# Date 2008-01-16 Time 03:54:57 PST -0800 (1200484497.23 s)
#phil __OFF__

Command line arguments: "../99.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5450
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 99

-------------------------------------------------------------------------------
  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: (68.4938, 47.8686, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95056
Completeness in resolution range: 0.943593
Completeness with d_max=infinity: 0.940739

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9212
                             d_min =   1.9506

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: (68.4938, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95056
Completeness in resolution range: 0.943593
Completeness with d_max=infinity: 0.940739

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9216 -  4.1746 [2179/2208]  1958   221  10.1%
  bin  2:  4.1746 -  3.3255 [2091/2114]  1885   206   9.9%
  bin  3:  3.3255 -  2.9087 [2060/2085]  1851   209  10.1%
  bin  4:  2.9087 -  2.6444 [2029/2056]  1834   195   9.6%
  bin  5:  2.6444 -  2.4557 [2036/2069]  1825   211  10.4%
  bin  6:  2.4557 -  2.3115 [2025/2053]  1835   190   9.4%
  bin  7:  2.3115 -  2.1961 [2005/2041]  1798   207  10.3%
  bin  8:  2.1961 -  2.1008 [2003/2045]  1801   202  10.1%
  bin  9:  2.1008 -  2.0201 [1954/2029]  1760   194   9.9%
  bin 10:  2.0201 -  1.9506 [1207/2060]  1083   124  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_99/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.12 -     1.88: 21
        1.88 -     2.63: 143
        2.63 -     3.39: 4377
        3.39 -     4.14: 9529
        4.14 -     4.90: 14828
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.125 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.171 3.040 -x+1/2,-y+1,z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.319 3.270 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.359 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.375 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28893 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_99/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_99/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.8686 84.23025 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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5045   r_free= 0.5035   ksol= 0.00   Bsol= 0.00   scale= 0.877    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.302482                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6565 0.99   1416  159 0.4137 0.4213      6.6275      6.6823|
|  2:  4.6565 -  3.7148 0.99   1356  148 0.4549 0.4366      6.8633       6.843|
|  3:  3.7148 -  3.2507 0.99   1341  149 0.4752 0.4715      6.7108      6.7944|
|  4:  3.2507 -  2.9560 0.98   1317  141 0.4913 0.4820      6.5481      6.5292|
|  5:  2.9560 -  2.7456 0.99   1320  152 0.5267 0.5103      6.3912      6.3662|
|  6:  2.7456 -  2.5846 0.99   1318  145 0.5263 0.5241      6.2913      6.2034|
|  7:  2.5846 -  2.4557 0.98   1285  148 0.5449 0.5239      6.2664      6.2017|
|  8:  2.4557 -  2.3493 0.98   1317  136 0.5492 0.5780      6.1841      6.2383|
|  9:  2.3493 -  2.2591 0.99   1289  143 0.5754 0.5720       6.133      6.1573|
| 10:  2.2591 -  2.1814 0.99   1292  148 0.5420 0.5575      6.1216      6.1337|
| 11:  2.1814 -  2.1134 0.97   1283  140 0.5507 0.5769      6.0346      6.0418|
| 12:  2.1134 -  2.0532 0.98   1281  148 0.5428 0.5291        5.97      6.0054|
| 13:  2.0532 -  1.9992 0.90   1168  130 0.5361 0.5646      5.8953      5.8899|
| 14:  1.9992 -  1.9506 0.49    647   72 0.5458 0.5303      5.8475      5.6945|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6565  1416   159  0.62  41.44   0.81     0.65      93746.32|
|  2:  4.6565 -  3.7148  1356   148  0.62  41.94   0.88     0.72     137017.91|
|  3:  3.7148 -  3.2507  1341   149  0.51  50.77   0.91     0.71     143000.90|
|  4:  3.2507 -  2.9560  1317   141  0.43  57.60   0.91     0.63     121806.05|
|  5:  2.9560 -  2.7456  1320   152  0.35  63.27   0.87     0.53      94584.21|
|  6:  2.7456 -  2.5846  1318   145  0.31  66.87   0.87     0.45      79558.92|
|  7:  2.5846 -  2.4557  1285   148  0.25  71.35   0.87     0.34      73194.87|
|  8:  2.4557 -  2.3493  1317   136  0.19  75.48   0.88     0.30      70057.10|
|  9:  2.3493 -  2.2591  1289   143  0.15  78.96   0.87     0.24      66708.47|
| 10:  2.2591 -  2.1814  1292   148  0.15  78.50   0.95     0.24      60085.44|
| 11:  2.1814 -  2.1134  1283   140  0.13  80.58   0.91     0.20      55909.94|
| 12:  2.1134 -  2.0532  1281   148  0.12  81.01   0.94     0.20      52035.83|
| 13:  2.0532 -  1.9992  1168   130  0.11  81.51   0.95     0.19      44821.54|
| 14:  1.9992 -  1.9506   647    72  0.14  79.70   0.92     0.20      34667.59|
|alpha:            min =        0.19 max =            0.72 mean =         0.41|
|beta:             min =    34667.59 max =       143000.90 mean =     83014.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.30|
|phase err.(work): min =        0.00 max =           90.00 mean =        66.89|
|phase err.(test): min =        0.00 max =           90.00 mean =        66.92|
|-----------------------------------------------------------------------------|

============================== 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 = 20.768330             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.117   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.654066              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.266   (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 |  1.125 -  1.502:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.502 -  1.880:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.880 -  2.257:       51 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.257 -  2.635:       92 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.635 -  3.012:     2009 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.012 -  3.390:     2368 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.390 -  3.767:     4035 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.767 -  4.145:     5494 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.145 -  4.522:     6601 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.522 -  4.900:     8227 |
|-----------------------------------------------------------------------------|
|-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 |        0.271 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.125 |       1.834 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5045   r_free= 0.5035   ksol= 0.00   Bsol= 0.00   scale= 0.877    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.302482                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4987   r_free= 0.4961   ksol= 0.30   Bsol= 20.00   scale= 0.909   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,1.83,0.65,0.00,0.00,0.00); trace/3= 0.41                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.300082                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.899079             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.770   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.117028              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.752   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4987      final r-factor (work) = 0.4100          |
| start r-factor (free) = 0.4961      final r-factor (free) = 0.4309          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.4938 = 16.90 * 0.50 * 6.2989 + 1.00 * 0.2710                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.7663 = 16.90 * 0.50 * 6.2270 + 1.00 * 0.1507                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4100      final r-factor (work) = 0.3671          |
| start r-factor (free) = 0.4309      final r-factor (free) = 0.4413          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1889 = 2.12 * 1.00 * 6.2270 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0250 = 2.12 * 1.00 * 6.1385 + 1.00 * 0.0296                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.24  22.59    None  None   None       |
|    all(noH): 2823   0      0.00    100.24  22.59    None  None   None       |
|    Sol.    : 438    0      0.00    100.24  41.26    None  None   None       |
|    Mac.    : 2385   0      0.00    96.97   19.17    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 -  10.024:  806   |   5:    50.120 -  60.145:  148        |
|      1:    10.024 -  20.048:  758   |   6:    60.145 -  70.169:   68        |
|      2:    20.048 -  30.072:  463   |   7:    70.169 -  80.193:   34        |
|      3:    30.072 -  40.096:  315   |   8:    80.193 -  90.217:   18        |
|      4:    40.096 -  50.120:  202   |   9:    90.217 - 100.241:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3671 r_free = 0.4413             target_work(ml) = 6.145         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3666 r_free = 0.4404             target_work(ml) = 6.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3666   r_free= 0.4404   ksol= 0.30   Bsol= 20.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,1.83,0.65,0.00,0.00,0.00); trace/3= 0.41                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.144490                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3657   r_free= 0.4390   ksol= 0.33   Bsol= 50.00   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,1.81,1.07,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.143462                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.070594             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.822   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.333611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.544  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3657      final r-factor (work) = 0.3014          |
| start r-factor (free) = 0.4390      final r-factor (free) = 0.3700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.4885 = 16.07 * 0.50 * 6.1402 + 1.00 * 0.1503                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.9523 = 16.07 * 0.50 * 6.0787 + 1.00 * 0.1078                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3014      final r-factor (work) = 0.2755          |
| start r-factor (free) = 0.3700      final r-factor (free) = 0.3533          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1360 = 1.33 * 1.00 * 6.0787 + 1.00 * 0.0293                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9587 = 1.33 * 1.00 * 5.9509 + 1.00 * 0.0226                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.83  21.20    None  None   None       |
|    all(noH): 2823   0      0.00    110.83  21.20    None  None   None       |
|    Sol.    : 438    0      0.00    103.48  43.19    None  None   None       |
|    Mac.    : 2385   0      0.00    110.83  17.16    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 -  11.083: 1016   |   5:    55.414 -  66.497:   94        |
|      1:    11.083 -  22.166:  840   |   6:    66.497 -  77.580:   59        |
|      2:    22.166 -  33.248:  405   |   7:    77.580 -  88.663:   24        |
|      3:    33.248 -  44.331:  219   |   8:    88.663 -  99.745:   12        |
|      4:    44.331 -  55.414:  149   |   9:    99.745 - 110.828:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2755 r_free = 0.3533             target_work(ml) = 5.927         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2754 r_free = 0.3529             target_work(ml) = 5.926         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2754   r_free= 0.3529   ksol= 0.33   Bsol= 50.00   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,1.81,1.07,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.925641                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2751   r_free= 0.3525   ksol= 0.33   Bsol= 50.00   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.65,0.27,0.00,0.00,0.00); trace/3= -0.07                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.924378                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.675607              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.636  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.276382              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.779  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2751      final r-factor (work) = 0.2215          |
| start r-factor (free) = 0.3525      final r-factor (free) = 0.2873          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9700 = 6.68 * 0.50 * 5.9507 + 1.00 * 0.1078                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6024 = 6.68 * 0.50 * 5.8510 + 1.00 * 0.0728                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2215      final r-factor (work) = 0.2054          |
| start r-factor (free) = 0.2873      final r-factor (free) = 0.2595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6387 = 0.28 * 1.00 * 5.8510 + 1.00 * 0.0216                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5928 = 0.28 * 1.00 * 5.7105 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.37  19.26    None  None   None       |
|    all(noH): 2823   0      0.00    105.37  19.26    None  None   None       |
|    Sol.    : 438    0      3.91    101.36  42.23    None  None   None       |
|    Mac.    : 2385   0      0.00    105.37  15.05    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 -  10.537: 1065   |   5:    52.687 -  63.225:   97        |
|      1:    10.537 -  21.075:  963   |   6:    63.225 -  73.762:   39        |
|      2:    21.075 -  31.612:  295   |   7:    73.762 -  84.299:   20        |
|      3:    31.612 -  42.150:  188   |   8:    84.299 -  94.837:   13        |
|      4:    42.150 -  52.687:  137   |   9:    94.837 - 105.374:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2054 r_free = 0.2595             target_work(ml) = 5.659         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2047 r_free = 0.2585             target_work(ml) = 5.657         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2047   r_free= 0.2585   ksol= 0.33   Bsol= 50.00   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.65,0.27,0.00,0.00,0.00); trace/3= -0.07                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.657195                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2035   r_free= 0.2568   ksol= 0.32   Bsol= 40.13   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-0.84,-1.34,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.655791                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.459839              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.720  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.462103              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.580   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2035      final r-factor (work) = 0.1676          |
| start r-factor (free) = 0.2568      final r-factor (free) = 0.2166          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0996 = 2.46 * 0.50 * 5.7135 + 1.00 * 0.0724                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9130 = 2.46 * 0.50 * 5.5740 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1676      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2166      final r-factor (free) = 0.2083          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1612 = 1.46 * 1.00 * 5.5740 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9774 = 1.46 * 1.00 * 5.4472 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.72  19.29    None  None   None       |
|    all(noH): 2823   0      0.00    109.72  19.29    None  None   None       |
|    Sol.    : 438    0      0.00    102.88  47.24    None  None   None       |
|    Mac.    : 2385   0      0.00    109.72  14.16    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 -  10.972: 1187   |   5:    54.861 -  65.833:   92        |
|      1:    10.972 -  21.944:  966   |   6:    65.833 -  76.805:   63        |
|      2:    21.944 -  32.917:  215   |   7:    76.805 -  87.778:   29        |
|      3:    32.917 -  43.889:  136   |   8:    87.778 -  98.750:   12        |
|      4:    43.889 -  54.861:  114   |   9:    98.750 - 109.722:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1543 r_free = 0.2083             target_work(ml) = 5.426         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1541 r_free = 0.2082             target_work(ml) = 5.426         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1541   r_free= 0.2082   ksol= 0.32   Bsol= 40.13   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-0.84,-1.34,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.425876                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1546   r_free= 0.2082   ksol= 0.31   Bsol= 40.13   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.20,-1.27,-1.83,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.427456                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.960864              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.098  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.100087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.332  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1546      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.2082      final r-factor (free) = 0.1880          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1261 = 2.96 * 0.50 * 5.4502 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0113 = 2.96 * 0.50 * 5.3676 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1331      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.1880      final r-factor (free) = 0.1768          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5502 = 0.10 * 1.00 * 5.3676 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5445 = 0.10 * 1.00 * 5.3113 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.28  18.07    None  None   None       |
|    all(noH): 2823   0      0.00    105.28  18.07    None  None   None       |
|    Sol.    : 438    0      2.61    98.85   42.49    None  None   None       |
|    Mac.    : 2385   0      0.00    105.28  13.58    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 -  10.528: 1078   |   5:    52.641 -  63.170:   82        |
|      1:    10.528 -  21.057: 1132   |   6:    63.170 -  73.698:   45        |
|      2:    21.057 -  31.585:  196   |   7:    73.698 -  84.226:   18        |
|      3:    31.585 -  42.113:  136   |   8:    84.226 -  94.755:   12        |
|      4:    42.113 -  52.641:  120   |   9:    94.755 - 105.283:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1322 r_free = 0.1768             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1319 r_free = 0.1766             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1319   r_free= 0.1766   ksol= 0.31   Bsol= 40.13   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.20,-1.27,-1.83,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278441                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6565 0.99   1416  159 0.1010 0.1413      5.4308      5.6191|
|  2:  4.6565 -  3.7148 0.99   1356  148 0.0943 0.1194       5.527      5.7631|
|  3:  3.7148 -  3.2507 0.99   1341  149 0.1213 0.1719       5.598      5.9362|
|  4:  3.2507 -  2.9560 0.98   1317  141 0.1496 0.1765       5.598      5.7484|
|  5:  2.9560 -  2.7456 0.99   1320  152 0.1594 0.1846      5.4696      5.5928|
|  6:  2.7456 -  2.5846 0.99   1318  145 0.1527 0.2398      5.3693      5.6049|
|  7:  2.5846 -  2.4557 0.98   1285  148 0.1441 0.1854      5.2952       5.469|
|  8:  2.4557 -  2.3493 0.98   1317  136 0.1467 0.1814      5.2356      5.4203|
|  9:  2.3493 -  2.2591 0.99   1289  143 0.1448 0.2029      5.1657       5.377|
| 10:  2.2591 -  2.1814 0.99   1292  148 0.1371 0.1908      5.1193       5.307|
| 11:  2.1814 -  2.1134 0.97   1283  140 0.1362 0.1997      5.0354      5.2898|
| 12:  2.1134 -  2.0532 0.98   1281  148 0.1379 0.1954      4.9873      5.2473|
| 13:  2.0532 -  1.9992 0.90   1168  130 0.1343 0.1990      4.9096       5.176|
| 14:  1.9992 -  1.9506 0.49    647   72 0.1350 0.1811      4.8569      4.9827|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6565  1416   159  0.93  10.47   0.98     0.95       8704.76|
|  2:  4.6565 -  3.7148  1356   148  0.94   9.47   1.03     1.02      11099.33|
|  3:  3.7148 -  3.2507  1341   149  0.92  13.20   1.04     1.03      13030.83|
|  4:  3.2507 -  2.9560  1317   141  0.90  16.25   1.03     1.02      13056.59|
|  5:  2.9560 -  2.7456  1320   152  0.88  18.58   1.02     0.99      10727.10|
|  6:  2.7456 -  2.5846  1318   145  0.88  18.63   0.99     0.95       9127.51|
|  7:  2.5846 -  2.4557  1285   148  0.88  18.31   1.00     0.96       8027.60|
|  8:  2.4557 -  2.3493  1317   136  0.88  18.61   1.02     0.99       7411.46|
|  9:  2.3493 -  2.2591  1289   143  0.88  18.56   1.02     0.99       6384.04|
| 10:  2.2591 -  2.1814  1292   148  0.89  17.56   1.02     0.98       5746.65|
| 11:  2.1814 -  2.1134  1283   140  0.89  18.02   1.02     0.98       5041.50|
| 12:  2.1134 -  2.0532  1281   148  0.89  17.25   1.02     1.01       4526.23|
| 13:  2.0532 -  1.9992  1168   130  0.88  18.10   1.02     1.02       4100.36|
| 14:  1.9992 -  1.9506   647    72  0.88  18.58   1.00     0.95       3601.51|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     3601.51 max =        13056.59 mean =      8131.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.39|
|phase err.(test): min =        0.00 max =           89.89 mean =        16.02|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1765   ksol= 0.32   Bsol= 40.13   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.43,-1.60,-2.05,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.278638                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1765   ksol= 0.32   Bsol= 40.13   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.43,-1.60,-2.05,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.278638                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6565 0.99   1416  159 0.1010 0.1419      5.4341       5.621|
|  2:  4.6565 -  3.7148 0.99   1356  148 0.0941 0.1189      5.5262      5.7608|
|  3:  3.7148 -  3.2507 0.99   1341  149 0.1213 0.1718      5.5972      5.9359|
|  4:  3.2507 -  2.9560 0.98   1317  141 0.1496 0.1765       5.598      5.7487|
|  5:  2.9560 -  2.7456 0.99   1320  152 0.1595 0.1846      5.4696      5.5926|
|  6:  2.7456 -  2.5846 0.99   1318  145 0.1527 0.2396      5.3691      5.6048|
|  7:  2.5846 -  2.4557 0.98   1285  148 0.1441 0.1855       5.295      5.4689|
|  8:  2.4557 -  2.3493 0.98   1317  136 0.1466 0.1815      5.2358      5.4212|
|  9:  2.3493 -  2.2591 0.99   1289  143 0.1446 0.2030      5.1656      5.3769|
| 10:  2.2591 -  2.1814 0.99   1292  148 0.1371 0.1908      5.1193      5.3078|
| 11:  2.1814 -  2.1134 0.97   1283  140 0.1362 0.1998      5.0353      5.2897|
| 12:  2.1134 -  2.0532 0.98   1281  148 0.1380 0.1955      4.9879      5.2477|
| 13:  2.0532 -  1.9992 0.90   1168  130 0.1343 0.1988        4.91      5.1757|
| 14:  1.9992 -  1.9506 0.49    647   72 0.1350 0.1811      4.8568      4.9826|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6565  1416   159  0.93  10.54   0.98     0.95       8802.87|
|  2:  4.6565 -  3.7148  1356   148  0.94   9.48   1.02     1.01      11112.04|
|  3:  3.7148 -  3.2507  1341   149  0.92  13.17   1.04     1.02      12990.89|
|  4:  3.2507 -  2.9560  1317   141  0.90  16.24   1.02     1.01      13052.34|
|  5:  2.9560 -  2.7456  1320   152  0.88  18.57   1.01     0.99      10721.49|
|  6:  2.7456 -  2.5846  1318   145  0.88  18.62   0.98     0.94       9122.42|
|  7:  2.5846 -  2.4557  1285   148  0.88  18.31   0.99     0.95       8028.49|
|  8:  2.4557 -  2.3493  1317   136  0.88  18.61   1.01     0.98       7418.29|
|  9:  2.3493 -  2.2591  1289   143  0.88  18.55   1.00     0.98       6387.89|
| 10:  2.2591 -  2.1814  1292   148  0.89  17.56   1.01     0.97       5749.38|
| 11:  2.1814 -  2.1134  1283   140  0.89  18.02   1.01     0.96       5043.06|
| 12:  2.1134 -  2.0532  1281   148  0.89  17.26   1.00     0.99       4531.35|
| 13:  2.0532 -  1.9992  1168   130  0.88  18.10   1.01     1.00       4101.48|
| 14:  1.9992 -  1.9506   647    72  0.88  18.58   0.99     0.94       3598.44|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     3598.44 max =        13052.34 mean =      8137.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.39|
|phase err.(test): min =        0.00 max =           89.96 mean =        16.04|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.29  18.07    None  None   None       |
|    all(noH): 2823   0      0.00    105.29  18.07    None  None   None       |
|    Sol.    : 438    0      2.61    98.85   42.50    None  None   None       |
|    Mac.    : 2385   0      0.00    105.29  13.58    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 -  10.531: 1078   |   5:    52.644 -  63.173:   82        |
|      1:    10.531 -  21.060: 1132   |   6:    63.173 -  73.701:   45        |
|      2:    21.060 -  31.588:  196   |   7:    73.701 -  84.229:   18        |
|      3:    31.588 -  42.116:  136   |   8:    84.229 -  94.758:   12        |
|      4:    42.116 -  52.644:  120   |   9:    94.758 - 105.286:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.415 - 5.917
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 314
   mapped sites are within: 0.719 - 5.917

peak=    9.684 closest distance to " O   HOH Z 138 " =    1.501
peak=    8.881 closest distance to " CB  SER A 216 " =    1.100
peak=    7.228 closest distance to " O   HOH Z 102 " =    1.254
peak=    6.526 closest distance to " O   HOH Z  92 " =    1.944
peak=    6.510 closest distance to " O   HOH Z  45 " =    1.365
peak=    6.356 closest distance to " O   HOH Z 120 " =    1.465
peak=    6.301 closest distance to " O   HOH Z  46 " =    1.383
peak=    6.239 closest distance to " O   HOH Z 199 " =    1.733
peak=    5.883 closest distance to " O   HOH Z 278 " =    1.655
peak=    5.546 closest distance to " O   HOH Z 117 " =    1.615
peak=    5.542 closest distance to " O   HOH Z 404 " =    1.312
peak=    5.470 closest distance to " O   HOH Z 401 " =    2.096
peak=    5.465 closest distance to " O   HOH Z 389 " =    2.020
peak=    5.296 closest distance to " O   HOH Z  52 " =    1.706
peak=    5.222 closest distance to " CG  PRO A  54 " =    1.217
peak=    5.220 closest distance to " O   HOH Z 124 " =    1.548
peak=    5.148 closest distance to " O   HOH Z  97 " =    1.736
peak=    5.016 closest distance to " O   HOH Z 402 " =    1.680
peak=    4.995 closest distance to " O   HOH Z 193 " =    1.913
peak=    4.948 closest distance to " O   HOH Z  80 " =    2.139
peak=    4.947 closest distance to " O   HOH Z  65 " =    1.155
peak=    4.946 closest distance to " O   HOH Z 247 " =    1.539
peak=    4.896 closest distance to " NH2 ARG A  56 " =    2.105
peak=    4.871 closest distance to " C   PRO A 198 " =    1.679
peak=    4.840 closest distance to " O   HOH Z 116 " =    1.235
peak=    4.828 closest distance to " O   HOH Z 416 " =    1.279
peak=    4.828 closest distance to " CG AARG A 275 " =    1.219
peak=    4.776 closest distance to " CB  ARG A 275 " =    0.991
peak=    4.765 closest distance to " CG  GLN A  77 " =    0.910
peak=    4.757 closest distance to " OD1 ASN A  60 " =    0.998
peak=    4.742 closest distance to " CA  TYR A  30 " =    1.059
peak=    4.739 closest distance to " O   HOH Z 163 " =    1.749
peak=    4.620 closest distance to " O   HOH Z  68 " =    1.823
peak=    4.614 closest distance to " O   HOH Z 412 " =    3.486
peak=    4.591 closest distance to " O   HOH Z  43 " =    1.718
peak=    4.584 closest distance to " CB  ASN A 187 " =    1.856
peak=    4.568 closest distance to " CD  ARG A 269 " =    1.063
peak=    4.554 closest distance to " O   HOH Z 214 " =    1.439
peak=    4.515 closest distance to " O   HOH Z 406 " =    1.556
peak=    4.465 closest distance to " CG  ARG A  66 " =    1.309
peak=    4.424 closest distance to " O   HOH Z 127 " =    1.201
peak=    4.396 closest distance to " CB  SER A  63 " =    1.221
peak=    4.377 closest distance to " O   HOH Z 128 " =    1.923
peak=    4.374 closest distance to " O   HOH Z  49 " =    1.281
peak=    4.366 closest distance to " CG  PRO A 213 " =    1.322
peak=    4.349 closest distance to " O   HOH Z 203 " =    1.910
peak=    4.346 closest distance to " O   HOH Z 134 " =    2.183
peak=    4.312 closest distance to " O   HOH Z 316 " =    2.329
peak=    4.304 closest distance to " O   HOH Z 155 " =    1.790
peak=    4.294 closest distance to " O   HOH Z 279 " =    1.082
peak=    4.290 closest distance to " O   HOH Z 209 " =    2.292
peak=    4.251 closest distance to " O   HOH Z 154 " =    1.954
peak=    4.233 closest distance to " CB  GLN A  73 " =    0.965
peak=    4.225 closest distance to " CG  PRO A 198 " =    1.405
peak=    4.210 closest distance to " CG  PRO A  90 " =    1.371
peak=    4.206 closest distance to " O   HOH Z 249 " =    1.357
peak=    4.195 closest distance to " O   HOH Z 236 " =    1.512
peak=    4.191 closest distance to " O   HOH Z 133 " =    1.412
peak=    4.186 closest distance to " O   HOH Z 132 " =    1.985
peak=    4.175 closest distance to " CB  VAL A 265 " =    1.298
peak=    4.174 closest distance to " O   HOH Z 232 " =    2.261
peak=    4.172 closest distance to " NH2 ARG A  56 " =    1.368
peak=    4.154 closest distance to " O   HOH Z 394 " =    1.619
peak=    4.142 closest distance to " CB  ASN A 285 " =    0.942
peak=    4.140 closest distance to " CA  ALA A  21 " =    1.080
peak=    4.080 closest distance to " O   SER A  87 " =    2.167
peak=    4.077 closest distance to " O   HOH Z 234 " =    3.697
peak=    4.040 closest distance to " O   HOH Z 427 " =    3.242
peak=    4.024 closest distance to " NZ  LYS A 117 " =    3.345
peak=    4.011 closest distance to " NH1AARG A 275 " =    1.270
peak=    3.995 closest distance to " O   HOH Z 433 " =    1.591
peak=    3.993 closest distance to " CD  ARG A 195 " =    1.078
peak=    3.990 closest distance to " CB  SER A 141 " =    0.924
peak=    3.977 closest distance to " CB  VAL A 202 " =    1.689
peak=    3.966 closest distance to " NZ  LYS A 117 " =    0.907
peak=    3.950 closest distance to " O   HOH Z 276 " =    1.780
peak=    3.940 closest distance to " O   HOH Z 371 " =    3.177
peak=    3.924 closest distance to " O   HOH Z 369 " =    2.096
peak=    3.912 closest distance to " CB  GLN A 223 " =    1.414
peak=    3.908 closest distance to " NH2 ARG A 156 " =    1.218
peak=    3.893 closest distance to " O   HOH Z 210 " =    1.114
peak=    3.877 closest distance to " O   HOH Z 272 " =    1.927
peak=    3.876 closest distance to " O   HOH Z 132 " =    2.361
peak=    3.875 closest distance to " O   HOH Z 196 " =    1.268
peak=    3.872 closest distance to " CB  GLU A 152 " =    1.081
peak=    3.866 closest distance to " NH2AARG A 145 " =    2.033
peak=    3.865 closest distance to " ND2 ASN A 187 " =    1.725
peak=    3.862 closest distance to " CB  GLN A 194 " =    0.903
peak=    3.861 closest distance to " O   HOH Z 431 " =    1.275
peak=    3.855 closest distance to " O   HOH Z 424 " =    0.986
peak=    3.854 closest distance to " CD  PRO A  54 " =    0.951
peak=    3.853 closest distance to " O   HOH Z  85 " =    1.911
peak=    3.852 closest distance to " CB AVAL A  41 " =    1.037
peak=    3.846 closest distance to " O   HOH Z 225 " =    2.143
peak=    3.843 closest distance to " O   HOH Z  11 " =    1.347
peak=    3.842 closest distance to " O   HOH Z 192 " =    1.788
peak=    3.834 closest distance to " CG  LYS A 166 " =    1.531
peak=    3.833 closest distance to " O   HOH Z 130 " =    1.149
peak=    3.831 closest distance to " O   HOH Z 365 " =    1.425
peak=    3.829 closest distance to " O   HOH Z 326 " =    1.520
peak=    3.828 closest distance to " O   HOH Z 315 " =    1.770
peak=    3.822 closest distance to " O   GLY A  91 " =    1.349
peak=    3.818 closest distance to " O   HOH Z 298 " =    2.029
peak=    3.817 closest distance to " O   HOH Z 334 " =    1.738
peak=    3.794 closest distance to " O   HOH Z 408 " =    1.840
peak=    3.781 closest distance to " O   HOH Z  97 " =    1.804
peak=    3.776 closest distance to " OD1 ASP A 253 " =    1.886
peak=    3.767 closest distance to " O   HOH Z 156 " =    2.496
peak=    3.767 closest distance to " CB  SER A  62 " =    0.817
peak=    3.760 closest distance to " N   ASN A  39 " =    1.167
peak=    3.757 closest distance to " CE  LYS A 119 " =    1.126
peak=    3.757 closest distance to " CG2 ILE A 120 " =    1.203
peak=    3.749 closest distance to " O   HOH Z  63 " =    2.147
peak=    3.735 closest distance to " O   HOH Z 109 " =    1.604
peak=    3.734 closest distance to " O   HOH Z 402 " =    2.460
peak=    3.730 closest distance to " CD  LYS A  76 " =    1.555
peak=    3.713 closest distance to " CG  PRO A 243 " =    1.317
peak=    3.710 closest distance to " O   HOH Z 425 " =    1.482
peak=    3.699 closest distance to " OH  TYR A  30 " =    1.371
peak=    3.697 closest distance to " O   HOH Z 368 " =    1.137
peak=    3.686 closest distance to " CB  TRP A 179 " =    0.958
peak=    3.683 closest distance to " OE1 GLN A  11 " =    1.877
peak=    3.680 closest distance to " O   HOH Z 339 " =    1.319
peak=    3.680 closest distance to " O   ARG A 102 " =    2.285
peak=    3.674 closest distance to " CD  ARG A 139 " =    1.323
peak=    3.673 closest distance to " O   HOH Z 414 " =    1.748
peak=    3.662 closest distance to " O  BHOH Z  74 " =    1.368
peak=    3.660 closest distance to " CB  GLN A 183 " =    1.145
peak=    3.655 closest distance to " O   HOH Z  38 " =    1.442
peak=    3.653 closest distance to " O   HOH Z  40 " =    1.917
peak=    3.652 closest distance to " CA  ALA A  51 " =    0.963
peak=    3.652 closest distance to " O   HOH Z  15 " =    2.238
peak=    3.650 closest distance to " O   HOH Z 128 " =    1.498
peak=    3.642 closest distance to " O   HOH Z 108 " =    1.645
peak=    3.642 closest distance to " O   HOH Z 345 " =    2.164
peak=    3.633 closest distance to " O   HOH Z 255 " =    1.203
peak=    3.631 closest distance to " CB  ARG A 102 " =    0.818
peak=    3.631 closest distance to " O   HOH Z 423 " =    1.963
peak=    3.630 closest distance to " O   HOH Z 287 " =    1.832
peak=    3.620 closest distance to " O   HOH Z 279 " =    2.102
peak=    3.613 closest distance to " CG1 ILE A  33 " =    1.212
peak=    3.607 closest distance to " O   HOH Z  48 " =    1.798
peak=    3.607 closest distance to " O   HOH Z 154 " =    2.189
peak=    3.600 closest distance to " O   HOH Z  78 " =    1.666
peak=    3.600 closest distance to " CB  ASP A 191 " =    1.196
peak=    3.597 closest distance to " O   HOH Z 145 " =    1.972
peak=    3.591 closest distance to " O   HOH Z 361 " =    2.871
peak=    3.589 closest distance to " CB  ASN A 148 " =    1.847
peak=    3.586 closest distance to " O   HOH Z   6 " =    2.257
peak=    3.581 closest distance to " OG BSER A 210 " =    1.328
peak=    3.573 closest distance to " CB  GLN A  58 " =    0.988
peak=    3.572 closest distance to " O   HOH Z 132 " =    1.863
peak=    3.563 closest distance to " CH2 TRP A 274 " =    2.157
peak=    3.556 closest distance to " O   HOH Z 225 " =    1.943
peak=    3.554 closest distance to " NE2 GLN A  11 " =    1.055
peak=    3.543 closest distance to " O   HOH Z 222 " =    1.317
peak=    3.541 closest distance to " O   SER A 164 " =    0.994
peak=    3.540 closest distance to " O   HOH Z 124 " =    2.934
peak=    3.539 closest distance to " O   HOH Z  44 " =    1.998
peak=    3.539 closest distance to " O   HOH Z 113 " =    2.252
peak=    3.538 closest distance to " CG  MET A 185 " =    1.298
peak=    3.537 closest distance to " O   HOH Z 129 " =    3.056
peak=    3.536 closest distance to " CB  PRO A 163 " =    3.909
peak=    3.523 closest distance to " O   HOH Z 246 " =    1.672
peak=    3.520 closest distance to " O   HOH Z  39 " =    1.670
peak=    3.518 closest distance to " CD2 LEU A 297 " =    1.059
peak=    3.517 closest distance to " O   HOH Z 192 " =    1.429
peak=    3.517 closest distance to " O   HOH Z 114 " =    1.885
peak=    3.504 closest distance to " O   HOH Z  35 " =    2.051
peak=    3.500 closest distance to " CG2 THR A 220 " =    0.787
peak=    3.492 closest distance to " CA  THR A 221 " =    1.035
peak=    3.483 closest distance to " CB ASER A 164 " =    0.880
peak=    3.479 closest distance to " O   HOH Z  54 " =    1.309
peak=    3.474 closest distance to " O   HOH Z 195 " =    3.745
peak=    3.470 closest distance to " O   HOH Z 193 " =    2.235
peak=    3.470 closest distance to " NE2 HIS A 115 " =    0.866
peak=    3.462 closest distance to " O   HOH Z 217 " =    2.146
peak=    3.460 closest distance to " CB  PRO A 198 " =    1.375
peak=    3.460 closest distance to " O   HOH Z  63 " =    1.952
peak=    3.455 closest distance to " O   ALA A 165 " =    1.137
peak=    3.449 closest distance to " CG2 VAL A 197 " =    1.235
peak=    3.444 closest distance to " O   HOH Z 428 " =    1.126
peak=    3.442 closest distance to " O   HOH Z  56 " =    2.000
peak=    3.439 closest distance to " CB  ARG A 139 " =    1.320
peak=    3.438 closest distance to " O   HOH Z 108 " =    1.922
peak=    3.437 closest distance to " O   HOH Z 274 " =    2.159
peak=    3.430 closest distance to " O   HOH Z   1 " =    2.883
peak=    3.428 closest distance to " CB  SER A   3 " =    1.297
peak=    3.427 closest distance to " O   HOH Z 138 " =    1.450
peak=    3.423 closest distance to " NZ  LYS A 119 " =    1.404
peak=    3.423 closest distance to " O   HOH Z 227 " =    1.669
peak=    3.413 closest distance to " CB  GLU A 277 " =    0.735
peak=    3.412 closest distance to " O   HOH Z 189 " =    1.753
peak=    3.407 closest distance to " O   HOH Z 298 " =    2.123
peak=    3.406 closest distance to " O   HOH Z 303 " =    2.133
peak=    3.404 closest distance to " O   HOH Z 120 " =    1.932
peak=    3.404 closest distance to " O   HOH Z 377 " =    1.192
peak=    3.402 closest distance to " CG  PRO A 280 " =    0.719
peak=    3.400 closest distance to " O   HOH Z 426 " =    1.664
peak=    3.400 closest distance to " CB  GLU A 128 " =    1.325
peak=    3.398 closest distance to " O   HOH Z 427 " =    3.289
peak=    3.396 closest distance to " CB  ASN A 148 " =    1.182
peak=    3.396 closest distance to " CB  LEU A 228 " =    1.350
peak=    3.396 closest distance to " NE1 TRP A 274 " =    0.766
peak=    3.395 closest distance to " CB  SER A  26 " =    0.977
peak=    3.394 closest distance to " CB  TYR A 169 " =    0.763
peak=    3.391 closest distance to " N   ASN A 252 " =    1.086
peak=    3.381 closest distance to " CA  ARG A  66 " =    1.039
peak=    3.376 closest distance to " O   GLY A  57 " =    0.991
peak=    3.375 closest distance to " O   HOH Z 114 " =    5.917
peak=    3.375 closest distance to " O   HOH Z 291 " =    1.723
peak=    3.374 closest distance to " O   HOH Z 173 " =    2.154
peak=    3.374 closest distance to " CB  ARG A 190 " =    1.838
peak=    3.372 closest distance to " CD2 TRP A 179 " =    1.464
peak=    3.371 closest distance to " CD2 PHE A 225 " =    1.208
peak=    3.369 closest distance to " CG1BVAL A  72 " =    1.597
peak=    3.367 closest distance to " O   HOH Z 111 " =    3.593
peak=    3.365 closest distance to " CZ2 TRP A 179 " =    1.800
peak=    3.363 closest distance to " O   HOH Z 173 " =    1.716
peak=    3.361 closest distance to " ND1 HIS A  81 " =    1.295
peak=    3.356 closest distance to " O   HOH Z 380 " =    1.927
peak=    3.355 closest distance to " CB  TRP A 179 " =    1.670
peak=    3.344 closest distance to " O   HOH Z  66 " =    2.184
peak=    3.339 closest distance to " CA  ALA A 233 " =    1.482
peak=    3.337 closest distance to " O   HOH Z  85 " =    1.896
peak=    3.336 closest distance to " OD2 ASP A 286 " =    2.420
peak=    3.332 closest distance to " O   HOH Z 357 " =    1.170
peak=    3.331 closest distance to " O   HOH Z 166 " =    1.358
peak=    3.319 closest distance to " CA  ASN A 215 " =    1.005
peak=    3.319 closest distance to " O   HOH Z 137 " =    1.751
peak=    3.317 closest distance to " O   HOH Z  78 " =    2.298
peak=    3.316 closest distance to " CB  GLN A  88 " =    1.129
peak=    3.316 closest distance to " O   HOH Z 403 " =    2.258
peak=    3.313 closest distance to " CD BLYS A 290 " =    1.029
peak=    3.309 closest distance to " CA  ASP A 191 " =    0.951
peak=    3.302 closest distance to " O   HOH Z 136 " =    1.085
peak=    3.302 closest distance to " O   HOH Z 170 " =    1.682
peak=    3.301 closest distance to " N   HIS A 108 " =    1.804
peak=    3.296 closest distance to " CA  ARG A  36 " =    1.138
peak=    3.288 closest distance to " O   HOH Z 327 " =    1.812
peak=    3.287 closest distance to " CA  GLY A 196 " =    0.949
peak=    3.285 closest distance to " O   HOH Z 188 " =    1.083
peak=    3.281 closest distance to " CA  ALA A 295 " =    0.962
peak=    3.279 closest distance to " O   HOH Z 346 " =    1.441
peak=    3.268 closest distance to " NH1 ARG A  14 " =    1.064
peak=    3.267 closest distance to " O   HOH Z 150 " =    1.488
peak=    3.265 closest distance to " CD  LYS A 193 " =    1.052
peak=    3.262 closest distance to " CD2 LEU A 255 " =    1.015
peak=    3.261 closest distance to " O   HOH Z 154 " =    2.991
peak=    3.258 closest distance to " CB  PRO A  90 " =    2.010
peak=    3.251 closest distance to " O   HOH Z 380 " =    3.032
peak=    3.248 closest distance to " O   HOH Z 118 " =    1.457
peak=    3.246 closest distance to " O   HOH Z 155 " =    2.648
peak=    3.241 closest distance to " O   HOH Z 145 " =    2.122
peak=    3.238 closest distance to " CD  LYS A 119 " =    1.793
peak=    3.238 closest distance to " CA  SER A  63 " =    1.467
peak=    3.237 closest distance to " CD2 HIS A  81 " =    1.490
peak=    3.237 closest distance to " CD  LYS A 166 " =    1.492
peak=    3.237 closest distance to " N   GLY A 133 " =    0.722
peak=    3.235 closest distance to " O   HOH Z 130 " =    2.473
peak=    3.233 closest distance to " O   HOH Z 278 " =    1.564
peak=    3.233 closest distance to " O   HOH Z 395 " =    1.453
peak=    3.232 closest distance to " NH1BARG A 145 " =    1.402
peak=    3.228 closest distance to " O   HOH Z 412 " =    3.461
peak=    3.222 closest distance to " CB  LEU A   5 " =    1.047
peak=    3.222 closest distance to " O   HOH Z  50 " =    1.656
peak=    3.220 closest distance to " O   HOH Z 215 " =    1.703
peak=    3.217 closest distance to " O   HOH Z 197 " =    1.950
peak=    3.215 closest distance to " O   HOH Z 158 " =    3.382
peak=    3.214 closest distance to " N   ASP A 162 " =    1.467
peak=    3.205 closest distance to " O   HOH Z 357 " =    1.640
peak=    3.202 closest distance to " CB  TRP A 123 " =    1.345
peak=    3.195 closest distance to " O   HOH Z 343 " =    2.283
peak=    3.194 closest distance to " O   HOH Z  50 " =    2.996
peak=    3.194 closest distance to " O   HOH Z  59 " =    1.881
peak=    3.192 closest distance to " O   HOH Z 214 " =    2.930
peak=    3.192 closest distance to " CA  SER A  87 " =    0.927
peak=    3.187 closest distance to " CB  ALA A 248 " =    1.375
peak=    3.182 closest distance to " O   HOH Z 379 " =    1.621
peak=    3.178 closest distance to " O   HOH Z 147 " =    0.967
peak=    3.177 closest distance to " O   HOH Z 241 " =    2.041
peak=    3.174 closest distance to " CB  ALA A  34 " =    0.820
peak=    3.168 closest distance to " O   HOH Z 261 " =    2.131
peak=    3.158 closest distance to " O   HOH Z 261 " =    1.726
peak=    3.156 closest distance to " O   HOH Z 142 " =    1.229
peak=    3.155 closest distance to " OG ASER A 216 " =    1.545
peak=    3.155 closest distance to " OG1 THR A 294 " =    2.361
peak=    3.145 closest distance to " O   HOH Z 142 " =    1.295
peak=    3.139 closest distance to " CA  LYS A 117 " =    1.253
peak=    3.133 closest distance to " OG BSER A 164 " =    2.280
peak=    3.130 closest distance to " O   HOH Z  88 " =    3.487
peak=    3.128 closest distance to " O   HOH Z 258 " =    2.211
peak=    3.126 closest distance to " OG  SER A 245 " =    1.426
peak=    3.125 closest distance to " CB  MET A  47 " =    1.290
peak=    3.125 closest distance to " O   HOH Z 336 " =    1.583
peak=    3.124 closest distance to " ND2 ASN A 209 " =    1.589
peak=    3.120 closest distance to " CA  ILE A  20 " =    0.734
peak=    3.117 closest distance to " O   HOH Z 424 " =    3.764
peak=    3.116 closest distance to " N   ARG A 156 " =    1.463
peak=    3.115 closest distance to " CA  LEU A 282 " =    1.123
peak=    3.114 closest distance to " O   HOH Z 128 " =    1.373
peak=    3.114 closest distance to " O   ASN A 217 " =    1.189
peak=    3.113 closest distance to " O   HOH Z 298 " =    3.916
peak=    3.106 closest distance to " CB  PHE A  16 " =    1.225
peak=    3.081 closest distance to " O   HOH Z 268 " =    1.585
peak=    3.080 closest distance to " O   HOH Z 434 " =    4.916
peak=    3.061 closest distance to " NE BARG A 145 " =    0.902
peak=    3.037 closest distance to " O   HOH Z   1 " =    2.776
peak=    3.025 closest distance to " O   HOH Z  40 " =    2.471
peak=    3.005 closest distance to " NH2AARG A 190 " =    1.291

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.501 - 5.353
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 201
   mapped sites are within: 0.708 - 5.353

peak=   -4.929 closest distance to " O   HOH Z  52 " =    1.104
peak=   -4.722 closest distance to " CD1 TRP A 179 " =    1.057
peak=   -4.713 closest distance to " O   HOH Z 401 " =    0.749
peak=   -4.568 closest distance to " O   HOH Z 210 " =    0.856
peak=   -4.453 closest distance to " O   HOH Z  13 " =    1.566
peak=   -4.434 closest distance to " O   HOH Z 221 " =    1.227
peak=   -4.360 closest distance to " C   HIS A 108 " =    1.068
peak=   -4.351 closest distance to " O   HOH Z 102 " =    0.815
peak=   -4.339 closest distance to " C   THR A 279 " =    1.255
peak=   -4.320 closest distance to " OG ASER A 216 " =    0.950
peak=   -4.302 closest distance to " O   HOH Z 198 " =    1.097
peak=   -4.285 closest distance to " O   HOH Z 423 " =    2.366
peak=   -4.269 closest distance to " O   HOH Z 422 " =    1.103
peak=   -4.197 closest distance to " O   HOH Z 266 " =    4.267
peak=   -4.102 closest distance to " O   HOH Z 290 " =    0.708
peak=   -4.072 closest distance to " O   HOH Z 120 " =    0.962
peak=   -4.033 closest distance to " OG  SER A  97 " =    2.105
peak=   -4.031 closest distance to " O   TRP A  92 " =    1.861
peak=   -4.027 closest distance to " CG2 THR A 182 " =    2.399
peak=   -4.025 closest distance to " CD2 LEU A 237 " =    2.847
peak=   -4.008 closest distance to " CA  VAL A  67 " =    2.818
peak=   -3.978 closest distance to " O   HOH Z  29 " =    0.800
peak=   -3.968 closest distance to " C   GLY A  91 " =    1.470
peak=   -3.906 closest distance to " ND2 ASN A  39 " =    1.239
peak=   -3.901 closest distance to " CA  SER A 164 " =    1.924
peak=   -3.887 closest distance to " O   GLN A  11 " =    1.166
peak=   -3.841 closest distance to " O  BHOH Z 338 " =    1.591
peak=   -3.841 closest distance to " O   HOH Z 147 " =    0.917
peak=   -3.836 closest distance to " O   PRO A  54 " =    1.648
peak=   -3.812 closest distance to " O   HOH Z 418 " =    1.302
peak=   -3.803 closest distance to " O   SER A 273 " =    1.134
peak=   -3.756 closest distance to " CB  SER A  26 " =    1.591
peak=   -3.725 closest distance to " C   GLY A 133 " =    1.192
peak=   -3.720 closest distance to " CD2 TYR A  30 " =    2.882
peak=   -3.719 closest distance to " O   GLN A  58 " =    0.865
peak=   -3.710 closest distance to " OG ASER A 134 " =    1.289
peak=   -3.699 closest distance to " CG2AVAL A  41 " =    2.790
peak=   -3.687 closest distance to " O   HOH Z  71 " =    1.245
peak=   -3.683 closest distance to " O   SER A 146 " =    0.917
peak=   -3.682 closest distance to " O   LEU A 300 " =    2.537
peak=   -3.672 closest distance to " O   HOH Z 396 " =    1.653
peak=   -3.672 closest distance to " NE2 GLN A  88 " =    2.136
peak=   -3.671 closest distance to " OXT GLY A 302 " =    2.770
peak=   -3.671 closest distance to " O   HOH Z 222 " =    1.226
peak=   -3.667 closest distance to " N   GLY A  17 " =    1.397
peak=   -3.656 closest distance to " CD1 PHE A  59 " =    1.807
peak=   -3.652 closest distance to " N   ASP A 286 " =    2.146
peak=   -3.636 closest distance to " CG BARG A 275 " =    1.226
peak=   -3.633 closest distance to " OG  SER A  63 " =    1.023
peak=   -3.628 closest distance to " CD  ARG A 156 " =    1.884
peak=   -3.625 closest distance to " CD2 LEU A 300 " =    2.696
peak=   -3.624 closest distance to " O   PRO A 198 " =    1.398
peak=   -3.623 closest distance to " CE1 PHE A 204 " =    2.463
peak=   -3.621 closest distance to " O   ALA A 161 " =    1.418
peak=   -3.609 closest distance to " CE  MET A  93 " =    1.201
peak=   -3.605 closest distance to " C   ILE A 239 " =    2.323
peak=   -3.604 closest distance to " O   HOH Z 165 " =    1.833
peak=   -3.597 closest distance to " O   HOH Z 109 " =    5.353
peak=   -3.589 closest distance to " CG  ASP A 231 " =    0.756
peak=   -3.582 closest distance to " O   HOH Z 428 " =    1.219
peak=   -3.577 closest distance to " C   PRO A 213 " =    1.530
peak=   -3.520 closest distance to " NH2 ARG A  79 " =    1.954
peak=   -3.518 closest distance to " O   VAL A 174 " =    1.993
peak=   -3.516 closest distance to " O   HOH Z 109 " =    3.070
peak=   -3.516 closest distance to " CB  ARG A 156 " =    2.349
peak=   -3.514 closest distance to " CD  ARG A 195 " =    5.003
peak=   -3.509 closest distance to " O   HOH Z 118 " =    3.561
peak=   -3.509 closest distance to " O   HOH Z 389 " =    1.065
peak=   -3.507 closest distance to " O   HOH Z 178 " =    0.721
peak=   -3.500 closest distance to " O   HOH Z  64 " =    0.934
peak=   -3.500 closest distance to " CB  PHE A 208 " =    2.334
peak=   -3.496 closest distance to " O   HOH Z 427 " =    1.578
peak=   -3.493 closest distance to " N   MET A 188 " =    2.012
peak=   -3.491 closest distance to " O   HOH Z 377 " =    1.011
peak=   -3.491 closest distance to " CG2BVAL A  41 " =    2.227
peak=   -3.484 closest distance to " O   LYS A 193 " =    1.749
peak=   -3.482 closest distance to " OG  SER A 273 " =    2.065
peak=   -3.477 closest distance to " O   HOH Z  39 " =    1.087
peak=   -3.472 closest distance to " CD  GLN A 223 " =    1.140
peak=   -3.464 closest distance to " O   HOH Z  56 " =    1.111
peak=   -3.454 closest distance to " SD  MET A 105 " =    2.399
peak=   -3.453 closest distance to " O   HOH Z 120 " =    1.280
peak=   -3.451 closest distance to " O   LEU A 228 " =    2.196
peak=   -3.448 closest distance to " N   ALA A 248 " =    1.884
peak=   -3.448 closest distance to " NH1 ARG A 195 " =    2.526
peak=   -3.447 closest distance to " O   THR A  52 " =    2.038
peak=   -3.434 closest distance to " N   GLN A  58 " =    1.139
peak=   -3.429 closest distance to " OD2 ASP A 107 " =    1.035
peak=   -3.423 closest distance to " CB  ASP A 162 " =    2.384
peak=   -3.422 closest distance to " CD  GLU A   2 " =    1.609
peak=   -3.419 closest distance to " O   PRO A 198 " =    1.146
peak=   -3.418 closest distance to " O   HOH Z 426 " =    2.322
peak=   -3.410 closest distance to " O   HOH Z 227 " =    0.802
peak=   -3.406 closest distance to " O   HOH Z  17 " =    1.062
peak=   -3.404 closest distance to " CZ  ARG A 156 " =    1.191
peak=   -3.402 closest distance to " ND2 ASN A  69 " =    1.742
peak=   -3.398 closest distance to " CD1 LEU A 101 " =    2.504
peak=   -3.385 closest distance to " CB  LEU A 167 " =    1.992
peak=   -3.385 closest distance to " CG  GLN A  73 " =    1.071
peak=   -3.381 closest distance to " O   HOH Z 364 " =    5.173
peak=   -3.380 closest distance to " CE1 HIS A  81 " =    1.533
peak=   -3.378 closest distance to " N   GLN A 122 " =    1.639
peak=   -3.377 closest distance to " OG  SER A  32 " =    0.996
peak=   -3.369 closest distance to " CE1 TYR A 247 " =    2.307
peak=   -3.359 closest distance to " CD2 HIS A 115 " =    1.106
peak=   -3.353 closest distance to " OG BSER A 134 " =    1.475
peak=   -3.350 closest distance to " C   SER A 206 " =    1.445
peak=   -3.348 closest distance to " O   HOH Z 176 " =    1.487
peak=   -3.343 closest distance to " O   HOH Z 216 " =    3.319
peak=   -3.340 closest distance to " O   ASN A 187 " =    1.487
peak=   -3.339 closest distance to " CZ  TYR A 169 " =    1.863
peak=   -3.338 closest distance to " O   HOH Z 196 " =    1.896
peak=   -3.337 closest distance to " CG2 ILE A  49 " =    2.619
peak=   -3.333 closest distance to " O   HOH Z 193 " =    1.284
peak=   -3.332 closest distance to " O   HOH Z 196 " =    1.893
peak=   -3.328 closest distance to " CD2 PHE A  61 " =    2.096
peak=   -3.327 closest distance to " OD1 ASP A 200 " =    1.175
peak=   -3.324 closest distance to " N   GLN A  58 " =    2.055
peak=   -3.321 closest distance to " C   GLN A 144 " =    0.774
peak=   -3.318 closest distance to " CG  PRO A 198 " =    1.809
peak=   -3.312 closest distance to " CG  GLU A 152 " =    1.104
peak=   -3.308 closest distance to " O   HOH Z 380 " =    4.565
peak=   -3.306 closest distance to " O   HOH Z 166 " =    1.316
peak=   -3.305 closest distance to " CB  ASP A 132 " =    2.263
peak=   -3.305 closest distance to " N   ALA A 226 " =    1.982
peak=   -3.303 closest distance to " O   VAL A 197 " =    1.098
peak=   -3.303 closest distance to " C   SER A 271 " =    1.316
peak=   -3.299 closest distance to " CG  ARG A 259 " =    2.731
peak=   -3.295 closest distance to " OG  SER A   3 " =    1.337
peak=   -3.289 closest distance to " ND2 ASN A 173 " =    1.238
peak=   -3.288 closest distance to " CD  LYS A 289 " =    2.452
peak=   -3.284 closest distance to " CB  ALA A 248 " =    2.000
peak=   -3.279 closest distance to " CE3 TRP A 150 " =    2.385
peak=   -3.276 closest distance to " O   TYR A  15 " =    1.591
peak=   -3.273 closest distance to " O   HOH Z  35 " =    1.805
peak=   -3.271 closest distance to " CB  SER A  63 " =    3.062
peak=   -3.266 closest distance to " O   HOH Z 222 " =    1.461
peak=   -3.265 closest distance to " CZ  TYR A 172 " =    1.793
peak=   -3.264 closest distance to " O   LEU A 222 " =    1.354
peak=   -3.263 closest distance to " O   HOH Z 424 " =    3.436
peak=   -3.262 closest distance to " CB  PRO A 163 " =    2.885
peak=   -3.254 closest distance to " O   HOH Z  15 " =    1.574
peak=   -3.243 closest distance to " O   LEU A 167 " =    1.353
peak=   -3.238 closest distance to " O   HOH Z 151 " =    1.948
peak=   -3.234 closest distance to " OG1 THR A  82 " =    1.025
peak=   -3.233 closest distance to " O   HOH Z 251 " =    1.042
peak=   -3.231 closest distance to " N   SER A 206 " =    1.854
peak=   -3.230 closest distance to " O   ARG A  66 " =    1.047
peak=   -3.229 closest distance to " O   HOH Z 135 " =    1.694
peak=   -3.227 closest distance to " O   GLN A  77 " =    1.994
peak=   -3.216 closest distance to " CA  TYR A  68 " =    2.817
peak=   -3.214 closest distance to " CD  GLU A 236 " =    0.925
peak=   -3.213 closest distance to " CA  GLY A 133 " =    1.793
peak=   -3.211 closest distance to " OD1 ASN A 285 " =    0.876
peak=   -3.201 closest distance to " ND2 ASN A 301 " =    2.032
peak=   -3.197 closest distance to " CE1 PHE A 155 " =    1.040
peak=   -3.194 closest distance to " O   HOH Z  37 " =    1.661
peak=   -3.192 closest distance to " SG  CYS A 254 " =    3.143
peak=   -3.188 closest distance to " O   HOH Z 424 " =    1.176
peak=   -3.186 closest distance to " O   HOH Z 391 " =    1.269
peak=   -3.183 closest distance to " N   LEU A 282 " =    2.704
peak=   -3.181 closest distance to " CD1 ILE A 151 " =    2.356
peak=   -3.178 closest distance to " C   ASN A 170 " =    1.256
peak=   -3.178 closest distance to " CD2 PHE A  59 " =    2.407
peak=   -3.173 closest distance to " CD  GLN A  88 " =    0.779
peak=   -3.172 closest distance to " CG  GLN A 103 " =    2.128
peak=   -3.171 closest distance to " O   ALA A   1 " =    1.881
peak=   -3.170 closest distance to " O   HOH Z  24 " =    1.094
peak=   -3.165 closest distance to " O   GLY A 196 " =    0.916
peak=   -3.157 closest distance to " CE2 TRP A 274 " =    1.216
peak=   -3.154 closest distance to " O   HOH Z 318 " =    1.525
peak=   -3.153 closest distance to " SD  MET A 188 " =    1.155
peak=   -3.149 closest distance to " O   HOH Z  79 " =    1.680
peak=   -3.148 closest distance to " NE2 GLN A 103 " =    1.494
peak=   -3.145 closest distance to " O   HOH Z 138 " =    1.611
peak=   -3.142 closest distance to " CD2 LEU A 237 " =    2.116
peak=   -3.138 closest distance to " ND2 ASN A 252 " =    1.524
peak=   -3.135 closest distance to " O   HOH Z 246 " =    1.423
peak=   -3.131 closest distance to " N   ALA A  43 " =    2.402
peak=   -3.128 closest distance to " NH2 ARG A  66 " =    1.793
peak=   -3.124 closest distance to " O   HOH Z 212 " =    2.355
peak=   -3.124 closest distance to " O   HOH Z 130 " =    2.089
peak=   -3.124 closest distance to " CG  LYS A 193 " =    1.981
peak=   -3.123 closest distance to " C   LEU A 143 " =    1.108
peak=   -3.118 closest distance to " O   HOH Z 363 " =    2.291
peak=   -3.117 closest distance to " C   GLY A  13 " =    0.997
peak=   -3.107 closest distance to " CE  MET A 105 " =    1.964
peak=   -3.103 closest distance to " CD  GLN A  58 " =    1.448
peak=   -3.100 closest distance to " CG1AVAL A  41 " =    2.523
peak=   -3.098 closest distance to " O   HOH Z 109 " =    2.930
peak=   -3.092 closest distance to " O   HOH Z 231 " =    1.010
peak=   -3.081 closest distance to " O   HOH Z 416 " =    0.713
peak=   -3.066 closest distance to " OG ASER A 134 " =    0.911
peak=   -3.031 closest distance to " O   HOH Z  65 " =    1.301
peak=   -3.021 closest distance to " O   GLY A 241 " =    2.265
peak=   -3.009 closest distance to " OG BSER A 134 " =    1.683

================= 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    :  0.5045 0.5035   6.302482e+00   6.299272e+00
   1_bss:  0.4987 0.4961   6.300082e+00   6.290631e+00
   1_xyz:  0.4100 0.4309   6.190627e+00   6.221120e+00
   1_adp:  0.3671 0.4413   6.145353e+00   6.236561e+00
   1_occ:  0.3666 0.4404   6.144490e+00   6.236274e+00
   2_bss:  0.3657 0.4390   6.143462e+00   6.235966e+00
   2_xyz:  0.3014 0.3700   5.981655e+00   6.129793e+00
   2_adp:  0.2755 0.3533   5.926687e+00   6.093369e+00
   2_occ:  0.2754 0.3529   5.925641e+00   6.092726e+00
   3_bss:  0.2751 0.3525   5.924378e+00   6.090256e+00
   3_xyz:  0.2215 0.2873   5.738009e+00   5.935628e+00
   3_adp:  0.2054 0.2595   5.659166e+00   5.843333e+00
   3_occ:  0.2047 0.2585   5.657195e+00   5.841653e+00
   4_bss:  0.2035 0.2568   5.655791e+00   5.838053e+00
   4_xyz:  0.1676 0.2166   5.485915e+00   5.685070e+00
   4_adp:  0.1543 0.2083   5.426252e+00   5.642853e+00
   4_occ:  0.1541 0.2082   5.425876e+00   5.642971e+00
   5_bss:  0.1546 0.2082   5.427456e+00   5.642694e+00
   5_xyz:  0.1331 0.1880   5.311203e+00   5.546635e+00
   5_adp:  0.1322 0.1768   5.280153e+00   5.490253e+00
   5_occ:  0.1319 0.1766   5.278441e+00   5.489520e+00
   5_bss:  0.1318 0.1765   5.278638e+00   5.489576e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000  -1.249   1.826   0.654   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -1.249   1.826   0.654   0.000   0.000   0.000
   1_adp:  0.300  20.000  -1.249   1.826   0.654   0.000   0.000   0.000
   1_occ:  0.300  20.000  -1.249   1.826   0.654   0.000   0.000   0.000
   2_bss:  0.328  50.000  -0.607   1.806   1.074   0.000   0.000   0.000
   2_xyz:  0.328  50.000  -0.607   1.806   1.074   0.000   0.000   0.000
   2_adp:  0.328  50.000  -0.607   1.806   1.074   0.000   0.000   0.000
   2_occ:  0.328  50.000  -0.607   1.806   1.074   0.000   0.000   0.000
   3_bss:  0.328  50.000  -1.134   0.646   0.271   0.000   0.000   0.000
   3_xyz:  0.328  50.000  -1.134   0.646   0.271   0.000   0.000   0.000
   3_adp:  0.328  50.000  -1.134   0.646   0.271   0.000   0.000   0.000
   3_occ:  0.328  50.000  -1.134   0.646   0.271   0.000   0.000   0.000
   4_bss:  0.317  40.129  -2.754  -0.841  -1.345  -0.000  -0.000  -0.000
   4_xyz:  0.317  40.129  -2.754  -0.841  -1.345  -0.000  -0.000  -0.000
   4_adp:  0.317  40.129  -2.754  -0.841  -1.345  -0.000  -0.000  -0.000
   4_occ:  0.317  40.129  -2.754  -0.841  -1.345  -0.000  -0.000  -0.000
   5_bss:  0.312  40.129  -3.195  -1.269  -1.829  -0.000  -0.000  -0.000
   5_xyz:  0.312  40.129  -3.195  -1.269  -1.829  -0.000  -0.000  -0.000
   5_adp:  0.312  40.129  -3.195  -1.269  -1.829  -0.000  -0.000  -0.000
   5_occ:  0.312  40.129  -3.195  -1.269  -1.829  -0.000  -0.000  -0.000
   5_bss:  0.320  40.132  -3.428  -1.598  -2.049  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.897 0.3033  0.4134    82993.862
   1_bss:  65.814 0.3162  0.4421    79994.802
   1_xyz:  51.565 0.4995  0.6905    56120.731
   1_adp:  52.965 0.4817  0.6891    59158.365
   1_occ:  53.046 0.4805  0.6852    58989.267
   2_bss:  52.958 0.4814  0.6970    58571.486
   2_xyz:  42.180 0.6140  0.8823    39167.147
   2_adp:  38.795 0.6556  0.9062    34648.126
   2_occ:  38.720 0.6565  0.9068    34512.607
   3_bss:  38.576 0.6581  0.8824    34238.629
   3_xyz:  30.212 0.7537  0.9812    21935.229
   3_adp:  26.036 0.8003  1.0199    17685.258
   3_occ:  25.977 0.8010  1.0203    17656.565
   4_bss:  25.843 0.8022  0.9628    17431.849
   4_xyz:  21.059 0.8510  0.9935    12163.597
   4_adp:  19.893 0.8628  0.9895    11130.918
   4_occ:  19.891 0.8628  0.9894    11137.617
   5_bss:  19.899 0.8627  0.9730    11150.486
   5_xyz:  17.708 0.8830  0.9847     9024.405
   5_adp:  16.374 0.8955  0.9884     8151.435
   5_occ:  16.351 0.8956  0.9884     8129.204
   5_bss:  16.353 0.8956  0.9793     8135.414
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.7105e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.7105e-01
   1_xyz:   1.651  0.013  0.092 16.360  0.007  4.107   1.5072e-01
   1_adp:   1.651  0.013  0.092 16.360  0.007  4.107   1.5072e-01
   1_occ:   1.651  0.013  0.092 16.360  0.007  4.107   1.5072e-01
   2_bss:   1.651  0.013  0.092 16.360  0.007  4.107   1.5072e-01
   2_xyz:   1.388  0.010  0.091 15.588  0.006  4.101   1.0779e-01
   2_adp:   1.388  0.010  0.091 15.588  0.006  4.101   1.0779e-01
   2_occ:   1.388  0.010  0.091 15.588  0.006  4.101   1.0779e-01
   3_bss:   1.388  0.010  0.091 15.588  0.006  4.101   1.0779e-01
   3_xyz:   1.098  0.008  0.069 14.878  0.005  4.115   7.2794e-02
   3_adp:   1.098  0.008  0.069 14.878  0.005  4.115   7.2794e-02
   3_occ:   1.098  0.008  0.069 14.878  0.005  4.115   7.2794e-02
   4_bss:   1.098  0.008  0.069 14.878  0.005  4.115   7.2794e-02
   4_xyz:   0.994  0.006  0.068 14.244  0.004  4.113   5.7415e-02
   4_adp:   0.994  0.006  0.068 14.244  0.004  4.113   5.7415e-02
   4_occ:   0.994  0.006  0.068 14.244  0.004  4.113   5.7415e-02
   5_bss:   0.994  0.006  0.068 14.244  0.004  4.113   5.7415e-02
   5_xyz:   1.081  0.007  0.073 14.655  0.004  4.108   6.4831e-02
   5_adp:   1.081  0.007  0.073 14.655  0.004  4.108   6.4831e-02
   5_occ:   1.081  0.007  0.073 14.655  0.004  4.108   6.4831e-02
   5_bss:   1.081  0.007  0.073 14.655  0.004  4.108   6.4831e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.125   2.4634e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.125   2.4634e-01
   1_xyz:  11.110  0.118  0.273 86.347  0.059  1.958   1.1311e-01
   1_adp:  11.110  0.118  0.273 86.347  0.059  1.958   1.1311e-01
   1_occ:  11.110  0.118  0.273 86.347  0.059  1.958   1.1311e-01
   2_bss:  11.110  0.118  0.273 86.347  0.059  1.958   1.1311e-01
   2_xyz:   9.511  0.073  0.328 89.107  0.041  2.166   9.6623e-02
   2_adp:   9.511  0.073  0.328 89.107  0.041  2.166   9.6623e-02
   2_occ:   9.511  0.073  0.328 89.107  0.041  2.166   9.6623e-02
   3_bss:   9.511  0.073  0.328 89.107  0.041  2.166   9.6623e-02
   3_xyz:   7.534  0.039  0.233 80.927  0.034  2.231   5.9501e-02
   3_adp:   7.534  0.039  0.233 80.927  0.034  2.231   5.9501e-02
   3_occ:   7.534  0.039  0.233 80.927  0.034  2.231   5.9501e-02
   4_bss:   7.534  0.039  0.233 80.927  0.034  2.231   5.9501e-02
   4_xyz:   7.510  0.047  0.205 77.943  0.038  2.290   6.1734e-02
   4_adp:   7.510  0.047  0.205 77.943  0.038  2.290   6.1734e-02
   4_occ:   7.510  0.047  0.205 77.943  0.038  2.290   6.1734e-02
   5_bss:   7.510  0.047  0.205 77.943  0.038  2.290   6.1734e-02
   5_xyz:   7.843  0.044  0.240 81.796  0.032  2.237   4.7106e-02
   5_adp:   7.843  0.044  0.240 81.796  0.032  2.237   4.7106e-02
   5_occ:   7.843  0.044  0.240 81.796  0.032  2.237   4.7106e-02
   5_bss:   7.843  0.044  0.240 81.796  0.032  2.237   4.7106e-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: 100.24   0.00  22.59  96.97   0.00  19.17 100.24   0.00  41.26
   1_occ: 100.24   0.00  22.59  96.97   0.00  19.17 100.24   0.00  41.26
   2_bss: 100.24   0.00  22.59  96.97   0.00  19.17 100.24   0.00  41.26
   2_xyz: 100.24   0.00  22.59  96.97   0.00  19.17 100.24   0.00  41.26
   2_adp: 110.83   0.00  21.20 110.83   0.00  17.16 103.48   0.00  43.19
   2_occ: 110.83   0.00  21.20 110.83   0.00  17.16 103.48   0.00  43.19
   3_bss: 110.83   0.00  21.20 110.83   0.00  17.16 103.48   0.00  43.19
   3_xyz: 110.83   0.00  21.20 110.83   0.00  17.16 103.48   0.00  43.19
   3_adp: 105.37   0.00  19.26 105.37   0.00  15.05 101.36   3.91  42.23
   3_occ: 105.37   0.00  19.26 105.37   0.00  15.05 101.36   3.91  42.23
   4_bss: 105.37   0.00  19.26 105.37   0.00  15.05 101.36   3.91  42.23
   4_xyz: 105.37   0.00  19.26 105.37   0.00  15.05 101.36   3.91  42.23
   4_adp: 109.72   0.00  19.29 109.72   0.00  14.16 102.88   0.00  47.24
   4_occ: 109.72   0.00  19.29 109.72   0.00  14.16 102.88   0.00  47.24
   5_bss: 109.72   0.00  19.29 109.72   0.00  14.16 102.88   0.00  47.24
   5_xyz: 109.72   0.00  19.29 109.72   0.00  14.16 102.88   0.00  47.24
   5_adp: 105.28   0.00  18.07 105.28   0.00  13.58  98.85   2.61  42.49
   5_occ: 105.28   0.00  18.07 105.28   0.00  13.58  98.85   2.61  42.49
   5_bss: 105.29   0.00  18.07 105.29   0.00  13.58  98.85   2.61  42.50
------------------------------------------------------------------------
 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:    3.892    0.027    0.389
   1_adp:    3.892    0.027    0.389
   1_occ:    3.892    0.027    0.389
   2_bss:    3.892    0.027    0.389
   2_xyz:    2.836    0.094    0.636
   2_adp:    2.836    0.094    0.636
   2_occ:    2.836    0.094    0.636
   3_bss:    2.836    0.094    0.636
   3_xyz:    3.024    0.098    0.771
   3_adp:    3.024    0.098    0.771
   3_occ:    3.024    0.098    0.771
   4_bss:    3.024    0.098    0.771
   4_xyz:    2.879    0.088    0.852
   4_adp:    2.879    0.088    0.852
   4_occ:    2.879    0.088    0.852
   5_bss:    2.879    0.088    0.852
   5_xyz:    2.828    0.077    0.902
   5_adp:    2.828    0.077    0.902
   5_occ:    2.828    0.077    0.902
   5_bss:    2.828    0.077    0.902
------------------------------------------------------------------------

CPU time actual refinement: 356.14


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_99/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_99/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_99/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_99/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_99/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.00 
  Macro-tasks:
    bulk solvent and scale       = 42.69  
    individual site refinement   = 153.56 
    weights calculation          = 31.83  
    collect and process          = 6.49   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 234.69 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 114.84 
    alpha_beta                      = 8.11   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 123.35 
    fmodel                         = 6.99   
    r_factors                      = 0.29   
    phase_errors                   = 10.18  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 267.67 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.086 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    614 calls, 114.56 s
gradients_fft:          559 calls, 110.43 s

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

# Date 2008-01-16 Time 04:01:06 PST -0800 (1200484866.71 s)
Start R-work = 0.5045, R-free = 0.5035 (no bulk solvent and anisotropic scale)
Final R-work = 0.1581, R-free = 0.2008 (no bulk solvent and anisotropic scale)

Start R-work = 0.4987, R-free = 0.4961
Final R-work = 0.1318, R-free = 0.1765