2.227   1.0191e-01
   2_bss:  14.962  0.116  0.505 87.636  0.042  2.227   1.0191e-01
   2_xyz:   8.762  0.075  0.272 87.291  0.026  1.989   5.8837e-02
   2_adp:   8.762  0.075  0.272 87.291  0.026  1.989   5.8837e-02
   2_occ:   8.762  0.075  0.272 87.291  0.026  1.989   5.8837e-02
   3_bss:   8.762  0.075  0.272 87.291  0.026  1.989   5.8837e-02
   3_xyz:   8.221  0.090  0.295 84.862  0.033  2.209   5.9996e-02
   3_adp:   8.221  0.090  0.295 84.862  0.033  2.209   5.9996e-02
   3_occ:   8.221  0.090  0.295 84.862  0.033  2.209   5.9996e-02
   4_bss:   8.221  0.090  0.295 84.862  0.033  2.209   5.9996e-02
   4_xyz:   6.692  0.051  0.219 80.730  0.034  2.118   5.2696e-02
   4_adp:   6.692  0.051  0.219 80.730  0.034  2.118   5.2696e-02
   4_occ:   6.692  0.051  0.219 80.730  0.034  2.118   5.2696e-02
   5_bss:   6.692  0.051  0.219 80.730  0.034  2.118   5.2696e-02
   5_xyz:   7.975  0.065  0.525 86.911  0.033  2.249   6.1735e-02
   5_adp:   7.975  0.065  0.525 86.911  0.033  2.249   6.1735e-02
   5_occ:   7.975  0.065  0.525 86.911  0.033  2.249   6.1735e-02
   5_bss:   7.975  0.065  0.525 86.911  0.033  2.249   6.1735e-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:  73.69   0.00  13.43  58.83   0.00  11.45  73.69   0.00  24.22
   1_occ:  73.69   0.00  13.43  58.83   0.00  11.45  73.69   0.00  24.22
   2_bss:  73.69   0.00  13.43  58.83   0.00  11.45  73.69   0.00  24.22
   2_xyz:  73.69   0.00  13.43  58.83   0.00  11.45  73.69   0.00  24.22
   2_adp:  74.39   0.00  13.01  60.15   0.00  10.70  74.39   0.00  25.57
   2_occ:  74.39   0.00  13.01  60.15   0.00  10.70  74.39   0.00  25.57
   3_bss:  74.39   0.00  13.01  60.15   0.00  10.70  74.39   0.00  25.57
   3_xyz:  74.39   0.00  13.01  60.15   0.00  10.70  74.39   0.00  25.57
   3_adp:  98.10   0.00  15.57  96.66   0.00  11.67  98.10   0.59  36.78
   3_occ:  98.10   0.00  15.57  96.66   0.00  11.67  98.10   0.59  36.78
   4_bss:  98.10   0.00  15.57  96.66   0.00  11.67  98.10   0.59  36.78
   4_xyz:  98.10   0.00  15.57  96.66   0.00  11.67  98.10   0.59  36.78
   4_adp:  97.41   0.00  14.44  97.41   0.00  10.19  94.38   0.00  37.59
   4_occ:  97.41   0.00  14.44  97.41   0.00  10.19  94.38   0.00  37.59
   5_bss:  97.41   0.00  14.44  97.41   0.00  10.19  94.38   0.00  37.59
   5_xyz:  97.41   0.00  14.44  97.41   0.00  10.19  94.38   0.00  37.59
   5_adp:  98.54   0.00  14.21  98.10   0.00   9.48  98.54   1.78  39.96
   5_occ:  98.54   0.00  14.21  98.10   0.00   9.48  98.54   1.78  39.96
   5_bss: 100.84   2.30  16.51 100.40   2.30  11.78 100.84   4.07  42.26
------------------------------------------------------------------------
 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:    1.078    0.015    0.410
   1_adp:    1.078    0.015    0.410
   1_occ:    1.078    0.015    0.410
   2_bss:    1.078    0.015    0.410
   2_xyz:    1.846    0.022    0.561
   2_adp:    1.846    0.022    0.561
   2_occ:    1.846    0.022    0.561
   3_bss:    1.846    0.022    0.561
   3_xyz:    1.560    0.047    0.661
   3_adp:    1.560    0.047    0.661
   3_occ:    1.560    0.047    0.661
   4_bss:    1.560    0.047    0.661
   4_xyz:    1.848    0.064    0.757
   4_adp:    1.848    0.064    0.757
   4_occ:    1.848    0.064    0.757
   5_bss:    1.848    0.064    0.757
   5_xyz:    1.948    0.069    0.846
   5_adp:    1.948    0.069    0.846
   5_occ:    1.948    0.069    0.846
   5_bss:    1.948    0.069    0.846
------------------------------------------------------------------------

CPU time actual refinement: 296.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_840/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_840/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_840/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_840/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_840/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 296.45 
  Macro-tasks:
    bulk solvent and scale       = 34.72  
    individual site refinement   = 126.90 
    weights calculation          = 27.29  
    collect and process          = 5.40   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 194.44 
  Micro-tasks:
    mask                            = 2.55   
    f_calc                          = 93.25  
    alpha_beta                      = 7.07   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 103.04 
    fmodel                         = 6.12   
    r_factors                      = 0.22   
    phase_errors                   = 8.39   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 221.88 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.122 micro seconds
Total CPU time: 5.13 minutes
from_scatterers_fft:    657 calls, 92.98 s
gradients_fft:          601 calls, 91.31 s

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

# Date 2008-01-16 Time 02:32:31 PST -0800 (1200479551.67 s)
Start R-work = 0.4904, R-free = 0.4754 (no bulk solvent and anisotropic scale)
Final R-work = 0.1549, R-free = 0.2042 (no bulk solvent and anisotropic scale)

Start R-work = 0.4829, R-free = 0.4695
Final R-work = 0.1396, R-free = 0.1887