# Date 2008-01-16 Time 02:21:38 PST -0800 (1200478898.40 s)
#phil __OFF__

Command line arguments: "../796.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29232
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 796

-------------------------------------------------------------------------------
  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, 47.1647, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99109
Completeness in resolution range: 0.967884
Completeness with d_max=infinity: 0.964833

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9911

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99109
Completeness in resolution range: 0.967884
Completeness with d_max=infinity: 0.964833

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2602 [2117/2144]  1906   211  10.0%
  bin  2:  4.2602 -  3.3942 [2041/2057]  1836   205  10.0%
  bin  3:  3.3942 -  2.9689 [2018/2037]  1814   204  10.1%
  bin  4:  2.9689 -  2.6992 [2000/2030]  1805   195   9.8%
  bin  5:  2.6992 -  2.5067 [1984/2003]  1784   200  10.1%
  bin  6:  2.5067 -  2.3595 [1954/1979]  1762   192   9.8%
  bin  7:  2.3595 -  2.2417 [1971/2004]  1770   201  10.2%
  bin  8:  2.2417 -  2.1444 [1957/1988]  1761   196  10.0%
  bin  9:  2.1444 -  2.0621 [1961/2003]  1766   195   9.9%
  bin 10:  2.0621 -  1.9911 [1586/1994]  1426   160  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_796/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2201
        3.04 -     3.66: 4644
        3.66 -     4.28: 9007
        4.28 -     4.90: 12336
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.081 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.335 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28193 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_796/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_796/model_refine_001.geo

CPU time processing inputs: 9.14


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


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


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


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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4150   r_free= 0.4005   ksol= 0.00   Bsol= 0.00   scale= 0.831    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.200752                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7514 0.99   1378  154 0.3551 0.3327         6.5      6.4141|
|  2:  4.7514 -  3.7913 0.99   1334  145 0.3046 0.3153      6.5825      6.6206|
|  3:  3.7913 -  3.3179 0.99   1302  146 0.3514 0.3346      6.5139      6.5293|
|  4:  3.3179 -  3.0172 0.99   1289  145 0.3862 0.3441      6.4184      6.2968|
|  5:  3.0172 -  2.8025 0.99   1281  141 0.4280 0.4195      6.2799      6.3157|
|  6:  2.8025 -  2.6382 0.99   1285  143 0.4373 0.4988      6.2064      6.2172|
|  7:  2.6382 -  2.5067 0.99   1276  141 0.4630 0.4240      6.2009       6.118|
|  8:  2.5067 -  2.3980 0.98   1267  143 0.4601 0.4278      6.1299      6.0873|
|  9:  2.3980 -  2.3060 0.98   1271  140 0.4638 0.4631      6.0794      6.0636|
| 10:  2.3060 -  2.2267 0.99   1246  142 0.4741 0.4758      6.0756       6.063|
| 11:  2.2267 -  2.1573 0.99   1275  139 0.4743 0.4089      6.0069      5.9728|
| 12:  2.1573 -  2.0958 0.97   1241  137 0.4793 0.4602      5.9612      5.9821|
| 13:  2.0958 -  2.0408 0.99   1252  142 0.4958 0.5126      5.8648       5.873|
| 14:  2.0408 -  1.9911 0.72    933  101 0.4868 0.4478      5.8218      5.7088|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7514  1378   154  0.75  30.02   0.82     0.77      54523.62|
|  2:  4.7514 -  3.7913  1334   145  0.80  26.63   0.92     0.83      65120.90|
|  3:  3.7913 -  3.3179  1302   146  0.74  32.18   0.88     0.82      66839.10|
|  4:  3.3179 -  3.0172  1289   145  0.69  36.46   0.85     0.74      60111.13|
|  5:  3.0172 -  2.8025  1281   141  0.59  44.69   0.78     0.66      55115.04|
|  6:  2.8025 -  2.6382  1285   143  0.57  46.29   0.78     0.63      49980.47|
|  7:  2.6382 -  2.5067  1276   141  0.56  47.15   0.76     0.62      45976.22|
|  8:  2.5067 -  2.3980  1267   143  0.56  47.44   0.77     0.63      41280.50|
|  9:  2.3980 -  2.3060  1271   140  0.56  47.14   0.76     0.62      36633.01|
| 10:  2.3060 -  2.2267  1246   142  0.56  47.64   0.78     0.62      33965.47|
| 11:  2.2267 -  2.1573  1275   139  0.54  49.46   0.79     0.60      32239.95|
| 12:  2.1573 -  2.0958  1241   137  0.49  52.74   0.79     0.57      33064.18|
| 13:  2.0958 -  2.0408  1252   142  0.46  55.63   0.76     0.54      29741.62|
| 14:  2.0408 -  1.9911   933   101  0.50  52.28   0.75     0.54      23731.78|
|alpha:            min =        0.54 max =            0.83 mean =         0.66|
|beta:             min =    23731.78 max =        66839.10 mean =     45530.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.98 mean =        43.62|
|phase err.(test): min =        0.00 max =           90.00 mean =        43.64|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.750362              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.897   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.524025              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.959   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      674 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1508 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2621 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3888 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5054 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6576 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7668 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.937 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.642 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    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= 0.4238   r_free= 0.4083   ksol= 0.00   Bsol= 0.00   scale= 0.799    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.208523                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4061   r_free= 0.3896   ksol= 0.34   Bsol= 20.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.49,8.63,8.05,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.196980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.433687              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.007   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.542350              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.737   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4061      final r-factor (work) = 0.2907          |
| start r-factor (free) = 0.3896      final r-factor (free) = 0.3177          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.9453 = 6.43 * 0.50 * 6.2199 + 1.00 * 53.9368                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4455 = 6.43 * 0.50 * 6.0105 + 1.00 * 0.1106                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2907      final r-factor (work) = 0.2196          |
| start r-factor (free) = 0.3177      final r-factor (free) = 0.2520          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2745 = 0.54 * 1.00 * 6.0105 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1535 = 0.54 * 1.00 * 5.7953 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    54.17   9.82     None  None   None       |
|    all(noH): 2823   0      0.00    54.17   9.82     None  None   None       |
|    Sol.    : 438    0      0.00    54.17   26.55    None  None   None       |
|    Mac.    : 2385   0      0.00    46.89   6.75     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.418: 1296   |   5:    27.088 -  32.505:  106        |
|      1:     5.418 -  10.835:  757   |   6:    32.505 -  37.922:   86        |
|      2:    10.835 -  16.253:  252   |   7:    37.922 -  43.340:   68        |
|      3:    16.253 -  21.670:  118   |   8:    43.340 -  48.757:   17        |
|      4:    21.670 -  27.088:  120   |   9:    48.757 -  54.175:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2196 r_free = 0.2520             target_work(ml) = 5.690         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2191 r_free = 0.2516             target_work(ml) = 5.688         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2191   r_free= 0.2516   ksol= 0.34   Bsol= 20.00   scale= 1.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.49,8.63,8.05,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.688077                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2142   r_free= 0.2446   ksol= 0.34   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.06,4.88,5.10,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.685982                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.969468              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.090   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.263475              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.831  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2142      final r-factor (work) = 0.1483          |
| start r-factor (free) = 0.2446      final r-factor (free) = 0.1844          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7394 = 2.97 * 0.50 * 5.8120 + 1.00 * 0.1101                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2424 = 2.97 * 0.50 * 5.5091 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1483      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.1844      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4619 = 0.26 * 1.00 * 5.5091 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4275 = 0.26 * 1.00 * 5.3172 + 1.00 * 0.0265                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    54.95   10.31    None  None   None       |
|    all(noH): 2823   0      0.00    54.95   10.31    None  None   None       |
|    Sol.    : 438    0      0.65    54.95   29.47    None  None   None       |
|    Mac.    : 2385   0      0.00    51.15   6.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.495: 1350   |   5:    27.473 -  32.968:   89        |
|      1:     5.495 -  10.989:  688   |   6:    32.968 -  38.462:  116        |
|      2:    10.989 -  16.484:  253   |   7:    38.462 -  43.957:   90        |
|      3:    16.484 -  21.979:  108   |   8:    43.957 -  49.452:   29        |
|      4:    21.979 -  27.473:   92   |   9:    49.452 -  54.946:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1369 r_free = 0.1747             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1368 r_free = 0.1746             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1746   ksol= 0.34   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.06,4.88,5.10,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.291790                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1366   r_free= 0.1745   ksol= 0.34   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.90,4.48,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.293254                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.361950              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.599  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.052337              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.676   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3469 = 2.36 * 0.50 * 5.3209 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2448 = 2.36 * 0.50 * 5.2331 + 1.00 * 0.0646                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5259 = 1.05 * 1.00 * 5.2331 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4508 = 1.05 * 1.00 * 5.1671 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.29   11.11    None  None   None       |
|    all(noH): 2823   0      0.00    70.29   11.11    None  None   None       |
|    Sol.    : 438    0      0.38    68.43   33.43    None  None   None       |
|    Mac.    : 2385   0      0.00    70.29   7.01     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 -   7.029: 1632   |   5:    35.144 -  42.172:   89        |
|      1:     7.029 -  14.057:  554   |   6:    42.172 -  49.201:   93        |
|      2:    14.057 -  21.086:  176   |   7:    49.201 -  56.230:   56        |
|      3:    21.086 -  28.115:  111   |   8:    56.230 -  63.258:   20        |
|      4:    28.115 -  35.144:   84   |   9:    63.258 -  70.287:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1572             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1573             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1573   ksol= 0.34   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.90,4.48,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161578                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1573   ksol= 0.33   Bsol= 47.51   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.90,4.48,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.161131                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.451722              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.019  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.309767              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.489  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8148 = 1.45 * 0.50 * 5.1666 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8017 = 1.45 * 0.50 * 5.1633 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6137 = 0.31 * 1.00 * 5.1633 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6323 = 0.31 * 1.00 * 5.1684 + 1.00 * 0.0314                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.64   10.91    None  None   None       |
|    all(noH): 2823   0      0.00    71.64   10.91    None  None   None       |
|    Sol.    : 438    0      0.64    66.35   32.43    None  None   None       |
|    Mac.    : 2385   0      0.00    71.64   6.96     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.164: 1666   |   5:    35.819 -  42.983:   80        |
|      1:     7.164 -  14.328:  544   |   6:    42.983 -  50.146:   78        |
|      2:    14.328 -  21.491:  167   |   7:    50.146 -  57.310:   43        |
|      3:    21.491 -  28.655:  108   |   8:    57.310 -  64.474:   16        |
|      4:    28.655 -  35.819:  114   |   9:    64.474 -  71.638:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1153 r_free = 0.1571             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1153 r_free = 0.1571             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1571   ksol= 0.33   Bsol= 47.51   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.90,4.48,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163555                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1571   ksol= 0.33   Bsol= 47.51   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.90,4.48,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163555                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.714841              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.221  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.728419              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.306   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0694 = 2.71 * 0.50 * 5.1681 + 1.00 * 0.0540                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0517 = 2.71 * 0.50 * 5.1426 + 1.00 * 0.0711                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7819 = 0.73 * 1.00 * 5.1426 + 1.00 * 0.0359                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7500 = 0.73 * 1.00 * 5.1306 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.19   11.08    None  None   None       |
|    all(noH): 2823   0      0.00    80.19   11.08    None  None   None       |
|    Sol.    : 438    0      0.46    70.87   33.25    None  None   None       |
|    Mac.    : 2385   0      0.00    80.19   7.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.019: 1758   |   5:    40.095 -  48.115:   96        |
|      1:     8.019 -  16.038:  505   |   6:    48.115 -  56.134:   61        |
|      2:    16.038 -  24.057:  148   |   7:    56.134 -  64.153:   22        |
|      3:    24.057 -  32.076:  111   |   8:    64.153 -  72.172:    9        |
|      4:    32.076 -  40.095:  108   |   9:    72.172 -  80.191:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1094 r_free = 0.1557             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1093 r_free = 0.1557             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1557   ksol= 0.33   Bsol= 47.51   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.90,4.48,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133819                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7514 0.99   1378  154 0.0990 0.1311      5.3815      5.5291|
|  2:  4.7514 -  3.7913 0.99   1334  145 0.0846 0.1091      5.4264      5.6177|
|  3:  3.7913 -  3.3179 0.99   1302  146 0.1029 0.1500      5.4547      5.8582|
|  4:  3.3179 -  3.0172 0.99   1289  145 0.1169 0.1482        5.44      5.5748|
|  5:  3.0172 -  2.8025 0.99   1281  141 0.1300 0.1725      5.3146      5.5423|
|  6:  2.8025 -  2.6382 0.99   1285  143 0.1169 0.1744      5.1969      5.4179|
|  7:  2.6382 -  2.5067 0.99   1276  141 0.1232 0.1671      5.1599      5.4128|
|  8:  2.5067 -  2.3980 0.98   1267  143 0.1142 0.1737      5.0648      5.3568|
|  9:  2.3980 -  2.3060 0.98   1271  140 0.1147 0.1796      5.0326      5.3245|
| 10:  2.3060 -  2.2267 0.99   1246  142 0.1078 0.1605      4.9528      5.1532|
| 11:  2.2267 -  2.1573 0.99   1275  139 0.1115 0.1822       4.934      5.3024|
| 12:  2.1573 -  2.0958 0.97   1241  137 0.1084 0.1644      4.8684      5.1552|
| 13:  2.0958 -  2.0408 0.99   1252  142 0.1134 0.1749      4.7892      5.0773|
| 14:  2.0408 -  1.9911 0.72    933  101 0.1056 0.1737        4.67      4.9134|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7514  1378   154  0.94   9.00   0.98     0.96       7174.81|
|  2:  4.7514 -  3.7913  1334   145  0.95   7.80   1.01     1.00       8893.74|
|  3:  3.7913 -  3.3179  1302   146  0.94  11.01   1.02     1.01      10100.43|
|  4:  3.3179 -  3.0172  1289   145  0.92  13.13   1.00     0.99      10116.58|
|  5:  3.0172 -  2.8025  1281   141  0.90  15.83   0.99     0.96       8114.97|
|  6:  2.8025 -  2.6382  1285   143  0.90  15.59   0.98     0.95       6991.03|
|  7:  2.6382 -  2.5067  1276   141  0.91  15.55   0.99     0.95       6130.14|
|  8:  2.5067 -  2.3980  1267   143  0.91  14.97   0.99     0.97       5327.10|
|  9:  2.3980 -  2.3060  1271   140  0.91  15.46   1.01     0.98       5099.43|
| 10:  2.3060 -  2.2267  1246   142  0.91  15.33   1.00     0.96       4387.34|
| 11:  2.2267 -  2.1573  1275   139  0.90  16.46   1.00     0.96       4400.27|
| 12:  2.1573 -  2.0958  1241   137  0.92  14.68   1.00     0.99       3858.38|
| 13:  2.0958 -  2.0408  1252   142  0.90  16.14   1.00     0.99       3378.07|
| 14:  2.0408 -  1.9911   933   101  0.91  14.60   0.98     0.94       2555.04|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2555.04 max =        10116.58 mean =      6287.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.77 mean =        13.90|
|phase err.(test): min =        0.00 max =           87.02 mean =        13.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1561   ksol= 0.32   Bsol= 49.38   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-0.08,0.59,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1561   ksol= 0.32   Bsol= 49.38   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-0.08,0.59,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135017                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7514 0.99   1378  154 0.1001 0.1316      5.3895      5.5262|
|  2:  4.7514 -  3.7913 0.99   1334  145 0.0855 0.1092      5.4344      5.6209|
|  3:  3.7913 -  3.3179 0.99   1302  146 0.1030 0.1492      5.4566       5.845|
|  4:  3.3179 -  3.0172 0.99   1289  145 0.1168 0.1489      5.4376      5.5772|
|  5:  3.0172 -  2.8025 0.99   1281  141 0.1300 0.1723      5.3139      5.5413|
|  6:  2.8025 -  2.6382 0.99   1285  143 0.1168 0.1746      5.1965      5.4195|
|  7:  2.6382 -  2.5067 0.99   1276  141 0.1232 0.1683      5.1605      5.4148|
|  8:  2.5067 -  2.3980 0.98   1267  143 0.1141 0.1740       5.065      5.3574|
|  9:  2.3980 -  2.3060 0.98   1271  140 0.1146 0.1798      5.0328      5.3253|
| 10:  2.3060 -  2.2267 0.99   1246  142 0.1075 0.1610      4.9534      5.1557|
| 11:  2.2267 -  2.1573 0.99   1275  139 0.1114 0.1823      4.9341      5.3028|
| 12:  2.1573 -  2.0958 0.97   1241  137 0.1082 0.1641      4.8685      5.1549|
| 13:  2.0958 -  2.0408 0.99   1252  142 0.1132 0.1751      4.7888      5.0784|
| 14:  2.0408 -  1.9911 0.72    933  101 0.1057 0.1735      4.6695      4.9128|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7514  1378   154  0.94   9.21   0.98     0.95       7284.05|
|  2:  4.7514 -  3.7913  1334   145  0.95   7.90   1.01     1.00       8929.00|
|  3:  3.7913 -  3.3179  1302   146  0.94  11.05   1.02     1.01      10109.15|
|  4:  3.3179 -  3.0172  1289   145  0.92  13.07   1.00     0.99      10019.11|
|  5:  3.0172 -  2.8025  1281   141  0.90  15.81   0.99     0.96       8103.73|
|  6:  2.8025 -  2.6382  1285   143  0.90  15.60   0.98     0.95       6992.24|
|  7:  2.6382 -  2.5067  1276   141  0.91  15.55   0.99     0.96       6139.78|
|  8:  2.5067 -  2.3980  1267   143  0.91  14.99   0.99     0.97       5339.30|
|  9:  2.3980 -  2.3060  1271   140  0.91  15.47   1.01     0.98       5112.94|
| 10:  2.3060 -  2.2267  1246   142  0.91  15.34   1.00     0.96       4398.15|
| 11:  2.2267 -  2.1573  1275   139  0.90  16.48   1.00     0.96       4409.76|
| 12:  2.1573 -  2.0958  1241   137  0.92  14.70   1.00     0.99       3866.61|
| 13:  2.0958 -  2.0408  1252   142  0.90  16.13   1.01     0.99       3377.91|
| 14:  2.0408 -  1.9911   933   101  0.91  14.58   0.98     0.95       2549.42|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2549.42 max =        10109.15 mean =      6295.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.92|
|phase err.(test): min =        0.00 max =           87.74 mean =        13.44|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.94    84.13   15.02    None  None   None       |
|    all(noH): 2823   0      3.94    84.13   15.02    None  None   None       |
|    Sol.    : 438    0      4.40    74.81   37.19    None  None   None       |
|    Mac.    : 2385   0      3.94    84.13   10.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.940 -  11.959: 1758   |   5:    44.036 -  52.055:   96        |
|      1:    11.959 -  19.978:  505   |   6:    52.055 -  60.074:   61        |
|      2:    19.978 -  27.997:  148   |   7:    60.074 -  68.093:   22        |
|      3:    27.997 -  36.017:  111   |   8:    68.093 -  76.112:    9        |
|      4:    36.017 -  44.036:  108   |   9:    76.112 -  84.131:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.327 - 4.774
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 308
   mapped sites are within: 0.732 - 4.774

peak=   10.199 closest distance to " CG2 VAL A 230 " =    1.305
peak=    6.479 closest distance to " CG2 VAL A 296 " =    1.097
peak=    6.261 closest distance to " NH2 ARG A  56 " =    2.276
peak=    6.183 closest distance to " CG  LEU A   5 " =    1.189
peak=    5.965 closest distance to " CG  LEU A 228 " =    1.163
peak=    5.360 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.329 closest distance to " CD2 LEU A   5 " =    1.181
peak=    5.302 closest distance to " CB  VAL A 230 " =    1.204
peak=    5.301 closest distance to " CB  VAL A 296 " =    1.081
peak=    5.228 closest distance to " CG  PRO A  54 " =    1.219
peak=    5.122 closest distance to " CB  SER A  63 " =    1.284
peak=    5.030 closest distance to " CB  GLN A 183 " =    1.301
peak=    4.971 closest distance to " NE2 GLN A  11 " =    1.095
peak=    4.928 closest distance to " O   HOH Z 126 " =    1.949
peak=    4.733 closest distance to " CB  PRO A  54 " =    0.906
peak=    4.630 closest distance to " CG  PRO A 213 " =    1.209
peak=    4.615 closest distance to " CB  ARG A 275 " =    0.877
peak=    4.589 closest distance to " O   HOH Z 272 " =    1.923
peak=    4.587 closest distance to " O   HOH Z 209 " =    2.327
peak=    4.545 closest distance to " O   HOH Z 368 " =    2.241
peak=    4.473 closest distance to " C   PRO A 198 " =    1.486
peak=    4.459 closest distance to " O   HOH Z 298 " =    1.855
peak=    4.442 closest distance to " O   HOH Z 369 " =    2.162
peak=    4.390 closest distance to " O   HOH Z 142 " =    1.559
peak=    4.353 closest distance to " OD1 ASN A  69 " =    2.620
peak=    4.331 closest distance to " O   HOH Z 232 " =    2.373
peak=    4.279 closest distance to " O   SER A  87 " =    2.296
peak=    4.269 closest distance to " O   HOH Z 427 " =    3.005
peak=    4.268 closest distance to " CB  GLU A 152 " =    1.192
peak=    4.237 closest distance to " O   HOH Z 193 " =    1.802
peak=    4.213 closest distance to " O   HOH Z 316 " =    3.083
peak=    4.197 closest distance to " O   HOH Z  54 " =    2.398
peak=    4.190 closest distance to " O   HOH Z  15 " =    2.121
peak=    4.187 closest distance to " O   HOH Z 423 " =    1.781
peak=    4.173 closest distance to " O   HOH Z  66 " =    2.288
peak=    4.171 closest distance to " O   HOH Z  63 " =    2.061
peak=    4.152 closest distance to " CB  SER A   3 " =    1.256
peak=    4.150 closest distance to " O   HOH Z 203 " =    1.727
peak=    4.150 closest distance to " CG  PRO A 243 " =    1.120
peak=    4.108 closest distance to " ND2 ASN A 187 " =    1.461
peak=    4.102 closest distance to " O   HOH Z 346 " =    1.596
peak=    4.100 closest distance to " O   HOH Z 158 " =    3.119
peak=    4.092 closest distance to " O   HOH Z 403 " =    1.649
peak=    4.086 closest distance to " CB  GLU A 277 " =    3.600
peak=    4.084 closest distance to " O   HOH Z  61 " =    1.680
peak=    4.081 closest distance to " O   HOH Z  43 " =    2.041
peak=    4.062 closest distance to " O   HOH Z 303 " =    2.065
peak=    4.061 closest distance to " O   HOH Z  78 " =    1.697
peak=    4.046 closest distance to " CB  GLU A 128 " =    1.042
peak=    4.046 closest distance to " CB  ASN A 148 " =    1.399
peak=    4.042 closest distance to " CB  ASN A 187 " =    1.469
peak=    4.042 closest distance to " CA  TYR A  30 " =    0.972
peak=    4.029 closest distance to " O   HOH Z 234 " =    3.631
peak=    4.021 closest distance to " CG  PRO A 198 " =    1.133
peak=    4.016 closest distance to " O   HOH Z  40 " =    1.558
peak=    4.010 closest distance to " CB  ARG A  79 " =    1.429
peak=    3.998 closest distance to " O   HOH Z 126 " =    1.838
peak=    3.993 closest distance to " CD2 LEU A 228 " =    1.103
peak=    3.991 closest distance to " O   HOH Z 263 " =    1.661
peak=    3.975 closest distance to " CB  ARG A 190 " =    1.620
peak=    3.972 closest distance to " O   HOH Z 248 " =    1.646
peak=    3.935 closest distance to " O   HOH Z 189 " =    2.625
peak=    3.927 closest distance to " CB  TRP A 266 " =    0.965
peak=    3.927 closest distance to " O   HOH Z 236 " =    1.961
peak=    3.927 closest distance to " CG  ARG A  66 " =    2.748
peak=    3.927 closest distance to " CB  VAL A 265 " =    1.308
peak=    3.912 closest distance to " CG1BVAL A  72 " =    1.690
peak=    3.896 closest distance to " O   HOH Z 280 " =    2.933
peak=    3.863 closest distance to " CB  ARG A 139 " =    0.917
peak=    3.855 closest distance to " O   HOH Z 411 " =    3.725
peak=    3.846 closest distance to " O   HOH Z  97 " =    1.991
peak=    3.837 closest distance to " O   HOH Z 197 " =    3.004
peak=    3.832 closest distance to " CB  ASP A 140 " =    0.950
peak=    3.831 closest distance to " O   HOH Z 402 " =    1.477
peak=    3.809 closest distance to " CB  TRP A 179 " =    1.406
peak=    3.786 closest distance to " O   MET A 105 " =    1.831
peak=    3.775 closest distance to " O   HOH Z 261 " =    2.108
peak=    3.771 closest distance to " CB AVAL A  41 " =    1.044
peak=    3.769 closest distance to " O   HOH Z 344 " =    3.014
peak=    3.764 closest distance to " O   HOH Z 214 " =    2.149
peak=    3.748 closest distance to " NH2 ARG A 156 " =    1.155
peak=    3.743 closest distance to " O   HOH Z  59 " =    2.165
peak=    3.734 closest distance to " O   HOH Z  88 " =    3.144
peak=    3.722 closest distance to " CG1 ILE A  33 " =    1.255
peak=    3.720 closest distance to " CZ  PHE A 218 " =    1.086
peak=    3.718 closest distance to " CA  ALA A  51 " =    0.953
peak=    3.705 closest distance to " CA  ALA A  21 " =    1.157
peak=    3.684 closest distance to " CB  VAL A 202 " =    1.562
peak=    3.664 closest distance to " CE1 TYR A 186 " =    1.289
peak=    3.664 closest distance to " O   HOH Z 425 " =    1.313
peak=    3.660 closest distance to " CA  LYS A 117 " =    1.245
peak=    3.658 closest distance to " O   HOH Z 422 " =    2.658
peak=    3.655 closest distance to " O   HOH Z 147 " =    1.748
peak=    3.647 closest distance to " O   HOH Z 193 " =    2.041
peak=    3.644 closest distance to " CA  THR A 221 " =    0.920
peak=    3.643 closest distance to " CB  ASN A  39 " =    0.886
peak=    3.641 closest distance to " CG1 ILE A  49 " =    1.453
peak=    3.635 closest distance to " O   HOH Z 128 " =    2.111
peak=    3.634 closest distance to " CA  THR A 264 " =    0.748
peak=    3.634 closest distance to " CB  LEU A 143 " =    1.154
peak=    3.623 closest distance to " O   HOH Z  97 " =    2.576
peak=    3.620 closest distance to " CD  LYS A 166 " =    1.312
peak=    3.619 closest distance to " CB  ALA A   9 " =    1.592
peak=    3.619 closest distance to " OD2 ASP A 286 " =    2.846
peak=    3.614 closest distance to " O   HOH Z  48 " =    1.696
peak=    3.612 closest distance to " CD BLYS A 290 " =    1.041
peak=    3.612 closest distance to " O   HOH Z 371 " =    3.265
peak=    3.608 closest distance to " CG2 THR A 221 " =    1.207
peak=    3.607 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.590 closest distance to " O   HOH Z  80 " =    1.647
peak=    3.588 closest distance to " CA  ARG A 195 " =    1.219
peak=    3.585 closest distance to " O   HOH Z 133 " =    1.599
peak=    3.585 closest distance to " CB  ALA A 291 " =    1.413
peak=    3.584 closest distance to " O   HOH Z  19 " =    2.268
peak=    3.577 closest distance to " O   HOH Z 329 " =    3.905
peak=    3.573 closest distance to " O   TRP A 274 " =    1.876
peak=    3.570 closest distance to " O   HOH Z 345 " =    3.271
peak=    3.563 closest distance to " CD2 TRP A 179 " =    1.393
peak=    3.561 closest distance to " O   HOH Z 145 " =    2.148
peak=    3.554 closest distance to " CA  ASN A 215 " =    1.223
peak=    3.553 closest distance to " CG  MET A 185 " =    1.155
peak=    3.552 closest distance to " O   HOH Z 291 " =    1.657
peak=    3.549 closest distance to " O   HOH Z 417 " =    3.239
peak=    3.546 closest distance to " CA  ALA A 158 " =    1.212
peak=    3.543 closest distance to " O   HOH Z 180 " =    2.121
peak=    3.538 closest distance to " CB  THR A  31 " =    1.657
peak=    3.536 closest distance to " O   HOH Z 407 " =    2.422
peak=    3.534 closest distance to " O   HOH Z 426 " =    1.548
peak=    3.534 closest distance to " O   HOH Z 273 " =    2.713
peak=    3.534 closest distance to " CB  ASN A 142 " =    1.121
peak=    3.533 closest distance to " N   VAL A 126 " =    1.364
peak=    3.528 closest distance to " N   ASN A  39 " =    1.247
peak=    3.526 closest distance to " CB  ALA A 248 " =    1.523
peak=    3.513 closest distance to " CB  THR A 157 " =    1.191
peak=    3.509 closest distance to " OG BSER A 164 " =    2.219
peak=    3.508 closest distance to " O   HOH Z 245 " =    1.399
peak=    3.507 closest distance to " CB  LEU A 228 " =    1.274
peak=    3.502 closest distance to " O   HOH Z 437 " =    1.892
peak=    3.487 closest distance to " O   HOH Z 135 " =    1.832
peak=    3.486 closest distance to " O   HOH Z  40 " =    2.308
peak=    3.482 closest distance to " O   HOH Z 250 " =    1.351
peak=    3.481 closest distance to " CB  SER A 212 " =    1.135
peak=    3.481 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.476 closest distance to " O   HOH Z 172 " =    3.687
peak=    3.474 closest distance to " O   HOH Z 368 " =    3.563
peak=    3.471 closest distance to " CD1 LEU A 300 " =    1.192
peak=    3.469 closest distance to " CA  ASP A 140 " =    1.208
peak=    3.469 closest distance to " CD  ARG A 159 " =    0.754
peak=    3.468 closest distance to " O   HOH Z 171 " =    2.430
peak=    3.468 closest distance to " ND2 ASN A 249 " =    1.873
peak=    3.462 closest distance to " NZ  LYS A 117 " =    3.292
peak=    3.458 closest distance to " O   HOH Z  21 " =    1.675
peak=    3.458 closest distance to " O   ASP A 124 " =    1.139
peak=    3.453 closest distance to " O   HOH Z 299 " =    4.310
peak=    3.445 closest distance to " O   HOH Z 366 " =    3.030
peak=    3.440 closest distance to " O   HOH Z 261 " =    1.529
peak=    3.438 closest distance to " O   HOH Z 295 " =    1.534
peak=    3.437 closest distance to " O   HOH Z 305 " =    3.586
peak=    3.437 closest distance to " NH2 ARG A  79 " =    1.373
peak=    3.436 closest distance to " O   HOH Z 290 " =    0.992
peak=    3.436 closest distance to " NH1AARG A 145 " =    1.103
peak=    3.436 closest distance to " CD1 LEU A   5 " =    1.365
peak=    3.435 closest distance to " O   HOH Z 250 " =    1.414
peak=    3.433 closest distance to " CB  TRP A 150 " =    1.381
peak=    3.425 closest distance to " CG  LEU A 167 " =    1.182
peak=    3.420 closest distance to " ND2 ASN A 110 " =    1.635
peak=    3.418 closest distance to " O   HOH Z 227 " =    1.692
peak=    3.417 closest distance to " O   ALA A 158 " =    1.401
peak=    3.412 closest distance to " O   HOH Z 417 " =    2.114
peak=    3.410 closest distance to " O   HOH Z 134 " =    1.376
peak=    3.409 closest distance to " O   HOH Z 285 " =    3.020
peak=    3.408 closest distance to " N   SER A 135 " =    1.437
peak=    3.407 closest distance to " OG  SER A  22 " =    2.837
peak=    3.396 closest distance to " OG1 THR A 294 " =    2.368
peak=    3.389 closest distance to " CB  ARG A  79 " =    0.890
peak=    3.388 closest distance to " ND1 HIS A  81 " =    1.663
peak=    3.383 closest distance to " O   HOH Z 313 " =    1.741
peak=    3.379 closest distance to " CA  ASP A 162 " =    1.083
peak=    3.375 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.374 closest distance to " O   HOH Z 108 " =    2.599
peak=    3.370 closest distance to " CD  ARG A 269 " =    0.946
peak=    3.368 closest distance to " O   HOH Z 420 " =    2.010
peak=    3.364 closest distance to " CG2 ILE A  20 " =    1.440
peak=    3.362 closest distance to " O   HOH Z 132 " =    2.655
peak=    3.360 closest distance to " O   HOH Z  48 " =    1.439
peak=    3.358 closest distance to " CG  MET A 185 " =    1.094
peak=    3.352 closest distance to " CA  LEU A 282 " =    1.052
peak=    3.351 closest distance to " NH2AARG A 275 " =    3.586
peak=    3.351 closest distance to " O   HOH Z 175 " =    2.112
peak=    3.349 closest distance to " CG  GLN A  77 " =    2.149
peak=    3.347 closest distance to " CB  SER A  26 " =    1.664
peak=    3.343 closest distance to " CA  MET A  40 " =    1.117
peak=    3.343 closest distance to " CG2 VAL A 257 " =    0.866
peak=    3.343 closest distance to " CA  VAL A  41 " =    0.830
peak=    3.339 closest distance to " O   HOH Z 102 " =    1.266
peak=    3.339 closest distance to " CZ  PHE A 192 " =    0.998
peak=    3.333 closest distance to " CB  HIS A 108 " =    0.788
peak=    3.332 closest distance to " O   HOH Z 148 " =    3.260
peak=    3.330 closest distance to " O   HOH Z  66 " =    2.302
peak=    3.329 closest distance to " CA  VAL A 126 " =    0.861
peak=    3.325 closest distance to " N   ARG A 190 " =    1.064
peak=    3.321 closest distance to " CA  TYR A 116 " =    1.369
peak=    3.320 closest distance to " O   HOH Z 193 " =    1.613
peak=    3.319 closest distance to " CB  GLN A 205 " =    1.084
peak=    3.319 closest distance to " O  BHOH Z 338 " =    2.394
peak=    3.318 closest distance to " O   HOH Z  54 " =    1.542
peak=    3.309 closest distance to " O   HOH Z 425 " =    2.040
peak=    3.306 closest distance to " CA  ALA A 295 " =    1.064
peak=    3.306 closest distance to " CA  ALA A 291 " =    0.944
peak=    3.306 closest distance to " CD2 LEU A   5 " =    0.732
peak=    3.303 closest distance to " CD  LYS A 119 " =    1.515
peak=    3.301 closest distance to " O   HOH Z 189 " =    2.743
peak=    3.300 closest distance to " CB  ILE A  20 " =    1.451
peak=    3.299 closest distance to " O   HOH Z   1 " =    2.039
peak=    3.289 closest distance to " CB  GLU A  46 " =    1.059
peak=    3.289 closest distance to " O   ALA A 165 " =    1.447
peak=    3.288 closest distance to " CA  ALA A 233 " =    1.322
peak=    3.287 closest distance to " CB  MET A  47 " =    1.152
peak=    3.287 closest distance to " O   HOH Z 327 " =    1.810
peak=    3.275 closest distance to " N   ASN A 127 " =    1.238
peak=    3.273 closest distance to " CB  SER A 216 " =    0.784
peak=    3.272 closest distance to " CB  ILE A 120 " =    1.328
peak=    3.271 closest distance to " O   HOH Z 421 " =    1.763
peak=    3.270 closest distance to " CB  MET A  40 " =    0.822
peak=    3.267 closest distance to " CA  ASP A 191 " =    0.902
peak=    3.266 closest distance to " O   HOH Z 116 " =    1.787
peak=    3.266 closest distance to " O   HOH Z 406 " =    1.619
peak=    3.264 closest distance to " CA  SER A 146 " =    1.723
peak=    3.260 closest distance to " NE2 GLN A  77 " =    3.309
peak=    3.257 closest distance to " OG BSER A 134 " =    2.997
peak=    3.257 closest distance to " O   HOH Z   9 " =    2.003
peak=    3.257 closest distance to " CA  ALA A  84 " =    1.459
peak=    3.255 closest distance to " O   HOH Z 353 " =    2.698
peak=    3.254 closest distance to " O   HOH Z  49 " =    2.503
peak=    3.252 closest distance to " O   HOH Z 151 " =    1.804
peak=    3.251 closest distance to " CB  GLN A 278 " =    0.880
peak=    3.245 closest distance to " NZ  LYS A  48 " =    1.366
peak=    3.244 closest distance to " O   HOH Z 133 " =    2.461
peak=    3.243 closest distance to " O   HOH Z 435 " =    1.976
peak=    3.243 closest distance to " O   HOH Z 359 " =    1.817
peak=    3.242 closest distance to " O   HOH Z 383 " =    2.063
peak=    3.234 closest distance to " O   HOH Z 423 " =    3.036
peak=    3.234 closest distance to " CB  GLN A  89 " =    1.172
peak=    3.229 closest distance to " O   HOH Z 216 " =    2.718
peak=    3.228 closest distance to " O   ARG A  56 " =    2.801
peak=    3.225 closest distance to " CD1 ILE A  33 " =    1.602
peak=    3.224 closest distance to " N   ASP A 162 " =    1.354
peak=    3.221 closest distance to " CB  ALA A 248 " =    0.996
peak=    3.220 closest distance to " CB  SER A 273 " =    0.813
peak=    3.220 closest distance to " O   HOH Z  20 " =    1.495
peak=    3.218 closest distance to " O   HOH Z 126 " =    1.657
peak=    3.218 closest distance to " CA  ARG A  36 " =    1.077
peak=    3.213 closest distance to " CG  GLN A  88 " =    1.060
peak=    3.211 closest distance to " CB  ASN A 110 " =    1.206
peak=    3.207 closest distance to " CB  GLN A  88 " =    1.184
peak=    3.206 closest distance to " O   HOH Z  10 " =    1.799
peak=    3.204 closest distance to " CA  LYS A 290 " =    1.250
peak=    3.203 closest distance to " O   HOH Z 156 " =    3.344
peak=    3.197 closest distance to " O   HOH Z 403 " =    1.367
peak=    3.192 closest distance to " CD1 ILE A 106 " =    0.978
peak=    3.190 closest distance to " N   ARG A 156 " =    1.325
peak=    3.190 closest distance to " O   HOH Z 341 " =    1.901
peak=    3.189 closest distance to " O   HOH Z 166 " =    3.585
peak=    3.188 closest distance to " CG2 ILE A 120 " =    1.237
peak=    3.186 closest distance to " CB  VAL A 268 " =    0.862
peak=    3.185 closest distance to " O   HOH Z 409 " =    3.376
peak=    3.185 closest distance to " O   HOH Z 359 " =    3.781
peak=    3.179 closest distance to " N   PHE A 130 " =    1.282
peak=    3.173 closest distance to " NZ  LYS A  76 " =    1.381
peak=    3.171 closest distance to " O   HOH Z   4 " =    1.822
peak=    3.167 closest distance to " CA  MET A 105 " =    0.974
peak=    3.159 closest distance to " C   TYR A 214 " =    1.479
peak=    3.159 closest distance to " CG2 THR A 294 " =    1.717
peak=    3.149 closest distance to " CG BARG A 275 " =    1.353
peak=    3.142 closest distance to " O   HOH Z 281 " =    4.774
peak=    3.138 closest distance to " CB  ASN A 215 " =    1.163
peak=    3.136 closest distance to " O   HOH Z 173 " =    2.228
peak=    3.134 closest distance to " CA  SER A  87 " =    1.012
peak=    3.132 closest distance to " CB  LYS A 117 " =    1.143
peak=    3.129 closest distance to " O   HOH Z 124 " =    1.279
peak=    3.122 closest distance to " OE2 GLU A  53 " =    2.030
peak=    3.122 closest distance to " O   THR A  31 " =    1.552
peak=    3.122 closest distance to " CA  ASN A 176 " =    1.075
peak=    3.117 closest distance to " CA  ALA A 154 " =    0.994
peak=    3.114 closest distance to " CB  SER A 245 " =    3.176
peak=    3.112 closest distance to " NE2 HIS A 207 " =    1.691
peak=    3.106 closest distance to " O   HOH Z 427 " =    3.187
peak=    3.104 closest distance to " CG  LYS A  76 " =    0.982
peak=    3.103 closest distance to " O   ALA A   1 " =    1.570
peak=    3.101 closest distance to " O   HOH Z 163 " =    1.459
peak=    3.095 closest distance to " O   HOH Z 258 " =    1.884
peak=    3.087 closest distance to " CA  ILE A 106 " =    0.773
peak=    3.079 closest distance to " CZ3 TRP A  85 " =    0.970
peak=    3.076 closest distance to " O   HOH Z  61 " =    1.606
peak=    3.074 closest distance to " O   HOH Z 141 " =    1.491
peak=    3.071 closest distance to " O   GLN A 278 " =    1.518
peak=    3.067 closest distance to " O   HOH Z 256 " =    2.341
peak=    3.060 closest distance to " CB  ALA A 100 " =    1.225
peak=    3.053 closest distance to " O   HOH Z 201 " =    3.163
peak=    3.012 closest distance to " NH1BARG A 190 " =    2.122

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.778 - 5.485
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 213
   mapped sites are within: 0.778 - 5.485

peak=   -5.518 closest distance to " CG2 VAL A 230 " =    0.869
peak=   -4.584 closest distance to " CD  ARG A 156 " =    2.002
peak=   -4.502 closest distance to " O   HOH Z 266 " =    4.920
peak=   -4.430 closest distance to " SG  CYS A 254 " =    3.202
peak=   -4.346 closest distance to " CB  PRO A 243 " =    2.607
peak=   -4.246 closest distance to " CB  ALA A 161 " =    2.572
peak=   -4.223 closest distance to " C   HIS A 108 " =    1.213
peak=   -4.082 closest distance to " CG  GLN A 223 " =    2.133
peak=   -4.051 closest distance to " O   HOH Z 290 " =    1.211
peak=   -4.049 closest distance to " CD2 LEU A 300 " =    2.793
peak=   -4.032 closest distance to " O   HOH Z 196 " =    2.180
peak=   -4.019 closest distance to " O   HOH Z 351 " =    1.532
peak=   -4.014 closest distance to " O   PRO A 163 " =    2.155
peak=   -4.012 closest distance to " CG2BVAL A  41 " =    2.597
peak=   -3.976 closest distance to " O   HOH Z 231 " =    1.973
peak=   -3.911 closest distance to " CD  GLN A  58 " =    1.128
peak=   -3.904 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -3.901 closest distance to " CG2 VAL A 296 " =    1.242
peak=   -3.899 closest distance to " O   HOH Z 166 " =    1.917
peak=   -3.893 closest distance to " O   HOH Z 114 " =    3.159
peak=   -3.892 closest distance to " O   VAL A  67 " =    2.734
peak=   -3.855 closest distance to " OXT GLY A 302 " =    2.891
peak=   -3.848 closest distance to " NE2 GLN A  88 " =    2.044
peak=   -3.820 closest distance to " C   ALA A 158 " =    1.278
peak=   -3.817 closest distance to " OG  SER A  97 " =    2.250
peak=   -3.799 closest distance to " OG BSER A 134 " =    1.154
peak=   -3.787 closest distance to " CG  ASP A 231 " =    0.778
peak=   -3.787 closest distance to " CA  ASP A 298 " =    1.028
peak=   -3.783 closest distance to " O   HOH Z  11 " =    1.896
peak=   -3.777 closest distance to " CG1 VAL A 250 " =    2.777
peak=   -3.766 closest distance to " CG1 VAL A 112 " =    2.810
peak=   -3.752 closest distance to " NH2AARG A 275 " =    5.174
peak=   -3.734 closest distance to " CZ3 TRP A 179 " =    1.226
peak=   -3.698 closest distance to " N   GLN A  58 " =    1.612
peak=   -3.688 closest distance to " O   HOH Z  63 " =    1.099
peak=   -3.688 closest distance to " N   ALA A 226 " =    2.091
peak=   -3.683 closest distance to " O   HOH Z 389 " =    1.931
peak=   -3.638 closest distance to " O   HOH Z 283 " =    2.217
peak=   -3.637 closest distance to " ND2 ASN A  45 " =    1.340
peak=   -3.631 closest distance to " CD1 LEU A 228 " =    2.262
peak=   -3.618 closest distance to " CB  PHE A 192 " =    1.854
peak=   -3.613 closest distance to " O   HOH Z  13 " =    1.453
peak=   -3.607 closest distance to " CB  ALA A 248 " =    2.099
peak=   -3.603 closest distance to " O   HOH Z 435 " =    2.766
peak=   -3.601 closest distance to " CB  ALA A 291 " =    2.308
peak=   -3.594 closest distance to " CG1 VAL A 112 " =    2.572
peak=   -3.594 closest distance to " N   ALA A  43 " =    2.614
peak=   -3.593 closest distance to " CG2 ILE A 263 " =    2.395
peak=   -3.591 closest distance to " NH2 ARG A  79 " =    1.993
peak=   -3.572 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.560 closest distance to " NE2 GLN A 103 " =    1.715
peak=   -3.559 closest distance to " O   HOH Z 394 " =    1.546
peak=   -3.558 closest distance to " O   HOH Z 103 " =    1.815
peak=   -3.552 closest distance to " CE  MET A 105 " =    2.146
peak=   -3.547 closest distance to " CD  ARG A 139 " =    1.633
peak=   -3.546 closest distance to " O   HOH Z 102 " =    1.611
peak=   -3.544 closest distance to " O   HOH Z 211 " =    1.663
peak=   -3.543 closest distance to " CB  PRO A 280 " =    2.128
peak=   -3.540 closest distance to " N   THR A 235 " =    1.380
peak=   -3.531 closest distance to " O   HOH Z  47 " =    1.558
peak=   -3.530 closest distance to " CD1 LEU A 101 " =    2.444
peak=   -3.526 closest distance to " O   HOH Z 198 " =    2.302
peak=   -3.525 closest distance to " O   HOH Z  43 " =    1.709
peak=   -3.525 closest distance to " ND2 ASN A 187 " =    1.664
peak=   -3.522 closest distance to " C   ASN A 285 " =    2.385
peak=   -3.519 closest distance to " CG  TRP A 266 " =    1.889
peak=   -3.518 closest distance to " C   ASN A 187 " =    1.892
peak=   -3.512 closest distance to " O   HOH Z 311 " =    3.772
peak=   -3.504 closest distance to " O   HOH Z 350 " =    1.716
peak=   -3.495 closest distance to " CB  ALA A  43 " =    2.477
peak=   -3.492 closest distance to " CG1 VAL A 197 " =    2.262
peak=   -3.486 closest distance to " OG  SER A  26 " =    1.274
peak=   -3.481 closest distance to " O   HOH Z  44 " =    2.107
peak=   -3.481 closest distance to " O   HOH Z 353 " =    2.088
peak=   -3.477 closest distance to " CG  GLU A 277 " =    1.118
peak=   -3.470 closest distance to " O   HOH Z 185 " =    2.363
peak=   -3.469 closest distance to " CD  LYS A 289 " =    2.510
peak=   -3.464 closest distance to " O   HOH Z 407 " =    3.076
peak=   -3.463 closest distance to " OD1 ASN A 148 " =    1.516
peak=   -3.462 closest distance to " CE3 TRP A 150 " =    2.097
peak=   -3.452 closest distance to " OD1 ASN A  39 " =    2.198
peak=   -3.446 closest distance to " O   HOH Z  10 " =    1.494
peak=   -3.444 closest distance to " OG ASER A 134 " =    1.217
peak=   -3.443 closest distance to " CB  ALA A 248 " =    2.389
peak=   -3.442 closest distance to " O   VAL A 189 " =    2.588
peak=   -3.439 closest distance to " CD1 PHE A  59 " =    2.024
peak=   -3.433 closest distance to " OG BSER A 134 " =    1.724
peak=   -3.426 closest distance to " CZ  TYR A 169 " =    1.693
peak=   -3.425 closest distance to " O   HOH Z 198 " =    1.453
peak=   -3.425 closest distance to " CD1 LEU A 101 " =    2.627
peak=   -3.424 closest distance to " CE2 PHE A 218 " =    2.547
peak=   -3.423 closest distance to " O   HOH Z 292 " =    4.488
peak=   -3.413 closest distance to " CB  ASP A 132 " =    2.287
peak=   -3.408 closest distance to " N   SER A 212 " =    2.028
peak=   -3.405 closest distance to " O   HOH Z 426 " =    1.674
peak=   -3.403 closest distance to " CG  ARG A 269 " =    2.366
peak=   -3.401 closest distance to " O   HOH Z 241 " =    1.292
peak=   -3.399 closest distance to " O   PRO A 198 " =    1.246
peak=   -3.398 closest distance to " OD1 ASN A 187 " =    1.595
peak=   -3.389 closest distance to " CG  PHE A 283 " =    2.839
peak=   -3.385 closest distance to " O   HOH Z  19 " =    2.266
peak=   -3.383 closest distance to " CB  ALA A 291 " =    2.182
peak=   -3.381 closest distance to " N   THR A 157 " =    1.525
peak=   -3.379 closest distance to " CG  ASP A  50 " =    2.408
peak=   -3.372 closest distance to " O   SER A 271 " =    2.099
peak=   -3.368 closest distance to " CD2 LEU A 167 " =    1.749
peak=   -3.366 closest distance to " O   HOH Z  52 " =    1.581
peak=   -3.365 closest distance to " O   HOH Z 165 " =    1.914
peak=   -3.362 closest distance to " CE BMET A  47 " =    1.872
peak=   -3.360 closest distance to " O   HOH Z 339 " =    1.853
peak=   -3.358 closest distance to " NZ  LYS A 119 " =    3.524
peak=   -3.355 closest distance to " CB  ASP A 132 " =    2.341
peak=   -3.353 closest distance to " CA  GLY A 241 " =    3.074
peak=   -3.347 closest distance to " CG1 VAL A 296 " =    1.374
peak=   -3.347 closest distance to " OG  SER A  62 " =    1.691
peak=   -3.328 closest distance to " O   HOH Z 265 " =    2.114
peak=   -3.327 closest distance to " O   HOH Z  60 " =    2.061
peak=   -3.327 closest distance to " O   HOH Z 113 " =    2.385
peak=   -3.324 closest distance to " O   HOH Z 234 " =    4.150
peak=   -3.320 closest distance to " O   LEU A 167 " =    1.505
peak=   -3.315 closest distance to " NH1 ARG A 195 " =    2.576
peak=   -3.315 closest distance to " O   HOH Z  17 " =    1.577
peak=   -3.308 closest distance to " O   HOH Z 222 " =    1.493
peak=   -3.305 closest distance to " O   SER A  95 " =    1.639
peak=   -3.304 closest distance to " O   GLY A 196 " =    1.096
peak=   -3.302 closest distance to " CA  GLY A 203 " =    2.413
peak=   -3.298 closest distance to " CB  ASP A 171 " =    2.321
peak=   -3.296 closest distance to " CA  GLY A 133 " =    2.281
peak=   -3.295 closest distance to " N   ASP A 171 " =    2.362
peak=   -3.294 closest distance to " O   HOH Z  38 " =    1.568
peak=   -3.292 closest distance to " O   PRO A 198 " =    1.333
peak=   -3.290 closest distance to " N   PHE A  59 " =    2.165
peak=   -3.287 closest distance to " O   VAL A 125 " =    2.314
peak=   -3.286 closest distance to " O   HOH Z 298 " =    2.660
peak=   -3.285 closest distance to " O   HOH Z  11 " =    2.129
peak=   -3.283 closest distance to " OG  SER A  87 " =    1.444
peak=   -3.269 closest distance to " O   HOH Z 191 " =    5.485
peak=   -3.267 closest distance to " C   LEU A 143 " =    1.051
peak=   -3.263 closest distance to " CZ  PHE A  59 " =    1.595
peak=   -3.261 closest distance to " CG  GLU A  53 " =    1.620
peak=   -3.260 closest distance to " NH2 ARG A  66 " =    1.831
peak=   -3.260 closest distance to " O   HOH Z  22 " =    2.447
peak=   -3.257 closest distance to " CG1 VAL A 230 " =    1.911
peak=   -3.255 closest distance to " CD1 TYR A 247 " =    2.400
peak=   -3.250 closest distance to " O   MET A  40 " =    2.688
peak=   -3.248 closest distance to " O   HOH Z 134 " =    2.702
peak=   -3.248 closest distance to " OXT GLY A 302 " =    3.381
peak=   -3.241 closest distance to " O   HOH Z 193 " =    1.880
peak=   -3.235 closest distance to " CB  ASN A  69 " =    1.165
peak=   -3.227 closest distance to " O   HOH Z 372 " =    2.396
peak=   -3.216 closest distance to " N   SER A 276 " =    1.343
peak=   -3.213 closest distance to " CG2 VAL A 112 " =    2.493
peak=   -3.211 closest distance to " O   HOH Z 252 " =    4.036
peak=   -3.208 closest distance to " O   GLY A  80 " =    2.534
peak=   -3.206 closest distance to " CG  LEU A 228 " =    1.034
peak=   -3.205 closest distance to " O   ALA A  10 " =    1.801
peak=   -3.198 closest distance to " CD  PRO A 213 " =    2.206
peak=   -3.194 closest distance to " O   LYS A 117 " =    1.680
peak=   -3.194 closest distance to " CD2 PHE A  61 " =    2.435
peak=   -3.190 closest distance to " CG  MET A 105 " =    0.903
peak=   -3.181 closest distance to " CD2 LEU A 237 " =    2.709
peak=   -3.179 closest distance to " O   ALA A 161 " =    1.680
peak=   -3.176 closest distance to " N   ALA A 248 " =    2.496
peak=   -3.173 closest distance to " CD1 ILE A 199 " =    2.492
peak=   -3.172 closest distance to " O   GLN A 240 " =    2.141
peak=   -3.172 closest distance to " CB  ASN A  39 " =    2.228
peak=   -3.163 closest distance to " OG1 THR A 178 " =    1.316
peak=   -3.159 closest distance to " ND2 ASN A  60 " =    1.670
peak=   -3.158 closest distance to " C   MET A 188 " =    1.450
peak=   -3.156 closest distance to " O   HOH Z 295 " =    1.503
peak=   -3.156 closest distance to " O   HOH Z 431 " =    1.791
peak=   -3.152 closest distance to " CD2 TYR A 247 " =    2.289
peak=   -3.151 closest distance to " OH  TYR A 214 " =    1.254
peak=   -3.150 closest distance to " N   ALA A 248 " =    1.623
peak=   -3.149 closest distance to " O   HOH Z 275 " =    1.477
peak=   -3.145 closest distance to " O   HOH Z 244 " =    2.013
peak=   -3.141 closest distance to " OG  SER A 206 " =    1.707
peak=   -3.141 closest distance to " O   ALA A  51 " =    1.353
peak=   -3.141 closest distance to " O   HOH Z 326 " =    5.187
peak=   -3.139 closest distance to " C   ASP A 231 " =    2.624
peak=   -3.136 closest distance to " O   HOH Z 389 " =    4.682
peak=   -3.132 closest distance to " O   HOH Z 111 " =    2.337
peak=   -3.127 closest distance to " N   SER A   3 " =    2.051
peak=   -3.126 closest distance to " O   HOH Z 313 " =    1.714
peak=   -3.123 closest distance to " O   SER A 276 " =    1.618
peak=   -3.113 closest distance to " O   GLY A  80 " =    2.538
peak=   -3.110 closest distance to " O   HOH Z 175 " =    4.284
peak=   -3.108 closest distance to " O   HOH Z 377 " =    1.810
peak=   -3.106 closest distance to " O   SER A  22 " =    2.230
peak=   -3.106 closest distance to " N   GLN A  77 " =    1.511
peak=   -3.105 closest distance to " CG  PRO A 163 " =    2.584
peak=   -3.103 closest distance to " O   HOH Z  90 " =    1.680
peak=   -3.101 closest distance to " CZ  PHE A  38 " =    2.281
peak=   -3.100 closest distance to " O   HOH Z 262 " =    2.834
peak=   -3.097 closest distance to " O   HOH Z 353 " =    2.050
peak=   -3.092 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.091 closest distance to " C   LEU A 222 " =    0.817
peak=   -3.091 closest distance to " OD1 ASP A 171 " =    1.564
peak=   -3.089 closest distance to " ND2 ASN A  60 " =    1.401
peak=   -3.086 closest distance to " O   HOH Z 357 " =    1.942
peak=   -3.086 closest distance to " CB  ASP A 132 " =    2.282
peak=   -3.084 closest distance to " CG  ASN A 301 " =    2.053
peak=   -3.084 closest distance to " CA  SER A  62 " =    2.629
peak=   -3.083 closest distance to " OE2 GLU A   2 " =    1.820
peak=   -3.081 closest distance to " O   HOH Z 123 " =    2.434
peak=   -3.074 closest distance to " CD1 ILE A 151 " =    2.340
peak=   -3.073 closest distance to " SG ACYS A 201 " =    2.043
peak=   -3.072 closest distance to " O   HOH Z 313 " =    1.115
peak=   -3.072 closest distance to " O   HOH Z 139 " =    3.095
peak=   -3.068 closest distance to " N   ALA A 248 " =    1.892
peak=   -3.058 closest distance to " O   HOH Z 409 " =    4.852
peak=   -3.044 closest distance to " O   HOH Z 111 " =    1.253

================= 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    :  0.4150 0.4005   6.200752e+00   6.175065e+00
   1_bss:  0.4061 0.3896   6.196980e+00   6.160322e+00
   1_xyz:  0.2907 0.3177   5.944536e+00   6.006742e+00
   1_adp:  0.2196 0.2520   5.689547e+00   5.812455e+00
   1_occ:  0.2191 0.2516   5.688077e+00   5.812706e+00
   2_bss:  0.2142 0.2446   5.685982e+00   5.805527e+00
   2_xyz:  0.1483 0.1844   5.358972e+00   5.544388e+00
   2_adp:  0.1369 0.1747   5.292414e+00   5.491890e+00
   2_occ:  0.1368 0.1746   5.291790e+00   5.491396e+00
   3_bss:  0.1366 0.1745   5.293254e+00   5.493151e+00
   3_xyz:  0.1197 0.1600   5.186837e+00   5.412087e+00
   3_adp:  0.1148 0.1572   5.161520e+00   5.399108e+00
   3_occ:  0.1147 0.1573   5.161578e+00   5.399375e+00
   4_bss:  0.1147 0.1573   5.161131e+00   5.399119e+00
   4_xyz:  0.1150 0.1583   5.166163e+00   5.403350e+00
   4_adp:  0.1153 0.1571   5.163986e+00   5.396228e+00
   4_occ:  0.1153 0.1571   5.163555e+00   5.395694e+00
   5_bss:  0.1153 0.1571   5.163555e+00   5.395694e+00
   5_xyz:  0.1101 0.1552   5.134122e+00   5.383168e+00
   5_adp:  0.1094 0.1557   5.133647e+00   5.386599e+00
   5_occ:  0.1093 0.1557   5.133819e+00   5.386859e+00
   5_bss:  0.1096 0.1561   5.135017e+00   5.386583e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.342  20.001   7.485   8.626   8.049   0.000   0.000   0.000
   1_xyz:  0.342  20.001   7.485   8.626   8.049   0.000   0.000   0.000
   1_adp:  0.342  20.001   7.485   8.626   8.049   0.000   0.000   0.000
   1_occ:  0.342  20.001   7.485   8.626   8.049   0.000   0.000   0.000
   2_bss:  0.342  50.001   4.060   4.879   5.102   0.000   0.000   0.000
   2_xyz:  0.342  50.001   4.060   4.879   5.102   0.000   0.000   0.000
   2_adp:  0.342  50.001   4.060   4.879   5.102   0.000   0.000   0.000
   2_occ:  0.342  50.001   4.060   4.879   5.102   0.000   0.000   0.000
   3_bss:  0.342  50.001   3.346   3.905   4.477   0.000   0.000   0.000
   3_xyz:  0.342  50.001   3.346   3.905   4.477   0.000   0.000   0.000
   3_adp:  0.342  50.001   3.346   3.905   4.477   0.000   0.000   0.000
   3_occ:  0.342  50.001   3.346   3.905   4.477   0.000   0.000   0.000
   4_bss:  0.328  47.514   3.346   3.905   4.477   0.000   0.000   0.000
   4_xyz:  0.328  47.514   3.346   3.905   4.477   0.000   0.000   0.000
   4_adp:  0.328  47.514   3.346   3.905   4.477   0.000   0.000   0.000
   4_occ:  0.328  47.514   3.346   3.905   4.477   0.000   0.000   0.000
   5_bss:  0.328  47.514   3.346   3.905   4.477   0.000   0.000   0.000
   5_xyz:  0.328  47.514   3.346   3.905   4.477   0.000   0.000   0.000
   5_adp:  0.328  47.514   3.346   3.905   4.477   0.000   0.000   0.000
   5_occ:  0.328  47.514   3.346   3.905   4.477   0.000   0.000   0.000
   5_bss:  0.322  49.381  -0.508  -0.081   0.589  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.621 0.6013  0.6616    45531.030
   1_bss:  43.096 0.6055  0.8477    42898.892
   1_xyz:  33.545 0.7171  0.9763    26986.905
   1_adp:  24.369 0.8193  1.0645    15874.678
   1_occ:  24.376 0.8191  1.0643    15865.163
   2_bss:  24.096 0.8219  0.9448    15547.256
   2_xyz:  17.334 0.8864  0.9900     8673.300
   2_adp:  16.083 0.8979  0.9978     7840.823
   2_occ:  16.081 0.8979  0.9976     7835.274
   3_bss:  16.116 0.8977  0.9696     7902.233
   3_xyz:  14.376 0.9121  0.9756     6645.314
   3_adp:  14.125 0.9143  0.9753     6457.207
   3_occ:  14.127 0.9143  0.9751     6461.469
   4_bss:  14.126 0.9143  0.9749     6453.469
   4_xyz:  14.172 0.9140  0.9740     6498.722
   4_adp:  14.004 0.9154  0.9743     6415.329
   4_occ:  13.994 0.9155  0.9741     6411.170
   5_bss:  13.994 0.9155  0.9741     6411.170
   5_xyz:  13.763 0.9172  0.9753     6255.391
   5_adp:  13.843 0.9166  0.9734     6284.489
   5_occ:  13.850 0.9165  0.9733     6287.879
   5_bss:  13.874 0.9163  0.9735     6296.135
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3937e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3937e+01
   1_xyz:   1.464  0.011  0.099 17.684  0.006  4.124   1.1057e-01
   1_adp:   1.464  0.011  0.099 17.684  0.006  4.124   1.1057e-01
   1_occ:   1.464  0.011  0.099 17.684  0.006  4.124   1.1057e-01
   2_bss:   1.464  0.011  0.099 17.684  0.006  4.124   1.1057e-01
   2_xyz:   1.005  0.007  0.075 16.096  0.004  4.125   6.2958e-02
   2_adp:   1.005  0.007  0.075 16.096  0.004  4.125   6.2958e-02
   2_occ:   1.005  0.007  0.075 16.096  0.004  4.125   6.2958e-02
   3_bss:   1.005  0.007  0.075 16.096  0.004  4.125   6.2958e-02
   3_xyz:   1.031  0.008  0.085 15.693  0.004  4.133   6.4576e-02
   3_adp:   1.031  0.008  0.085 15.693  0.004  4.133   6.4576e-02
   3_occ:   1.031  0.008  0.085 15.693  0.004  4.133   6.4576e-02
   4_bss:   1.031  0.008  0.085 15.693  0.004  4.133   6.4576e-02
   4_xyz:   0.918  0.006  0.075 15.329  0.003  4.133   5.3866e-02
   4_adp:   0.918  0.006  0.075 15.329  0.003  4.133   5.3866e-02
   4_occ:   0.918  0.006  0.075 15.329  0.003  4.133   5.3866e-02
   5_bss:   0.918  0.006  0.075 15.329  0.003  4.133   5.3866e-02
   5_xyz:   1.088  0.009  0.090 15.578  0.004  4.125   7.1109e-02
   5_adp:   1.088  0.009  0.090 15.578  0.004  4.125   7.1109e-02
   5_occ:   1.088  0.009  0.090 15.578  0.004  4.125   7.1109e-02
   5_bss:   1.088  0.009  0.090 15.578  0.004  4.125   7.1109e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9937e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9937e+00
   1_xyz:  12.106  0.130  0.415 88.016  0.041  2.265   8.3253e-02
   1_adp:  12.106  0.130  0.415 88.016  0.041  2.265   8.3253e-02
   1_occ:  12.106  0.130  0.415 88.016  0.041  2.265   8.3253e-02
   2_bss:  12.106  0.130  0.415 88.016  0.041  2.265   8.3253e-02
   2_xyz:   7.883  0.062  0.385 81.854  0.034  2.344   4.5838e-02
   2_adp:   7.883  0.062  0.385 81.854  0.034  2.344   4.5838e-02
   2_occ:   7.883  0.062  0.385 81.854  0.034  2.344   4.5838e-02
   3_bss:   7.883  0.062  0.385 81.854  0.034  2.344   4.5838e-02
   3_xyz:   6.856  0.047  0.609 83.634  0.039  2.357   4.9049e-02
   3_adp:   6.856  0.047  0.609 83.634  0.039  2.357   4.9049e-02
   3_occ:   6.856  0.047  0.609 83.634  0.039  2.357   4.9049e-02
   4_bss:   6.856  0.047  0.609 83.634  0.039  2.357   4.9049e-02
   4_xyz:   7.171  0.039  0.462 82.497  0.038  2.395   3.6900e-02
   4_adp:   7.171  0.039  0.462 82.497  0.038  2.395   3.6900e-02
   4_occ:   7.171  0.039  0.462 82.497  0.038  2.395   3.6900e-02
   5_bss:   7.171  0.039  0.462 82.497  0.038  2.395   3.6900e-02
   5_xyz:   7.388  0.046  0.665 83.002  0.041  2.295   4.9778e-02
   5_adp:   7.388  0.046  0.665 83.002  0.041  2.295   4.9778e-02
   5_occ:   7.388  0.046  0.665 83.002  0.041  2.295   4.9778e-02
   5_bss:   7.388  0.046  0.665 83.002  0.041  2.295   4.9778e-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:  54.17   0.00   9.82  46.89   0.00   6.75  54.17   0.00  26.55
   1_occ:  54.17   0.00   9.82  46.89   0.00   6.75  54.17   0.00  26.55
   2_bss:  54.17   0.00   9.82  46.89   0.00   6.75  54.17   0.00  26.55
   2_xyz:  54.17   0.00   9.82  46.89   0.00   6.75  54.17   0.00  26.55
   2_adp:  54.95   0.00  10.31  51.15   0.00   6.79  54.95   0.65  29.47
   2_occ:  54.95   0.00  10.31  51.15   0.00   6.79  54.95   0.65  29.47
   3_bss:  54.95   0.00  10.31  51.15   0.00   6.79  54.95   0.65  29.47
   3_xyz:  54.95   0.00  10.31  51.15   0.00   6.79  54.95   0.65  29.47
   3_adp:  70.29   0.00  11.11  70.29   0.00   7.01  68.43   0.38  33.43
   3_occ:  70.29   0.00  11.11  70.29   0.00   7.01  68.43   0.38  33.43
   4_bss:  70.29   0.00  11.11  70.29   0.00   7.01  68.43   0.38  33.43
   4_xyz:  70.29   0.00  11.11  70.29   0.00   7.01  68.43   0.38  33.43
   4_adp:  71.64   0.00  10.91  71.64   0.00   6.96  66.35   0.64  32.43
   4_occ:  71.64   0.00  10.91  71.64   0.00   6.96  66.35   0.64  32.43
   5_bss:  71.64   0.00  10.91  71.64   0.00   6.96  66.35   0.64  32.43
   5_xyz:  71.64   0.00  10.91  71.64   0.00   6.96  66.35   0.64  32.43
   5_adp:  80.19   0.00  11.08  80.19   0.00   7.01  70.87   0.46  33.25
   5_occ:  80.19   0.00  11.08  80.19   0.00   7.01  70.87   0.46  33.25
   5_bss:  84.13   3.94  15.02  84.13   3.94  10.95  74.81   4.40  37.19
------------------------------------------------------------------------
 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:    1.167    0.015    0.401
   1_adp:    1.167    0.015    0.401
   1_occ:    1.167    0.015    0.401
   2_bss:    1.167    0.015    0.401
   2_xyz:    1.418    0.015    0.478
   2_adp:    1.418    0.015    0.478
   2_occ:    1.418    0.015    0.478
   3_bss:    1.418    0.015    0.478
   3_xyz:    1.399    0.034    0.508
   3_adp:    1.399    0.034    0.508
   3_occ:    1.399    0.034    0.508
   4_bss:    1.399    0.034    0.508
   4_xyz:    1.501    0.031    0.513
   4_adp:    1.501    0.031    0.513
   4_occ:    1.501    0.031    0.513
   5_bss:    1.501    0.031    0.513
   5_xyz:    1.446    0.023    0.520
   5_adp:    1.446    0.023    0.520
   5_occ:    1.446    0.023    0.520
   5_bss:    1.446    0.023    0.520
------------------------------------------------------------------------

CPU time actual refinement: 323.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_796/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_796/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_796/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_796/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_796/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.00 
  Macro-tasks:
    bulk solvent and scale       = 42.25  
    individual site refinement   = 133.07 
    weights calculation          = 32.34  
    collect and process          = 6.66   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 214.42 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 96.01  
    alpha_beta                      = 8.45   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 108.07 
    fmodel                         = 7.36   
    r_factors                      = 0.15   
    phase_errors                   = 11.09  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 234.37 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.504 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    648 calls, 95.71 s
gradients_fft:          593 calls, 94.16 s

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

# Date 2008-01-16 Time 02:27:15 PST -0800 (1200479235.32 s)
Start R-work = 0.4150, R-free = 0.4005 (no bulk solvent and anisotropic scale)
Final R-work = 0.1266, R-free = 0.1713 (no bulk solvent and anisotropic scale)

Start R-work = 0.4061, R-free = 0.3896
Final R-work = 0.1096, R-free = 0.1561