# Date 2008-01-16 Time 03:58:04 PST -0800 (1200484684.92 s)
#phil __OFF__

Command line arguments: "../126.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21149
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 126

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 45.7567, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.81, per 1000 atoms: 1.00


================================== 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: (68.845, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7736 1.95216
Completeness in resolution range: 0.958882
Completeness with d_max=infinity: 0.955934

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7736
                             d_min =   1.9522

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: (68.845, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7736 1.95216
Completeness in resolution range: 0.958882
Completeness with d_max=infinity: 0.955934

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7740 -  4.1771 [2149/2173]  1930   219  10.2%
  bin  2:  4.1771 -  3.3279 [2053/2073]  1849   204   9.9%
  bin  3:  3.3279 -  2.9109 [2034/2053]  1836   198   9.7%
  bin  4:  2.9109 -  2.6464 [2014/2044]  1810   204  10.1%
  bin  5:  2.6464 -  2.4577 [1999/2018]  1798   201  10.1%
  bin  6:  2.4577 -  2.3133 [2007/2032]  1803   204  10.2%
  bin  7:  2.3133 -  2.1979 [1980/2008]  1781   199  10.1%
  bin  8:  2.1979 -  2.1025 [1963/1999]  1768   195   9.9%
  bin  9:  2.1025 -  2.0218 [1961/2003]  1771   190   9.7%
  bin 10:  2.0218 -  1.9522 [1429/2026]  1284   145  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_126/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: 0.11 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:
        1.37 -     2.07: 28
        2.07 -     2.78: 655
        2.78 -     3.49: 4648
        3.49 -     4.19: 9621
        4.19 -     4.90: 14098
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.367 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.453 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.542 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.634 3.040 -x+1,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  ... (remaining 29045 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 =====================


==================== 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/noshake/run_126/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_126/model_refine_001.geo

CPU time processing inputs: 7.94


============================ 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 = 68.845 45.75675 86.39 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4600   r_free= 0.4547   ksol= 0.00   Bsol= 0.00   scale= 0.910    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.275101                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7740 -  4.6589 0.99   1393  154 0.3846 0.3794      6.5796      6.5859|
|  2:  4.6589 -  3.7173 0.99   1339  152 0.3990 0.3730      6.7982      6.7721|
|  3:  3.7173 -  3.2531 0.99   1304  142 0.4422 0.4274      6.7042      6.7285|
|  4:  3.2531 -  2.9583 0.99   1313  146 0.4473 0.4317      6.5352       6.538|
|  5:  2.9583 -  2.7477 0.99   1295  146 0.4949 0.4655      6.3689      6.3706|
|  6:  2.7477 -  2.5866 0.99   1304  143 0.4837 0.5065      6.2738      6.2092|
|  7:  2.5866 -  2.4577 0.99   1275  143 0.4955 0.4796      6.2297      6.1372|
|  8:  2.4577 -  2.3511 0.98   1274  139 0.4958 0.5266      6.1811      6.2154|
|  9:  2.3511 -  2.2609 0.98   1283  146 0.4871 0.4962      6.1114      6.1799|
| 10:  2.2609 -  2.1832 1.00   1296  141 0.5012 0.5217      6.1015      6.0822|
| 11:  2.1832 -  2.1151 0.97   1253  139 0.4968 0.5270       6.013      6.0351|
| 12:  2.1151 -  2.0548 0.98   1260  142 0.4857 0.4476      5.9584      6.0053|
| 13:  2.0548 -  2.0009 0.99   1274  136 0.4875 0.4755      5.8689      5.8227|
| 14:  2.0009 -  1.9522 0.59    767   90 0.5247 0.4985      5.9001      5.7776|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7740 -  4.6589  1393   154  0.68  36.40   0.82     0.74      80505.44|
|  2:  4.6589 -  3.7173  1339   152  0.69  36.45   0.91     0.81     113250.77|
|  3:  3.7173 -  3.2531  1304   142  0.59  44.72   0.93     0.78     118644.20|
|  4:  3.2531 -  2.9583  1313   146  0.50  51.72   0.94     0.70     106810.98|
|  5:  2.9583 -  2.7477  1295   146  0.43  57.08   0.90     0.62      80220.86|
|  6:  2.7477 -  2.5866  1304   143  0.42  58.12   0.89     0.59      69001.74|
|  7:  2.5866 -  2.4577  1275   143  0.39  60.64   0.95     0.56      63399.54|
|  8:  2.4577 -  2.3511  1274   139  0.37  62.49   0.93     0.53      59666.44|
|  9:  2.3511 -  2.2609  1283   146  0.36  63.13   0.95     0.52      55723.33|
| 10:  2.2609 -  2.1832  1296   141  0.38  61.79   0.96     0.56      47280.35|
| 11:  2.1832 -  2.1151  1253   139  0.37  61.91   0.97     0.59      44709.16|
| 12:  2.1151 -  2.0548  1260   142  0.40  59.75   1.01     0.62      38090.19|
| 13:  2.0548 -  2.0009  1274   136  0.40  60.17   0.98     0.63      33077.74|
| 14:  2.0009 -  1.9522   767    90  0.47  55.04   0.99     0.65      25550.15|
|alpha:            min =        0.52 max =            0.81 mean =         0.64|
|beta:             min =    25550.15 max =       118644.20 mean =     68518.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.75|
|phase err.(test): min =        0.00 max =           89.99 mean =        54.59|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.842607             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.500   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.143558              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.681   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.367 -  1.720:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.720 -  2.074:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.074 -  2.427:       56 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.427 -  2.780:      599 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.780 -  3.133:     2211 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.133 -  3.487:     2437 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.487 -  3.840:     4627 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.840 -  4.193:     4994 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.193 -  4.547:     6359 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.547 -  4.900:     7739 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.212 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.105    4.900  1.367 |       0.970 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.294)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4600   r_free= 0.4547   ksol= 0.00   Bsol= 0.00   scale= 0.910    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.275101                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4500   r_free= 0.4448   ksol= 0.35   Bsol= 21.63   scale= 0.928   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,2.18,-1.88,0.00,-0.00,-0.00); trace/3= -0.30                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.268557                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.119143             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.245   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.107601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.518   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4500      final r-factor (work) = 0.3599          |
| start r-factor (free) = 0.4448      final r-factor (free) = 0.4002          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.1881 = 12.12 * 0.50 * 6.2671 + 1.00 * 0.2121                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.4951 = 12.12 * 0.50 * 6.1637 + 1.00 * 0.1457                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3599      final r-factor (work) = 0.3287          |
| start r-factor (free) = 0.4002      final r-factor (free) = 0.4132          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8331 = 1.11 * 1.00 * 6.1637 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7502 = 1.11 * 1.00 * 6.0778 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.294)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.84   17.94    None  None   None       |
|    all(noH): 2823   0      0.00    87.84   17.94    None  None   None       |
|    Sol.    : 438    0      0.00    87.84   33.80    None  None   None       |
|    Mac.    : 2385   0      0.00    78.55   15.03    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 -   8.784:  776   |   5:    43.920 -  52.704:   88        |
|      1:     8.784 -  17.568:  885   |   6:    52.704 -  61.488:   42        |
|      2:    17.568 -  26.352:  539   |   7:    61.488 -  70.272:   17        |
|      3:    26.352 -  35.136:  315   |   8:    70.272 -  79.056:    9        |
|      4:    35.136 -  43.920:  151   |   9:    79.056 -  87.840:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3287 r_free = 0.4132             target_work(ml) = 6.088         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3284 r_free = 0.4139             target_work(ml) = 6.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3284   r_free= 0.4139   ksol= 0.35   Bsol= 21.63   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,2.18,-1.88,0.00,-0.00,-0.00); trace/3= -0.30                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.087762                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3273   r_free= 0.4102   ksol= 0.35   Bsol= 52.50   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,1.25,-0.05,0.00,-0.00,-0.00); trace/3= 0.09                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.084619                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.164387             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.155  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.645601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.681  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3273      final r-factor (work) = 0.2719          |
| start r-factor (free) = 0.4102      final r-factor (free) = 0.3484          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.0438 = 10.16 * 0.50 * 6.0797 + 1.00 * 0.1457                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.6875 = 10.16 * 0.50 * 6.0186 + 1.00 * 0.0996                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2719      final r-factor (work) = 0.2556          |
| start r-factor (free) = 0.3484      final r-factor (free) = 0.3386          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9033 = 0.65 * 1.00 * 6.0186 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8528 = 0.65 * 1.00 * 5.9076 + 1.00 * 0.0388                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.294)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.31   17.51    None  None   None       |
|    all(noH): 2823   0      0.00    81.31   17.51    None  None   None       |
|    Sol.    : 438    0      1.43    81.31   35.44    None  None   None       |
|    Mac.    : 2385   0      0.00    80.04   14.22    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 -   8.132:  751   |   5:    40.657 -  48.789:  100        |
|      1:     8.132 -  16.263:  923   |   6:    48.789 -  56.920:   70        |
|      2:    16.263 -  24.395:  486   |   7:    56.920 -  65.052:   28        |
|      3:    24.395 -  32.526:  264   |   8:    65.052 -  73.183:   11        |
|      4:    32.526 -  40.657:  184   |   9:    73.183 -  81.315:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2556 r_free = 0.3386             target_work(ml) = 5.895         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2554 r_free = 0.3386             target_work(ml) = 5.894         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2554   r_free= 0.3386   ksol= 0.35   Bsol= 52.50   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,1.25,-0.05,0.00,-0.00,-0.00); trace/3= 0.09                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.894098                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2557   r_free= 0.3371   ksol= 0.34   Bsol= 53.16   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,0.36,0.41,0.00,0.00,0.00); trace/3= -0.07                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.891930                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.278942              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.191  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.531295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.626   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2557      final r-factor (work) = 0.2159          |
| start r-factor (free) = 0.3371      final r-factor (free) = 0.2828          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7389 = 4.28 * 0.50 * 5.9077 + 1.00 * 0.0996                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5229 = 4.28 * 0.50 * 5.8240 + 1.00 * 0.0627                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2159      final r-factor (work) = 0.1980          |
| start r-factor (free) = 0.2828      final r-factor (free) = 0.2713          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.4046 = 4.53 * 1.00 * 5.8240 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 25.7835 = 4.53 * 1.00 * 5.6858 + 1.00 * 0.0193                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.294)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.68  18.89    None  None   None       |
|    all(noH): 2823   0      0.00    109.68  18.89    None  None   None       |
|    Sol.    : 438    0      3.28    109.68  45.99    None  None   None       |
|    Mac.    : 2385   0      0.00    100.57  13.91    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 -  10.968: 1249   |   5:    54.842 -  65.810:   93        |
|      1:    10.968 -  21.937:  835   |   6:    65.810 -  76.778:   66        |
|      2:    21.937 -  32.905:  268   |   7:    76.778 -  87.747:   29        |
|      3:    32.905 -  43.873:  154   |   8:    87.747 -  98.715:    7        |
|      4:    43.873 -  54.842:  117   |   9:    98.715 - 109.684:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1980 r_free = 0.2713             target_work(ml) = 5.667         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1977 r_free = 0.2710             target_work(ml) = 5.667         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1977   r_free= 0.2710   ksol= 0.34   Bsol= 53.16   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,0.36,0.41,0.00,0.00,0.00); trace/3= -0.07                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.666506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1976   r_free= 0.2707   ksol= 0.32   Bsol= 48.11   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.46,0.45,-0.00,0.00,0.00); trace/3= -0.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.663872                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.708446              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.500  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.289357              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.884  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1976      final r-factor (work) = 0.1599          |
| start r-factor (free) = 0.2707      final r-factor (free) = 0.2224          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4469 = 4.71 * 0.50 * 5.6853 + 1.00 * 0.0623                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1925 = 4.71 * 0.50 * 5.5766 + 1.00 * 0.0640                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1599      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.2224      final r-factor (free) = 0.1992          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6327 = 0.29 * 1.00 * 5.5766 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5854 = 0.29 * 1.00 * 5.4338 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.294)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.07  17.20    None  None   None       |
|    all(noH): 2823   0      0.00    100.07  17.20    None  None   None       |
|    Sol.    : 438    0      5.74    100.07  42.75    None  None   None       |
|    Mac.    : 2385   0      0.00    96.76   12.51    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 -  10.007: 1240   |   5:    50.033 -  60.040:   92        |
|      1:    10.007 -  20.013:  930   |   6:    60.040 -  70.046:   68        |
|      2:    20.013 -  30.020:  204   |   7:    70.046 -  80.053:   22        |
|      3:    30.020 -  40.027:  150   |   8:    80.053 -  90.060:    8        |
|      4:    40.027 -  50.033:  104   |   9:    90.060 - 100.066:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1475 r_free = 0.1992             target_work(ml) = 5.374         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1472 r_free = 0.1985             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1472   r_free= 0.1985   ksol= 0.32   Bsol= 48.11   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.46,0.45,-0.00,0.00,0.00); trace/3= -0.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.371731                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1472   r_free= 0.1981   ksol= 0.31   Bsol= 39.96   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-1.31,0.06,-0.00,0.00,0.00); trace/3= -0.98                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.370333                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.222033              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.173  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.499   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1472      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1981      final r-factor (free) = 0.1770          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8176 = 3.22 * 0.50 * 5.4336 + 1.00 * 0.0640                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6199 = 3.22 * 0.50 * 5.3127 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1273      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9118 = 0.55 * 1.00 * 5.3127 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8655 = 0.55 * 1.00 * 5.2302 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.294)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.61   16.87    None  None   None       |
|    all(noH): 2823   0      0.00    99.61   16.87    None  None   None       |
|    Sol.    : 438    0      5.58    99.61   42.98    None  None   None       |
|    Mac.    : 2385   0      0.00    98.21   12.08    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 -   9.961: 1254   |   5:    49.807 -  59.768:   81        |
|      1:     9.961 -  19.923:  945   |   6:    59.768 -  69.729:   69        |
|      2:    19.923 -  29.884:  204   |   7:    69.729 -  79.691:   29        |
|      3:    29.884 -  39.845:  119   |   8:    79.691 -  89.652:    9        |
|      4:    39.845 -  49.807:  107   |   9:    89.652 -  99.614:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1220 r_free = 0.1708             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1706             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1706   ksol= 0.31   Bsol= 39.96   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-1.31,0.06,-0.00,0.00,0.00); trace/3= -0.98                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.210902                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7740 -  4.6589 0.99   1393  154 0.1002 0.1363      5.3978      5.6061|
|  2:  4.6589 -  3.7173 0.99   1339  152 0.0890 0.1255      5.4875      5.7413|
|  3:  3.7173 -  3.2531 0.99   1304  142 0.1170 0.1545      5.5656      5.8753|
|  4:  3.2531 -  2.9583 0.99   1313  146 0.1357 0.1973      5.5462      5.7502|
|  5:  2.9583 -  2.7477 0.99   1295  146 0.1471 0.1821      5.4144      5.6221|
|  6:  2.7477 -  2.5866 0.99   1304  143 0.1339 0.1972      5.2827      5.5171|
|  7:  2.5866 -  2.4577 0.99   1275  143 0.1369 0.1828      5.2284      5.4176|
|  8:  2.4577 -  2.3511 0.98   1274  139 0.1334 0.1768      5.1655      5.3911|
|  9:  2.3511 -  2.2609 0.98   1283  146 0.1277 0.1872      5.0898      5.3429|
| 10:  2.2609 -  2.1832 1.00   1296  141 0.1196 0.1734      5.0102      5.1724|
| 11:  2.1832 -  2.1151 0.97   1253  139 0.1253 0.2000       5.004      5.3628|
| 12:  2.1151 -  2.0548 0.98   1260  142 0.1248 0.1831       4.952      5.2589|
| 13:  2.0548 -  2.0009 0.99   1274  136 0.1227 0.1953      4.8366       5.116|
| 14:  2.0009 -  1.9522 0.59    767   90 0.1107 0.1565       4.719      4.9093|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7740 -  4.6589  1393   154  0.93   9.78   0.99     0.96       7624.64|
|  2:  4.6589 -  3.7173  1339   152  0.95   8.73   1.04     1.02      10365.29|
|  3:  3.7173 -  3.2531  1304   142  0.92  12.92   1.06     1.05      12743.50|
|  4:  3.2531 -  2.9583  1313   146  0.90  15.78   1.03     1.01      12643.55|
|  5:  2.9583 -  2.7477  1295   146  0.89  17.12   1.02     0.99       9613.07|
|  6:  2.7477 -  2.5866  1304   143  0.88  17.82   0.99     0.96       8138.48|
|  7:  2.5866 -  2.4577  1275   143  0.89  17.45   1.01     0.98       7068.80|
|  8:  2.4577 -  2.3511  1274   139  0.89  16.98   1.01     1.00       6359.80|
|  9:  2.3511 -  2.2609  1283   146  0.91  15.72   1.02     0.97       5297.79|
| 10:  2.2609 -  2.1832  1296   141  0.89  17.05   1.02     0.98       4898.59|
| 11:  2.1832 -  2.1151  1253   139  0.89  17.57   1.02     0.97       4940.34|
| 12:  2.1151 -  2.0548  1260   142  0.89  17.38   1.03     1.03       4587.09|
| 13:  2.0548 -  2.0009  1274   136  0.89  17.16   1.03     1.01       3665.32|
| 14:  2.0009 -  1.9522   767    90  0.92  14.63   1.01     0.98       2785.76|
|alpha:            min =        0.96 max =            1.05 mean =         0.99|
|beta:             min =     2785.76 max =        12743.50 mean =      7363.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.40|
|phase err.(test): min =        0.00 max =           88.86 mean =        14.75|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1707   ksol= 0.31   Bsol= 39.96   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.54,-0.10,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211781                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1707   ksol= 0.31   Bsol= 39.96   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.54,-0.10,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211781                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7740 -  4.6589 0.99   1393  154 0.1008 0.1379      5.4026      5.6116|
|  2:  4.6589 -  3.7173 0.99   1339  152 0.0905 0.1268      5.4973      5.7452|
|  3:  3.7173 -  3.2531 0.99   1304  142 0.1177 0.1543      5.5703      5.8747|
|  4:  3.2531 -  2.9583 0.99   1313  146 0.1363 0.1975      5.5463      5.7501|
|  5:  2.9583 -  2.7477 0.99   1295  146 0.1470 0.1819      5.4149      5.6193|
|  6:  2.7477 -  2.5866 0.99   1304  143 0.1340 0.1968      5.2815      5.5141|
|  7:  2.5866 -  2.4577 0.99   1275  143 0.1368 0.1836      5.2277      5.4197|
|  8:  2.4577 -  2.3511 0.98   1274  139 0.1330 0.1762      5.1637       5.388|
|  9:  2.3511 -  2.2609 0.98   1283  146 0.1276 0.1872      5.0888      5.3429|
| 10:  2.2609 -  2.1832 1.00   1296  141 0.1195 0.1738      5.0092      5.1735|
| 11:  2.1832 -  2.1151 0.97   1253  139 0.1250 0.1994      5.0028       5.362|
| 12:  2.1151 -  2.0548 0.98   1260  142 0.1247 0.1830      4.9515      5.2586|
| 13:  2.0548 -  2.0009 0.99   1274  136 0.1225 0.1950      4.8358      5.1148|
| 14:  2.0009 -  1.9522 0.59    767   90 0.1106 0.1557       4.718      4.9068|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7740 -  4.6589  1393   154  0.93   9.81   0.98     0.95       7758.96|
|  2:  4.6589 -  3.7173  1339   152  0.95   8.82   1.03     1.02      10468.12|
|  3:  3.7173 -  3.2531  1304   142  0.92  12.93   1.05     1.05      12818.87|
|  4:  3.2531 -  2.9583  1313   146  0.90  15.74   1.02     1.00      12605.78|
|  5:  2.9583 -  2.7477  1295   146  0.89  17.14   1.02     0.99       9622.79|
|  6:  2.7477 -  2.5866  1304   143  0.88  17.81   0.99     0.95       8121.04|
|  7:  2.5866 -  2.4577  1275   143  0.89  17.47   1.00     0.97       7070.38|
|  8:  2.4577 -  2.3511  1274   139  0.89  16.97   1.01     0.99       6348.33|
|  9:  2.3511 -  2.2609  1283   146  0.91  15.71   1.01     0.96       5294.34|
| 10:  2.2609 -  2.1832  1296   141  0.89  17.05   1.01     0.97       4893.40|
| 11:  2.1832 -  2.1151  1253   139  0.89  17.56   1.01     0.96       4935.61|
| 12:  2.1151 -  2.0548  1260   142  0.89  17.38   1.02     1.02       4583.76|
| 13:  2.0548 -  2.0009  1274   136  0.89  17.14   1.01     1.00       3659.30|
| 14:  2.0009 -  1.9522   767    90  0.92  14.61   1.00     0.97       2780.55|
|alpha:            min =        0.95 max =            1.05 mean =         0.99|
|beta:             min =     2780.55 max =        12818.87 mean =      7381.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.40|
|phase err.(test): min =        0.00 max =           87.54 mean =        14.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.294)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.62   16.88    None  None   None       |
|    all(noH): 2823   0      0.00    99.62   16.88    None  None   None       |
|    Sol.    : 438    0      5.58    99.62   42.98    None  None   None       |
|    Mac.    : 2385   0      0.00    98.21   12.08    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:     0.003 -   9.964: 1254   |   5:    49.810 -  59.771:   81        |
|      1:     9.964 -  19.926:  945   |   6:    59.771 -  69.732:   69        |
|      2:    19.926 -  29.887:  204   |   7:    69.732 -  79.694:   29        |
|      3:    29.887 -  39.848:  119   |   8:    79.694 -  89.655:    9        |
|      4:    39.848 -  49.810:  107   |   9:    89.655 -  99.616:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.604 - 5.736
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 307
   mapped sites are within: 0.745 - 5.736

peak=   10.170 closest distance to " O   HOH Z 178 " =    1.654
peak=    7.536 closest distance to " O   HOH Z 385 " =    2.200
peak=    6.723 closest distance to " O   HOH Z 130 " =    1.352
peak=    6.612 closest distance to " O   HOH Z 422 " =    1.245
peak=    6.586 closest distance to " O   HOH Z 431 " =    2.004
peak=    6.355 closest distance to " O   HOH Z 117 " =    1.809
peak=    6.203 closest distance to " O   HOH Z 245 " =    1.232
peak=    6.126 closest distance to " O   HOH Z 142 " =    1.913
peak=    6.103 closest distance to " O   HOH Z 427 " =    1.614
peak=    5.795 closest distance to " O   HOH Z  65 " =    1.680
peak=    5.779 closest distance to " NE2 GLN A  11 " =    1.318
peak=    5.767 closest distance to " O   HOH Z 375 " =    1.479
peak=    5.741 closest distance to " O   HOH Z 112 " =    1.603
peak=    5.560 closest distance to " CB  ARG A 275 " =    1.054
peak=    5.547 closest distance to " O   HOH Z  49 " =    1.342
peak=    5.537 closest distance to " O   HOH Z 289 " =    1.279
peak=    5.526 closest distance to " O   HOH Z 416 " =    1.315
peak=    5.504 closest distance to " O   HOH Z 126 " =    2.159
peak=    5.372 closest distance to " O   HOH Z  29 " =    1.401
peak=    5.290 closest distance to " O   HOH Z 417 " =    2.613
peak=    5.253 closest distance to " O   HOH Z 124 " =    1.558
peak=    5.232 closest distance to " CB  PRO A  54 " =    1.080
peak=    5.163 closest distance to " O   HOH Z 211 " =    1.270
peak=    5.058 closest distance to " O   HOH Z   7 " =    1.633
peak=    5.057 closest distance to " O   HOH Z 145 " =    1.626
peak=    5.052 closest distance to " O   HOH Z  92 " =    1.540
peak=    5.051 closest distance to " O   HOH Z 222 " =    1.258
peak=    4.985 closest distance to " O   HOH Z 236 " =    1.571
peak=    4.904 closest distance to " O   HOH Z  61 " =    1.567
peak=    4.889 closest distance to " O   HOH Z 390 " =    1.143
peak=    4.848 closest distance to " O   HOH Z  78 " =    1.682
peak=    4.834 closest distance to " CG  PRO A  54 " =    1.303
peak=    4.723 closest distance to " O   HOH Z 414 " =    1.431
peak=    4.692 closest distance to " O   HOH Z 193 " =    1.581
peak=    4.686 closest distance to " NH2 ARG A  56 " =    1.988
peak=    4.667 closest distance to " CB  ASN A 148 " =    1.426
peak=    4.643 closest distance to " O   HOH Z  57 " =    2.418
peak=    4.635 closest distance to " O   HOH Z   9 " =    1.231
peak=    4.544 closest distance to " O   HOH Z 293 " =    1.450
peak=    4.512 closest distance to " O   HOH Z 427 " =    1.542
peak=    4.456 closest distance to " O   HOH Z 298 " =    1.819
peak=    4.438 closest distance to " NZ  LYS A 117 " =    2.896
peak=    4.436 closest distance to " CG  PRO A 213 " =    1.285
peak=    4.436 closest distance to " O   HOH Z 424 " =    1.159
peak=    4.429 closest distance to " O   HOH Z 213 " =    1.687
peak=    4.429 closest distance to " O   HOH Z 380 " =    2.036
peak=    4.401 closest distance to " O   HOH Z 232 " =    2.200
peak=    4.398 closest distance to " O   HOH Z  63 " =    1.687
peak=    4.384 closest distance to " O   HOH Z 130 " =    2.269
peak=    4.380 closest distance to " O   HOH Z 166 " =    1.841
peak=    4.379 closest distance to " O   HOH Z 287 " =    1.973
peak=    4.370 closest distance to " O   HOH Z 132 " =    1.130
peak=    4.355 closest distance to " CB  GLN A 223 " =    1.507
peak=    4.349 closest distance to " O   HOH Z  11 " =    1.932
peak=    4.298 closest distance to " O   SER A  87 " =    2.502
peak=    4.293 closest distance to " O   HOH Z 371 " =    1.749
peak=    4.228 closest distance to " O   HOH Z 378 " =    1.013
peak=    4.222 closest distance to " O   HOH Z 423 " =    1.727
peak=    4.186 closest distance to " NH1AARG A 145 " =    1.160
peak=    4.183 closest distance to " O   HOH Z 158 " =    1.219
peak=    4.173 closest distance to " O   HOH Z 214 " =    1.365
peak=    4.156 closest distance to " O   HOH Z 426 " =    1.118
peak=    4.153 closest distance to " O   HOH Z 403 " =    1.433
peak=    4.146 closest distance to " O   HOH Z 434 " =    1.380
peak=    4.142 closest distance to " O   HOH Z 358 " =    1.228
peak=    4.099 closest distance to " OG ASER A 258 " =    3.020
peak=    4.089 closest distance to " O   HOH Z  69 " =    1.109
peak=    4.076 closest distance to " CB  SER A 276 " =    1.209
peak=    4.075 closest distance to " O   HOH Z 425 " =    2.057
peak=    4.068 closest distance to " O   HOH Z 272 " =    1.765
peak=    4.061 closest distance to " O   HOH Z 327 " =    1.716
peak=    4.041 closest distance to " O   HOH Z 418 " =    1.058
peak=    4.041 closest distance to " CB  SER A  63 " =    1.365
peak=    4.037 closest distance to " CB  THR A  31 " =    1.570
peak=    4.029 closest distance to " O   HOH Z 405 " =    1.492
peak=    4.015 closest distance to " O   HOH Z  59 " =    1.476
peak=    3.996 closest distance to " NE2 GLN A  58 " =    4.008
peak=    3.991 closest distance to " O   HOH Z  39 " =    1.232
peak=    3.971 closest distance to " O   HOH Z 365 " =    1.576
peak=    3.961 closest distance to " O   HOH Z 361 " =    3.629
peak=    3.961 closest distance to " OE1 GLN A  77 " =    1.252
peak=    3.942 closest distance to " O   PRO A 198 " =    1.320
peak=    3.939 closest distance to " CE  LYS A 119 " =    1.318
peak=    3.924 closest distance to " O   HOH Z 212 " =    1.766
peak=    3.917 closest distance to " O   HOH Z 227 " =    2.010
peak=    3.893 closest distance to " NZ  LYS A 117 " =    1.259
peak=    3.886 closest distance to " O   HOH Z 425 " =    1.433
peak=    3.880 closest distance to " CB  GLN A 183 " =    1.089
peak=    3.869 closest distance to " O   HOH Z 222 " =    2.375
peak=    3.861 closest distance to " CB  PHE A 130 " =    0.981
peak=    3.854 closest distance to " CA  TYR A  30 " =    1.017
peak=    3.852 closest distance to " O   HOH Z  30 " =    1.554
peak=    3.850 closest distance to " O   HOH Z 106 " =    2.558
peak=    3.846 closest distance to " O   HOH Z 371 " =    2.132
peak=    3.834 closest distance to " O   HOH Z 347 " =    1.023
peak=    3.818 closest distance to " O   HOH Z 424 " =    3.004
peak=    3.805 closest distance to " CD  LYS A 166 " =    1.468
peak=    3.800 closest distance to " O   HOH Z 244 " =    1.557
peak=    3.794 closest distance to " O   HOH Z 365 " =    2.318
peak=    3.793 closest distance to " OG BSER A 164 " =    2.081
peak=    3.777 closest distance to " O   HOH Z 402 " =    1.483
peak=    3.772 closest distance to " O   HOH Z 352 " =    1.362
peak=    3.747 closest distance to " NE1 TRP A 274 " =    1.048
peak=    3.733 closest distance to " O   HOH Z 394 " =    1.784
peak=    3.724 closest distance to " N   ALA A   1 " =    1.239
peak=    3.712 closest distance to " O   HOH Z 412 " =    2.187
peak=    3.711 closest distance to " CA  ASN A 127 " =    0.982
peak=    3.701 closest distance to " O   HOH Z 415 " =    1.120
peak=    3.699 closest distance to " O   HOH Z  51 " =    1.925
peak=    3.687 closest distance to " CG  TRP A 179 " =    2.113
peak=    3.682 closest distance to " CB  ARG A 190 " =    1.831
peak=    3.677 closest distance to " CB  ASN A  39 " =    0.891
peak=    3.664 closest distance to " O   HOH Z 392 " =    1.254
peak=    3.662 closest distance to " O   HOH Z  93 " =    1.900
peak=    3.654 closest distance to " O   HOH Z  68 " =    2.025
peak=    3.653 closest distance to " O   HOH Z  22 " =    1.932
peak=    3.651 closest distance to " CA  PHE A 283 " =    1.357
peak=    3.648 closest distance to " O   HOH Z 419 " =    2.136
peak=    3.642 closest distance to " CB  GLU A 128 " =    0.993
peak=    3.641 closest distance to " O   HOH Z   6 " =    2.059
peak=    3.638 closest distance to " O   HOH Z 218 " =    2.155
peak=    3.637 closest distance to " O   HOH Z 119 " =    4.064
peak=    3.632 closest distance to " N   ALA A   1 " =    2.544
peak=    3.627 closest distance to " O   HOH Z  65 " =    1.526
peak=    3.601 closest distance to " CG2 VAL A 232 " =    1.064
peak=    3.600 closest distance to " CB  ASN A 215 " =    1.147
peak=    3.600 closest distance to " N   GLN A 278 " =    1.055
peak=    3.596 closest distance to " CB  ALA A 114 " =    1.306
peak=    3.595 closest distance to " CB  GLU A 152 " =    1.245
peak=    3.595 closest distance to " CB  GLU A 277 " =    1.015
peak=    3.592 closest distance to " CB  GLU A 277 " =    3.478
peak=    3.591 closest distance to " CG  PRO A 198 " =    1.270
peak=    3.578 closest distance to " OG1 THR A 221 " =    1.330
peak=    3.575 closest distance to " O   HOH Z  28 " =    1.174
peak=    3.573 closest distance to " CG2 THR A 221 " =    1.272
peak=    3.573 closest distance to " OD1 ASN A  45 " =    1.230
peak=    3.570 closest distance to " CA  MET A  40 " =    1.238
peak=    3.566 closest distance to " CB  LEU A 300 " =    1.001
peak=    3.564 closest distance to " CD2 LEU A 167 " =    1.258
peak=    3.561 closest distance to " CE  LYS A  76 " =    0.939
peak=    3.558 closest distance to " O   HOH Z 386 " =    1.412
peak=    3.558 closest distance to " O   HOH Z 234 " =    3.480
peak=    3.548 closest distance to " CD2 TYR A 186 " =    0.945
peak=    3.547 closest distance to " OD1 ASN A  69 " =    2.458
peak=    3.545 closest distance to " O   HOH Z  30 " =    2.114
peak=    3.544 closest distance to " CG2 VAL A 257 " =    0.881
peak=    3.543 closest distance to " O   HOH Z 155 " =    1.858
peak=    3.540 closest distance to " O   ALA A 165 " =    1.293
peak=    3.530 closest distance to " O   HOH Z  97 " =    1.890
peak=    3.528 closest distance to " O   HOH Z  26 " =    1.486
peak=    3.527 closest distance to " O   HOH Z   7 " =    3.528
peak=    3.522 closest distance to " O   HOH Z 119 " =    1.335
peak=    3.507 closest distance to " CB  ALA A   1 " =    1.047
peak=    3.504 closest distance to " CG  GLN A  11 " =    2.188
peak=    3.502 closest distance to " O   HOH Z  44 " =    2.946
peak=    3.501 closest distance to " O   HOH Z 389 " =    1.354
peak=    3.495 closest distance to " O   HOH Z 117 " =    2.897
peak=    3.491 closest distance to " CB  TRP A 179 " =    1.305
peak=    3.483 closest distance to " O   HOH Z 189 " =    2.704
peak=    3.482 closest distance to " NH1AARG A 275 " =    1.011
peak=    3.480 closest distance to " CA  LEU A 282 " =    1.030
peak=    3.478 closest distance to " OG BSER A 210 " =    1.385
peak=    3.476 closest distance to " CG  PRO A  90 " =    1.249
peak=    3.475 closest distance to " O   HOH Z 126 " =    1.417
peak=    3.468 closest distance to " O   HOH Z 156 " =    3.152
peak=    3.465 closest distance to " O   HOH Z 207 " =    2.132
peak=    3.464 closest distance to " O   HOH Z 128 " =    1.983
peak=    3.461 closest distance to " O   HOH Z  55 " =    1.638
peak=    3.456 closest distance to " CB  SER A 216 " =    0.916
peak=    3.449 closest distance to " N   GLU A   2 " =    1.290
peak=    3.448 closest distance to " CA  ALA A 129 " =    1.172
peak=    3.446 closest distance to " O   HOH Z 261 " =    2.010
peak=    3.444 closest distance to " CD1 ILE A 263 " =    1.316
peak=    3.443 closest distance to " CG2 ILE A 120 " =    1.114
peak=    3.442 closest distance to " O   HOH Z  50 " =    1.817
peak=    3.442 closest distance to " O   HOH Z 413 " =    1.612
peak=    3.441 closest distance to " CG  LYS A  76 " =    1.648
peak=    3.436 closest distance to " CA  ARG A 195 " =    1.480
peak=    3.425 closest distance to " OE2 GLU A  53 " =    1.996
peak=    3.423 closest distance to " O   HOH Z 248 " =    1.851
peak=    3.416 closest distance to " CG1 ILE A 120 " =    1.611
peak=    3.415 closest distance to " O   HOH Z  32 " =    2.082
peak=    3.412 closest distance to " CB  ASN A  74 " =    1.031
peak=    3.409 closest distance to " CB  ALA A 114 " =    1.241
peak=    3.408 closest distance to " O   HOH Z 173 " =    2.197
peak=    3.407 closest distance to " O   HOH Z  17 " =    1.718
peak=    3.404 closest distance to " O   HOH Z 203 " =    1.444
peak=    3.403 closest distance to " O   HOH Z 150 " =    1.259
peak=    3.401 closest distance to " CB  VAL A 230 " =    0.881
peak=    3.398 closest distance to " O   HOH Z 151 " =    1.716
peak=    3.395 closest distance to " O   HOH Z  47 " =    1.540
peak=    3.393 closest distance to " CA  GLY A 241 " =    3.779
peak=    3.389 closest distance to " CA  ASN A 215 " =    1.012
peak=    3.380 closest distance to " O   HOH Z  40 " =    1.858
peak=    3.380 closest distance to " CA  ALA A 299 " =    0.938
peak=    3.374 closest distance to " O   HOH Z 329 " =    3.783
peak=    3.374 closest distance to " O   HOH Z  44 " =    1.696
peak=    3.371 closest distance to " CB  GLN A  89 " =    1.339
peak=    3.357 closest distance to " CB  TRP A 266 " =    1.225
peak=    3.355 closest distance to " O   HOH Z 162 " =    1.988
peak=    3.354 closest distance to " CB  SER A   3 " =    1.165
peak=    3.354 closest distance to " NH2 ARG A  14 " =    1.321
peak=    3.351 closest distance to " O   HOH Z 128 " =    1.990
peak=    3.350 closest distance to " O   HOH Z 158 " =    2.954
peak=    3.349 closest distance to " CB  VAL A 265 " =    1.202
peak=    3.346 closest distance to " O   HOH Z  80 " =    1.968
peak=    3.341 closest distance to " O   HOH Z 139 " =    1.138
peak=    3.340 closest distance to " CD  GLN A  58 " =    5.736
peak=    3.339 closest distance to " O   HOH Z 258 " =    2.181
peak=    3.338 closest distance to " O   HOH Z 423 " =    1.744
peak=    3.338 closest distance to " N   PHE A 130 " =    1.207
peak=    3.336 closest distance to " CG  LEU A 167 " =    1.283
peak=    3.336 closest distance to " CD  PRO A 243 " =    1.571
peak=    3.333 closest distance to " O   HOH Z 113 " =    1.958
peak=    3.330 closest distance to " CZ3 TRP A 266 " =    1.170
peak=    3.329 closest distance to " O   HOH Z  61 " =    1.573
peak=    3.327 closest distance to " CG AARG A 275 " =    1.020
peak=    3.325 closest distance to " CB  SER A 273 " =    0.993
peak=    3.323 closest distance to " O   HOH Z  69 " =    2.055
peak=    3.320 closest distance to " CB  SER A 212 " =    1.219
peak=    3.316 closest distance to " O   HOH Z 122 " =    1.795
peak=    3.312 closest distance to " O   HOH Z 145 " =    2.278
peak=    3.307 closest distance to " CB  THR A 157 " =    1.086
peak=    3.305 closest distance to " NZ  LYS A 119 " =    2.371
peak=    3.305 closest distance to " O   HOH Z 181 " =    2.122
peak=    3.298 closest distance to " ND1 HIS A  81 " =    1.369
peak=    3.292 closest distance to " CE1 PHE A  61 " =    1.497
peak=    3.292 closest distance to " O   HOH Z 368 " =    1.866
peak=    3.290 closest distance to " O   HOH Z 419 " =    1.748
peak=    3.279 closest distance to " O   HOH Z  88 " =    2.600
peak=    3.272 closest distance to " CB  ASN A 110 " =    1.060
peak=    3.271 closest distance to " O   HOH Z 344 " =    3.046
peak=    3.267 closest distance to " O   HOH Z 299 " =    2.528
peak=    3.265 closest distance to " NZ BLYS A 290 " =    0.842
peak=    3.264 closest distance to " CA  PRO A 243 " =    1.291
peak=    3.263 closest distance to " O   HOH Z 334 " =    1.720
peak=    3.262 closest distance to " O   HOH Z  64 " =    2.045
peak=    3.261 closest distance to " O   HOH Z 438 " =    2.332
peak=    3.257 closest distance to " CB  ASN A 142 " =    1.067
peak=    3.255 closest distance to " CB  ARG A 138 " =    0.815
peak=    3.255 closest distance to " O   HOH Z 363 " =    1.070
peak=    3.254 closest distance to " O   HOH Z 379 " =    1.491
peak=    3.246 closest distance to " O   HOH Z 213 " =    1.907
peak=    3.244 closest distance to " CD1 LEU A 281 " =    0.969
peak=    3.242 closest distance to " CG  MET A 185 " =    1.594
peak=    3.242 closest distance to " O   HOH Z 128 " =    3.134
peak=    3.241 closest distance to " O   HOH Z 359 " =    1.390
peak=    3.238 closest distance to " OG  SER A  22 " =    2.649
peak=    3.237 closest distance to " CZ  PHE A  38 " =    1.236
peak=    3.237 closest distance to " CG1 VAL A 174 " =    1.525
peak=    3.235 closest distance to " ND2 ASN A 187 " =    1.601
peak=    3.233 closest distance to " O   HOH Z 389 " =    2.807
peak=    3.230 closest distance to " NH2BARG A 145 " =    1.967
peak=    3.228 closest distance to " O   HOH Z 222 " =    1.854
peak=    3.227 closest distance to " O   HOH Z 152 " =    2.367
peak=    3.227 closest distance to " O   HOH Z  67 " =    1.710
peak=    3.224 closest distance to " O   HOH Z 418 " =    1.608
peak=    3.222 closest distance to " O   HOH Z 158 " =    2.479
peak=    3.221 closest distance to " O   HOH Z 384 " =    1.226
peak=    3.221 closest distance to " O   HOH Z 189 " =    2.150
peak=    3.218 closest distance to " CD  ARG A 159 " =    0.813
peak=    3.213 closest distance to " CB  MET A  40 " =    0.867
peak=    3.209 closest distance to " O   GLY A 302 " =    2.457
peak=    3.206 closest distance to " O   HOH Z 218 " =    1.858
peak=    3.198 closest distance to " O   HOH Z 302 " =    1.358
peak=    3.191 closest distance to " O   HOH Z 365 " =    1.715
peak=    3.188 closest distance to " CB  PHE A 225 " =    1.189
peak=    3.174 closest distance to " CA  ILE A 234 " =    0.981
peak=    3.174 closest distance to " O   HOH Z  43 " =    2.236
peak=    3.171 closest distance to " O   HOH Z 367 " =    2.327
peak=    3.170 closest distance to " CB  SER A  99 " =    0.989
peak=    3.167 closest distance to " O   HOH Z 431 " =    1.247
peak=    3.162 closest distance to " CD2 TRP A 179 " =    1.349
peak=    3.159 closest distance to " CB  MET A 105 " =    1.065
peak=    3.155 closest distance to " O   HOH Z 357 " =    1.782
peak=    3.148 closest distance to " O   HOH Z   1 " =    1.758
peak=    3.146 closest distance to " CA  ALA A  21 " =    1.230
peak=    3.145 closest distance to " O   ASN A  74 " =    1.332
peak=    3.142 closest distance to " CG2BVAL A  41 " =    0.745
peak=    3.141 closest distance to " CB  VAL A 202 " =    1.583
peak=    3.138 closest distance to " CE AMET A  47 " =    1.295
peak=    3.138 closest distance to " ND2 ASN A 249 " =    0.804
peak=    3.132 closest distance to " CB  GLN A 278 " =    0.792
peak=    3.130 closest distance to " NE AARG A 275 " =    1.480
peak=    3.130 closest distance to " NE2 GLN A  73 " =    1.482
peak=    3.129 closest distance to " CB  ASN A 176 " =    1.215
peak=    3.129 closest distance to " O   HOH Z 214 " =    1.791
peak=    3.126 closest distance to " O   HOH Z  88 " =    2.542
peak=    3.120 closest distance to " CB  ASP A 140 " =    0.941
peak=    3.117 closest distance to " OE1 GLU A   2 " =    1.537
peak=    3.116 closest distance to " O   HOH Z 175 " =    1.917
peak=    3.115 closest distance to " SD BMET A  47 " =    1.223
peak=    3.114 closest distance to " O   HOH Z 214 " =    3.293
peak=    3.100 closest distance to " CG2 ILE A  20 " =    1.817
peak=    3.082 closest distance to " CA  MET A 105 " =    0.807
peak=    3.081 closest distance to " CA  ALA A 292 " =    0.931
peak=    3.078 closest distance to " OG1 THR A 246 " =    1.280
peak=    3.066 closest distance to " O   HOH Z 225 " =    1.531
peak=    3.063 closest distance to " N   HIS A  86 " =    1.875
peak=    3.036 closest distance to " O   HOH Z 194 " =    1.892
peak=    3.031 closest distance to " CG2 ILE A  20 " =    1.150
peak=    3.019 closest distance to " O   HOH Z 153 " =    3.473

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.649 - 5.130
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 219
   mapped sites are within: 0.774 - 5.130

peak=   -4.845 closest distance to " O   HOH Z 385 " =    0.976
peak=   -4.482 closest distance to " O   PRO A 198 " =    1.161
peak=   -4.283 closest distance to " O   SER A  22 " =    2.575
peak=   -4.220 closest distance to " O   HOH Z 313 " =    1.102
peak=   -4.205 closest distance to " O   HOH Z  60 " =    1.926
peak=   -4.202 closest distance to " O   HOH Z  24 " =    1.038
peak=   -4.071 closest distance to " OG  SER A  97 " =    2.073
peak=   -4.037 closest distance to " CB  ALA A 248 " =    2.123
peak=   -3.986 closest distance to " O   MET A  40 " =    2.920
peak=   -3.971 closest distance to " OG BSER A 134 " =    1.335
peak=   -3.963 closest distance to " N   THR A 157 " =    1.506
peak=   -3.947 closest distance to " ND2 ASN A 209 " =    1.956
peak=   -3.932 closest distance to " N   ALA A   1 " =    1.327
peak=   -3.911 closest distance to " O   HOH Z 298 " =    1.069
peak=   -3.886 closest distance to " CZ  PHE A  59 " =    1.349
peak=   -3.883 closest distance to " O   SER A 135 " =    1.546
peak=   -3.880 closest distance to " O   HOH Z 347 " =    0.920
peak=   -3.875 closest distance to " O   HOH Z  69 " =    1.791
peak=   -3.873 closest distance to " O   PHE A 218 " =    1.375
peak=   -3.860 closest distance to " O   HOH Z 372 " =    2.582
peak=   -3.860 closest distance to " OD2 ASP A 171 " =    1.933
peak=   -3.859 closest distance to " CB  ASN A  39 " =    2.196
peak=   -3.852 closest distance to " O   HOH Z  88 " =    1.661
peak=   -3.829 closest distance to " CB  GLN A  55 " =    1.247
peak=   -3.818 closest distance to " OE1 GLU A 277 " =    1.948
peak=   -3.806 closest distance to " O   HOH Z 387 " =    2.470
peak=   -3.775 closest distance to " O   HOH Z 103 " =    1.483
peak=   -3.767 closest distance to " CD  ARG A 156 " =    1.948
peak=   -3.758 closest distance to " O   HOH Z 244 " =    1.297
peak=   -3.754 closest distance to " O   ILE A  49 " =    1.684
peak=   -3.736 closest distance to " SG  CYS A 254 " =    3.342
peak=   -3.736 closest distance to " N   GLN A  58 " =    1.242
peak=   -3.727 closest distance to " CZ2 TRP A 274 " =    0.940
peak=   -3.726 closest distance to " O   HOH Z 236 " =    2.312
peak=   -3.703 closest distance to " CA  GLY A  98 " =    1.682
peak=   -3.702 closest distance to " O   HOH Z 290 " =    0.958
peak=   -3.701 closest distance to " O   HOH Z 407 " =    2.685
peak=   -3.699 closest distance to " CD2 TYR A 293 " =    1.817
peak=   -3.698 closest distance to " O   HOH Z 102 " =    1.581
peak=   -3.681 closest distance to " CD2 LEU A 237 " =    2.476
peak=   -3.672 closest distance to " OG  SER A  63 " =    1.496
peak=   -3.634 closest distance to " O   HOH Z 351 " =    1.554
peak=   -3.606 closest distance to " CB  ALA A 291 " =    2.152
peak=   -3.603 closest distance to " O   VAL A  67 " =    2.552
peak=   -3.601 closest distance to " O   HOH Z 183 " =    1.555
peak=   -3.600 closest distance to " O   HOH Z 274 " =    3.221
peak=   -3.599 closest distance to " O   HOH Z   1 " =    1.173
peak=   -3.599 closest distance to " O   HOH Z 198 " =    1.678
peak=   -3.593 closest distance to " O   ASP A 191 " =    1.920
peak=   -3.589 closest distance to " O   HOH Z 131 " =    4.153
peak=   -3.580 closest distance to " OXT GLY A 302 " =    2.958
peak=   -3.574 closest distance to " O   HOH Z 147 " =    1.046
peak=   -3.570 closest distance to " O   HOH Z  39 " =    1.271
peak=   -3.569 closest distance to " CB  ASP A 132 " =    2.471
peak=   -3.567 closest distance to " CB  ALA A  43 " =    2.135
peak=   -3.562 closest distance to " O   HOH Z 288 " =    1.425
peak=   -3.560 closest distance to " CG  ARG A 219 " =    2.280
peak=   -3.559 closest distance to " O   HOH Z 412 " =    4.695
peak=   -3.541 closest distance to " O   HOH Z 292 " =    1.558
peak=   -3.527 closest distance to " O   HOH Z 100 " =    1.260
peak=   -3.523 closest distance to " OE1 GLN A 183 " =    1.346
peak=   -3.521 closest distance to " CD1 ILE A 239 " =    2.362
peak=   -3.513 closest distance to " O   HOH Z  76 " =    1.313
peak=   -3.511 closest distance to " O   VAL A 174 " =    2.264
peak=   -3.507 closest distance to " CA  GLY A 133 " =    1.958
peak=   -3.503 closest distance to " CG2 ILE A  20 " =    2.702
peak=   -3.500 closest distance to " OE2 GLU A 152 " =    1.111
peak=   -3.500 closest distance to " N   ALA A 248 " =    1.564
peak=   -3.491 closest distance to " O   HOH Z  22 " =    2.836
peak=   -3.489 closest distance to " O   HOH Z  90 " =    2.428
peak=   -3.487 closest distance to " O   HOH Z  77 " =    1.842
peak=   -3.484 closest distance to " O   SER A  95 " =    1.360
peak=   -3.483 closest distance to " OG  SER A  63 " =    1.187
peak=   -3.473 closest distance to " CG  MET A 105 " =    0.932
peak=   -3.472 closest distance to " C   ILE A 239 " =    2.001
peak=   -3.472 closest distance to " O   HOH Z 337 " =    1.520
peak=   -3.470 closest distance to " O   HOH Z 211 " =    1.583
peak=   -3.457 closest distance to " O   HOH Z 185 " =    1.879
peak=   -3.454 closest distance to " CD1 LEU A 101 " =    2.217
peak=   -3.452 closest distance to " O   HOH Z 165 " =    2.442
peak=   -3.451 closest distance to " O   HOH Z 231 " =    2.063
peak=   -3.450 closest distance to " O   HOH Z 195 " =    1.810
peak=   -3.445 closest distance to " CB  SER A 210 " =    1.213
peak=   -3.437 closest distance to " OG  SER A  87 " =    1.216
peak=   -3.437 closest distance to " O   ALA A 161 " =    1.731
peak=   -3.434 closest distance to " O   HOH Z 286 " =    1.809
peak=   -3.423 closest distance to " NE  ARG A  36 " =    1.836
peak=   -3.419 closest distance to " ND2 ASN A 285 " =    1.728
peak=   -3.411 closest distance to " OD1 ASN A 187 " =    1.522
peak=   -3.411 closest distance to " OD2 ASP A  27 " =    1.655
peak=   -3.409 closest distance to " OD1 ASN A 148 " =    1.700
peak=   -3.408 closest distance to " OD2 ASP A 191 " =    1.509
peak=   -3.401 closest distance to " OG  SER A 273 " =    1.839
peak=   -3.399 closest distance to " CD2 PHE A  61 " =    2.457
peak=   -3.398 closest distance to " OD2 ASP A  50 " =    1.284
peak=   -3.389 closest distance to " CG  PRO A 243 " =    1.463
peak=   -3.385 closest distance to " NH2 ARG A  79 " =    2.022
peak=   -3.384 closest distance to " O   ALA A  10 " =    1.706
peak=   -3.376 closest distance to " O   HOH Z 265 " =    2.100
peak=   -3.374 closest distance to " O   HOH Z 250 " =    1.183
peak=   -3.373 closest distance to " N   ALA A   1 " =    1.083
peak=   -3.370 closest distance to " OD2 ASP A 171 " =    1.377
peak=   -3.365 closest distance to " CG  GLN A  58 " =    1.253
peak=   -3.362 closest distance to " CG2BVAL A  72 " =    1.466
peak=   -3.358 closest distance to " O   HOH Z 368 " =    2.566
peak=   -3.357 closest distance to " O   HOH Z 415 " =    1.124
peak=   -3.356 closest distance to " CD  GLU A 236 " =    1.121
peak=   -3.349 closest distance to " ND2 ASN A 187 " =    1.464
peak=   -3.343 closest distance to " O   HOH Z 122 " =    2.418
peak=   -3.342 closest distance to " O   HOH Z  64 " =    1.168
peak=   -3.341 closest distance to " O   GLY A  80 " =    2.586
peak=   -3.332 closest distance to " CG  ASP A 231 " =    0.824
peak=   -3.332 closest distance to " O   HOH Z 426 " =    1.395
peak=   -3.331 closest distance to " N   ARG A 275 " =    0.774
peak=   -3.331 closest distance to " CG  GLU A 152 " =    1.279
peak=   -3.329 closest distance to " CB  CYS A 201 " =    2.267
peak=   -3.324 closest distance to " N   VAL A  72 " =    1.707
peak=   -3.322 closest distance to " NE1 TRP A 179 " =    1.264
peak=   -3.322 closest distance to " N   VAL A 125 " =    2.117
peak=   -3.321 closest distance to " O   HOH Z 428 " =    2.238
peak=   -3.321 closest distance to " O   HOH Z 163 " =    1.949
peak=   -3.320 closest distance to " O   HOH Z 266 " =    4.596
peak=   -3.313 closest distance to " OG BSER A 210 " =    2.346
peak=   -3.312 closest distance to " O   HOH Z 425 " =    0.943
peak=   -3.307 closest distance to " CB  ALA A 100 " =    1.800
peak=   -3.301 closest distance to " CE  LYS A  76 " =    3.063
peak=   -3.300 closest distance to " CA  GLY A 241 " =    2.147
peak=   -3.299 closest distance to " O   HOH Z 297 " =    3.697
peak=   -3.295 closest distance to " O   THR A 235 " =    1.496
peak=   -3.293 closest distance to " O   PRO A  54 " =    1.656
peak=   -3.291 closest distance to " O   HOH Z 197 " =    3.340
peak=   -3.290 closest distance to " CE2 PHE A 218 " =    2.395
peak=   -3.290 closest distance to " OG  SER A 245 " =    1.378
peak=   -3.289 closest distance to " OE1 GLN A 223 " =    2.031
peak=   -3.288 closest distance to " O   HOH Z 214 " =    1.536
peak=   -3.288 closest distance to " ND2 ASN A  39 " =    1.177
peak=   -3.284 closest distance to " O   HOH Z  28 " =    2.076
peak=   -3.281 closest distance to " CG  LEU A  83 " =    2.064
peak=   -3.278 closest distance to " CG1 ILE A 263 " =    1.937
peak=   -3.277 closest distance to " O   TRP A  70 " =    1.430
peak=   -3.274 closest distance to " OG ASER A 216 " =    1.011
peak=   -3.272 closest distance to " O   SER A 271 " =    2.064
peak=   -3.266 closest distance to " OG BSER A 134 " =    1.828
peak=   -3.266 closest distance to " CB  ASN A  45 " =    1.862
peak=   -3.264 closest distance to " C   ALA A 114 " =    2.144
peak=   -3.258 closest distance to " O   HOH Z 426 " =    2.085
peak=   -3.256 closest distance to " ND2 ASN A  60 " =    4.211
peak=   -3.256 closest distance to " O   HOH Z 137 " =    1.440
peak=   -3.250 closest distance to " O   HOH Z  56 " =    1.991
peak=   -3.249 closest distance to " O   HOH Z 140 " =    1.566
peak=   -3.243 closest distance to " O   GLU A 152 " =    1.407
peak=   -3.242 closest distance to " CB  ALA A   7 " =    1.870
peak=   -3.240 closest distance to " CZ  ARG A  36 " =    1.345
peak=   -3.237 closest distance to " NH2 ARG A 219 " =    1.633
peak=   -3.235 closest distance to " CZ2 TRP A  92 " =    2.730
peak=   -3.232 closest distance to " OG  SER A 245 " =    1.733
peak=   -3.229 closest distance to " O   HOH Z 393 " =    2.626
peak=   -3.229 closest distance to " N   ALA A 226 " =    2.007
peak=   -3.224 closest distance to " CB  LEU A  25 " =    2.603
peak=   -3.221 closest distance to " C   ALA A 158 " =    1.506
peak=   -3.221 closest distance to " CD  GLN A 278 " =    1.279
peak=   -3.219 closest distance to " O   HOH Z  88 " =    2.622
peak=   -3.216 closest distance to " O   HOH Z 289 " =    1.786
peak=   -3.213 closest distance to " O   HOH Z 404 " =    1.491
peak=   -3.213 closest distance to " C   HIS A 207 " =    1.296
peak=   -3.213 closest distance to " O   HOH Z  79 " =    1.502
peak=   -3.207 closest distance to " N   SER A 206 " =    1.863
peak=   -3.204 closest distance to " O   THR A 220 " =    1.712
peak=   -3.201 closest distance to " O   HOH Z 422 " =    3.155
peak=   -3.200 closest distance to " CD2 TYR A 293 " =    2.144
peak=   -3.199 closest distance to " CE3 TRP A  70 " =    2.037
peak=   -3.196 closest distance to " CB  PHE A 192 " =    1.930
peak=   -3.192 closest distance to " O   HOH Z 388 " =    2.085
peak=   -3.191 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.191 closest distance to " O   HOH Z 423 " =    1.914
peak=   -3.190 closest distance to " O   HOH Z   4 " =    0.930
peak=   -3.185 closest distance to " C   HIS A 108 " =    1.290
peak=   -3.180 closest distance to " CE  MET A 105 " =    2.395
peak=   -3.169 closest distance to " O   HOH Z  99 " =    3.786
peak=   -3.161 closest distance to " C   ASN A 285 " =    1.985
peak=   -3.159 closest distance to " CG  GLN A  88 " =    0.794
peak=   -3.156 closest distance to " CB  ASP A  27 " =    2.267
peak=   -3.150 closest distance to " CB  ALA A 227 " =    2.358
peak=   -3.145 closest distance to " CB  ALA A 114 " =    2.353
peak=   -3.143 closest distance to " N   GLN A  58 " =    1.992
peak=   -3.143 closest distance to " C   VAL A 265 " =    0.850
peak=   -3.138 closest distance to " CE3 TRP A 274 " =    2.350
peak=   -3.138 closest distance to " O   HOH Z 213 " =    1.386
peak=   -3.137 closest distance to " N   ARG A 159 " =    1.882
peak=   -3.132 closest distance to " O   HOH Z 359 " =    1.576
peak=   -3.121 closest distance to " O   HOH Z 348 " =    1.981
peak=   -3.119 closest distance to " O   HOH Z 283 " =    2.311
peak=   -3.118 closest distance to " CB  ILE A  33 " =    2.833
peak=   -3.116 closest distance to " O   HOH Z 198 " =    1.801
peak=   -3.113 closest distance to " NE2 GLN A  55 " =    1.139
peak=   -3.111 closest distance to " O   PRO A 163 " =    1.100
peak=   -3.111 closest distance to " NE2 GLN A 278 " =    1.744
peak=   -3.110 closest distance to " O   HOH Z 126 " =    1.928
peak=   -3.110 closest distance to " CB  TYR A  15 " =    2.100
peak=   -3.110 closest distance to " O   HOH Z 413 " =    4.491
peak=   -3.108 closest distance to " CZ  TYR A 169 " =    1.786
peak=   -3.105 closest distance to " O   ALA A   1 " =    1.294
peak=   -3.104 closest distance to " CG  ARG A 259 " =    2.662
peak=   -3.098 closest distance to " O   ALA A 180 " =    1.058
peak=   -3.097 closest distance to " CG  ARG A 219 " =    2.311
peak=   -3.091 closest distance to " OE1 GLN A  58 " =    5.130
peak=   -3.089 closest distance to " O   HOH Z 166 " =    1.456
peak=   -3.088 closest distance to " ND2 ASN A 249 " =    2.348
peak=   -3.079 closest distance to " CZ3 TRP A 123 " =    1.929
peak=   -3.079 closest distance to " CB  TRP A 274 " =    2.759
peak=   -3.075 closest distance to " CG2 ILE A 151 " =    2.449
peak=   -3.071 closest distance to " CG  TRP A  85 " =    0.940
peak=   -3.071 closest distance to " CZ  PHE A  38 " =    2.516
peak=   -3.065 closest distance to " O   HOH Z 193 " =    1.932
peak=   -3.059 closest distance to " OG BSER A  99 " =    1.157
peak=   -3.057 closest distance to " O   HOH Z 414 " =    1.432
peak=   -3.048 closest distance to " CG  GLN A  58 " =    0.873

================= 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    :  0.4600 0.4547   6.275101e+00   6.266731e+00
   1_bss:  0.4500 0.4448   6.268557e+00   6.251757e+00
   1_xyz:  0.3599 0.4002   6.125306e+00   6.188140e+00
   1_adp:  0.3287 0.4132   6.087604e+00   6.200806e+00
   1_occ:  0.3284 0.4139   6.087762e+00   6.201348e+00
   2_bss:  0.3273 0.4102   6.084619e+00   6.199483e+00
   2_xyz:  0.2719 0.3484   5.929933e+00   6.085576e+00
   2_adp:  0.2556 0.3386   5.894539e+00   6.061024e+00
   2_occ:  0.2554 0.3386   5.894098e+00   6.060794e+00
   3_bss:  0.2557 0.3371   5.891930e+00   6.058931e+00
   3_xyz:  0.2159 0.2828   5.727503e+00   5.912625e+00
   3_adp:  0.1980 0.2713   5.667174e+00   5.877503e+00
   3_occ:  0.1977 0.2710   5.666506e+00   5.876713e+00
   4_bss:  0.1976 0.2707   5.663872e+00   5.873767e+00
   4_xyz:  0.1599 0.2224   5.463984e+00   5.703825e+00
   4_adp:  0.1475 0.1992   5.373877e+00   5.604369e+00
   4_occ:  0.1472 0.1985   5.371731e+00   5.601737e+00
   5_bss:  0.1472 0.1981   5.370333e+00   5.599730e+00
   5_xyz:  0.1273 0.1770   5.249435e+00   5.488684e+00
   5_adp:  0.1220 0.1708   5.211507e+00   5.454125e+00
   5_occ:  0.1219 0.1706   5.210902e+00   5.453236e+00
   5_bss:  0.1222 0.1707   5.211781e+00   5.453237e+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:  0.355  21.631  -1.187   2.178  -1.877   0.000  -0.000  -0.000
   1_xyz:  0.355  21.631  -1.187   2.178  -1.877   0.000  -0.000  -0.000
   1_adp:  0.355  21.631  -1.187   2.178  -1.877   0.000  -0.000  -0.000
   1_occ:  0.355  21.631  -1.187   2.178  -1.877   0.000  -0.000  -0.000
   2_bss:  0.349  52.498  -0.937   1.251  -0.052   0.000  -0.000  -0.000
   2_xyz:  0.349  52.498  -0.937   1.251  -0.052   0.000  -0.000  -0.000
   2_adp:  0.349  52.498  -0.937   1.251  -0.052   0.000  -0.000  -0.000
   2_occ:  0.349  52.498  -0.937   1.251  -0.052   0.000  -0.000  -0.000
   3_bss:  0.342  53.164  -0.968   0.356   0.410   0.000   0.000   0.000
   3_xyz:  0.342  53.164  -0.968   0.356   0.410   0.000   0.000   0.000
   3_adp:  0.342  53.164  -0.968   0.356   0.410   0.000   0.000   0.000
   3_occ:  0.342  53.164  -0.968   0.356   0.410   0.000   0.000   0.000
   4_bss:  0.321  48.106  -1.252  -0.457   0.451  -0.000   0.000   0.000
   4_xyz:  0.321  48.106  -1.252  -0.457   0.451  -0.000   0.000   0.000
   4_adp:  0.321  48.106  -1.252  -0.457   0.451  -0.000   0.000   0.000
   4_occ:  0.321  48.106  -1.252  -0.457   0.451  -0.000   0.000   0.000
   5_bss:  0.311  39.957  -1.694  -1.310   0.055  -0.000   0.000   0.000
   5_xyz:  0.311  39.957  -1.694  -1.310   0.055  -0.000   0.000   0.000
   5_adp:  0.311  39.957  -1.694  -1.310   0.055  -0.000   0.000   0.000
   5_occ:  0.311  39.957  -1.694  -1.310   0.055  -0.000   0.000   0.000
   5_bss:  0.310  39.959  -1.898  -1.540  -0.096  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.731 0.4625  0.6366    68517.676
   1_bss:  53.844 0.4724  0.6443    65149.661
   1_xyz:  45.870 0.5713  0.7619    49145.641
   1_adp:  47.136 0.5553  0.7353    51864.787
   1_occ:  47.266 0.5537  0.7321    52057.760
   2_bss:  46.717 0.5601  0.7533    50888.101
   2_xyz:  37.571 0.6705  0.8914    34180.106
   2_adp:  35.869 0.6909  0.9000    32006.743
   2_occ:  35.862 0.6910  0.8998    31978.376
   3_bss:  35.680 0.6929  0.8966    31630.819
   3_xyz:  28.543 0.7733  0.9704    20964.471
   3_adp:  27.023 0.7900  0.9651    19157.441
   3_occ:  26.998 0.7902  0.9652    19109.174
   4_bss:  26.908 0.7910  0.9537    18932.215
   4_xyz:  21.736 0.8435  0.9934    12473.103
   4_adp:  18.843 0.8725  1.0082    10081.424
   4_occ:  18.773 0.8731  1.0082     9994.885
   5_bss:  18.707 0.8736  0.9873     9915.514
   5_xyz:  16.160 0.8966  0.9977     7859.279
   5_adp:  15.347 0.9039  0.9939     7388.231
   5_occ:  15.332 0.9039  0.9938     7363.120
   5_bss:  15.337 0.9039  0.9868     7381.149
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.105   2.1212e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.105   2.1212e-01
   1_xyz:   1.609  0.012  0.110 15.702  0.006  4.104   1.4566e-01
   1_adp:   1.609  0.012  0.110 15.702  0.006  4.104   1.4566e-01
   1_occ:   1.609  0.012  0.110 15.702  0.006  4.104   1.4566e-01
   2_bss:   1.609  0.012  0.110 15.702  0.006  4.104   1.4566e-01
   2_xyz:   1.348  0.010  0.098 15.241  0.006  4.104   9.9557e-02
   2_adp:   1.348  0.010  0.098 15.241  0.006  4.104   9.9557e-02
   2_occ:   1.348  0.010  0.098 15.241  0.006  4.104   9.9557e-02
   3_bss:   1.348  0.010  0.098 15.241  0.006  4.104   9.9557e-02
   3_xyz:   1.028  0.007  0.070 14.309  0.004  4.111   6.2690e-02
   3_adp:   1.028  0.007  0.070 14.309  0.004  4.111   6.2690e-02
   3_occ:   1.028  0.007  0.070 14.309  0.004  4.111   6.2690e-02
   4_bss:   1.028  0.007  0.070 14.309  0.004  4.111   6.2690e-02
   4_xyz:   1.055  0.007  0.073 14.525  0.004  4.110   6.3973e-02
   4_adp:   1.055  0.007  0.073 14.525  0.004  4.110   6.3973e-02
   4_occ:   1.055  0.007  0.073 14.525  0.004  4.110   6.3973e-02
   5_bss:   1.055  0.007  0.073 14.525  0.004  4.110   6.3973e-02
   5_xyz:   1.026  0.007  0.071 14.580  0.004  4.107   6.1032e-02
   5_adp:   1.026  0.007  0.071 14.580  0.004  4.107   6.1032e-02
   5_occ:   1.026  0.007  0.071 14.580  0.004  4.107   6.1032e-02
   5_bss:   1.026  0.007  0.071 14.580  0.004  4.107   6.1032e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.367   2.3852e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.367   2.3852e-01
   1_xyz:  10.139  0.077  0.466 74.036  0.038  1.980   1.0177e-01
   1_adp:  10.139  0.077  0.466 74.036  0.038  1.980   1.0177e-01
   1_occ:  10.139  0.077  0.466 74.036  0.038  1.980   1.0177e-01
   2_bss:  10.139  0.077  0.466 74.036  0.038  1.980   1.0177e-01
   2_xyz:   9.743  0.049  0.325 78.710  0.045  2.047   1.0145e-01
   2_adp:   9.743  0.049  0.325 78.710  0.045  2.047   1.0145e-01
   2_occ:   9.743  0.049  0.325 78.710  0.045  2.047   1.0145e-01
   3_bss:   9.743  0.049  0.325 78.710  0.045  2.047   1.0145e-01
   3_xyz:   8.071  0.056  0.254 77.223  0.028  2.318   4.7886e-02
   3_adp:   8.071  0.056  0.254 77.223  0.028  2.318   4.7886e-02
   3_occ:   8.071  0.056  0.254 77.223  0.028  2.318   4.7886e-02
   4_bss:   8.071  0.056  0.254 77.223  0.028  2.318   4.7886e-02
   4_xyz:   8.786  0.047  0.273 79.458  0.031  2.300   5.7020e-02
   4_adp:   8.786  0.047  0.273 79.458  0.031  2.300   5.7020e-02
   4_occ:   8.786  0.047  0.273 79.458  0.031  2.300   5.7020e-02
   5_bss:   8.786  0.047  0.273 79.458  0.031  2.300   5.7020e-02
   5_xyz:   8.038  0.051  0.239 82.006  0.034  2.281   4.6078e-02
   5_adp:   8.038  0.051  0.239 82.006  0.034  2.281   4.6078e-02
   5_occ:   8.038  0.051  0.239 82.006  0.034  2.281   4.6078e-02
   5_bss:   8.038  0.051  0.239 82.006  0.034  2.281   4.6078e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  87.84   0.00  17.94  78.55   0.00  15.03  87.84   0.00  33.80
   1_occ:  87.84   0.00  17.94  78.55   0.00  15.03  87.84   0.00  33.80
   2_bss:  87.84   0.00  17.94  78.55   0.00  15.03  87.84   0.00  33.80
   2_xyz:  87.84   0.00  17.94  78.55   0.00  15.03  87.84   0.00  33.80
   2_adp:  81.31   0.00  17.51  80.04   0.00  14.22  81.31   1.43  35.44
   2_occ:  81.31   0.00  17.51  80.04   0.00  14.22  81.31   1.43  35.44
   3_bss:  81.31   0.00  17.51  80.04   0.00  14.22  81.31   1.43  35.44
   3_xyz:  81.31   0.00  17.51  80.04   0.00  14.22  81.31   1.43  35.44
   3_adp: 109.68   0.00  18.89 100.57   0.00  13.91 109.68   3.28  45.99
   3_occ: 109.68   0.00  18.89 100.57   0.00  13.91 109.68   3.28  45.99
   4_bss: 109.68   0.00  18.89 100.57   0.00  13.91 109.68   3.28  45.99
   4_xyz: 109.68   0.00  18.89 100.57   0.00  13.91 109.68   3.28  45.99
   4_adp: 100.07   0.00  17.20  96.76   0.00  12.51 100.07   5.74  42.75
   4_occ: 100.07   0.00  17.20  96.76   0.00  12.51 100.07   5.74  42.75
   5_bss: 100.07   0.00  17.20  96.76   0.00  12.51 100.07   5.74  42.75
   5_xyz: 100.07   0.00  17.20  96.76   0.00  12.51 100.07   5.74  42.75
   5_adp:  99.61   0.00  16.87  98.21   0.00  12.08  99.61   5.58  42.98
   5_occ:  99.61   0.00  16.87  98.21   0.00  12.08  99.61   5.58  42.98
   5_bss:  99.62   0.00  16.88  98.21   0.00  12.08  99.62   5.58  42.98
------------------------------------------------------------------------
 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:    1.917    0.022    0.394
   1_adp:    1.917    0.022    0.394
   1_occ:    1.917    0.022    0.394
   2_bss:    1.917    0.022    0.394
   2_xyz:    1.524    0.025    0.559
   2_adp:    1.524    0.025    0.559
   2_occ:    1.524    0.025    0.559
   3_bss:    1.524    0.025    0.559
   3_xyz:    1.692    0.065    0.685
   3_adp:    1.692    0.065    0.685
   3_occ:    1.692    0.065    0.685
   4_bss:    1.692    0.065    0.685
   4_xyz:    1.755    0.037    0.788
   4_adp:    1.755    0.037    0.788
   4_occ:    1.755    0.037    0.788
   5_bss:    1.755    0.037    0.788
   5_xyz:    1.888    0.079    0.832
   5_adp:    1.888    0.079    0.832
   5_occ:    1.888    0.079    0.832
   5_bss:    1.888    0.079    0.832
------------------------------------------------------------------------

CPU time actual refinement: 297.35


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_126/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/noshake/run_126/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_126/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_126/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_126/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 297.23 
  Macro-tasks:
    bulk solvent and scale       = 37.39  
    individual site refinement   = 125.81 
    weights calculation          = 24.75  
    collect and process          = 5.38   
    model show statistics        = 0.07   
    TOTAL for macro-tasks        = 193.40 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 94.88  
    alpha_beta                      = 6.90   
    target                          = 0.96   
    gradients_wrt_atomic_parameters = 103.79 
    fmodel                         = 5.97   
    r_factors                      = 0.23   
    phase_errors                   = 8.63   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 224.05 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.194 micro seconds
Total CPU time: 5.15 minutes
from_scatterers_fft:    652 calls, 94.63 s
gradients_fft:          597 calls, 92.37 s

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

# Date 2008-01-16 Time 04:03:14 PST -0800 (1200484994.11 s)
Start R-work = 0.4600, R-free = 0.4547 (no bulk solvent and anisotropic scale)
Final R-work = 0.1417, R-free = 0.1856 (no bulk solvent and anisotropic scale)

Start R-work = 0.4500, R-free = 0.4448
Final R-work = 0.1222, R-free = 0.1707