# Date 2008-01-16 Time 02:03:58 PST -0800 (1200477838.87 s)
#phil __OFF__

Command line arguments: "../678.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27123
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 678

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.1647, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.00058
Completeness in resolution range: 0.972545
Completeness with d_max=infinity: 0.969465

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0342
                             d_min =   2.0006

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.00058
Completeness in resolution range: 0.972545
Completeness with d_max=infinity: 0.969465

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0346 -  4.2801 [2117/2141]  1903   214  10.1%
  bin  2:  4.2801 -  3.4103 [2037/2056]  1836   201   9.9%
  bin  3:  3.4103 -  2.9830 [2007/2026]  1808   199   9.9%
  bin  4:  2.9830 -  2.7120 [1981/2011]  1777   204  10.3%
  bin  5:  2.7120 -  2.5186 [1983/2002]  1787   196   9.9%
  bin  6:  2.5186 -  2.3707 [1964/1989]  1769   195   9.9%
  bin  7:  2.3707 -  2.2524 [1953/1981]  1758   195  10.0%
  bin  8:  2.2524 -  2.1546 [1945/1981]  1750   195  10.0%
  bin  9:  2.1546 -  2.0719 [1929/1971]  1735   194  10.1%
  bin 10:  2.0719 -  2.0006 [1673/1984]  1507   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_678/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: 12
        2.42 -     3.04: 2181
        3.04 -     3.66: 4602
        3.66 -     4.28: 8967
        4.28 -     4.90: 12307
  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 "  2.046 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.155 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.239 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28064 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_678/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_678/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.16465 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4256   r_free= 0.4094   ksol= 0.00   Bsol= 0.00   scale= 0.821    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.215935                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7734 0.99   1380  153 0.3544 0.3273      6.5124      6.4152|
|  2:  4.7734 -  3.8091 0.99   1311  149 0.3145 0.3328      6.6042      6.7028|
|  3:  3.8091 -  3.3336 0.99   1306  145 0.3696 0.3420      6.5527      6.5133|
|  4:  3.3336 -  3.0315 0.99   1289  136 0.4025 0.3706      6.4387      6.3474|
|  5:  3.0315 -  2.8158 0.99   1268  144 0.4390 0.4371      6.3045       6.323|
|  6:  2.8158 -  2.6507 0.99   1276  145 0.4453 0.4989      6.2271      6.1733|
|  7:  2.6507 -  2.5186 0.99   1281  142 0.4701 0.4615       6.195      6.1499|
|  8:  2.5186 -  2.4094 0.98   1261  136 0.4796 0.4139      6.1485      6.0924|
|  9:  2.4094 -  2.3170 0.98   1252  143 0.4741 0.4621      6.0829      6.0882|
| 10:  2.3170 -  2.2373 0.99   1262  136 0.4963 0.4473      6.1131      6.0099|
| 11:  2.2373 -  2.1676 0.98   1261  142 0.4826 0.4423      6.0106      6.0012|
| 12:  2.1676 -  2.1058 0.97   1230  139 0.4960 0.4736        5.96      5.9998|
| 13:  2.1058 -  2.0505 1.00   1262  137 0.4901 0.4741      5.8795       5.842|
| 14:  2.0505 -  2.0006 0.78    991  112 0.4996 0.4515      5.8476      5.7232|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7734  1380   153  0.75  29.43   0.81     0.77      53203.20|
|  2:  4.7734 -  3.8091  1311   149  0.79  27.37   0.91     0.82      69025.37|
|  3:  3.8091 -  3.3336  1306   145  0.72  33.26   0.87     0.79      72158.96|
|  4:  3.3336 -  3.0315  1289   136  0.66  38.47   0.83     0.71      64347.57|
|  5:  3.0315 -  2.8158  1268   144  0.58  45.84   0.78     0.64      57884.37|
|  6:  2.8158 -  2.6507  1276   145  0.56  47.49   0.76     0.61      52984.91|
|  7:  2.6507 -  2.5186  1281   142  0.53  50.03   0.75     0.59      49291.99|
|  8:  2.5186 -  2.4094  1261   136  0.53  49.59   0.77     0.60      43240.25|
|  9:  2.4094 -  2.3170  1252   143  0.55  47.88   0.74     0.62      38026.38|
| 10:  2.3170 -  2.2373  1262   136  0.55  48.15   0.76     0.63      34704.03|
| 11:  2.2373 -  2.1676  1261   142  0.53  49.94   0.77     0.61      33520.95|
| 12:  2.1676 -  2.1058  1230   139  0.49  53.37   0.78     0.58      33016.51|
| 13:  2.1058 -  2.0505  1262   137  0.49  53.37   0.76     0.56      28615.73|
| 14:  2.0505 -  2.0006   991   112  0.54  49.21   0.73     0.57      21628.67|
|alpha:            min =        0.56 max =            0.82 mean =         0.65|
|beta:             min =    21628.67 max =        72158.96 mean =     47169.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.98 mean =        44.26|
|phase err.(test): min =        0.00 max =           89.88 mean =        44.44|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.859670              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.204   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561223              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.858   (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:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2607 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3882 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5024 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6546 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7682 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.073 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.652 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4338   r_free= 0.4080   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.225282                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4175   r_free= 0.3925   ksol= 0.33   Bsol= 20.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.06,8.36,9.71,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.212340                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.338312              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.070   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.526618              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.018   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4175      final r-factor (work) = 0.3007          |
| start r-factor (free) = 0.3925      final r-factor (free) = 0.3187          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.8279 = 6.34 * 0.50 * 6.2336 + 1.00 * 54.0728                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2223 = 6.34 * 0.50 * 6.0292 + 1.00 * 0.1149                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3007      final r-factor (work) = 0.2342          |
| start r-factor (free) = 0.3187      final r-factor (free) = 0.2647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1898 = 0.53 * 1.00 * 6.0292 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0775 = 0.53 * 1.00 * 5.8231 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.04   10.40    None  None   None       |
|    all(noH): 2823   0      0.00    67.04   10.40    None  None   None       |
|    Sol.    : 438    0      0.00    67.04   27.40    None  None   None       |
|    Mac.    : 2385   0      0.00    55.96   7.28     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 -   6.704: 1457   |   5:    33.518 -  40.221:   85        |
|      1:     6.704 -  13.407:  689   |   6:    40.221 -  46.925:   65        |
|      2:    13.407 -  20.111:  246   |   7:    46.925 -  53.628:   18        |
|      3:    20.111 -  26.814:  139   |   8:    53.628 -  60.332:    6        |
|      4:    26.814 -  33.518:  117   |   9:    60.332 -  67.036:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2342 r_free = 0.2647             target_work(ml) = 5.742         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2334 r_free = 0.2652             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2334   r_free= 0.2652   ksol= 0.33   Bsol= 20.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.06,8.36,9.71,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.740818                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2275   r_free= 0.2603   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,4.69,6.01,0.00,0.00,0.00); trace/3= 4.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.738376                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.690747              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.172   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.280796              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.571  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2275      final r-factor (work) = 0.1572          |
| start r-factor (free) = 0.2603      final r-factor (free) = 0.1913          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9709 = 2.69 * 0.50 * 5.8393 + 1.00 * 0.1148                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5414 = 2.69 * 0.50 * 5.5592 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1572      final r-factor (work) = 0.1440          |
| start r-factor (free) = 0.1913      final r-factor (free) = 0.1796          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5720 = 0.28 * 1.00 * 5.5592 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5549 = 0.28 * 1.00 * 5.3604 + 1.00 * 0.0497                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.30   10.87    None  None   None       |
|    all(noH): 2823   0      0.00    65.30   10.87    None  None   None       |
|    Sol.    : 438    0      0.61    65.30   31.47    None  None   None       |
|    Mac.    : 2385   0      0.00    61.83   7.08     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 -   6.531: 1497   |   5:    32.653 -  39.183:   92        |
|      1:     6.531 -  13.061:  667   |   6:    39.183 -  45.713:   97        |
|      2:    13.061 -  19.592:  179   |   7:    45.713 -  52.244:   61        |
|      3:    19.592 -  26.122:  103   |   8:    52.244 -  58.774:   15        |
|      4:    26.122 -  32.653:  108   |   9:    58.774 -  65.305:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1440 r_free = 0.1796             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1438 r_free = 0.1797             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1438   r_free= 0.1797   ksol= 0.33   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,4.69,6.01,0.00,0.00,0.00); trace/3= 4.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.332969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1437   r_free= 0.1804   ksol= 0.33   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.84,4.96,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.334778                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.700110              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.652  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.087090              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.620   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3036 = 2.70 * 0.50 * 5.3638 + 1.00 * 0.0622                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1627 = 2.70 * 0.50 * 5.2539 + 1.00 * 0.0697                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7259 = 1.09 * 1.00 * 5.2539 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6377 = 1.09 * 1.00 * 5.1736 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.28   11.39    None  None   None       |
|    all(noH): 2823   0      0.00    72.28   11.39    None  None   None       |
|    Sol.    : 438    0      0.00    67.03   34.26    None  None   None       |
|    Mac.    : 2385   0      0.00    72.28   7.18     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 -   7.228: 1637   |   5:    36.138 -  43.366:   82        |
|      1:     7.228 -  14.455:  554   |   6:    43.366 -  50.593:   90        |
|      2:    14.455 -  21.683:  177   |   7:    50.593 -  57.821:   55        |
|      3:    21.683 -  28.911:  100   |   8:    57.821 -  65.049:   21        |
|      4:    28.911 -  36.138:  101   |   9:    65.049 -  72.276:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1590             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1162 r_free = 0.1590             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1590   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.84,4.96,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170670                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1590   ksol= 0.33   Bsol= 52.24   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.72,4.84,0.00,0.00,0.00); trace/3= 3.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170435                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.413401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.658  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259740              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.605  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7256 = 1.41 * 0.50 * 5.1732 + 1.00 * 0.0697                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7123 = 1.41 * 0.50 * 5.1766 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3580 = 0.26 * 1.00 * 5.1766 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3580 = 0.26 * 1.00 * 5.1836 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.53   11.21    None  None   None       |
|    all(noH): 2823   0      0.00    72.53   11.21    None  None   None       |
|    Sol.    : 438    0      0.70    66.50   33.59    None  None   None       |
|    Mac.    : 2385   0      0.00    72.53   7.10     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 -   7.253: 1665   |   5:    36.266 -  43.520:   82        |
|      1:     7.253 -  14.507:  544   |   6:    43.520 -  50.773:   84        |
|      2:    14.507 -  21.760:  170   |   7:    50.773 -  58.026:   47        |
|      3:    21.760 -  29.013:  101   |   8:    58.026 -  65.279:   22        |
|      4:    29.013 -  36.266:  103   |   9:    65.279 -  72.532:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1590             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1590             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1590   ksol= 0.33   Bsol= 52.24   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.72,4.84,0.00,0.00,0.00); trace/3= 3.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.178964                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1587   ksol= 0.33   Bsol= 52.24   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.72,4.84,0.00,0.00,0.00); trace/3= 3.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179336                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.518458              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.153  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.760165              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.871  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9899 = 1.52 * 0.50 * 5.1837 + 1.00 * 0.0543                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9815 = 1.52 * 0.50 * 5.1673 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.7764 = 5.76 * 1.00 * 5.1673 + 1.00 * 0.0116                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.7121 = 5.76 * 1.00 * 5.1556 + 1.00 * 0.0151                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.84   11.52    None  None   None       |
|    all(noH): 2823   0      0.00    83.84   11.52    None  None   None       |
|    Sol.    : 438    0      0.13    78.35   34.94    None  None   None       |
|    Mac.    : 2385   0      0.00    83.84   7.22     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 -   8.384: 1777   |   5:    41.918 -  50.302:   88        |
|      1:     8.384 -  16.767:  484   |   6:    50.302 -  58.685:   64        |
|      2:    16.767 -  25.151:  152   |   7:    58.685 -  67.069:   24        |
|      3:    25.151 -  33.535:  105   |   8:    67.069 -  75.453:   14        |
|      4:    33.535 -  41.918:  111   |   9:    75.453 -  83.836:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1141 r_free = 0.1583             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1583             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1583   ksol= 0.33   Bsol= 52.24   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.72,4.84,0.00,0.00,0.00); trace/3= 3.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.163326                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7734 0.99   1380  153 0.1019 0.1275      5.4039      5.5137|
|  2:  4.7734 -  3.8091 0.99   1311  149 0.0858 0.1074      5.4386      5.6263|
|  3:  3.8091 -  3.3336 0.99   1306  145 0.1061 0.1465      5.4773      5.8323|
|  4:  3.3336 -  3.0315 0.99   1289  136 0.1205 0.1541      5.4506      5.5905|
|  5:  3.0315 -  2.8158 0.99   1268  144 0.1349 0.1710      5.3495      5.5476|
|  6:  2.8158 -  2.6507 0.99   1276  145 0.1222 0.1942      5.2289      5.5126|
|  7:  2.6507 -  2.5186 0.99   1281  142 0.1302 0.1702      5.1957      5.3673|
|  8:  2.5186 -  2.4094 0.98   1261  136 0.1218 0.1734      5.1173      5.3964|
|  9:  2.4094 -  2.3170 0.98   1252  143 0.1217 0.1936      5.0711      5.3512|
| 10:  2.3170 -  2.2373 0.99   1262  136 0.1162 0.1697      4.9999      5.2268|
| 11:  2.2373 -  2.1676 0.98   1261  142 0.1175 0.1710      4.9669       5.233|
| 12:  2.1676 -  2.1058 0.97   1230  139 0.1178 0.1696      4.9085      5.2346|
| 13:  2.1058 -  2.0505 1.00   1262  137 0.1157 0.1759      4.8223      5.0752|
| 14:  2.0505 -  2.0006 0.78    991  112 0.1074 0.1835      4.6956      4.9927|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7734  1380   153  0.94   9.38   0.97     0.95       7449.18|
|  2:  4.7734 -  3.8091  1311   149  0.95   7.75   1.01     0.99       8787.87|
|  3:  3.8091 -  3.3336  1306   145  0.94  10.88   1.02     1.02      10108.66|
|  4:  3.3336 -  3.0315  1289   136  0.92  13.12   1.00     0.99       9975.00|
|  5:  3.0315 -  2.8158  1268   144  0.90  15.91   1.00     0.97       8538.34|
|  6:  2.8158 -  2.6507  1276   145  0.90  16.10   0.98     0.95       7352.61|
|  7:  2.6507 -  2.5186  1281   142  0.90  16.02   0.98     0.95       6523.09|
|  8:  2.5186 -  2.4094  1261   136  0.91  15.44   0.99     0.96       5718.65|
|  9:  2.4094 -  2.3170  1252   143  0.90  16.10   1.00     0.97       5475.61|
| 10:  2.3170 -  2.2373  1262   136  0.89  16.38   0.99     0.94       4676.03|
| 11:  2.2373 -  2.1676  1261   142  0.90  16.23   0.99     0.95       4597.78|
| 12:  2.1676 -  2.1058  1230   139  0.91  15.87   1.01     0.99       4136.66|
| 13:  2.1058 -  2.0505  1262   137  0.90  15.98   0.99     0.96       3506.99|
| 14:  2.0505 -  2.0006   991   112  0.91  14.87   0.97     0.93       2657.38|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2657.38 max =        10108.66 mean =      6485.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.22|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.76|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1583   ksol= 0.32   Bsol= 55.93   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.21,0.94,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.163225                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1583   ksol= 0.32   Bsol= 55.93   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.21,0.94,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.163225                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7734 0.99   1380  153 0.1018 0.1275      5.4028      5.5131|
|  2:  4.7734 -  3.8091 0.99   1311  149 0.0859 0.1074       5.439      5.6269|
|  3:  3.8091 -  3.3336 0.99   1306  145 0.1061 0.1466      5.4777      5.8326|
|  4:  3.3336 -  3.0315 0.99   1289  136 0.1205 0.1540      5.4506      5.5905|
|  5:  3.0315 -  2.8158 0.99   1268  144 0.1349 0.1710      5.3493      5.5473|
|  6:  2.8158 -  2.6507 0.99   1276  145 0.1222 0.1942      5.2287      5.5123|
|  7:  2.6507 -  2.5186 0.99   1281  142 0.1302 0.1703      5.1957      5.3675|
|  8:  2.5186 -  2.4094 0.98   1261  136 0.1219 0.1734      5.1174      5.3964|
|  9:  2.4094 -  2.3170 0.98   1252  143 0.1216 0.1936      5.0711      5.3511|
| 10:  2.3170 -  2.2373 0.99   1262  136 0.1162 0.1697      4.9998       5.227|
| 11:  2.2373 -  2.1676 0.98   1261  142 0.1174 0.1709      4.9668      5.2327|
| 12:  2.1676 -  2.1058 0.97   1230  139 0.1178 0.1695      4.9084      5.2343|
| 13:  2.1058 -  2.0505 1.00   1262  137 0.1157 0.1758      4.8221      5.0752|
| 14:  2.0505 -  2.0006 0.78    991  112 0.1074 0.1833      4.6954      4.9922|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7734  1380   153  0.94   9.37   0.97     0.95       7433.01|
|  2:  4.7734 -  3.8091  1311   149  0.95   7.75   1.01     0.99       8788.64|
|  3:  3.8091 -  3.3336  1306   145  0.94  10.88   1.02     1.02      10119.13|
|  4:  3.3336 -  3.0315  1289   136  0.92  13.12   1.00     0.99       9974.32|
|  5:  3.0315 -  2.8158  1268   144  0.90  15.91   1.00     0.97       8534.02|
|  6:  2.8158 -  2.6507  1276   145  0.90  16.10   0.98     0.96       7349.66|
|  7:  2.6507 -  2.5186  1281   142  0.90  16.02   0.98     0.95       6523.30|
|  8:  2.5186 -  2.4094  1261   136  0.91  15.45   0.99     0.97       5718.85|
|  9:  2.4094 -  2.3170  1252   143  0.90  16.11   1.00     0.97       5477.22|
| 10:  2.3170 -  2.2373  1262   136  0.89  16.38   0.99     0.95       4674.68|
| 11:  2.2373 -  2.1676  1261   142  0.90  16.22   0.99     0.96       4597.05|
| 12:  2.1676 -  2.1058  1230   139  0.91  15.86   1.01     0.99       4135.31|
| 13:  2.1058 -  2.0505  1262   137  0.90  15.97   0.99     0.97       3505.08|
| 14:  2.0505 -  2.0006   991   112  0.91  14.86   0.97     0.93       2654.79|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2654.79 max =        10119.13 mean =      6484.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.22|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.76|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.95    87.79   15.48    None  None   None       |
|    all(noH): 2823   0      3.95    87.79   15.48    None  None   None       |
|    Sol.    : 438    0      4.09    82.31   38.90    None  None   None       |
|    Mac.    : 2385   0      3.95    87.79   11.18    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:     3.955 -  12.338: 1777   |   5:    45.873 -  54.256:   88        |
|      1:    12.338 -  20.722:  484   |   6:    54.256 -  62.640:   64        |
|      2:    20.722 -  29.105:  152   |   7:    62.640 -  71.024:   24        |
|      3:    29.105 -  37.489:  105   |   8:    71.024 -  79.407:   14        |
|      4:    37.489 -  45.873:  111   |   9:    79.407 -  87.791:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.230 - 4.603
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 316
   mapped sites are within: 0.703 - 4.603

peak=   10.813 closest distance to " CG2 VAL A 230 " =    1.429
peak=    7.545 closest distance to " CG2 VAL A 296 " =    1.163
peak=    6.369 closest distance to " CG  LEU A   5 " =    1.192
peak=    6.129 closest distance to " NH2 ARG A  56 " =    2.278
peak=    5.678 closest distance to " CG  LEU A 228 " =    1.173
peak=    5.617 closest distance to " CB  GLN A 223 " =    1.422
peak=    5.583 closest distance to " CG  PRO A  54 " =    1.343
peak=    5.417 closest distance to " CD2 LEU A   5 " =    1.139
peak=    5.073 closest distance to " CB  PRO A  54 " =    0.978
peak=    4.891 closest distance to " CB  ARG A 275 " =    0.930
peak=    4.873 closest distance to " CB  GLN A 183 " =    1.300
peak=    4.827 closest distance to " CG  PRO A 198 " =    1.218
peak=    4.800 closest distance to " NE2 GLN A  11 " =    1.078
peak=    4.770 closest distance to " O   HOH Z 142 " =    1.723
peak=    4.715 closest distance to " CB  VAL A 230 " =    1.171
peak=    4.693 closest distance to " O   HOH Z 232 " =    2.330
peak=    4.665 closest distance to " CG  PRO A 213 " =    1.208
peak=    4.613 closest distance to " CB  SER A  63 " =    1.250
peak=    4.577 closest distance to " CB  VAL A 296 " =    1.036
peak=    4.534 closest distance to " CZ  PHE A 218 " =    1.134
peak=    4.487 closest distance to " O   HOH Z 369 " =    2.258
peak=    4.484 closest distance to " O   HOH Z 126 " =    2.025
peak=    4.354 closest distance to " CG  PRO A 243 " =    1.119
peak=    4.349 closest distance to " O   HOH Z  78 " =    1.693
peak=    4.317 closest distance to " O   HOH Z 427 " =    3.044
peak=    4.297 closest distance to " O   HOH Z  43 " =    2.029
peak=    4.295 closest distance to " CA  TYR A  30 " =    0.936
peak=    4.291 closest distance to " O   HOH Z 265 " =    2.302
peak=    4.271 closest distance to " O   HOH Z 298 " =    1.859
peak=    4.268 closest distance to " O   HOH Z 209 " =    2.295
peak=    4.259 closest distance to " O   HOH Z  61 " =    1.730
peak=    4.253 closest distance to " O   HOH Z 189 " =    2.933
peak=    4.223 closest distance to " O   SER A  87 " =    2.301
peak=    4.220 closest distance to " CB  ARG A 190 " =    1.607
peak=    4.197 closest distance to " C   PRO A 198 " =    1.564
peak=    4.195 closest distance to " O   HOH Z 346 " =    1.601
peak=    4.188 closest distance to " CB  GLU A 128 " =    1.068
peak=    4.188 closest distance to " CB  ASN A 148 " =    1.356
peak=    4.182 closest distance to " CB  TRP A 266 " =    1.005
peak=    4.177 closest distance to " CB  ARG A  79 " =    1.465
peak=    4.151 closest distance to " O   HOH Z 402 " =    1.446
peak=    4.139 closest distance to " O   HOH Z 368 " =    2.265
peak=    4.127 closest distance to " O   HOH Z 248 " =    1.469
peak=    4.126 closest distance to " O   HOH Z 316 " =    3.124
peak=    4.086 closest distance to " CD2 LEU A 228 " =    1.141
peak=    4.067 closest distance to " O   HOH Z 272 " =    1.885
peak=    4.059 closest distance to " O   HOH Z 423 " =    1.787
peak=    4.058 closest distance to " O   HOH Z 234 " =    3.692
peak=    4.056 closest distance to " ND2 ASN A 187 " =    1.494
peak=    4.026 closest distance to " O   HOH Z 214 " =    2.245
peak=    4.005 closest distance to " O   HOH Z 280 " =    2.946
peak=    4.005 closest distance to " CB  VAL A 202 " =    1.574
peak=    4.000 closest distance to " O   HOH Z 236 " =    2.006
peak=    3.995 closest distance to " O   HOH Z 303 " =    2.060
peak=    3.989 closest distance to " O   HOH Z 411 " =    3.848
peak=    3.970 closest distance to " OD1 ASN A  69 " =    2.572
peak=    3.954 closest distance to " CA  ALA A  51 " =    0.937
peak=    3.945 closest distance to " O   HOH Z  63 " =    1.973
peak=    3.928 closest distance to " O   HOH Z  19 " =    2.221
peak=    3.920 closest distance to " O   HOH Z 261 " =    1.808
peak=    3.915 closest distance to " CB  ASN A 142 " =    1.214
peak=    3.910 closest distance to " CB  ASP A 140 " =    1.088
peak=    3.902 closest distance to " O   HOH Z 313 " =    1.767
peak=    3.898 closest distance to " CB  VAL A 265 " =    1.294
peak=    3.873 closest distance to " CA  ARG A 195 " =    1.192
peak=    3.862 closest distance to " CB  GLU A 277 " =    3.675
peak=    3.849 closest distance to " CG2 VAL A 257 " =    0.864
peak=    3.846 closest distance to " CB  GLU A 152 " =    1.173
peak=    3.836 closest distance to " O   HOH Z  15 " =    2.177
peak=    3.836 closest distance to " CA  ARG A  36 " =    1.058
peak=    3.832 closest distance to " CD  ARG A 269 " =    0.990
peak=    3.827 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.826 closest distance to " N   ASN A  39 " =    1.219
peak=    3.811 closest distance to " O   HOH Z 422 " =    2.644
peak=    3.808 closest distance to " O   HOH Z 158 " =    3.148
peak=    3.802 closest distance to " CD BLYS A 290 " =    0.970
peak=    3.794 closest distance to " CD  LYS A 166 " =    1.320
peak=    3.789 closest distance to " CE  LYS A  76 " =    0.867
peak=    3.775 closest distance to " NH1AARG A 145 " =    1.197
peak=    3.771 closest distance to " O   HOH Z 193 " =    1.750
peak=    3.769 closest distance to " CB  SER A   3 " =    1.254
peak=    3.768 closest distance to " O   HOH Z  80 " =    1.736
peak=    3.767 closest distance to " O   HOH Z 203 " =    1.702
peak=    3.752 closest distance to " O   HOH Z  59 " =    2.183
peak=    3.749 closest distance to " O   HOH Z 403 " =    1.636
peak=    3.738 closest distance to " CB  TRP A 179 " =    1.451
peak=    3.732 closest distance to " CG1 VAL A 153 " =    0.959
peak=    3.725 closest distance to " O   HOH Z 285 " =    2.670
peak=    3.717 closest distance to " ND2 ASN A 249 " =    1.905
peak=    3.707 closest distance to " O   HOH Z  40 " =    1.724
peak=    3.694 closest distance to " CE1 TYR A 186 " =    1.332
peak=    3.691 closest distance to " NH2 ARG A 156 " =    1.075
peak=    3.688 closest distance to " CD2 TRP A 179 " =    1.345
peak=    3.683 closest distance to " CA  VAL A 125 " =    1.247
peak=    3.683 closest distance to " O   HOH Z  97 " =    2.025
peak=    3.676 closest distance to " CA  VAL A  41 " =    0.792
peak=    3.675 closest distance to " CG1BVAL A  72 " =    1.780
peak=    3.674 closest distance to " CA  TYR A  30 " =    1.071
peak=    3.671 closest distance to " O   HOH Z 251 " =    1.501
peak=    3.664 closest distance to " CD2 LEU A   5 " =    0.703
peak=    3.662 closest distance to " CB  ALA A   9 " =    1.593
peak=    3.660 closest distance to " CA  ASN A 215 " =    1.148
peak=    3.655 closest distance to " CG1 ILE A  49 " =    1.544
peak=    3.650 closest distance to " CG  MET A 185 " =    1.236
peak=    3.636 closest distance to " CG  ARG A  66 " =    2.550
peak=    3.633 closest distance to " CB BVAL A  41 " =    1.179
peak=    3.625 closest distance to " O   HOH Z 250 " =    1.324
peak=    3.624 closest distance to " O   HOH Z 261 " =    1.741
peak=    3.622 closest distance to " O   HOH Z 353 " =    2.635
peak=    3.618 closest distance to " O   HOH Z  68 " =    2.237
peak=    3.617 closest distance to " CA  PHE A 283 " =    1.231
peak=    3.613 closest distance to " O   HOH Z 365 " =    2.907
peak=    3.590 closest distance to " CB  THR A  31 " =    1.576
peak=    3.579 closest distance to " CD  ARG A 159 " =    0.740
peak=    3.579 closest distance to " O   HOH Z 147 " =    1.752
peak=    3.578 closest distance to " CB  GLU A  46 " =    0.960
peak=    3.575 closest distance to " O   HOH Z  97 " =    2.417
peak=    3.572 closest distance to " O   HOH Z 102 " =    1.280
peak=    3.562 closest distance to " O   HOH Z 425 " =    1.319
peak=    3.560 closest distance to " OG BSER A 164 " =    2.274
peak=    3.560 closest distance to " O   HOH Z 371 " =    3.021
peak=    3.553 closest distance to " CB  ALA A 291 " =    1.327
peak=    3.553 closest distance to " NE2 GLN A  77 " =    3.290
peak=    3.552 closest distance to " O   HOH Z 290 " =    1.057
peak=    3.549 closest distance to " CA  ALA A 291 " =    0.840
peak=    3.549 closest distance to " CB  ARG A  79 " =    0.914
peak=    3.546 closest distance to " CA  THR A 264 " =    0.712
peak=    3.543 closest distance to " CG  LEU A 167 " =    1.187
peak=    3.540 closest distance to " CB  GLN A  89 " =    1.232
peak=    3.525 closest distance to " CD1 LEU A 300 " =    1.278
peak=    3.525 closest distance to " O   HOH Z 180 " =    2.188
peak=    3.522 closest distance to " O   HOH Z 273 " =    2.857
peak=    3.521 closest distance to " NZ  LYS A 117 " =    3.145
peak=    3.519 closest distance to " O   ASP A 124 " =    1.018
peak=    3.515 closest distance to " CA  ALA A  21 " =    1.118
peak=    3.503 closest distance to " CB  ALA A 248 " =    1.442
peak=    3.502 closest distance to " CA  LYS A 117 " =    1.244
peak=    3.498 closest distance to " O  BHOH Z 338 " =    2.424
peak=    3.496 closest distance to " CB  ALA A 104 " =    0.733
peak=    3.496 closest distance to " O   ASN A  74 " =    1.481
peak=    3.493 closest distance to " CZ  PHE A  38 " =    1.226
peak=    3.491 closest distance to " CH2 TRP A 266 " =    1.133
peak=    3.491 closest distance to " O   HOH Z 172 " =    3.673
peak=    3.474 closest distance to " CB  SER A  26 " =    1.827
peak=    3.460 closest distance to " O   HOH Z 126 " =    1.595
peak=    3.457 closest distance to " CG1 VAL A 296 " =    1.155
peak=    3.456 closest distance to " O   HOH Z  48 " =    1.609
peak=    3.455 closest distance to " O   HOH Z 247 " =    1.385
peak=    3.453 closest distance to " CB  ASN A 110 " =    1.190
peak=    3.448 closest distance to " O   HOH Z 368 " =    3.560
peak=    3.447 closest distance to " O   HOH Z 325 " =    2.174
peak=    3.446 closest distance to " CB  LYS A 117 " =    1.225
peak=    3.446 closest distance to " O   HOH Z 437 " =    1.724
peak=    3.444 closest distance to " CA  LEU A 282 " =    1.084
peak=    3.443 closest distance to " CG  MET A 185 " =    1.049
peak=    3.437 closest distance to " OE1 GLN A  55 " =    1.451
peak=    3.435 closest distance to " O   HOH Z 305 " =    3.696
peak=    3.428 closest distance to " CA  ALA A 158 " =    1.254
peak=    3.427 closest distance to " O   MET A 105 " =    1.876
peak=    3.423 closest distance to " CB  SER A 273 " =    0.873
peak=    3.420 closest distance to " O   HOH Z  21 " =    1.757
peak=    3.417 closest distance to " O   HOH Z 417 " =    2.573
peak=    3.414 closest distance to " CA  ASN A 127 " =    1.052
peak=    3.407 closest distance to " CB  MET A  47 " =    0.982
peak=    3.407 closest distance to " N   ASP A 162 " =    1.278
peak=    3.406 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.405 closest distance to " O   HOH Z 166 " =    3.835
peak=    3.404 closest distance to " CD2 LEU A 297 " =    0.952
peak=    3.403 closest distance to " CB  SER A 212 " =    1.166
peak=    3.395 closest distance to " O   HOH Z 145 " =    2.259
peak=    3.393 closest distance to " O   HOH Z 112 " =    1.663
peak=    3.389 closest distance to " CG2 THR A 221 " =    1.155
peak=    3.386 closest distance to " CA  GLY A 211 " =    1.342
peak=    3.386 closest distance to " O   GLN A 278 " =    1.331
peak=    3.386 closest distance to " O   HOH Z 128 " =    2.096
peak=    3.384 closest distance to " CB  THR A  52 " =    0.833
peak=    3.384 closest distance to " O   HOH Z 299 " =    4.316
peak=    3.384 closest distance to " CB  ARG A 139 " =    0.855
peak=    3.381 closest distance to " O   ALA A 165 " =    1.493
peak=    3.379 closest distance to " CB  THR A 157 " =    1.157
peak=    3.372 closest distance to " CG1 ILE A  33 " =    1.268
peak=    3.370 closest distance to " O   LYS A 290 " =    2.411
peak=    3.368 closest distance to " O   HOH Z 197 " =    3.093
peak=    3.368 closest distance to " O   HOH Z 407 " =    2.486
peak=    3.366 closest distance to " O   HOH Z 344 " =    2.995
peak=    3.362 closest distance to " CB  TRP A 150 " =    1.398
peak=    3.362 closest distance to " O   TRP A 274 " =    1.829
peak=    3.357 closest distance to " O   HOH Z 193 " =    2.044
peak=    3.352 closest distance to " N   PHE A 130 " =    1.259
peak=    3.352 closest distance to " N   VAL A 126 " =    1.465
peak=    3.349 closest distance to " O   HOH Z  88 " =    3.088
peak=    3.346 closest distance to " CB  LEU A 143 " =    1.234
peak=    3.339 closest distance to " CD1 ILE A  33 " =    1.701
peak=    3.335 closest distance to " ND2 ASN A 249 " =    0.857
peak=    3.333 closest distance to " CA  ASP A 191 " =    1.132
peak=    3.330 closest distance to " CB  GLN A 205 " =    1.038
peak=    3.328 closest distance to " O   HOH Z 359 " =    1.350
peak=    3.325 closest distance to " CB  LEU A 228 " =    1.256
peak=    3.322 closest distance to " O   HOH Z 258 " =    2.092
peak=    3.321 closest distance to " CE1 HIS A 108 " =    1.167
peak=    3.320 closest distance to " O   HOH Z 329 " =    4.063
peak=    3.318 closest distance to " CA  THR A 221 " =    0.921
peak=    3.316 closest distance to " O   HOH Z 435 " =    2.012
peak=    3.315 closest distance to " O   HOH Z 294 " =    1.601
peak=    3.313 closest distance to " O   HOH Z 148 " =    3.351
peak=    3.310 closest distance to " CB  HIS A 108 " =    0.800
peak=    3.307 closest distance to " N   GLY A 133 " =    3.710
peak=    3.305 closest distance to " N   SER A 135 " =    1.426
peak=    3.305 closest distance to " NE2 HIS A 207 " =    1.263
peak=    3.303 closest distance to " CB  MET A  40 " =    0.798
peak=    3.303 closest distance to " CG2 ILE A  20 " =    1.418
peak=    3.302 closest distance to " CA  TYR A 116 " =    1.471
peak=    3.300 closest distance to " CZ  PHE A 192 " =    0.986
peak=    3.297 closest distance to " N   ALA A 256 " =    1.075
peak=    3.296 closest distance to " O   HOH Z   4 " =    1.667
peak=    3.295 closest distance to " O   HOH Z 187 " =    2.323
peak=    3.286 closest distance to " CG  GLU A  37 " =    0.853
peak=    3.283 closest distance to " CA  MET A 105 " =    1.025
peak=    3.280 closest distance to " O   HOH Z 406 " =    1.477
peak=    3.279 closest distance to " O   HOH Z 383 " =    2.012
peak=    3.279 closest distance to " CZ3 TRP A  85 " =    0.929
peak=    3.267 closest distance to " O   ARG A  56 " =    2.908
peak=    3.261 closest distance to " NZ  LYS A  48 " =    1.302
peak=    3.261 closest distance to " CG AARG A 275 " =    1.087
peak=    3.259 closest distance to " CG  GLN A  88 " =    1.020
peak=    3.257 closest distance to " CA  ILE A 106 " =    0.737
peak=    3.253 closest distance to " CA  ALA A 295 " =    1.154
peak=    3.252 closest distance to " CB  PRO A 243 " =    1.473
peak=    3.251 closest distance to " O   HOH Z 193 " =    1.657
peak=    3.249 closest distance to " O   HOH Z 421 " =    1.915
peak=    3.247 closest distance to " CA  SER A  87 " =    1.066
peak=    3.244 closest distance to " O   HOH Z 263 " =    1.667
peak=    3.242 closest distance to " O   HOH Z 327 " =    1.813
peak=    3.240 closest distance to " CD1 ILE A 199 " =    0.804
peak=    3.240 closest distance to " O   HOH Z 171 " =    3.858
peak=    3.239 closest distance to " O   HOH Z 171 " =    2.317
peak=    3.236 closest distance to " CB  ASN A 215 " =    1.132
peak=    3.234 closest distance to " O   HOH Z 380 " =    1.894
peak=    3.230 closest distance to " CA  ALA A 154 " =    0.977
peak=    3.228 closest distance to " CA  ALA A 160 " =    0.872
peak=    3.226 closest distance to " N   ARG A 156 " =    1.432
peak=    3.222 closest distance to " CD  LYS A  76 " =    1.991
peak=    3.219 closest distance to " O   SER A 164 " =    1.261
peak=    3.217 closest distance to " O   HOH Z 216 " =    3.081
peak=    3.215 closest distance to " O   HOH Z 245 " =    1.320
peak=    3.209 closest distance to " CB  VAL A 268 " =    0.820
peak=    3.204 closest distance to " CG BARG A 102 " =    1.803
peak=    3.202 closest distance to " CG  GLN A 205 " =    0.911
peak=    3.201 closest distance to " OE1 GLU A   2 " =    2.013
peak=    3.196 closest distance to " O   HOH Z 133 " =    2.464
peak=    3.194 closest distance to " O   PRO A 213 " =    1.497
peak=    3.193 closest distance to " CA  ALA A 129 " =    1.470
peak=    3.189 closest distance to " CD  LYS A 119 " =    1.808
peak=    3.188 closest distance to " CA  ASP A 140 " =    1.256
peak=    3.188 closest distance to " ND1 HIS A  81 " =    1.680
peak=    3.186 closest distance to " OG  SER A  22 " =    2.760
peak=    3.184 closest distance to " CB  TYR A 247 " =    0.944
peak=    3.184 closest distance to " CA  SER A 146 " =    1.766
peak=    3.178 closest distance to " CG  LEU A 281 " =    1.057
peak=    3.177 closest distance to " O   HOH Z 361 " =    3.605
peak=    3.177 closest distance to " O   THR A 220 " =    1.252
peak=    3.175 closest distance to " O   HOH Z   1 " =    2.114
peak=    3.169 closest distance to " CG2 ILE A 120 " =    1.166
peak=    3.167 closest distance to " O   HOH Z 213 " =    1.956
peak=    3.165 closest distance to " O   GLN A  88 " =    1.664
peak=    3.164 closest distance to " CB  ALA A 242 " =    0.848
peak=    3.164 closest distance to " O   HOH Z 337 " =    3.566
peak=    3.163 closest distance to " O   HOH Z 426 " =    1.644
peak=    3.163 closest distance to " O   HOH Z 301 " =    1.889
peak=    3.157 closest distance to " O   HOH Z 291 " =    1.584
peak=    3.153 closest distance to " CD1 LEU A 228 " =    1.902
peak=    3.151 closest distance to " CE  LYS A  48 " =    1.122
peak=    3.149 closest distance to " O   HOH Z  90 " =    3.247
peak=    3.147 closest distance to " CA  ASP A 162 " =    1.091
peak=    3.146 closest distance to " O   HOH Z 350 " =    1.614
peak=    3.146 closest distance to " N   ASN A 127 " =    1.226
peak=    3.134 closest distance to " O   HOH Z 345 " =    3.303
peak=    3.134 closest distance to " CB  SER A 216 " =    0.848
peak=    3.132 closest distance to " O   HOH Z  10 " =    1.706
peak=    3.132 closest distance to " O   HOH Z 141 " =    1.586
peak=    3.129 closest distance to " OE2 GLU A  53 " =    1.934
peak=    3.124 closest distance to " CZ3 TRP A 274 " =    4.603
peak=    3.123 closest distance to " CA  LYS A 290 " =    1.095
peak=    3.111 closest distance to " CB  PHE A 204 " =    0.900
peak=    3.101 closest distance to " CA  ALA A 233 " =    1.493
peak=    3.100 closest distance to " O   HOH Z 124 " =    2.142
peak=    3.096 closest distance to " CB  GLN A 103 " =    0.985
peak=    3.094 closest distance to " CB  LEU A 300 " =    0.852
peak=    3.093 closest distance to " CA  ARG A 139 " =    1.077
peak=    3.090 closest distance to " O   ALA A 158 " =    1.333
peak=    3.084 closest distance to " CD  ARG A  66 " =    2.135
peak=    3.083 closest distance to " O   HOH Z 357 " =    1.988
peak=    3.082 closest distance to " CG2 ILE A 263 " =    0.892
peak=    3.081 closest distance to " CG2 ILE A 234 " =    0.832
peak=    3.079 closest distance to " O   HOH Z 116 " =    1.790
peak=    3.077 closest distance to " CB  ALA A  43 " =    0.822
peak=    3.067 closest distance to " CA  ARG A 102 " =    1.134
peak=    3.061 closest distance to " CD  ARG A  66 " =    2.596
peak=    3.056 closest distance to " C   ALA A 299 " =    0.945
peak=    3.036 closest distance to " O   HOH Z 260 " =    1.536
peak=    3.031 closest distance to " O   HOH Z 391 " =    2.892
peak=    3.030 closest distance to " CB  TYR A 116 " =    0.802

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.826 - 5.518
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 196
   mapped sites are within: 0.826 - 5.518

peak=   -4.700 closest distance to " CG2 VAL A 230 " =    0.826
peak=   -4.614 closest distance to " SG  CYS A 254 " =    3.390
peak=   -4.551 closest distance to " CD  GLN A  58 " =    1.063
peak=   -4.477 closest distance to " CD  ARG A 156 " =    2.036
peak=   -4.352 closest distance to " O   HOH Z 266 " =    5.388
peak=   -4.160 closest distance to " O   HOH Z 196 " =    2.197
peak=   -4.144 closest distance to " CB  PRO A 243 " =    2.682
peak=   -4.081 closest distance to " CG1 VAL A 112 " =    2.655
peak=   -4.073 closest distance to " C   HIS A 108 " =    1.135
peak=   -4.062 closest distance to " CB  PHE A 192 " =    1.961
peak=   -4.061 closest distance to " O   HOH Z 231 " =    2.114
peak=   -4.040 closest distance to " OG BSER A 134 " =    1.213
peak=   -4.025 closest distance to " O   ILE A 109 " =    2.615
peak=   -4.001 closest distance to " CG1 VAL A 112 " =    2.815
peak=   -3.975 closest distance to " CG1 VAL A 250 " =    2.741
peak=   -3.974 closest distance to " O   HOH Z 166 " =    1.928
peak=   -3.947 closest distance to " CA  ASP A 298 " =    1.043
peak=   -3.927 closest distance to " O   HOH Z 114 " =    3.027
peak=   -3.926 closest distance to " CG  GLN A 223 " =    2.209
peak=   -3.920 closest distance to " CA  VAL A  67 " =    2.883
peak=   -3.869 closest distance to " OXT GLY A 302 " =    2.872
peak=   -3.867 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -3.836 closest distance to " O   VAL A  67 " =    2.694
peak=   -3.825 closest distance to " OG  SER A  97 " =    2.288
peak=   -3.824 closest distance to " CE3 TRP A 150 " =    2.236
peak=   -3.794 closest distance to " O   PRO A 163 " =    2.156
peak=   -3.786 closest distance to " O   HOH Z 102 " =    1.712
peak=   -3.765 closest distance to " ND2 ASN A  45 " =    1.110
peak=   -3.741 closest distance to " CZ3 TRP A 179 " =    1.226
peak=   -3.739 closest distance to " N   ALA A 226 " =    2.095
peak=   -3.710 closest distance to " CG2 ILE A  49 " =    2.806
peak=   -3.706 closest distance to " O   HOH Z 351 " =    1.538
peak=   -3.690 closest distance to " ND2 ASN A 187 " =    1.617
peak=   -3.688 closest distance to " CE  MET A 105 " =    2.341
peak=   -3.662 closest distance to " CG  ASP A 231 " =    0.831
peak=   -3.644 closest distance to " NE2 GLN A  88 " =    1.993
peak=   -3.640 closest distance to " CB  ALA A 248 " =    2.328
peak=   -3.638 closest distance to " O   HOH Z 435 " =    2.755
peak=   -3.627 closest distance to " OD1 ASN A 148 " =    1.417
peak=   -3.615 closest distance to " O   HOH Z  37 " =    1.808
peak=   -3.611 closest distance to " CG2 VAL A 296 " =    1.427
peak=   -3.602 closest distance to " O   HOH Z 394 " =    1.558
peak=   -3.591 closest distance to " O   HOH Z 211 " =    1.525
peak=   -3.587 closest distance to " CA  GLY A 241 " =    3.126
peak=   -3.560 closest distance to " O   HOH Z 185 " =    2.383
peak=   -3.558 closest distance to " CG  ARG A 269 " =    2.514
peak=   -3.557 closest distance to " O   HOH Z  73 " =    2.203
peak=   -3.556 closest distance to " O   HOH Z  44 " =    2.209
peak=   -3.556 closest distance to " O   HOH Z 113 " =    2.386
peak=   -3.555 closest distance to " CD2 TYR A 293 " =    2.014
peak=   -3.551 closest distance to " O   SER A 271 " =    2.129
peak=   -3.549 closest distance to " O   HOH Z 377 " =    2.053
peak=   -3.541 closest distance to " O   HOH Z  60 " =    1.899
peak=   -3.534 closest distance to " SD BMET A  47 " =    1.050
peak=   -3.533 closest distance to " N   ALA A  43 " =    2.650
peak=   -3.527 closest distance to " ND2 ASN A  45 " =    1.695
peak=   -3.512 closest distance to " O   SER A 210 " =    1.915
peak=   -3.510 closest distance to " CG  GLU A 277 " =    1.134
peak=   -3.504 closest distance to " O   HOH Z  10 " =    1.496
peak=   -3.502 closest distance to " O   HOH Z 290 " =    1.205
peak=   -3.501 closest distance to " O   HOH Z  11 " =    1.869
peak=   -3.501 closest distance to " O   HOH Z 350 " =    1.886
peak=   -3.501 closest distance to " CD1 LEU A 101 " =    2.406
peak=   -3.496 closest distance to " O   HOH Z  52 " =    1.633
peak=   -3.494 closest distance to " CB  ALA A 248 " =    2.151
peak=   -3.485 closest distance to " O   HOH Z  19 " =    2.326
peak=   -3.485 closest distance to " C   MET A 188 " =    1.424
peak=   -3.483 closest distance to " NH2AARG A 275 " =    5.129
peak=   -3.474 closest distance to " O   PRO A 198 " =    1.226
peak=   -3.463 closest distance to " CG  HIS A  86 " =    1.077
peak=   -3.459 closest distance to " CG2 ILE A 263 " =    2.391
peak=   -3.457 closest distance to " O   HOH Z 292 " =    4.602
peak=   -3.444 closest distance to " C   GLY A  17 " =    1.252
peak=   -3.441 closest distance to " CB  ASP A 171 " =    2.286
peak=   -3.441 closest distance to " N   ALA A 248 " =    1.736
peak=   -3.439 closest distance to " C   ALA A 158 " =    1.252
peak=   -3.435 closest distance to " O   HOH Z 165 " =    1.916
peak=   -3.433 closest distance to " NE2 GLN A 194 " =    1.821
peak=   -3.427 closest distance to " CA  GLY A 203 " =    2.473
peak=   -3.423 closest distance to " CG1 VAL A 296 " =    1.379
peak=   -3.415 closest distance to " CB  ASP A 132 " =    2.362
peak=   -3.411 closest distance to " CZ  TYR A 169 " =    1.754
peak=   -3.408 closest distance to " CG  TRP A 266 " =    1.824
peak=   -3.404 closest distance to " N   ASP A 171 " =    2.370
peak=   -3.403 closest distance to " N   THR A  52 " =    1.662
peak=   -3.396 closest distance to " O   HOH Z 426 " =    1.669
peak=   -3.395 closest distance to " CG2 VAL A 296 " =    0.908
peak=   -3.395 closest distance to " O   VAL A 189 " =    2.617
peak=   -3.393 closest distance to " O   HOH Z 198 " =    2.161
peak=   -3.392 closest distance to " CD2 LEU A 167 " =    1.780
peak=   -3.390 closest distance to " CB  ALA A  10 " =    2.255
peak=   -3.389 closest distance to " O   HOH Z 353 " =    2.131
peak=   -3.386 closest distance to " OD2 ASP A  50 " =    2.324
peak=   -3.381 closest distance to " CB  GLN A  11 " =    1.779
peak=   -3.376 closest distance to " O   HOH Z 389 " =    1.960
peak=   -3.367 closest distance to " O   HOH Z  13 " =    1.659
peak=   -3.358 closest distance to " CE BMET A  47 " =    1.620
peak=   -3.355 closest distance to " NH2 ARG A  79 " =    2.101
peak=   -3.354 closest distance to " CB  ALA A  43 " =    2.606
peak=   -3.351 closest distance to " N   ASN A  60 " =    1.311
peak=   -3.351 closest distance to " O   HOH Z 149 " =    2.133
peak=   -3.349 closest distance to " NE2 GLN A 278 " =    1.905
peak=   -3.347 closest distance to " CB  PRO A 163 " =    2.521
peak=   -3.342 closest distance to " N   THR A 157 " =    1.486
peak=   -3.342 closest distance to " CE2 PHE A  61 " =    2.606
peak=   -3.329 closest distance to " CD  GLN A 223 " =    1.666
peak=   -3.325 closest distance to " CB  ALA A 291 " =    2.224
peak=   -3.322 closest distance to " O   ALA A  10 " =    1.757
peak=   -3.321 closest distance to " O   HOH Z 193 " =    1.630
peak=   -3.319 closest distance to " CD2 LEU A 300 " =    2.662
peak=   -3.317 closest distance to " O   HOH Z 359 " =    3.064
peak=   -3.313 closest distance to " NE2 GLN A 103 " =    1.788
peak=   -3.310 closest distance to " OD1 ASN A 187 " =    1.620
peak=   -3.305 closest distance to " CG1 VAL A  67 " =    3.103
peak=   -3.300 closest distance to " NH2 ARG A  79 " =    1.529
peak=   -3.300 closest distance to " O   HOH Z 128 " =    2.651
peak=   -3.298 closest distance to " O   ARG A  24 " =    2.093
peak=   -3.295 closest distance to " C   LEU A 143 " =    1.040
peak=   -3.291 closest distance to " CD1 ILE A 239 " =    2.181
peak=   -3.289 closest distance to " O   HOH Z 191 " =    5.518
peak=   -3.286 closest distance to " OG  SER A  87 " =    1.476
peak=   -3.282 closest distance to " O   HOH Z 431 " =    1.877
peak=   -3.279 closest distance to " O   ILE A 234 " =    1.180
peak=   -3.277 closest distance to " CA  GLY A 241 " =    2.346
peak=   -3.271 closest distance to " O   HOH Z 216 " =    1.546
peak=   -3.270 closest distance to " CB  ASN A  39 " =    2.330
peak=   -3.263 closest distance to " CA  GLY A 133 " =    2.340
peak=   -3.262 closest distance to " O   HOH Z 252 " =    4.037
peak=   -3.260 closest distance to " CD1 PHE A  59 " =    2.001
peak=   -3.259 closest distance to " OG ASER A 134 " =    1.270
peak=   -3.251 closest distance to " O   HOH Z 222 " =    1.582
peak=   -3.251 closest distance to " CA  GLY A  98 " =    1.942
peak=   -3.246 closest distance to " CG  PHE A 283 " =    2.816
peak=   -3.246 closest distance to " O   HOH Z 123 " =    2.499
peak=   -3.243 closest distance to " O   HOH Z 139 " =    3.140
peak=   -3.237 closest distance to " CB  ALA A 291 " =    2.269
peak=   -3.237 closest distance to " O   HOH Z 295 " =    1.573
peak=   -3.226 closest distance to " O   HOH Z 311 " =    3.788
peak=   -3.221 closest distance to " C   ASN A 187 " =    1.845
peak=   -3.220 closest distance to " O   HOH Z  38 " =    1.613
peak=   -3.216 closest distance to " O   HOH Z 407 " =    3.046
peak=   -3.209 closest distance to " O   SER A  95 " =    1.796
peak=   -3.207 closest distance to " CG2BVAL A  41 " =    1.727
peak=   -3.206 closest distance to " O   HOH Z 423 " =    2.076
peak=   -3.205 closest distance to " CB  ASN A  69 " =    1.175
peak=   -3.198 closest distance to " O   HOH Z 133 " =    1.390
peak=   -3.192 closest distance to " CZ2 TRP A 274 " =    0.970
peak=   -3.191 closest distance to " O   HOH Z 313 " =    1.215
peak=   -3.190 closest distance to " CD1 LEU A 228 " =    2.272
peak=   -3.189 closest distance to " CD2 TYR A 247 " =    2.304
peak=   -3.189 closest distance to " O   HOH Z 166 " =    1.626
peak=   -3.188 closest distance to " O   HOH Z   6 " =    1.640
peak=   -3.185 closest distance to " O   LEU A 167 " =    1.470
peak=   -3.182 closest distance to " CE1 TYR A 247 " =    2.673
peak=   -3.179 closest distance to " O   PHE A 218 " =    1.614
peak=   -3.178 closest distance to " CD1 LEU A  25 " =    2.476
peak=   -3.178 closest distance to " O   SER A 276 " =    1.722
peak=   -3.171 closest distance to " O   MET A  40 " =    2.775
peak=   -3.169 closest distance to " O   HOH Z 313 " =    1.727
peak=   -3.167 closest distance to " ND2 ASN A 252 " =    1.902
peak=   -3.166 closest distance to " CD  PRO A 243 " =    2.092
peak=   -3.165 closest distance to " O   LYS A  76 " =    1.400
peak=   -3.160 closest distance to " O   HOH Z 106 " =    1.831
peak=   -3.160 closest distance to " O   HOH Z  43 " =    1.754
peak=   -3.156 closest distance to " CG1 VAL A 230 " =    1.925
peak=   -3.155 closest distance to " CA  TYR A  68 " =    2.951
peak=   -3.151 closest distance to " CG1 VAL A 112 " =    2.790
peak=   -3.147 closest distance to " CG2 VAL A 189 " =    2.046
peak=   -3.144 closest distance to " CD2 HIS A 207 " =    2.415
peak=   -3.142 closest distance to " CG1 VAL A 125 " =    1.940
peak=   -3.142 closest distance to " O   ASN A 252 " =    1.413
peak=   -3.139 closest distance to " N   SER A 276 " =    1.355
peak=   -3.138 closest distance to " CG  GLU A  53 " =    1.478
peak=   -3.136 closest distance to " CD  PRO A 213 " =    2.054
peak=   -3.134 closest distance to " N   LYS A 289 " =    1.600
peak=   -3.131 closest distance to " C   ASP A 270 " =    1.225
peak=   -3.130 closest distance to " O   HOH Z 238 " =    1.105
peak=   -3.120 closest distance to " C   LEU A 222 " =    0.923
peak=   -3.115 closest distance to " CD1 ILE A 151 " =    2.395
peak=   -3.115 closest distance to " CD2 PHE A 225 " =    1.032
peak=   -3.111 closest distance to " O   ALA A 227 " =    1.576
peak=   -3.109 closest distance to " CA  VAL A 197 " =    1.053
peak=   -3.104 closest distance to " O   HOH Z 357 " =    2.054
peak=   -3.101 closest distance to " O   ALA A  51 " =    1.403
peak=   -3.095 closest distance to " N   ALA A 248 " =    2.329
peak=   -3.093 closest distance to " CB  TRP A  85 " =    2.513
peak=   -3.088 closest distance to " O   HOH Z  90 " =    1.670
peak=   -3.084 closest distance to " O   HOH Z 326 " =    5.096
peak=   -3.084 closest distance to " OG  SER A 206 " =    1.724
peak=   -3.074 closest distance to " CG1 VAL A 197 " =    2.289
peak=   -3.071 closest distance to " OG BSER A 134 " =    1.870
peak=   -3.067 closest distance to " CD1 LEU A   5 " =    2.531
peak=   -3.048 closest distance to " O   HOH Z 193 " =    2.026
peak=   -3.048 closest distance to " O   PRO A 198 " =    1.359
peak=   -3.005 closest distance to " N   GLN A  58 " =    2.056

================= 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    :  0.4256 0.4094   6.215935e+00   6.182180e+00
   1_bss:  0.4175 0.3925   6.212340e+00   6.165082e+00
   1_xyz:  0.3007 0.3187   5.970032e+00   6.005903e+00
   1_adp:  0.2342 0.2647   5.742495e+00   5.849515e+00
   1_occ:  0.2334 0.2652   5.740818e+00   5.851417e+00
   2_bss:  0.2275 0.2603   5.738376e+00   5.845325e+00
   2_xyz:  0.1572 0.1913   5.406173e+00   5.573818e+00
   2_adp:  0.1440 0.1796   5.333568e+00   5.516704e+00
   2_occ:  0.1438 0.1797   5.332969e+00   5.516548e+00
   3_bss:  0.1437 0.1804   5.334778e+00   5.518137e+00
   3_xyz:  0.1208 0.1603   5.192441e+00   5.411166e+00
   3_adp:  0.1162 0.1590   5.170978e+00   5.403394e+00
   3_occ:  0.1162 0.1590   5.170670e+00   5.403172e+00
   4_bss:  0.1162 0.1590   5.170435e+00   5.403086e+00
   4_xyz:  0.1175 0.1600   5.181006e+00   5.410523e+00
   4_adp:  0.1180 0.1590   5.179033e+00   5.402710e+00
   4_occ:  0.1180 0.1590   5.178964e+00   5.402878e+00
   5_bss:  0.1182 0.1587   5.179336e+00   5.401356e+00
   5_xyz:  0.1153 0.1568   5.161435e+00   5.391587e+00
   5_adp:  0.1141 0.1583   5.163360e+00   5.402300e+00
   5_occ:  0.1141 0.1583   5.163326e+00   5.402439e+00
   5_bss:  0.1141 0.1583   5.163225e+00   5.402381e+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:  0.333  20.001   7.057   8.364   9.708   0.000   0.000   0.000
   1_xyz:  0.333  20.001   7.057   8.364   9.708   0.000   0.000   0.000
   1_adp:  0.333  20.001   7.057   8.364   9.708   0.000   0.000   0.000
   1_occ:  0.333  20.001   7.057   8.364   9.708   0.000   0.000   0.000
   2_bss:  0.328  50.001   3.626   4.691   6.011   0.000   0.000   0.000
   2_xyz:  0.328  50.001   3.626   4.691   6.011   0.000   0.000   0.000
   2_adp:  0.328  50.001   3.626   4.691   6.011   0.000   0.000   0.000
   2_occ:  0.328  50.001   3.626   4.691   6.011   0.000   0.000   0.000
   3_bss:  0.326  50.001   3.066   3.845   4.957   0.000   0.000   0.000
   3_xyz:  0.326  50.001   3.066   3.845   4.957   0.000   0.000   0.000
   3_adp:  0.326  50.001   3.066   3.845   4.957   0.000   0.000   0.000
   3_occ:  0.326  50.001   3.066   3.845   4.957   0.000   0.000   0.000
   4_bss:  0.327  52.238   3.124   3.717   4.839   0.000   0.000   0.000
   4_xyz:  0.327  52.238   3.124   3.717   4.839   0.000   0.000   0.000
   4_adp:  0.327  52.238   3.124   3.717   4.839   0.000   0.000   0.000
   4_occ:  0.327  52.238   3.124   3.717   4.839   0.000   0.000   0.000
   5_bss:  0.327  52.238   3.124   3.717   4.839   0.000   0.000   0.000
   5_xyz:  0.327  52.238   3.124   3.717   4.839   0.000   0.000   0.000
   5_adp:  0.327  52.238   3.124   3.717   4.839   0.000   0.000   0.000
   5_occ:  0.327  52.238   3.124   3.717   4.839   0.000   0.000   0.000
   5_bss:  0.324  55.931  -0.738  -0.206   0.944   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.280 0.5933  0.6525    47168.883
   1_bss:  43.159 0.6057  0.8573    44232.872
   1_xyz:  33.737 0.7151  0.9760    27181.413
   1_adp:  25.964 0.8022  1.0551    17564.377
   1_occ:  26.005 0.8018  1.0541    17631.477
   2_bss:  25.746 0.8044  0.9289    17310.936
   2_xyz:  18.270 0.8779  0.9875     9341.237
   2_adp:  16.772 0.8918  0.9979     8320.481
   2_occ:  16.779 0.8917  0.9977     8321.993
   3_bss:  16.792 0.8917  0.9680     8373.617
   3_xyz:  14.438 0.9115  0.9763     6636.014
   3_adp:  14.246 0.9133  0.9743     6519.640
   3_occ:  14.238 0.9133  0.9742     6518.508
   4_bss:  14.231 0.9134  0.9723     6518.899
   4_xyz:  14.294 0.9132  0.9715     6618.615
   4_adp:  14.113 0.9147  0.9713     6522.144
   4_occ:  14.116 0.9147  0.9713     6525.590
   5_bss:  14.119 0.9146  0.9706     6503.202
   5_xyz:  13.941 0.9159  0.9717     6364.407
   5_adp:  14.171 0.9141  0.9665     6482.136
   5_occ:  14.172 0.9141  0.9665     6484.973
   5_bss:  14.170 0.9141  0.9686     6483.584
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4073e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4073e+01
   1_xyz:   1.501  0.011  0.101 17.774  0.006  4.126   1.1491e-01
   1_adp:   1.501  0.011  0.101 17.774  0.006  4.126   1.1491e-01
   1_occ:   1.501  0.011  0.101 17.774  0.006  4.126   1.1491e-01
   2_bss:   1.501  0.011  0.101 17.774  0.006  4.126   1.1491e-01
   2_xyz:   0.992  0.007  0.074 16.109  0.004  4.126   6.2186e-02
   2_adp:   0.992  0.007  0.074 16.109  0.004  4.126   6.2186e-02
   2_occ:   0.992  0.007  0.074 16.109  0.004  4.126   6.2186e-02
   3_bss:   0.992  0.007  0.074 16.109  0.004  4.126   6.2186e-02
   3_xyz:   1.073  0.009  0.087 15.801  0.004  4.137   6.9714e-02
   3_adp:   1.073  0.009  0.087 15.801  0.004  4.137   6.9714e-02
   3_occ:   1.073  0.009  0.087 15.801  0.004  4.137   6.9714e-02
   4_bss:   1.073  0.009  0.087 15.801  0.004  4.137   6.9714e-02
   4_xyz:   0.920  0.006  0.075 15.302  0.003  4.138   5.3990e-02
   4_adp:   0.920  0.006  0.075 15.302  0.003  4.138   5.3990e-02
   4_occ:   0.920  0.006  0.075 15.302  0.003  4.138   5.3990e-02
   5_bss:   0.920  0.006  0.075 15.302  0.003  4.138   5.3990e-02
   5_xyz:   0.972  0.007  0.079 15.255  0.003  4.126   5.8319e-02
   5_adp:   0.972  0.007  0.079 15.255  0.003  4.126   5.8319e-02
   5_occ:   0.972  0.007  0.079 15.255  0.003  4.126   5.8319e-02
   5_bss:   0.972  0.007  0.079 15.255  0.003  4.126   5.8319e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0112e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0112e+00
   1_xyz:  12.488  0.131  0.400 89.291  0.035  2.250   8.6688e-02
   1_adp:  12.488  0.131  0.400 89.291  0.035  2.250   8.6688e-02
   1_occ:  12.488  0.131  0.400 89.291  0.035  2.250   8.6688e-02
   2_bss:  12.488  0.131  0.400 89.291  0.035  2.250   8.6688e-02
   2_xyz:   7.380  0.066  0.344 81.827  0.032  2.346   5.7639e-02
   2_adp:   7.380  0.066  0.344 81.827  0.032  2.346   5.7639e-02
   2_occ:   7.380  0.066  0.344 81.827  0.032  2.346   5.7639e-02
   3_bss:   7.380  0.066  0.344 81.827  0.032  2.346   5.7639e-02
   3_xyz:   7.194  0.046  0.633 84.110  0.043  2.337   5.8385e-02
   3_adp:   7.194  0.046  0.633 84.110  0.043  2.337   5.8385e-02
   3_occ:   7.194  0.046  0.633 84.110  0.043  2.337   5.8385e-02
   4_bss:   7.194  0.046  0.633 84.110  0.043  2.337   5.8385e-02
   4_xyz:   6.897  0.041  0.460 82.031  0.038  2.414   3.3358e-02
   4_adp:   6.897  0.041  0.460 82.031  0.038  2.414   3.3358e-02
   4_occ:   6.897  0.041  0.460 82.031  0.038  2.414   3.3358e-02
   5_bss:   6.897  0.041  0.460 82.031  0.038  2.414   3.3358e-02
   5_xyz:   6.709  0.044  0.497 82.585  0.039  2.394   3.3936e-02
   5_adp:   6.709  0.044  0.497 82.585  0.039  2.394   3.3936e-02
   5_occ:   6.709  0.044  0.497 82.585  0.039  2.394   3.3936e-02
   5_bss:   6.709  0.044  0.497 82.585  0.039  2.394   3.3936e-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:  67.04   0.00  10.40  55.96   0.00   7.28  67.04   0.00  27.40
   1_occ:  67.04   0.00  10.40  55.96   0.00   7.28  67.04   0.00  27.40
   2_bss:  67.04   0.00  10.40  55.96   0.00   7.28  67.04   0.00  27.40
   2_xyz:  67.04   0.00  10.40  55.96   0.00   7.28  67.04   0.00  27.40
   2_adp:  65.30   0.00  10.87  61.83   0.00   7.08  65.30   0.61  31.47
   2_occ:  65.30   0.00  10.87  61.83   0.00   7.08  65.30   0.61  31.47
   3_bss:  65.30   0.00  10.87  61.83   0.00   7.08  65.30   0.61  31.47
   3_xyz:  65.30   0.00  10.87  61.83   0.00   7.08  65.30   0.61  31.47
   3_adp:  72.28   0.00  11.39  72.28   0.00   7.18  67.03   0.00  34.26
   3_occ:  72.28   0.00  11.39  72.28   0.00   7.18  67.03   0.00  34.26
   4_bss:  72.28   0.00  11.39  72.28   0.00   7.18  67.03   0.00  34.26
   4_xyz:  72.28   0.00  11.39  72.28   0.00   7.18  67.03   0.00  34.26
   4_adp:  72.53   0.00  11.21  72.53   0.00   7.10  66.50   0.70  33.59
   4_occ:  72.53   0.00  11.21  72.53   0.00   7.10  66.50   0.70  33.59
   5_bss:  72.53   0.00  11.21  72.53   0.00   7.10  66.50   0.70  33.59
   5_xyz:  72.53   0.00  11.21  72.53   0.00   7.10  66.50   0.70  33.59
   5_adp:  83.84   0.00  11.52  83.84   0.00   7.22  78.35   0.13  34.94
   5_occ:  83.84   0.00  11.52  83.84   0.00   7.22  78.35   0.13  34.94
   5_bss:  87.79   3.95  15.48  87.79   3.95  11.18  82.31   4.09  38.90
------------------------------------------------------------------------
 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:    1.202    0.011    0.401
   1_adp:    1.202    0.011    0.401
   1_occ:    1.202    0.011    0.401
   2_bss:    1.202    0.011    0.401
   2_xyz:    1.541    0.035    0.487
   2_adp:    1.541    0.035    0.487
   2_occ:    1.541    0.035    0.487
   3_bss:    1.541    0.035    0.487
   3_xyz:    1.486    0.018    0.518
   3_adp:    1.486    0.018    0.518
   3_occ:    1.486    0.018    0.518
   4_bss:    1.486    0.018    0.518
   4_xyz:    1.651    0.011    0.527
   4_adp:    1.651    0.011    0.527
   4_occ:    1.651    0.011    0.527
   5_bss:    1.651    0.011    0.527
   5_xyz:    1.668    0.015    0.535
   5_adp:    1.668    0.015    0.535
   5_occ:    1.668    0.015    0.535
   5_bss:    1.668    0.015    0.535
------------------------------------------------------------------------

CPU time actual refinement: 334.57


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_678/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_678/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_678/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_678/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_678/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.41 
  Macro-tasks:
    bulk solvent and scale       = 40.57  
    individual site refinement   = 138.93 
    weights calculation          = 32.41  
    collect and process          = 6.54   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 218.55 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 102.38 
    alpha_beta                      = 7.86   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.46 
    fmodel                         = 7.71   
    r_factors                      = 0.17   
    phase_errors                   = 11.14  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 246.92 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.624 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    677 calls, 102.08 s
gradients_fft:          621 calls, 100.26 s

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

# Date 2008-01-16 Time 02:09:46 PST -0800 (1200478186.53 s)
Start R-work = 0.4256, R-free = 0.4094 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1747 (no bulk solvent and anisotropic scale)

Start R-work = 0.4175, R-free = 0.3925
Final R-work = 0.1141, R-free = 0.1583