# Date 2008-01-16 Time 02:02:01 PST -0800 (1200477721.21 s)
#phil __OFF__

Command line arguments: "../657.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 = 18591
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 657

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 87.6859, 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: 3.26, 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: (70.25, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.9921
Completeness in resolution range: 0.964358
Completeness with d_max=infinity: 0.961376

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   1.9921

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.9921
Completeness in resolution range: 0.964358
Completeness with d_max=infinity: 0.961376

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2624 [2141/2165]  1923   218  10.2%
  bin  2:  4.2624 -  3.3960 [2042/2062]  1842   200   9.8%
  bin  3:  3.3960 -  2.9705 [2019/2038]  1816   203  10.1%
  bin  4:  2.9705 -  2.7006 [1996/2026]  1794   202  10.1%
  bin  5:  2.7006 -  2.5080 [2004/2023]  1806   198   9.9%
  bin  6:  2.5080 -  2.3607 [1985/2010]  1783   202  10.2%
  bin  7:  2.3607 -  2.2429 [1960/1988]  1767   193   9.8%
  bin  8:  2.2429 -  2.1455 [1964/2000]  1768   196  10.0%
  bin  9:  2.1455 -  2.0631 [1946/1988]  1755   191   9.8%
  bin 10:  2.0631 -  1.9921 [1532/2013]  1376   156  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_657/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: 15
        2.42 -     3.04: 2180
        3.04 -     3.66: 4653
        3.66 -     4.28: 8975
        4.28 -     4.90: 12332
  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  42 " - " O   HOH Z 183 "  1.863 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.904 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.007 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.116 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28150 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_657/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_657/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 87.68585 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 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4405   r_free= 0.4210   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.236520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7540 0.99   1389  152 0.3678 0.3379      6.5438      6.4409|
|  2:  4.7540 -  3.7933 0.99   1331  152 0.3290 0.3446      6.6486      6.7183|
|  3:  3.7933 -  3.3196 0.99   1299  143 0.3812 0.3451      6.5729      6.5369|
|  4:  3.3196 -  3.0188 0.99   1306  145 0.4298 0.3908      6.4803      6.3932|
|  5:  3.0188 -  2.8039 0.99   1282  145 0.4579 0.4387      6.3228      6.3259|
|  6:  2.8039 -  2.6395 0.99   1291  141 0.4588 0.5157      6.2388      6.1851|
|  7:  2.6395 -  2.5080 0.99   1283  143 0.4841 0.4861      6.2074       6.181|
|  8:  2.5080 -  2.3992 0.98   1273  137 0.4968 0.4405      6.1646      6.1458|
|  9:  2.3992 -  2.3072 0.98   1262  144 0.4783 0.4895      6.0855      6.1318|
| 10:  2.3072 -  2.2279 1.00   1279  143 0.5148 0.4251      6.1263      5.9971|
| 11:  2.2279 -  2.1584 0.97   1254  137 0.4964 0.4791      6.0236      6.0345|
| 12:  2.1584 -  2.0969 0.98   1251  142 0.5124 0.4684      5.9733      5.9824|
| 13:  2.0969 -  2.0418 0.99   1278  135 0.4977 0.4774      5.8661      5.8266|
| 14:  2.0418 -  1.9921 0.66    852  100 0.5078 0.4687      5.8681      5.7384|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7540  1389   152  0.75  30.19   0.81     0.77      56444.51|
|  2:  4.7540 -  3.7933  1331   152  0.78  28.31   0.90     0.83      74245.59|
|  3:  3.7933 -  3.3196  1299   143  0.71  34.73   0.87     0.80      77671.00|
|  4:  3.3196 -  3.0188  1306   145  0.64  40.73   0.82     0.70      71069.64|
|  5:  3.0188 -  2.8039  1282   145  0.55  48.22   0.78     0.62      63182.90|
|  6:  2.8039 -  2.6395  1291   141  0.50  52.01   0.74     0.56      59700.04|
|  7:  2.6395 -  2.5080  1283   143  0.46  54.85   0.75     0.53      56210.01|
|  8:  2.5080 -  2.3992  1273   137  0.47  54.43   0.74     0.54      49789.02|
|  9:  2.3992 -  2.3072  1262   144  0.51  51.59   0.75     0.57      43098.28|
| 10:  2.3072 -  2.2279  1279   143  0.51  51.13   0.76     0.59      37195.91|
| 11:  2.2279 -  2.1584  1254   137  0.50  51.88   0.76     0.59      35430.94|
| 12:  2.1584 -  2.0969  1251   142  0.47  54.53   0.77     0.56      33804.29|
| 13:  2.0969 -  2.0418  1278   135  0.46  55.79   0.73     0.54      30121.86|
| 14:  2.0418 -  1.9921   852   100  0.49  52.91   0.75     0.52      24243.06|
|alpha:            min =        0.52 max =            0.83 mean =         0.63|
|beta:             min =    24243.06 max =        77671.00 mean =     51749.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.93 mean =        46.89|
|phase err.(test): min =        0.00 max =           89.80 mean =        47.02|
|-----------------------------------------------------------------------------|

============================== 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 = 7.657326              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.472   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.647473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.115   (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:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2616 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3895 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5070 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6527 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7689 |
|-----------------------------------------------------------------------------|
|-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 |       53.975 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.709 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    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 = 11.994)------------------------------------------|
|    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 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4497   r_free= 0.4262   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.242577                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4322   r_free= 0.4103   ksol= 0.34   Bsol= 20.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.99,7.96,10.71,0.00,0.00,0.00); trace/3= 8.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.230631                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.963491              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.085   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.609188              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.320   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4322      final r-factor (work) = 0.3248          |
| start r-factor (free) = 0.4103      final r-factor (free) = 0.3434          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.7192 = 6.96 * 0.50 * 6.2453 + 1.00 * 53.9747                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.2918 = 6.96 * 0.50 * 6.0805 + 1.00 * 0.1210                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3248      final r-factor (work) = 0.2636          |
| start r-factor (free) = 0.3434      final r-factor (free) = 0.2996          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7189 = 0.61 * 1.00 * 6.0805 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6112 = 0.61 * 1.00 * 5.9085 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    58.80   10.95    None  None   None       |
|    all(noH): 2823   0      0.00    58.80   10.95    None  None   None       |
|    Sol.    : 438    0      0.00    58.80   27.52    None  None   None       |
|    Mac.    : 2385   0      0.00    51.97   7.90     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 -   5.880: 1171   |   5:    29.400 -  35.280:   93        |
|      1:     5.880 -  11.760:  772   |   6:    35.280 -  41.160:   67        |
|      2:    11.760 -  17.640:  346   |   7:    41.160 -  47.040:   46        |
|      3:    17.640 -  23.520:  160   |   8:    47.040 -  52.920:   20        |
|      4:    23.520 -  29.400:  136   |   9:    52.920 -  58.800:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2636 r_free = 0.2996             target_work(ml) = 5.858         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2630 r_free = 0.2998             target_work(ml) = 5.857         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2630   r_free= 0.2998   ksol= 0.34   Bsol= 20.00   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.99,7.96,10.71,0.00,0.00,0.00); trace/3= 8.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.856898                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2577   r_free= 0.2954   ksol= 0.34   Bsol= 47.91   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.69,4.09,7.07,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.854821                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.628134              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.597   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.366365              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.458  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2577      final r-factor (work) = 0.1804          |
| start r-factor (free) = 0.2954      final r-factor (free) = 0.2236          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8952 = 2.63 * 0.50 * 5.9165 + 1.00 * 0.1205                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5332 = 2.63 * 0.50 * 5.6873 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1804      final r-factor (work) = 0.1648          |
| start r-factor (free) = 0.2236      final r-factor (free) = 0.2104          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0953 = 0.37 * 1.00 * 5.6873 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0230 = 0.37 * 1.00 * 5.4887 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.38   11.34    None  None   None       |
|    all(noH): 2823   0      0.00    64.38   11.34    None  None   None       |
|    Sol.    : 438    0      0.54    64.38   32.06    None  None   None       |
|    Mac.    : 2385   0      0.00    55.36   7.54     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.438: 1376   |   5:    32.189 -  38.627:  113        |
|      1:     6.438 -  12.876:  717   |   6:    38.627 -  45.064:   96        |
|      2:    12.876 -  19.313:  240   |   7:    45.064 -  51.502:   52        |
|      3:    19.313 -  25.751:  109   |   8:    51.502 -  57.940:   26        |
|      4:    25.751 -  32.189:   88   |   9:    57.940 -  64.378:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1648 r_free = 0.2104             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1647 r_free = 0.2105             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1647   r_free= 0.2105   ksol= 0.34   Bsol= 47.91   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.69,4.09,7.07,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.462400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1639   r_free= 0.2107   ksol= 0.33   Bsol= 47.91   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.85,3.21,5.18,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.462611                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.613006              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.889  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.345429              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.963  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1639      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.2107      final r-factor (free) = 0.1745          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2392 = 2.61 * 0.50 * 5.4952 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0674 = 2.61 * 0.50 * 5.3586 + 1.00 * 0.0663                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1297      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2211 = 1.35 * 1.00 * 5.3586 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0581 = 1.35 * 1.00 * 5.2352 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.43   12.09    None  None   None       |
|    all(noH): 2823   0      0.00    77.43   12.09    None  None   None       |
|    Sol.    : 438    0      0.60    77.43   36.08    None  None   None       |
|    Mac.    : 2385   0      0.00    76.48   7.68     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 -   7.743: 1606   |   5:    38.717 -  46.460:   83        |
|      1:     7.743 -  15.487:  598   |   6:    46.460 -  54.204:   79        |
|      2:    15.487 -  23.230:  179   |   7:    54.204 -  61.947:   52        |
|      3:    23.230 -  30.974:   98   |   8:    61.947 -  69.690:   22        |
|      4:    30.974 -  38.717:   98   |   9:    69.690 -  77.434:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1228 r_free = 0.1702             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1227 r_free = 0.1702             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1702   ksol= 0.33   Bsol= 47.91   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.85,3.21,5.18,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.223104                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1698   ksol= 0.32   Bsol= 47.91   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.10,4.83,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.223195                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.214554              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.052  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.242861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.883  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1229      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1698      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8633 = 2.21 * 0.50 * 5.2353 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8212 = 2.21 * 0.50 * 5.1998 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2832 = 0.24 * 1.00 * 5.1998 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3751 = 0.24 * 1.00 * 5.1843 + 1.00 * 0.1161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.93   11.48    None  None   None       |
|    all(noH): 2823   0      0.00    76.93   11.48    None  None   None       |
|    Sol.    : 438    0      1.03    74.18   33.44    None  None   None       |
|    Mac.    : 2385   0      0.00    76.93   7.45     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.693: 1655   |   5:    38.467 -  46.160:   86        |
|      1:     7.693 -  15.387:  585   |   6:    46.160 -  53.854:   71        |
|      2:    15.387 -  23.080:  157   |   7:    53.854 -  61.547:   32        |
|      3:    23.080 -  30.774:  108   |   8:    61.547 -  69.241:   13        |
|      4:    30.774 -  38.467:  111   |   9:    69.241 -  76.934:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1602             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1162 r_free = 0.1601             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1601   ksol= 0.32   Bsol= 47.91   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.10,4.83,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.172794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1601   ksol= 0.32   Bsol= 47.91   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.10,4.83,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.172833                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.101625              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.315  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.714349              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.263   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1028 = 3.10 * 0.50 * 5.1839 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0679 = 3.10 * 0.50 * 5.1519 + 1.00 * 0.0783                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6956 = 0.71 * 1.00 * 5.1519 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6834 = 0.71 * 1.00 * 5.1390 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.11   11.54    None  None   None       |
|    all(noH): 2823   0      0.00    80.11   11.54    None  None   None       |
|    Sol.    : 438    0      0.89    74.66   33.97    None  None   None       |
|    Mac.    : 2385   0      0.00    80.11   7.42     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 -   8.011: 1700   |   5:    40.054 -  48.065:   85        |
|      1:     8.011 -  16.022:  545   |   6:    48.065 -  56.076:   66        |
|      2:    16.022 -  24.032:  162   |   7:    56.076 -  64.086:   26        |
|      3:    24.032 -  32.043:  106   |   8:    64.086 -  72.097:   15        |
|      4:    32.043 -  40.054:  115   |   9:    72.097 -  80.108:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1578             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1578             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1578   ksol= 0.32   Bsol= 47.91   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.10,4.83,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140743                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7540 0.99   1389  152 0.0994 0.1320      5.3846      5.5213|
|  2:  4.7540 -  3.7933 0.99   1331  152 0.0839 0.1119      5.4306      5.6433|
|  3:  3.7933 -  3.3196 0.99   1299  143 0.1042 0.1487      5.4735      5.8258|
|  4:  3.3196 -  3.0188 0.99   1306  145 0.1176 0.1709      5.4348      5.6191|
|  5:  3.0188 -  2.8039 0.99   1282  145 0.1291 0.1603      5.3199      5.5323|
|  6:  2.8039 -  2.6395 0.99   1291  141 0.1174 0.2126      5.1978      5.5313|
|  7:  2.6395 -  2.5080 0.99   1283  143 0.1268 0.1561      5.1739       5.321|
|  8:  2.5080 -  2.3992 0.98   1273  137 0.1152 0.1664      5.0735      5.3578|
|  9:  2.3992 -  2.3072 0.98   1262  144 0.1171 0.1846       5.049      5.3194|
| 10:  2.3072 -  2.2279 1.00   1279  143 0.1109 0.1703      4.9583       5.205|
| 11:  2.2279 -  2.1584 0.97   1254  137 0.1124 0.1712       4.951      5.2533|
| 12:  2.1584 -  2.0969 0.98   1251  142 0.1112 0.1764      4.8763      5.2448|
| 13:  2.0969 -  2.0418 0.99   1278  135 0.1094 0.1615      4.7796       5.007|
| 14:  2.0418 -  1.9921 0.66    852  100 0.0964 0.1668      4.6456       4.906|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7540  1389   152  0.94   9.18   0.98     0.95       7241.08|
|  2:  4.7540 -  3.7933  1331   152  0.95   7.97   1.01     1.00       9131.44|
|  3:  3.7933 -  3.3196  1299   143  0.94  11.11   1.02     1.02      10351.99|
|  4:  3.3196 -  3.0188  1306   145  0.92  13.34   1.00     0.98      10146.87|
|  5:  3.0188 -  2.8039  1282   145  0.90  15.56   1.00     0.98       8322.44|
|  6:  2.8039 -  2.6395  1291   141  0.90  16.19   0.98     0.95       7076.05|
|  7:  2.6395 -  2.5080  1283   143  0.91  15.62   0.98     0.95       6204.36|
|  8:  2.5080 -  2.3992  1273   137  0.91  15.25   0.99     0.97       5395.96|
|  9:  2.3992 -  2.3072  1262   144  0.91  15.47   1.01     0.97       5244.67|
| 10:  2.3072 -  2.2279  1279   143  0.90  16.11   1.00     0.96       4490.71|
| 11:  2.2279 -  2.1584  1254   137  0.90  16.35   1.00     0.96       4573.93|
| 12:  2.1584 -  2.0969  1251   142  0.90  15.91   1.01     1.00       4014.06|
| 13:  2.0969 -  2.0418  1278   135  0.90  15.95   1.00     0.97       3344.46|
| 14:  2.0418 -  1.9921   852   100  0.92  13.77   0.98     0.95       2508.28|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2508.28 max =        10351.99 mean =      6413.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.08|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1578   ksol= 0.32   Bsol= 51.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.72,-0.49,1.20,-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: 5.140627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1578   ksol= 0.32   Bsol= 51.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.72,-0.49,1.20,-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: 5.140627                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7540 0.99   1389  152 0.0993 0.1321      5.3838      5.5211|
|  2:  4.7540 -  3.7933 0.99   1331  152 0.0840 0.1120      5.4313      5.6444|
|  3:  3.7933 -  3.3196 0.99   1299  143 0.1042 0.1488       5.474      5.8264|
|  4:  3.3196 -  3.0188 0.99   1306  145 0.1176 0.1709      5.4349      5.6191|
|  5:  3.0188 -  2.8039 0.99   1282  145 0.1291 0.1602      5.3196      5.5316|
|  6:  2.8039 -  2.6395 0.99   1291  141 0.1174 0.2126      5.1975      5.5314|
|  7:  2.6395 -  2.5080 0.99   1283  143 0.1268 0.1562      5.1739      5.3211|
|  8:  2.5080 -  2.3992 0.98   1273  137 0.1153 0.1663      5.0737       5.358|
|  9:  2.3992 -  2.3072 0.98   1262  144 0.1171 0.1846      5.0489      5.3195|
| 10:  2.3072 -  2.2279 1.00   1279  143 0.1109 0.1702      4.9581       5.205|
| 11:  2.2279 -  2.1584 0.97   1254  137 0.1124 0.1711      4.9506      5.2524|
| 12:  2.1584 -  2.0969 0.98   1251  142 0.1111 0.1760      4.8758      5.2437|
| 13:  2.0969 -  2.0418 0.99   1278  135 0.1093 0.1616      4.7794      5.0077|
| 14:  2.0418 -  1.9921 0.66    852  100 0.0964 0.1667      4.6456      4.9052|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7540  1389   152  0.94   9.18   0.98     0.95       7234.36|
|  2:  4.7540 -  3.7933  1331   152  0.95   7.98   1.01     1.00       9139.93|
|  3:  3.7933 -  3.3196  1299   143  0.94  11.12   1.02     1.02      10368.62|
|  4:  3.3196 -  3.0188  1306   145  0.92  13.34   1.00     0.98      10147.32|
|  5:  3.0188 -  2.8039  1282   145  0.90  15.56   1.00     0.98       8319.21|
|  6:  2.8039 -  2.6395  1291   141  0.90  16.19   0.98     0.96       7071.75|
|  7:  2.6395 -  2.5080  1283   143  0.91  15.62   0.98     0.95       6205.02|
|  8:  2.5080 -  2.3992  1273   137  0.91  15.26   0.99     0.97       5397.34|
|  9:  2.3992 -  2.3072  1262   144  0.91  15.47   1.01     0.97       5247.02|
| 10:  2.3072 -  2.2279  1279   143  0.90  16.10   1.00     0.96       4487.16|
| 11:  2.2279 -  2.1584  1254   137  0.90  16.34   1.00     0.96       4568.51|
| 12:  2.1584 -  2.0969  1251   142  0.90  15.90   1.01     1.00       4008.78|
| 13:  2.0969 -  2.0418  1278   135  0.90  15.94   1.00     0.97       3341.53|
| 14:  2.0418 -  1.9921   852   100  0.92  13.77   0.98     0.95       2507.38|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2507.38 max =        10368.62 mean =      6413.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.07|
|phase err.(test): min =        0.00 max =           89.60 mean =        13.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.994)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.61    83.72   15.15    None  None   None       |
|    all(noH): 2823   0      3.61    83.72   15.15    None  None   None       |
|    Sol.    : 438    0      4.50    78.27   37.58    None  None   None       |
|    Mac.    : 2385   0      3.61    83.72   11.04    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:     3.612 -  11.623: 1700   |   5:    43.666 -  51.677:   85        |
|      1:    11.623 -  19.634:  545   |   6:    51.677 -  59.688:   66        |
|      2:    19.634 -  27.645:  162   |   7:    59.688 -  67.699:   26        |
|      3:    27.645 -  35.655:  106   |   8:    67.699 -  75.709:   15        |
|      4:    35.655 -  43.666:  115   |   9:    75.709 -  83.720:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.290 - 4.180
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 304
   mapped sites are within: 0.704 - 4.180

peak=   11.251 closest distance to " CB  VAL A 230 " =    1.494
peak=    7.550 closest distance to " CG2 VAL A 296 " =    1.165
peak=    6.374 closest distance to " CG  LEU A   5 " =    1.172
peak=    6.324 closest distance to " NH2 ARG A  56 " =    2.175
peak=    5.795 closest distance to " O   HOH Z 142 " =    1.934
peak=    5.678 closest distance to " NE2 GLN A  11 " =    1.184
peak=    5.603 closest distance to " CG  LEU A 228 " =    1.153
peak=    5.115 closest distance to " CD2 LEU A   5 " =    1.148
peak=    5.093 closest distance to " CB  GLN A 223 " =    1.490
peak=    5.089 closest distance to " CB  GLN A 183 " =    1.246
peak=    4.845 closest distance to " O   HOH Z   9 " =    1.501
peak=    4.844 closest distance to " O   HOH Z 232 " =    2.348
peak=    4.635 closest distance to " CB  ARG A 275 " =    0.932
peak=    4.569 closest distance to " O   HOH Z 265 " =    2.243
peak=    4.554 closest distance to " O   HOH Z  61 " =    1.691
peak=    4.548 closest distance to " O   HOH Z 427 " =    3.010
peak=    4.542 closest distance to " CB  ARG A  79 " =    1.515
peak=    4.515 closest distance to " O   SER A  87 " =    2.331
peak=    4.510 closest distance to " ND2 ASN A 187 " =    1.576
peak=    4.485 closest distance to " O   HOH Z 346 " =    1.602
peak=    4.459 closest distance to " O   HOH Z 126 " =    1.948
peak=    4.454 closest distance to " CB  VAL A 296 " =    1.047
peak=    4.359 closest distance to " CB  SER A  63 " =    1.245
peak=    4.355 closest distance to " O   HOH Z 303 " =    2.061
peak=    4.330 closest distance to " CZ  PHE A 218 " =    1.136
peak=    4.329 closest distance to " O   HOH Z 248 " =    1.592
peak=    4.273 closest distance to " CB  VAL A 265 " =    1.359
peak=    4.263 closest distance to " CG  PRO A 213 " =    1.190
peak=    4.262 closest distance to " O   HOH Z 369 " =    2.114
peak=    4.260 closest distance to " C   PRO A 198 " =    1.524
peak=    4.224 closest distance to " CB  TRP A 266 " =    1.048
peak=    4.208 closest distance to " O   HOH Z 298 " =    1.812
peak=    4.199 closest distance to " O   HOH Z 209 " =    2.292
peak=    4.190 closest distance to " O   HOH Z  43 " =    1.953
peak=    4.187 closest distance to " CB  ARG A 190 " =    1.495
peak=    4.180 closest distance to " O   HOH Z 158 " =    3.288
peak=    4.175 closest distance to " CB  VAL A 230 " =    1.128
peak=    4.164 closest distance to " CB  ASN A 142 " =    1.110
peak=    4.158 closest distance to " CB  GLU A 152 " =    1.229
peak=    4.132 closest distance to " O   HOH Z 313 " =    1.932
peak=    4.132 closest distance to " O   HOH Z 272 " =    1.836
peak=    4.125 closest distance to " CA  TYR A  30 " =    0.993
peak=    4.119 closest distance to " OG  SER A  97 " =    2.974
peak=    4.078 closest distance to " CB  ASN A 148 " =    1.364
peak=    4.048 closest distance to " O   HOH Z 425 " =    1.358
peak=    4.012 closest distance to " CB  ALA A   9 " =    1.620
peak=    4.011 closest distance to " O   HOH Z 287 " =    2.154
peak=    3.991 closest distance to " CB  ASP A 140 " =    0.995
peak=    3.977 closest distance to " CG  PRO A 243 " =    1.081
peak=    3.963 closest distance to " CG1 ILE A  49 " =    1.494
peak=    3.948 closest distance to " O   HOH Z  78 " =    1.673
peak=    3.940 closest distance to " O   HOH Z 411 " =    3.792
peak=    3.936 closest distance to " CA  ALA A  51 " =    0.946
peak=    3.934 closest distance to " O   HOH Z 214 " =    2.164
peak=    3.931 closest distance to " O   HOH Z 423 " =    1.779
peak=    3.928 closest distance to " N   PHE A 130 " =    1.283
peak=    3.923 closest distance to " CD2 LEU A 228 " =    1.111
peak=    3.921 closest distance to " CB  GLU A 277 " =    3.627
peak=    3.894 closest distance to " O   HOH Z 368 " =    2.177
peak=    3.873 closest distance to " O   HOH Z 126 " =    1.560
peak=    3.873 closest distance to " OG BSER A 164 " =    2.230
peak=    3.851 closest distance to " O   HOH Z 234 " =    3.660
peak=    3.832 closest distance to " O   HOH Z  92 " =    2.485
peak=    3.811 closest distance to " O   HOH Z 193 " =    1.834
peak=    3.808 closest distance to " OG ASER A 258 " =    3.090
peak=    3.806 closest distance to " O   HOH Z 261 " =    1.893
peak=    3.794 closest distance to " CG  PRO A 198 " =    1.256
peak=    3.789 closest distance to " CB  ASN A  39 " =    0.934
peak=    3.781 closest distance to " N   ASN A  39 " =    1.231
peak=    3.778 closest distance to " OD1 ASN A  69 " =    2.610
peak=    3.762 closest distance to " O   HOH Z 251 " =    1.595
peak=    3.758 closest distance to " O   HOH Z  10 " =    1.785
peak=    3.744 closest distance to " CG  LEU A 167 " =    1.236
peak=    3.733 closest distance to " O   HOH Z 126 " =    1.530
peak=    3.729 closest distance to " O   HOH Z 299 " =    4.180
peak=    3.726 closest distance to " O   HOH Z 371 " =    2.927
peak=    3.717 closest distance to " O   HOH Z  21 " =    1.738
peak=    3.716 closest distance to " CG2AVAL A  72 " =    1.701
peak=    3.712 closest distance to " O   HOH Z 180 " =    2.117
peak=    3.711 closest distance to " CG2 VAL A 257 " =    0.878
peak=    3.710 closest distance to " CD  ARG A  66 " =    2.661
peak=    3.706 closest distance to " O   HOH Z 389 " =    1.865
peak=    3.705 closest distance to " CB  PRO A  54 " =    0.785
peak=    3.690 closest distance to " CB AVAL A  41 " =    1.226
peak=    3.685 closest distance to " O   HOH Z 422 " =    2.626
peak=    3.682 closest distance to " NH1AARG A 145 " =    1.144
peak=    3.677 closest distance to " CA  ASN A 215 " =    1.120
peak=    3.671 closest distance to " CB  VAL A 202 " =    1.565
peak=    3.670 closest distance to " O   HOH Z 280 " =    3.018
peak=    3.653 closest distance to " O   HOH Z 261 " =    1.647
peak=    3.649 closest distance to " CD  ARG A 159 " =    0.704
peak=    3.648 closest distance to " CB  SER A   3 " =    1.276
peak=    3.628 closest distance to " CE  LYS A  76 " =    0.872
peak=    3.627 closest distance to " CA  ARG A 195 " =    1.175
peak=    3.627 closest distance to " CG  MET A 185 " =    1.189
peak=    3.619 closest distance to " O   HOH Z 197 " =    3.150
peak=    3.616 closest distance to " CB  THR A  82 " =    1.346
peak=    3.607 closest distance to " CB  GLU A 128 " =    0.958
peak=    3.603 closest distance to " O  BHOH Z 338 " =    2.396
peak=    3.601 closest distance to " O   HOH Z  40 " =    1.596
peak=    3.595 closest distance to " CD  LYS A 166 " =    1.322
peak=    3.594 closest distance to " CA  TYR A 116 " =    1.404
peak=    3.593 closest distance to " NZ  LYS A 117 " =    3.219
peak=    3.589 closest distance to " O   HOH Z 285 " =    2.469
peak=    3.583 closest distance to " CG2 ILE A  20 " =    1.478
peak=    3.582 closest distance to " O   HOH Z 193 " =    1.925
peak=    3.576 closest distance to " CB  SER A 212 " =    1.249
peak=    3.570 closest distance to " O   HOH Z 353 " =    2.550
peak=    3.568 closest distance to " O   HOH Z 329 " =    4.116
peak=    3.550 closest distance to " CD1 ILE A  33 " =    1.735
peak=    3.549 closest distance to " CG  MET A 185 " =    1.044
peak=    3.549 closest distance to " O   HOH Z 147 " =    1.791
peak=    3.539 closest distance to " CG1 VAL A 153 " =    0.973
peak=    3.529 closest distance to " CB  GLU A  46 " =    0.960
peak=    3.529 closest distance to " CA  LYS A 117 " =    1.195
peak=    3.526 closest distance to " CB  GLN A  88 " =    1.206
peak=    3.516 closest distance to " CA  ALA A 291 " =    0.866
peak=    3.509 closest distance to " CD2 TRP A 179 " =    1.318
peak=    3.508 closest distance to " O   HOH Z 403 " =    1.582
peak=    3.508 closest distance to " O   HOH Z 128 " =    2.186
peak=    3.503 closest distance to " CA  SER A  87 " =    0.985
peak=    3.500 closest distance to " O   HOH Z  97 " =    2.457
peak=    3.500 closest distance to " CB  ARG A 139 " =    0.951
peak=    3.497 closest distance to " O   HOH Z 409 " =    3.105
peak=    3.494 closest distance to " O   HOH Z   3 " =    1.933
peak=    3.486 closest distance to " O   HOH Z 145 " =    3.943
peak=    3.484 closest distance to " CA  THR A 264 " =    0.801
peak=    3.479 closest distance to " CB  THR A  31 " =    1.582
peak=    3.472 closest distance to " O   HOH Z  59 " =    1.928
peak=    3.466 closest distance to " O   HOH Z  30 " =    1.432
peak=    3.466 closest distance to " CB  LEU A 228 " =    1.230
peak=    3.465 closest distance to " CB  ASN A 148 " =    1.952
peak=    3.464 closest distance to " CG  GLN A  88 " =    1.087
peak=    3.463 closest distance to " O   HOH Z 145 " =    2.071
peak=    3.461 closest distance to " CB  LYS A 117 " =    1.240
peak=    3.461 closest distance to " O   HOH Z  88 " =    2.991
peak=    3.460 closest distance to " CB  ASN A 110 " =    1.076
peak=    3.459 closest distance to " O   HOH Z  66 " =    2.189
peak=    3.458 closest distance to " O   HOH Z  97 " =    1.988
peak=    3.457 closest distance to " O   HOH Z 402 " =    1.379
peak=    3.456 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.451 closest distance to " CB  ASN A 187 " =    1.149
peak=    3.444 closest distance to " O   HOH Z 359 " =    3.940
peak=    3.433 closest distance to " CA  ASP A 162 " =    1.016
peak=    3.431 closest distance to " O   HOH Z 273 " =    2.924
peak=    3.431 closest distance to " CD1 LEU A 228 " =    2.027
peak=    3.430 closest distance to " CA  ARG A  36 " =    1.048
peak=    3.426 closest distance to " CB  THR A 157 " =    1.169
peak=    3.412 closest distance to " O   ASP A 124 " =    1.115
peak=    3.407 closest distance to " O   HOH Z 148 " =    3.418
peak=    3.403 closest distance to " ND2 ASN A 249 " =    0.878
peak=    3.398 closest distance to " O   HOH Z 365 " =    2.996
peak=    3.397 closest distance to " NZ  LYS A  48 " =    1.233
peak=    3.394 closest distance to " CB  LEU A  83 " =    0.781
peak=    3.393 closest distance to " CB  ARG A 138 " =    0.945
peak=    3.391 closest distance to " O   HOH Z 406 " =    1.487
peak=    3.388 closest distance to " NE2 GLN A  77 " =    3.170
peak=    3.386 closest distance to " O   HOH Z 172 " =    3.533
peak=    3.386 closest distance to " O   HOH Z   9 " =    1.837
peak=    3.384 closest distance to " O   HOH Z 203 " =    1.653
peak=    3.383 closest distance to " CB  PRO A  90 " =    1.200
peak=    3.383 closest distance to " CE1 TYR A 186 " =    1.337
peak=    3.378 closest distance to " CZ3 TRP A 266 " =    1.126
peak=    3.368 closest distance to " OG1 THR A 294 " =    2.450
peak=    3.363 closest distance to " O   HOH Z 130 " =    2.117
peak=    3.358 closest distance to " O   HOH Z 417 " =    3.335
peak=    3.353 closest distance to " CA  ALA A 233 " =    1.065
peak=    3.353 closest distance to " CB  LEU A 143 " =    1.189
peak=    3.349 closest distance to " O   HOH Z 133 " =    2.513
peak=    3.344 closest distance to " O   HOH Z 213 " =    1.917
peak=    3.343 closest distance to " CA  ALA A  21 " =    1.151
peak=    3.341 closest distance to " O   HOH Z 419 " =    1.897
peak=    3.337 closest distance to " O   HOH Z 359 " =    1.360
peak=    3.336 closest distance to " CG2 THR A 221 " =    1.193
peak=    3.335 closest distance to " CB  TRP A 150 " =    1.350
peak=    3.335 closest distance to " O   HOH Z 132 " =    2.681
peak=    3.331 closest distance to " O   HOH Z 250 " =    1.312
peak=    3.329 closest distance to " CG2 ILE A 120 " =    1.196
peak=    3.328 closest distance to " O   HOH Z   1 " =    1.725
peak=    3.326 closest distance to " O   ALA A 291 " =    1.716
peak=    3.321 closest distance to " O   HOH Z 290 " =    1.086
peak=    3.319 closest distance to " CD1 LEU A  96 " =    0.715
peak=    3.318 closest distance to " CB  ALA A 291 " =    1.356
peak=    3.317 closest distance to " CB  MET A  40 " =    0.822
peak=    3.317 closest distance to " CG BARG A 102 " =    1.790
peak=    3.315 closest distance to " N   SER A 135 " =    1.332
peak=    3.310 closest distance to " O   MET A 105 " =    1.868
peak=    3.307 closest distance to " CA  VAL A 125 " =    1.187
peak=    3.301 closest distance to " N   ASP A 162 " =    1.188
peak=    3.298 closest distance to " O   HOH Z 128 " =    2.153
peak=    3.293 closest distance to " CB  ALA A 248 " =    1.036
peak=    3.293 closest distance to " CB  GLN A  89 " =    1.284
peak=    3.292 closest distance to " CB  ASP A 298 " =    1.189
peak=    3.285 closest distance to " O   HOH Z 425 " =    2.061
peak=    3.285 closest distance to " NH2AARG A 275 " =    3.556
peak=    3.284 closest distance to " CA  ARG A 159 " =    1.179
peak=    3.283 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.280 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.280 closest distance to " O   HOH Z 421 " =    2.001
peak=    3.279 closest distance to " CD1 ILE A 263 " =    1.227
peak=    3.279 closest distance to " O   HOH Z 368 " =    3.522
peak=    3.278 closest distance to " CB  ALA A 233 " =    1.367
peak=    3.278 closest distance to " CB  HIS A 108 " =    0.810
peak=    3.275 closest distance to " O   HOH Z   1 " =    1.798
peak=    3.273 closest distance to " O   HOH Z 286 " =    2.436
peak=    3.273 closest distance to " CG BARG A 275 " =    1.392
peak=    3.269 closest distance to " O   HOH Z 303 " =    2.969
peak=    3.266 closest distance to " CD  ARG A 195 " =    3.514
peak=    3.263 closest distance to " O   PHE A 192 " =    1.426
peak=    3.263 closest distance to " CD BLYS A 290 " =    1.102
peak=    3.262 closest distance to " O   HOH Z  90 " =    2.292
peak=    3.254 closest distance to " O   HOH Z 294 " =    1.507
peak=    3.250 closest distance to " CA  ALA A 158 " =    1.289
peak=    3.248 closest distance to " CB  SER A 216 " =    0.780
peak=    3.246 closest distance to " CB  SER A  26 " =    1.754
peak=    3.245 closest distance to " O   HOH Z  80 " =    1.538
peak=    3.241 closest distance to " OE2 GLU A   2 " =    1.872
peak=    3.239 closest distance to " CD1 ILE A 106 " =    0.969
peak=    3.236 closest distance to " CA  ASN A 217 " =    1.224
peak=    3.236 closest distance to " OE2 GLU A  53 " =    1.966
peak=    3.235 closest distance to " O   HOH Z 403 " =    1.428
peak=    3.235 closest distance to " CG  MET A 113 " =    1.196
peak=    3.234 closest distance to " O   HOH Z 187 " =    2.293
peak=    3.232 closest distance to " O   TRP A 274 " =    1.826
peak=    3.229 closest distance to " O   HOH Z 371 " =    3.380
peak=    3.229 closest distance to " O   HOH Z 291 " =    1.547
peak=    3.228 closest distance to " O   HOH Z 305 " =    3.483
peak=    3.227 closest distance to " N   ASN A 127 " =    1.257
peak=    3.220 closest distance to " ND1 HIS A  86 " =    1.779
peak=    3.218 closest distance to " O   HOH Z 263 " =    1.721
peak=    3.217 closest distance to " OG BSER A  99 " =    2.196
peak=    3.216 closest distance to " O   HOH Z 193 " =    1.706
peak=    3.215 closest distance to " O   ASN A 284 " =    1.713
peak=    3.213 closest distance to " O   PRO A  90 " =    1.487
peak=    3.209 closest distance to " O   HOH Z  85 " =    2.213
peak=    3.208 closest distance to " CD1 LEU A 300 " =    1.215
peak=    3.206 closest distance to " CZ  PHE A  38 " =    1.141
peak=    3.201 closest distance to " CG2 ILE A 234 " =    0.888
peak=    3.201 closest distance to " O   GLY A  75 " =    1.451
peak=    3.200 closest distance to " CE  LYS A  48 " =    1.153
peak=    3.198 closest distance to " CA  LEU A 282 " =    1.158
peak=    3.196 closest distance to " CB  SER A 273 " =    0.856
peak=    3.195 closest distance to " O   HOH Z  88 " =    3.292
peak=    3.194 closest distance to " O   HOH Z 380 " =    1.867
peak=    3.194 closest distance to " CB  ALA A  34 " =    1.042
peak=    3.193 closest distance to " O   HOH Z 437 " =    1.610
peak=    3.192 closest distance to " O   HOH Z  88 " =    2.719
peak=    3.189 closest distance to " CB  ALA A  43 " =    0.808
peak=    3.189 closest distance to " O   ARG A  56 " =    2.886
peak=    3.187 closest distance to " CB  THR A  52 " =    0.890
peak=    3.184 closest distance to " O   HOH Z 109 " =    2.539
peak=    3.181 closest distance to " CG  LYS A 119 " =    1.119
peak=    3.180 closest distance to " O   HOH Z  48 " =    1.598
peak=    3.176 closest distance to " NE2 HIS A 207 " =    1.288
peak=    3.174 closest distance to " CB  VAL A 268 " =    0.845
peak=    3.173 closest distance to " O   PHE A  61 " =    1.420
peak=    3.167 closest distance to " CA  GLY A 267 " =    0.874
peak=    3.162 closest distance to " O   HOH Z  89 " =    1.697
peak=    3.160 closest distance to " O   HOH Z 325 " =    2.226
peak=    3.160 closest distance to " O   HOH Z 234 " =    1.836
peak=    3.158 closest distance to " CB  GLN A 205 " =    1.127
peak=    3.149 closest distance to " CB  VAL A 257 " =    0.739
peak=    3.149 closest distance to " CB  GLN A 278 " =    0.908
peak=    3.143 closest distance to " O   HOH Z 421 " =    3.022
peak=    3.137 closest distance to " CA  MET A 105 " =    0.975
peak=    3.135 closest distance to " CA  ILE A 106 " =    0.758
peak=    3.135 closest distance to " O   ALA A 158 " =    1.410
peak=    3.134 closest distance to " CG2 THR A 294 " =    1.689
peak=    3.132 closest distance to " CG AARG A 275 " =    1.195
peak=    3.131 closest distance to " CB  PHE A 204 " =    0.894
peak=    3.128 closest distance to " CB  ILE A  20 " =    1.416
peak=    3.127 closest distance to " CD1 LEU A 261 " =    1.222
peak=    3.125 closest distance to " CA  VAL A  41 " =    0.805
peak=    3.124 closest distance to " N   GLN A 278 " =    1.314
peak=    3.123 closest distance to " CG  GLN A 278 " =    1.330
peak=    3.122 closest distance to " O   HOH Z 384 " =    3.306
peak=    3.122 closest distance to " CD  LYS A 119 " =    1.807
peak=    3.122 closest distance to " OG  SER A  22 " =    2.818
peak=    3.120 closest distance to " CB  SER A  62 " =    1.143
peak=    3.119 closest distance to " CG  LYS A  76 " =    0.888
peak=    3.116 closest distance to " CA  ALA A 154 " =    1.048
peak=    3.112 closest distance to " O   HOH Z 173 " =    2.161
peak=    3.110 closest distance to " O   HOH Z  89 " =    2.169
peak=    3.110 closest distance to " CG1 ILE A 151 " =    1.101
peak=    3.100 closest distance to " O   HOH Z 350 " =    1.630
peak=    3.100 closest distance to " O   HOH Z  29 " =    2.011
peak=    3.098 closest distance to " CB  TYR A 116 " =    0.866
peak=    3.094 closest distance to " OG  SER A  62 " =    2.907
peak=    3.083 closest distance to " CB  ASN A 173 " =    1.068
peak=    3.079 closest distance to " O   HOH Z 423 " =    2.819
peak=    3.075 closest distance to " CB  ALA A 114 " =    1.270
peak=    3.072 closest distance to " CB  ALA A 227 " =    1.011
peak=    3.063 closest distance to " O   HOH Z 238 " =    3.681
peak=    3.056 closest distance to " O   SER A 164 " =    1.265
peak=    3.055 closest distance to " ND1 HIS A  81 " =    1.756
peak=    3.040 closest distance to " CA  ILE A 234 " =    0.959
peak=    3.030 closest distance to " CG  LEU A 281 " =    1.014
peak=    3.029 closest distance to " O   GLN A 278 " =    1.511

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.751 - 5.522
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 204
   mapped sites are within: 0.751 - 5.522

peak=   -5.105 closest distance to " CG2 VAL A 230 " =    0.751
peak=   -4.472 closest distance to " CD  ARG A 156 " =    2.042
peak=   -4.454 closest distance to " CD  ARG A  14 " =    3.275
peak=   -4.413 closest distance to " OG BSER A 134 " =    1.267
peak=   -4.355 closest distance to " CB  PHE A 192 " =    1.955
peak=   -4.336 closest distance to " CD  GLN A  58 " =    1.005
peak=   -4.296 closest distance to " O   HOH Z 162 " =    2.690
peak=   -4.159 closest distance to " O   VAL A  67 " =    2.640
peak=   -4.157 closest distance to " O   HOH Z 266 " =    5.404
peak=   -4.120 closest distance to " CG1 VAL A 112 " =    2.660
peak=   -4.118 closest distance to " CG  GLN A 223 " =    2.093
peak=   -4.091 closest distance to " C   HIS A 108 " =    1.232
peak=   -4.067 closest distance to " O   HOH Z 185 " =    2.426
peak=   -4.031 closest distance to " CB  ALA A 248 " =    2.387
peak=   -4.024 closest distance to " O   HOH Z 231 " =    2.068
peak=   -3.999 closest distance to " CG2 VAL A 296 " =    1.293
peak=   -3.995 closest distance to " CG2 VAL A 202 " =    2.733
peak=   -3.980 closest distance to " CA  VAL A  67 " =    2.739
peak=   -3.934 closest distance to " O   HOH Z 290 " =    1.274
peak=   -3.932 closest distance to " CG2 ILE A  49 " =    2.797
peak=   -3.860 closest distance to " N   ALA A  43 " =    2.553
peak=   -3.850 closest distance to " O   HOH Z 211 " =    1.417
peak=   -3.849 closest distance to " CE2 TYR A  30 " =    2.717
peak=   -3.831 closest distance to " CD1 LEU A 255 " =    2.831
peak=   -3.828 closest distance to " O   HOH Z 351 " =    1.516
peak=   -3.815 closest distance to " O   HOH Z 114 " =    3.006
peak=   -3.811 closest distance to " O   HOH Z 394 " =    1.480
peak=   -3.797 closest distance to " O   HOH Z 429 " =    1.968
peak=   -3.793 closest distance to " O   HOH Z 196 " =    2.290
peak=   -3.790 closest distance to " O   HOH Z 166 " =    1.959
peak=   -3.786 closest distance to " CZ3 TRP A 179 " =    1.189
peak=   -3.784 closest distance to " CG1 VAL A 112 " =    2.814
peak=   -3.767 closest distance to " CB  ALA A  43 " =    2.491
peak=   -3.757 closest distance to " ND2 ASN A  45 " =    1.893
peak=   -3.741 closest distance to " CA  GLY A 241 " =    2.322
peak=   -3.737 closest distance to " CE BMET A  47 " =    1.423
peak=   -3.735 closest distance to " OXT GLY A 302 " =    2.973
peak=   -3.730 closest distance to " O   HOH Z  73 " =    2.282
peak=   -3.702 closest distance to " C   ILE A 239 " =    2.137
peak=   -3.699 closest distance to " O   HOH Z  11 " =    1.906
peak=   -3.698 closest distance to " O   PRO A 163 " =    2.076
peak=   -3.689 closest distance to " OG  SER A  97 " =    2.306
peak=   -3.666 closest distance to " CA  GLY A 241 " =    3.171
peak=   -3.649 closest distance to " N   THR A 157 " =    1.480
peak=   -3.645 closest distance to " CE3 TRP A 150 " =    2.078
peak=   -3.644 closest distance to " O   HOH Z  44 " =    2.312
peak=   -3.637 closest distance to " CG1 VAL A 250 " =    2.776
peak=   -3.632 closest distance to " CE  MET A 105 " =    2.378
peak=   -3.629 closest distance to " CB  PRO A 163 " =    2.450
peak=   -3.619 closest distance to " O   PRO A 198 " =    1.217
peak=   -3.602 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.591 closest distance to " O   VAL A 189 " =    2.584
peak=   -3.565 closest distance to " OG  SER A  87 " =    1.344
peak=   -3.559 closest distance to " NH2AARG A 275 " =    5.192
peak=   -3.548 closest distance to " C   MET A 188 " =    1.387
peak=   -3.541 closest distance to " CB  ALA A 291 " =    2.315
peak=   -3.536 closest distance to " CG2 ILE A 263 " =    2.329
peak=   -3.531 closest distance to " CD2 TYR A 293 " =    2.004
peak=   -3.527 closest distance to " O   HOH Z 389 " =    2.079
peak=   -3.522 closest distance to " O   HOH Z  13 " =    1.848
peak=   -3.511 closest distance to " ND2 ASN A 249 " =    2.410
peak=   -3.502 closest distance to " O   HOH Z 140 " =    1.798
peak=   -3.499 closest distance to " CB  ALA A 291 " =    2.218
peak=   -3.483 closest distance to " N   ALA A 248 " =    1.789
peak=   -3.473 closest distance to " O   HOH Z 103 " =    1.754
peak=   -3.467 closest distance to " CG  ASP A 231 " =    0.766
peak=   -3.455 closest distance to " O   HOH Z 407 " =    3.040
peak=   -3.452 closest distance to " CD2 LEU A 237 " =    2.815
peak=   -3.441 closest distance to " CG1 VAL A 125 " =    1.916
peak=   -3.438 closest distance to " O   GLY A  17 " =    1.229
peak=   -3.433 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.429 closest distance to " CD  PRO A 213 " =    2.137
peak=   -3.429 closest distance to " NE2 GLN A 194 " =    1.807
peak=   -3.425 closest distance to " N   HIS A 115 " =    2.143
peak=   -3.422 closest distance to " O   GLY A  80 " =    2.549
peak=   -3.422 closest distance to " CG  PRO A 163 " =    2.617
peak=   -3.420 closest distance to " CG  TRP A 266 " =    1.852
peak=   -3.409 closest distance to " C   LEU A 143 " =    1.050
peak=   -3.405 closest distance to " O   HOH Z  52 " =    1.515
peak=   -3.399 closest distance to " O   HOH Z 313 " =    1.189
peak=   -3.397 closest distance to " CG1 VAL A 112 " =    2.857
peak=   -3.393 closest distance to " CB  VAL A 230 " =    1.059
peak=   -3.386 closest distance to " O   HOH Z 243 " =    1.907
peak=   -3.381 closest distance to " OD1 ASN A 148 " =    1.410
peak=   -3.377 closest distance to " O   MET A  40 " =    2.821
peak=   -3.374 closest distance to " OH  TYR A 172 " =    1.778
peak=   -3.367 closest distance to " O   ARG A 145 " =    1.669
peak=   -3.360 closest distance to " OD1 ASN A 187 " =    1.569
peak=   -3.356 closest distance to " CG2 THR A 178 " =    2.222
peak=   -3.351 closest distance to " CZ  PHE A 192 " =    2.881
peak=   -3.348 closest distance to " O   HOH Z 359 " =    3.171
peak=   -3.346 closest distance to " NE2 GLN A 278 " =    1.821
peak=   -3.342 closest distance to " ND2 ASN A 252 " =    1.911
peak=   -3.340 closest distance to " O   HOH Z 131 " =    4.124
peak=   -3.340 closest distance to " CZ  TYR A 169 " =    1.700
peak=   -3.339 closest distance to " O   HOH Z 426 " =    1.592
peak=   -3.338 closest distance to " N   ALA A 248 " =    2.325
peak=   -3.338 closest distance to " O   SER A 271 " =    2.181
peak=   -3.329 closest distance to " O   PRO A 198 " =    1.354
peak=   -3.323 closest distance to " OG BSER A 134 " =    1.739
peak=   -3.323 closest distance to " O   HOH Z 136 " =    2.482
peak=   -3.323 closest distance to " O   HOH Z 102 " =    1.663
peak=   -3.320 closest distance to " CD1 LEU A 101 " =    2.310
peak=   -3.320 closest distance to " O   HOH Z 198 " =    2.077
peak=   -3.316 closest distance to " O   HOH Z  60 " =    1.913
peak=   -3.315 closest distance to " O   HOH Z 350 " =    1.766
peak=   -3.315 closest distance to " O   HOH Z 357 " =    2.022
peak=   -3.312 closest distance to " O   HOH Z 285 " =    2.012
peak=   -3.310 closest distance to " O   HOH Z  38 " =    1.716
peak=   -3.306 closest distance to " CG2 VAL A 296 " =    1.815
peak=   -3.306 closest distance to " C   ASP A 231 " =    2.488
peak=   -3.303 closest distance to " O   HOH Z 191 " =    5.522
peak=   -3.302 closest distance to " N   ASP A 171 " =    2.288
peak=   -3.302 closest distance to " N   THR A  52 " =    1.702
peak=   -3.302 closest distance to " O   HOH Z 166 " =    1.611
peak=   -3.298 closest distance to " CA  PRO A 243 " =    2.228
peak=   -3.298 closest distance to " OH  TYR A 247 " =    2.040
peak=   -3.297 closest distance to " ND2 ASN A 187 " =    1.473
peak=   -3.296 closest distance to " CD1 LEU A 228 " =    2.262
peak=   -3.289 closest distance to " C   LEU A 222 " =    0.759
peak=   -3.284 closest distance to " N   SER A 276 " =    1.412
peak=   -3.281 closest distance to " CD2 PHE A  61 " =    1.947
peak=   -3.280 closest distance to " CD1 PHE A  59 " =    2.036
peak=   -3.279 closest distance to " CD  ARG A 139 " =    1.631
peak=   -3.278 closest distance to " CG1 VAL A 197 " =    2.293
peak=   -3.277 closest distance to " O   GLY A 196 " =    1.249
peak=   -3.275 closest distance to " O   SER A 210 " =    1.834
peak=   -3.275 closest distance to " CG  HIS A  86 " =    1.098
peak=   -3.274 closest distance to " CG  GLU A 277 " =    1.246
peak=   -3.273 closest distance to " CG  ASP A 132 " =    2.328
peak=   -3.272 closest distance to " O   SER A 276 " =    1.613
peak=   -3.271 closest distance to " CA  GLY A  98 " =    1.839
peak=   -3.270 closest distance to " NE2 GLN A  88 " =    1.944
peak=   -3.269 closest distance to " CB  ASN A 252 " =    1.772
peak=   -3.265 closest distance to " O   HOH Z 313 " =    1.590
peak=   -3.261 closest distance to " CA  ASN A 110 " =    2.400
peak=   -3.260 closest distance to " CB  ASP A 171 " =    2.299
peak=   -3.259 closest distance to " CD  LYS A 289 " =    2.475
peak=   -3.252 closest distance to " O   SER A  22 " =    2.335
peak=   -3.250 closest distance to " CA  GLY A 203 " =    2.482
peak=   -3.250 closest distance to " N   SER A   3 " =    2.021
peak=   -3.250 closest distance to " O   PHE A 218 " =    1.597
peak=   -3.242 closest distance to " CB  TRP A  85 " =    2.700
peak=   -3.232 closest distance to " O   ALA A  10 " =    1.781
peak=   -3.228 closest distance to " O   HOH Z 275 " =    1.444
peak=   -3.224 closest distance to " O   HOH Z  10 " =    1.441
peak=   -3.222 closest distance to " CA  ASN A 127 " =    1.190
peak=   -3.221 closest distance to " O   HOH Z 189 " =    2.098
peak=   -3.220 closest distance to " CG2BVAL A  41 " =    1.791
peak=   -3.217 closest distance to " C   ALA A 158 " =    1.375
peak=   -3.216 closest distance to " NH2 ARG A  79 " =    2.040
peak=   -3.215 closest distance to " N   MET A 105 " =    2.653
peak=   -3.214 closest distance to " O   HOH Z 253 " =    3.861
peak=   -3.212 closest distance to " O   ASP A  27 " =    2.035
peak=   -3.212 closest distance to " O   HOH Z 281 " =    2.640
peak=   -3.211 closest distance to " O   ASN A 301 " =    1.574
peak=   -3.210 closest distance to " SG BCYS A 201 " =    2.051
peak=   -3.204 closest distance to " O   HOH Z 371 " =    2.161
peak=   -3.204 closest distance to " CB  GLN A  11 " =    1.882
peak=   -3.202 closest distance to " O   HOH Z 187 " =    1.779
peak=   -3.196 closest distance to " NE2 GLN A 278 " =    1.758
peak=   -3.194 closest distance to " O   HOH Z  51 " =    1.203
peak=   -3.194 closest distance to " CG  GLU A 152 " =    1.556
peak=   -3.193 closest distance to " O   HOH Z 138 " =    1.263
peak=   -3.190 closest distance to " O   ALA A 161 " =    1.733
peak=   -3.187 closest distance to " CG2 VAL A 189 " =    1.942
peak=   -3.186 closest distance to " CG  PHE A 283 " =    2.663
peak=   -3.186 closest distance to " O   ALA A  51 " =    1.334
peak=   -3.185 closest distance to " OG BSER A 210 " =    1.509
peak=   -3.181 closest distance to " CD1 ILE A 199 " =    2.478
peak=   -3.177 closest distance to " OE2 GLU A 152 " =    1.240
peak=   -3.175 closest distance to " O   HOH Z 295 " =    1.598
peak=   -3.173 closest distance to " O   HOH Z 134 " =    3.764
peak=   -3.170 closest distance to " OD1 ASP A 171 " =    1.726
peak=   -3.170 closest distance to " CA  SER A 135 " =    1.374
peak=   -3.165 closest distance to " O   LYS A 117 " =    1.756
peak=   -3.164 closest distance to " OD1 ASN A 301 " =    1.985
peak=   -3.158 closest distance to " O   HOH Z 193 " =    2.120
peak=   -3.154 closest distance to " O   HOH Z 252 " =    4.012
peak=   -3.153 closest distance to " O   HOH Z 216 " =    1.329
peak=   -3.152 closest distance to " CB  ASP A 132 " =    2.404
peak=   -3.151 closest distance to " CG1 VAL A 296 " =    1.466
peak=   -3.146 closest distance to " O   HOH Z 346 " =    1.805
peak=   -3.137 closest distance to " O   HOH Z 139 " =    3.116
peak=   -3.131 closest distance to " CD2 PHE A 225 " =    1.126
peak=   -3.131 closest distance to " OD2 ASP A 191 " =    1.323
peak=   -3.123 closest distance to " OD1 ASN A 249 " =    2.385
peak=   -3.117 closest distance to " O   ALA A   1 " =    1.745
peak=   -3.117 closest distance to " CD2 TYR A 247 " =    2.384
peak=   -3.111 closest distance to " OH  TYR A 214 " =    1.227
peak=   -3.105 closest distance to " O   HOH Z 116 " =    1.476
peak=   -3.104 closest distance to " CB  TRP A 177 " =    2.341
peak=   -3.103 closest distance to " O   HOH Z 431 " =    1.889
peak=   -3.102 closest distance to " CG  LEU A 228 " =    1.014
peak=   -3.100 closest distance to " O   HOH Z 353 " =    2.048
peak=   -3.095 closest distance to " O   HOH Z 390 " =    2.343
peak=   -3.094 closest distance to " O   ASP A 272 " =    2.292
peak=   -3.088 closest distance to " ND2 ASN A  60 " =    1.356
peak=   -3.083 closest distance to " O   HOH Z 193 " =    1.557
peak=   -3.076 closest distance to " ND2BASN A 224 " =    1.733
peak=   -3.065 closest distance to " OG  SER A 206 " =    1.725
peak=   -3.058 closest distance to " O   GLN A 240 " =    2.456
peak=   -3.048 closest distance to " CE1 TYR A 247 " =    2.726
peak=   -3.044 closest distance to " O   HOH Z   9 " =    2.740

================= 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    :  0.4405 0.4210   6.236520e+00   6.204401e+00
   1_bss:  0.4322 0.4103   6.230631e+00   6.190631e+00
   1_xyz:  0.3248 0.3434   6.030919e+00   6.059037e+00
   1_adp:  0.2636 0.2996   5.858059e+00   5.962981e+00
   1_occ:  0.2630 0.2998   5.856898e+00   5.964623e+00
   2_bss:  0.2577 0.2954   5.854821e+00   5.961633e+00
   2_xyz:  0.1804 0.2236   5.536194e+00   5.704205e+00
   2_adp:  0.1648 0.2104   5.462269e+00   5.646429e+00
   2_occ:  0.1647 0.2105   5.462400e+00   5.647628e+00
   3_bss:  0.1639 0.2107   5.462611e+00   5.647633e+00
   3_xyz:  0.1297 0.1745   5.261432e+00   5.480153e+00
   3_adp:  0.1228 0.1702   5.223383e+00   5.455485e+00
   3_occ:  0.1227 0.1702   5.223104e+00   5.455224e+00
   4_bss:  0.1229 0.1698   5.223195e+00   5.453810e+00
   4_xyz:  0.1160 0.1626   5.180412e+00   5.420393e+00
   4_adp:  0.1163 0.1602   5.173484e+00   5.403774e+00
   4_occ:  0.1162 0.1601   5.172794e+00   5.403176e+00
   5_bss:  0.1162 0.1601   5.172833e+00   5.403190e+00
   5_xyz:  0.1110 0.1578   5.144041e+00   5.391060e+00
   5_adp:  0.1100 0.1578   5.140929e+00   5.392357e+00
   5_occ:  0.1100 0.1578   5.140743e+00   5.392147e+00
   5_bss:  0.1100 0.1578   5.140627e+00   5.392103e+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:  0.343  20.001   6.985   7.965  10.710   0.000   0.000   0.000
   1_xyz:  0.343  20.001   6.985   7.965  10.710   0.000   0.000   0.000
   1_adp:  0.343  20.001   6.985   7.965  10.710   0.000   0.000   0.000
   1_occ:  0.343  20.001   6.985   7.965  10.710   0.000   0.000   0.000
   2_bss:  0.341  47.905   3.689   4.092   7.069   0.000   0.000   0.000
   2_xyz:  0.341  47.905   3.689   4.092   7.069   0.000   0.000   0.000
   2_adp:  0.341  47.905   3.689   4.092   7.069   0.000   0.000   0.000
   2_occ:  0.341  47.905   3.689   4.092   7.069   0.000   0.000   0.000
   3_bss:  0.325  47.905   2.853   3.211   5.179   0.000   0.000   0.000
   3_xyz:  0.325  47.905   2.853   3.211   5.179   0.000   0.000   0.000
   3_adp:  0.325  47.905   2.853   3.211   5.179   0.000   0.000   0.000
   3_occ:  0.325  47.905   2.853   3.211   5.179   0.000   0.000   0.000
   4_bss:  0.321  47.905   2.812   3.097   4.829   0.000   0.000   0.000
   4_xyz:  0.321  47.905   2.812   3.097   4.829   0.000   0.000   0.000
   4_adp:  0.321  47.905   2.812   3.097   4.829   0.000   0.000   0.000
   4_occ:  0.321  47.905   2.812   3.097   4.829   0.000   0.000   0.000
   5_bss:  0.324  47.905   2.812   3.097   4.829   0.000   0.000   0.000
   5_xyz:  0.324  47.905   2.812   3.097   4.829   0.000   0.000   0.000
   5_adp:  0.324  47.905   2.812   3.097   4.829   0.000   0.000   0.000
   5_occ:  0.324  47.905   2.812   3.097   4.829   0.000   0.000   0.000
   5_bss:  0.321  51.518  -0.715  -0.487   1.202  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.904 0.5605  0.6274    51749.730
   1_bss:  46.692 0.5615  0.8130    49450.887
   1_xyz:  36.461 0.6840  0.9531    31434.149
   1_adp:  30.425 0.7537  1.0332    23520.305
   1_occ:  30.498 0.7529  1.0314    23594.377
   2_bss:  30.208 0.7560  0.9098    23209.097
   2_xyz:  21.452 0.8476  0.9915    12365.633
   2_adp:  19.771 0.8644  1.0025    10999.544
   2_occ:  19.800 0.8641  1.0022    11014.163
   3_bss:  19.754 0.8646  0.9598    11027.762
   3_xyz:  16.036 0.8979  0.9796     7715.250
   3_adp:  15.453 0.9030  0.9785     7339.648
   3_occ:  15.448 0.9031  0.9786     7335.553
   4_bss:  15.435 0.9032  0.9726     7314.556
   4_xyz:  14.643 0.9100  0.9756     6780.756
   4_adp:  14.235 0.9135  0.9753     6579.598
   4_occ:  14.226 0.9135  0.9753     6572.529
   5_bss:  14.226 0.9135  0.9753     6572.870
   5_xyz:  14.000 0.9152  0.9767     6421.785
   5_adp:  14.028 0.9151  0.9730     6417.414
   5_occ:  14.024 0.9151  0.9730     6413.966
   5_bss:  14.022 0.9151  0.9742     6413.832
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3975e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3975e+01
   1_xyz:   1.546  0.012  0.102 18.080  0.006  4.123   1.2096e-01
   1_adp:   1.546  0.012  0.102 18.080  0.006  4.123   1.2096e-01
   1_occ:   1.546  0.012  0.102 18.080  0.006  4.123   1.2096e-01
   2_bss:   1.546  0.012  0.102 18.080  0.006  4.123   1.2096e-01
   2_xyz:   0.959  0.006  0.072 16.303  0.004  4.123   5.9784e-02
   2_adp:   0.959  0.006  0.072 16.303  0.004  4.123   5.9784e-02
   2_occ:   0.959  0.006  0.072 16.303  0.004  4.123   5.9784e-02
   3_bss:   0.959  0.006  0.072 16.303  0.004  4.123   5.9784e-02
   3_xyz:   1.032  0.008  0.081 16.264  0.003  4.134   6.6342e-02
   3_adp:   1.032  0.008  0.081 16.264  0.003  4.134   6.6342e-02
   3_occ:   1.032  0.008  0.081 16.264  0.003  4.134   6.6342e-02
   4_bss:   1.032  0.008  0.081 16.264  0.003  4.134   6.6342e-02
   4_xyz:   0.998  0.008  0.081 15.840  0.004  4.112   6.3501e-02
   4_adp:   0.998  0.008  0.081 15.840  0.004  4.112   6.3501e-02
   4_occ:   0.998  0.008  0.081 15.840  0.004  4.112   6.3501e-02
   5_bss:   0.998  0.008  0.081 15.840  0.004  4.112   6.3501e-02
   5_xyz:   1.123  0.010  0.091 15.909  0.004  4.114   7.8281e-02
   5_adp:   1.123  0.010  0.091 15.909  0.004  4.114   7.8281e-02
   5_occ:   1.123  0.010  0.091 15.909  0.004  4.114   7.8281e-02
   5_bss:   1.123  0.010  0.091 15.909  0.004  4.114   7.8281e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9980e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9980e+00
   1_xyz:  12.283  0.149  0.386 87.112  0.032  2.154   8.9508e-02
   1_adp:  12.283  0.149  0.386 87.112  0.032  2.154   8.9508e-02
   1_occ:  12.283  0.149  0.386 87.112  0.032  2.154   8.9508e-02
   2_bss:  12.283  0.149  0.386 87.112  0.032  2.154   8.9508e-02
   2_xyz:   5.738  0.046  0.255 85.407  0.036  2.379   4.4781e-02
   2_adp:   5.738  0.046  0.255 85.407  0.036  2.379   4.4781e-02
   2_occ:   5.738  0.046  0.255 85.407  0.036  2.379   4.4781e-02
   3_bss:   5.738  0.046  0.255 85.407  0.036  2.379   4.4781e-02
   3_xyz:   9.136  0.056  0.478 82.806  0.032  2.277   6.8804e-02
   3_adp:   9.136  0.056  0.478 82.806  0.032  2.277   6.8804e-02
   3_occ:   9.136  0.056  0.478 82.806  0.032  2.277   6.8804e-02
   4_bss:   9.136  0.056  0.478 82.806  0.032  2.277   6.8804e-02
   4_xyz:   6.744  0.042  0.477 82.875  0.038  2.354   5.2810e-02
   4_adp:   6.744  0.042  0.477 82.875  0.038  2.354   5.2810e-02
   4_occ:   6.744  0.042  0.477 82.875  0.038  2.354   5.2810e-02
   5_bss:   6.744  0.042  0.477 82.875  0.038  2.354   5.2810e-02
   5_xyz:   6.983  0.055  0.592 83.416  0.039  2.246   5.7963e-02
   5_adp:   6.983  0.055  0.592 83.416  0.039  2.246   5.7963e-02
   5_occ:   6.983  0.055  0.592 83.416  0.039  2.246   5.7963e-02
   5_bss:   6.983  0.055  0.592 83.416  0.039  2.246   5.7963e-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:  58.80   0.00  10.95  51.97   0.00   7.90  58.80   0.00  27.52
   1_occ:  58.80   0.00  10.95  51.97   0.00   7.90  58.80   0.00  27.52
   2_bss:  58.80   0.00  10.95  51.97   0.00   7.90  58.80   0.00  27.52
   2_xyz:  58.80   0.00  10.95  51.97   0.00   7.90  58.80   0.00  27.52
   2_adp:  64.38   0.00  11.34  55.36   0.00   7.54  64.38   0.54  32.06
   2_occ:  64.38   0.00  11.34  55.36   0.00   7.54  64.38   0.54  32.06
   3_bss:  64.38   0.00  11.34  55.36   0.00   7.54  64.38   0.54  32.06
   3_xyz:  64.38   0.00  11.34  55.36   0.00   7.54  64.38   0.54  32.06
   3_adp:  77.43   0.00  12.09  76.48   0.00   7.68  77.43   0.60  36.08
   3_occ:  77.43   0.00  12.09  76.48   0.00   7.68  77.43   0.60  36.08
   4_bss:  77.43   0.00  12.09  76.48   0.00   7.68  77.43   0.60  36.08
   4_xyz:  77.43   0.00  12.09  76.48   0.00   7.68  77.43   0.60  36.08
   4_adp:  76.93   0.00  11.48  76.93   0.00   7.45  74.18   1.03  33.44
   4_occ:  76.93   0.00  11.48  76.93   0.00   7.45  74.18   1.03  33.44
   5_bss:  76.93   0.00  11.48  76.93   0.00   7.45  74.18   1.03  33.44
   5_xyz:  76.93   0.00  11.48  76.93   0.00   7.45  74.18   1.03  33.44
   5_adp:  80.11   0.00  11.54  80.11   0.00   7.42  74.66   0.89  33.97
   5_occ:  80.11   0.00  11.54  80.11   0.00   7.42  74.66   0.89  33.97
   5_bss:  83.72   3.61  15.15  83.72   3.61  11.04  78.27   4.50  37.58
------------------------------------------------------------------------
 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:    1.226    0.018    0.402
   1_adp:    1.226    0.018    0.402
   1_occ:    1.226    0.018    0.402
   2_bss:    1.226    0.018    0.402
   2_xyz:    1.597    0.040    0.500
   2_adp:    1.597    0.040    0.500
   2_occ:    1.597    0.040    0.500
   3_bss:    1.597    0.040    0.500
   3_xyz:    1.623    0.031    0.546
   3_adp:    1.623    0.031    0.546
   3_occ:    1.623    0.031    0.546
   4_bss:    1.623    0.031    0.546
   4_xyz:    1.711    0.025    0.562
   4_adp:    1.711    0.025    0.562
   4_occ:    1.711    0.025    0.562
   5_bss:    1.711    0.025    0.562
   5_xyz:    1.695    0.020    0.574
   5_adp:    1.695    0.020    0.574
   5_occ:    1.695    0.020    0.574
   5_bss:    1.695    0.020    0.574
------------------------------------------------------------------------

CPU time actual refinement: 335.26


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_657/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_657/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_657/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_657/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_657/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.11 
  Macro-tasks:
    bulk solvent and scale       = 39.64  
    individual site refinement   = 141.42 
    weights calculation          = 32.04  
    collect and process          = 6.71   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.93 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 102.70 
    alpha_beta                      = 8.38   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 115.21 
    fmodel                         = 7.53   
    r_factors                      = 0.30   
    phase_errors                   = 11.07  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 248.43 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.619 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    677 calls, 102.37 s
gradients_fft:          622 calls, 100.82 s

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

# Date 2008-01-16 Time 02:07:50 PST -0800 (1200478070.74 s)
Start R-work = 0.4405, R-free = 0.4210 (no bulk solvent and anisotropic scale)
Final R-work = 0.1280, R-free = 0.1752 (no bulk solvent and anisotropic scale)

Start R-work = 0.4322, R-free = 0.4103
Final R-work = 0.1100, R-free = 0.1578