# Date 2008-01-16 Time 06:02:03 PST -0800 (1200492123.09 s)
#phil __OFF__

Command line arguments: "../984.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3745
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 984

-------------------------------------------------------------------------------
  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: (71.3037, 45.9914, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


================================== 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: (71.3037, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 1.96374
Completeness in resolution range: 0.938755
Completeness with d_max=infinity: 0.936063

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   1.9637

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: (71.3037, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 1.96374
Completeness in resolution range: 0.938755
Completeness with d_max=infinity: 0.936063

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1574 -  4.2035 [2193/2220]  1973   220  10.0%
  bin  2:  4.2035 -  3.3483 [2114/2134]  1903   211  10.0%
  bin  3:  3.3483 -  2.9285 [2069/2088]  1863   206  10.0%
  bin  4:  2.9285 -  2.6623 [2063/2093]  1854   209  10.1%
  bin  5:  2.6623 -  2.4724 [2044/2063]  1847   197   9.6%
  bin  6:  2.4724 -  2.3271 [2029/2054]  1819   210  10.3%
  bin  7:  2.3271 -  2.2110 [2044/2072]  1836   208  10.2%
  bin  8:  2.2110 -  2.1150 [2006/2042]  1806   200  10.0%
  bin  9:  2.1150 -  2.0338 [2014/2056]  1821   193   9.6%
  bin 10:  2.0338 -  1.9637 [1013/2045]   908   105  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_984/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:
        1.77 -     2.40: 30
        2.40 -     3.02: 2085
        3.02 -     3.65: 4670
        3.65 -     4.27: 9139
        4.27 -     4.90: 12441
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.775 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.994 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28360 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_984/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_984/model_refine_001.geo

CPU time processing inputs: 9.90


============================ 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 = 71.30375 45.9914 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4198   r_free= 0.4178   ksol= 0.00   Bsol= 0.00   scale= 0.920    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.232694                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1574 -  4.6891 0.99   1420  159 0.3498 0.3436      6.4998      6.4871|
|  2:  4.6891 -  3.7403 0.99   1365  152 0.3513 0.3409      6.7324      6.6656|
|  3:  3.7403 -  3.2729 0.99   1341  145 0.3749 0.3519      6.5841      6.6191|
|  4:  3.2729 -  2.9761 0.99   1343  154 0.4116 0.4353      6.4659      6.4892|
|  5:  2.9761 -  2.7642 0.99   1337  149 0.4437 0.4311      6.3174      6.3172|
|  6:  2.7642 -  2.6021 0.99   1315  145 0.4407 0.4587       6.222      6.1874|
|  7:  2.6021 -  2.4724 0.99   1319  139 0.4541 0.4296      6.1975      6.1432|
|  8:  2.4724 -  2.3652 0.98   1306  152 0.4584 0.4774      6.1251      6.1518|
|  9:  2.3652 -  2.2744 0.98   1290  145 0.4578 0.4803      6.0865      6.1119|
| 10:  2.2744 -  2.1962 1.00   1305  153 0.4722 0.4543      6.0555       6.034|
| 11:  2.1962 -  2.1277 0.98   1311  132 0.4666 0.4779      6.0076      6.0394|
| 12:  2.1277 -  2.0670 0.98   1278  149 0.4738 0.4865      5.9216       5.971|
| 13:  2.0670 -  2.0127 0.95   1253  132 0.4840 0.4665      5.8499      5.7969|
| 14:  2.0127 -  1.9637 0.34    447   53 0.5011 0.5071      5.8616      5.8269|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1574 -  4.6891  1420   159  0.74  31.05   0.83     0.78      60404.67|
|  2:  4.6891 -  3.7403  1365   152  0.76  29.91   0.93     0.86      82285.76|
|  3:  3.7403 -  3.2729  1341   145  0.67  38.24   0.95     0.85      89947.69|
|  4:  3.2729 -  2.9761  1343   154  0.59  45.03   0.93     0.78      84305.97|
|  5:  2.9761 -  2.7642  1337   149  0.51  51.40   0.91     0.71      69813.81|
|  6:  2.7642 -  2.6021  1315   145  0.49  52.58   0.92     0.68      60478.79|
|  7:  2.6021 -  2.4724  1319   139  0.47  54.18   0.95     0.65      54968.25|
|  8:  2.4724 -  2.3652  1306   152  0.46  55.34   0.93     0.64      49944.04|
|  9:  2.3652 -  2.2744  1290   145  0.46  55.23   0.96     0.65      45204.93|
| 10:  2.2744 -  2.1962  1305   153  0.47  54.90   0.96     0.67      40661.28|
| 11:  2.1962 -  2.1277  1311   132  0.44  56.80   0.99     0.67      40891.01|
| 12:  2.1277 -  2.0670  1278   149  0.41  59.22   0.96     0.62      37991.06|
| 13:  2.0670 -  2.0127  1253   132  0.37  62.06   0.96     0.61      34060.56|
| 14:  2.0127 -  1.9637   447    53  0.45  56.23   0.99     0.62      26586.30|
|alpha:            min =        0.61 max =            0.86 mean =         0.71|
|beta:             min =    26586.30 max =        89947.69 mean =     57324.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           90.00 mean =        49.59|
|phase err.(test): min =        0.00 max =           89.78 mean =        49.77|
|-----------------------------------------------------------------------------|

============================== 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 = 9.505435              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.032   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.894424              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.008   (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 |  1.775 -  2.087:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.087 -  2.400:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.400 -  2.712:      149 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.712 -  3.025:     1936 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.025 -  3.337:     1895 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.337 -  3.650:     2775 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.650 -  3.962:     4728 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.962 -  4.275:     4411 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.275 -  4.587:     5649 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.587 -  4.900:     6792 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.775 |       0.319 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    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: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4198   r_free= 0.4178   ksol= 0.00   Bsol= 0.00   scale= 0.920    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.232694                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4090   r_free= 0.4090   ksol= 0.35   Bsol= 50.00   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,2.86,-1.91,0.00,-0.00,-0.00); trace/3= 0.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.221844                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.296726              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.112   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.957354              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.762   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4090      final r-factor (work) = 0.2924          |
| start r-factor (free) = 0.4090      final r-factor (free) = 0.3311          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9774 = 8.30 * 0.50 * 6.2207 + 1.00 * 0.1718                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2905 = 8.30 * 0.50 * 6.0684 + 1.00 * 0.1165                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2924      final r-factor (work) = 0.2677          |
| start r-factor (free) = 0.3311      final r-factor (free) = 0.3443          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8157 = 0.96 * 1.00 * 6.0684 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6723 = 0.96 * 1.00 * 5.9084 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.55  18.16    None  None   None       |
|    all(noH): 2823   0      0.00    102.55  18.16    None  None   None       |
|    Sol.    : 438    0      2.92    102.55  39.79    None  None   None       |
|    Mac.    : 2385   0      0.00    67.14   14.19    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:     0.000 -  10.256:  969   |   5:    51.278 -  61.533:   78        |
|      1:    10.256 -  20.511: 1009   |   6:    61.533 -  71.788:   28        |
|      2:    20.511 -  30.767:  390   |   7:    71.788 -  82.044:   15        |
|      3:    30.767 -  41.022:  198   |   8:    82.044 -  92.299:    0        |
|      4:    41.022 -  51.278:  135   |   9:    92.299 - 102.555:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2677 r_free = 0.3443             target_work(ml) = 5.924         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2673 r_free = 0.3441             target_work(ml) = 5.923         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2673   r_free= 0.3441   ksol= 0.35   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,2.86,-1.91,0.00,-0.00,-0.00); trace/3= 0.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.922892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2659   r_free= 0.3403   ksol= 0.33   Bsol= 66.69   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.30,-1.24,-0.00,-0.00,-0.00); trace/3= -0.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.917779                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.479001              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.525   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.369657              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.977  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2659      final r-factor (work) = 0.2018          |
| start r-factor (free) = 0.3403      final r-factor (free) = 0.2613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3479 = 4.48 * 0.50 * 5.9082 + 1.00 * 0.1165                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0853 = 4.48 * 0.50 * 5.8128 + 1.00 * 0.0674                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2018      final r-factor (work) = 0.1848          |
| start r-factor (free) = 0.2613      final r-factor (free) = 0.2412          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1644 = 0.37 * 1.00 * 5.8128 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0905 = 0.37 * 1.00 * 5.6279 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.66  17.82    None  None   None       |
|    all(noH): 2823   0      0.00    100.66  17.82    None  None   None       |
|    Sol.    : 438    0      5.27    100.66  41.18    None  None   None       |
|    Mac.    : 2385   0      0.00    79.44   13.53    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 -  10.066: 1000   |   5:    50.331 -  60.397:   99        |
|      1:    10.066 -  20.132: 1098   |   6:    60.397 -  70.463:   36        |
|      2:    20.132 -  30.199:  268   |   7:    70.463 -  80.530:   14        |
|      3:    30.199 -  40.265:  169   |   8:    80.530 -  90.596:    0        |
|      4:    40.265 -  50.331:  138   |   9:    90.596 - 100.662:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1848 r_free = 0.2412             target_work(ml) = 5.591         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1847 r_free = 0.2409             target_work(ml) = 5.591         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1847   r_free= 0.2409   ksol= 0.33   Bsol= 66.69   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.30,-1.24,-0.00,-0.00,-0.00); trace/3= -0.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.591379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1844   r_free= 0.2397   ksol= 0.33   Bsol= 59.89   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-1.57,-0.97,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.588441                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.460451              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.310  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326002              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.929  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1844      final r-factor (work) = 0.1469          |
| start r-factor (free) = 0.2397      final r-factor (free) = 0.1966          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9905 = 2.46 * 0.50 * 5.6274 + 1.00 * 0.0674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8046 = 2.46 * 0.50 * 5.4876 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1469      final r-factor (work) = 0.1384          |
| start r-factor (free) = 0.1966      final r-factor (free) = 0.1883          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7991 = 0.33 * 1.00 * 5.4876 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7549 = 0.33 * 1.00 * 5.3549 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    97.59   17.50    None  None   None       |
|    all(noH): 2823   0      0.72    97.59   17.50    None  None   None       |
|    Sol.    : 438    0      5.12    97.59   41.83    None  None   None       |
|    Mac.    : 2385   0      0.72    81.73   13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.716 -  10.403: 1104   |   5:    49.152 -  58.839:  105        |
|      1:    10.403 -  20.090: 1042   |   6:    58.839 -  68.526:   50        |
|      2:    20.090 -  29.778:  233   |   7:    68.526 -  78.214:   19        |
|      3:    29.778 -  39.465:  139   |   8:    78.214 -  87.901:    3        |
|      4:    39.465 -  49.152:  127   |   9:    87.901 -  97.588:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1384 r_free = 0.1883             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1383 r_free = 0.1881             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1881   ksol= 0.33   Bsol= 59.89   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-1.57,-0.97,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331180                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1385   r_free= 0.1877   ksol= 0.33   Bsol= 59.89   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.46,-1.28,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.329644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.640357              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.592   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.555390              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.604  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1385      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1877      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1264 = 2.64 * 0.50 * 5.3575 + 1.00 * 0.0536                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0230 = 2.64 * 0.50 * 5.2757 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1691      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9392 = 0.56 * 1.00 * 5.2757 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8993 = 0.56 * 1.00 * 5.2030 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.03   17.47    None  None   None       |
|    all(noH): 2823   0      0.00    96.03   17.47    None  None   None       |
|    Sol.    : 438    0      3.75    96.03   42.20    None  None   None       |
|    Mac.    : 2385   0      0.00    91.05   12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.603:  969   |   5:    48.014 -  57.616:  111        |
|      1:     9.603 -  19.205: 1167   |   6:    57.616 -  67.219:   54        |
|      2:    19.205 -  28.808:  241   |   7:    67.219 -  76.822:   31        |
|      3:    28.808 -  38.411:  133   |   8:    76.822 -  86.424:    9        |
|      4:    38.411 -  48.014:  105   |   9:    86.424 -  96.027:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1658             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1659             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1659   ksol= 0.33   Bsol= 59.89   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.46,-1.28,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.192310                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1659   ksol= 0.32   Bsol= 53.86   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.59,-1.23,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.191999                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.471936              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.393  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.373578              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.689  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1659      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4883 = 2.47 * 0.50 * 5.2026 + 1.00 * 0.0581                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4548 = 2.47 * 0.50 * 5.1749 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9427 = 0.37 * 1.00 * 5.1749 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9357 = 0.37 * 1.00 * 5.1573 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.09    95.86   17.13    None  None   None       |
|    all(noH): 2823   0      0.09    95.86   17.13    None  None   None       |
|    Sol.    : 438    0      4.74    92.01   40.81    None  None   None       |
|    Mac.    : 2385   0      0.09    95.86   12.78    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:     0.094 -   9.670: 1000   |   5:    47.975 -  57.551:   88        |
|      1:     9.670 -  19.246: 1157   |   6:    57.551 -  67.127:   49        |
|      2:    19.246 -  28.823:  232   |   7:    67.127 -  76.703:   27        |
|      3:    28.823 -  38.399:  131   |   8:    76.703 -  86.280:    8        |
|      4:    38.399 -  47.975:  127   |   9:    86.280 -  95.856:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1584             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1585             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1585   ksol= 0.32   Bsol= 53.86   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.59,-1.23,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153281                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1574 -  4.6891 0.99   1420  159 0.0960 0.1293      5.3581      5.5771|
|  2:  4.6891 -  3.7403 0.99   1365  152 0.0841 0.1084      5.4369      5.6123|
|  3:  3.7403 -  3.2729 0.99   1341  145 0.1086 0.1597      5.4844      5.8429|
|  4:  3.2729 -  2.9761 0.99   1343  154 0.1257 0.1668      5.4575      5.6085|
|  5:  2.9761 -  2.7642 0.99   1337  149 0.1335 0.1727      5.3196      5.5549|
|  6:  2.7642 -  2.6021 0.99   1315  145 0.1221 0.1906      5.1954      5.4688|
|  7:  2.6021 -  2.4724 0.99   1319  139 0.1244 0.1546      5.1619      5.2991|
|  8:  2.4724 -  2.3652 0.98   1306  152 0.1179 0.1785      5.0696      5.3674|
|  9:  2.3652 -  2.2744 0.98   1290  145 0.1193 0.1777      5.0533      5.3191|
| 10:  2.2744 -  2.1962 1.00   1305  153 0.1117 0.1691      4.9495      5.1967|
| 11:  2.1962 -  2.1277 0.98   1311  132 0.1110 0.1809      4.9438      5.3244|
| 12:  2.1277 -  2.0670 0.98   1278  149 0.1131 0.1701      4.8721      5.1161|
| 13:  2.0670 -  2.0127 0.95   1253  132 0.1144 0.1686      4.7844      5.0216|
| 14:  2.0127 -  1.9637 0.34    447   53 0.0999 0.1460      4.6625      4.8772|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1574 -  4.6891  1420   159  0.94   8.84   0.98     0.95       6854.14|
|  2:  4.6891 -  3.7403  1365   152  0.95   8.02   1.01     1.01       9207.03|
|  3:  3.7403 -  3.2729  1341   145  0.93  11.44   1.03     1.02      10536.78|
|  4:  3.2729 -  2.9761  1343   154  0.91  14.20   1.01     0.98      10297.31|
|  5:  2.9761 -  2.7642  1337   149  0.90  15.63   1.00     0.98       8081.50|
|  6:  2.7642 -  2.6021  1315   145  0.90  15.98   0.99     0.97       6854.86|
|  7:  2.6021 -  2.4724  1319   139  0.91  15.40   1.00     0.97       6191.49|
|  8:  2.4724 -  2.3652  1306   152  0.90  15.97   0.98     0.95       5398.49|
|  9:  2.3652 -  2.2744  1290   145  0.90  16.05   1.00     0.96       5258.61|
| 10:  2.2744 -  2.1962  1305   153  0.90  16.24   1.00     0.97       4485.44|
| 11:  2.1962 -  2.1277  1311   132  0.90  15.89   0.99     0.94       4343.08|
| 12:  2.1277 -  2.0670  1278   149  0.91  15.92   1.01     1.01       4029.53|
| 13:  2.0670 -  2.0127  1253   132  0.90  16.67   1.00     0.97       3378.46|
| 14:  2.0127 -  1.9637   447    53  0.92  14.31   0.98     0.96       2633.25|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2633.25 max =        10536.78 mean =      6476.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.26|
|phase err.(test): min =        0.00 max =           89.50 mean =        13.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1579   ksol= 0.32   Bsol= 53.86   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.61,-1.14,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152088                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1579   ksol= 0.32   Bsol= 53.86   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.61,-1.14,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152088                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1574 -  4.6891 0.99   1420  159 0.0962 0.1270      5.3456      5.5438|
|  2:  4.6891 -  3.7403 0.99   1365  152 0.0843 0.1065      5.4335      5.6094|
|  3:  3.7403 -  3.2729 0.99   1341  145 0.1090 0.1589      5.4842      5.8385|
|  4:  3.2729 -  2.9761 0.99   1343  154 0.1258 0.1671       5.458        5.61|
|  5:  2.9761 -  2.7642 0.99   1337  149 0.1334 0.1725      5.3201      5.5537|
|  6:  2.7642 -  2.6021 0.99   1315  145 0.1222 0.1904      5.1956      5.4701|
|  7:  2.6021 -  2.4724 0.99   1319  139 0.1244 0.1548      5.1613      5.2999|
|  8:  2.4724 -  2.3652 0.98   1306  152 0.1178 0.1789      5.0695      5.3676|
|  9:  2.3652 -  2.2744 0.98   1290  145 0.1193 0.1772      5.0536      5.3183|
| 10:  2.2744 -  2.1962 1.00   1305  153 0.1116 0.1696      4.9497      5.1992|
| 11:  2.1962 -  2.1277 0.98   1311  132 0.1110 0.1809      4.9446      5.3243|
| 12:  2.1277 -  2.0670 0.98   1278  149 0.1131 0.1704      4.8721      5.1173|
| 13:  2.0670 -  2.0127 0.95   1253  132 0.1144 0.1683      4.7842      5.0205|
| 14:  2.0127 -  1.9637 0.34    447   53 0.0995 0.1460      4.6611      4.8757|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1574 -  4.6891  1420   159  0.94   8.58   0.97     0.95       6438.96|
|  2:  4.6891 -  3.7403  1365   152  0.95   7.79   1.01     1.01       8866.16|
|  3:  3.7403 -  3.2729  1341   145  0.93  11.32   1.03     1.02      10429.31|
|  4:  3.2729 -  2.9761  1343   154  0.91  14.22   1.01     0.98      10307.20|
|  5:  2.9761 -  2.7642  1337   149  0.90  15.64   1.00     0.98       8098.60|
|  6:  2.7642 -  2.6021  1315   145  0.90  15.98   0.99     0.97       6852.98|
|  7:  2.6021 -  2.4724  1319   139  0.91  15.40   1.00     0.97       6188.17|
|  8:  2.4724 -  2.3652  1306   152  0.90  15.99   0.98     0.95       5403.47|
|  9:  2.3652 -  2.2744  1290   145  0.90  16.06   1.00     0.96       5263.28|
| 10:  2.2744 -  2.1962  1305   153  0.90  16.26   1.00     0.97       4497.61|
| 11:  2.1962 -  2.1277  1311   132  0.90  15.92   0.99     0.94       4354.33|
| 12:  2.1277 -  2.0670  1278   149  0.91  15.94   1.01     1.01       4035.69|
| 13:  2.0670 -  2.0127  1253   132  0.90  16.67   1.00     0.98       3378.08|
| 14:  2.0127 -  1.9637   447    53  0.92  14.29   0.98     0.96       2626.79|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2626.79 max =        10429.31 mean =      6413.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.22|
|phase err.(test): min =        0.00 max =           89.45 mean =        13.73|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.09    95.86   17.13    None  None   None       |
|    all(noH): 2823   0      0.09    95.86   17.13    None  None   None       |
|    Sol.    : 438    0      4.74    92.01   40.81    None  None   None       |
|    Mac.    : 2385   0      0.09    95.86   12.78    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:     0.094 -   9.670: 1000   |   5:    47.974 -  57.551:   88        |
|      1:     9.670 -  19.246: 1157   |   6:    57.551 -  67.127:   49        |
|      2:    19.246 -  28.822:  232   |   7:    67.127 -  76.703:   27        |
|      3:    28.822 -  38.398:  131   |   8:    76.703 -  86.279:    8        |
|      4:    38.398 -  47.974:  127   |   9:    86.279 -  95.855:    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)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.606 - 4.686
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 320
   mapped sites are within: 0.719 - 4.686

peak=    6.830 closest distance to " NE2 GLN A  11 " =    1.321
peak=    5.477 closest distance to " CG  PRO A  54 " =    1.312
peak=    5.375 closest distance to " NH2 ARG A  56 " =    2.069
peak=    5.187 closest distance to " O   HOH Z 232 " =    2.255
peak=    5.181 closest distance to " O   HOH Z   7 " =    1.498
peak=    5.087 closest distance to " O   HOH Z 126 " =    1.990
peak=    5.075 closest distance to " O   HOH Z 417 " =    1.682
peak=    5.011 closest distance to " O   HOH Z 144 " =    1.694
peak=    4.971 closest distance to " CB  SER A  63 " =    1.283
peak=    4.961 closest distance to " O   HOH Z 427 " =    2.439
peak=    4.947 closest distance to " O   HOH Z 423 " =    1.990
peak=    4.934 closest distance to " CB  GLN A 223 " =    1.492
peak=    4.900 closest distance to " O   HOH Z 425 " =    1.485
peak=    4.872 closest distance to " O   HOH Z  63 " =    1.595
peak=    4.824 closest distance to " O   HOH Z 287 " =    2.072
peak=    4.709 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.695 closest distance to " CB  PRO A  54 " =    0.971
peak=    4.610 closest distance to " O   HOH Z 369 " =    2.211
peak=    4.605 closest distance to " CG  PRO A 213 " =    1.330
peak=    4.599 closest distance to " O   HOH Z 298 " =    2.053
peak=    4.552 closest distance to " C   PRO A 198 " =    1.521
peak=    4.546 closest distance to " CB  GLN A 183 " =    1.222
peak=    4.505 closest distance to " O   HOH Z  78 " =    1.645
peak=    4.487 closest distance to " O   HOH Z 419 " =    2.213
peak=    4.433 closest distance to " CB  ASN A 148 " =    1.369
peak=    4.422 closest distance to " O   HOH Z   2 " =    1.786
peak=    4.346 closest distance to " O   HOH Z 380 " =    1.767
peak=    4.333 closest distance to " CB  ARG A 275 " =    0.941
peak=    4.329 closest distance to " CB  GLU A 128 " =    1.029
peak=    4.313 closest distance to " ND2 ASN A 187 " =    1.536
peak=    4.287 closest distance to " O   HOH Z 133 " =    2.371
peak=    4.269 closest distance to " CB  SER A   3 " =    1.503
peak=    4.256 closest distance to " O   HOH Z   9 " =    1.346
peak=    4.238 closest distance to " O   HOH Z 209 " =    2.255
peak=    4.234 closest distance to " CB  ARG A 190 " =    1.725
peak=    4.190 closest distance to " CD  ARG A 159 " =    0.830
peak=    4.168 closest distance to " O   HOH Z 392 " =    1.290
peak=    4.161 closest distance to " CA  TYR A  30 " =    1.014
peak=    4.109 closest distance to " CG  LEU A 167 " =    1.279
peak=    4.108 closest distance to " CB  ASN A 187 " =    1.058
peak=    4.088 closest distance to " O   HOH Z   9 " =    1.982
peak=    4.076 closest distance to " O   HOH Z   1 " =    1.666
peak=    4.075 closest distance to " CG  TRP A 179 " =    2.190
peak=    4.073 closest distance to " O   HOH Z 437 " =    1.926
peak=    4.066 closest distance to " O   HOH Z 261 " =    1.837
peak=    4.059 closest distance to " CB  LEU A 228 " =    1.079
peak=    4.048 closest distance to " CG  PRO A  90 " =    1.178
peak=    4.033 closest distance to " O   HOH Z 132 " =    2.423
peak=    3.999 closest distance to " OG ASER A 258 " =    3.113
peak=    3.991 closest distance to " O   HOH Z   1 " =    1.845
peak=    3.986 closest distance to " O   HOH Z 193 " =    1.652
peak=    3.968 closest distance to " O   HOH Z  78 " =    2.243
peak=    3.966 closest distance to " ND1 HIS A  86 " =    1.748
peak=    3.954 closest distance to " O   HOH Z 183 " =    1.448
peak=    3.937 closest distance to " CG2 VAL A 257 " =    0.929
peak=    3.906 closest distance to " CB  SER A 216 " =    0.864
peak=    3.891 closest distance to " O   HOH Z 217 " =    2.870
peak=    3.886 closest distance to " O   SER A  87 " =    2.332
peak=    3.881 closest distance to " CG2 THR A 221 " =    1.015
peak=    3.870 closest distance to " O   HOH Z 236 " =    1.476
peak=    3.865 closest distance to " O   HOH Z 272 " =    1.803
peak=    3.860 closest distance to " CB  GLU A 152 " =    1.301
peak=    3.857 closest distance to " O   HOH Z  61 " =    1.581
peak=    3.834 closest distance to " O   HOH Z  61 " =    1.576
peak=    3.827 closest distance to " N   PHE A 130 " =    1.253
peak=    3.825 closest distance to " CG1 ILE A 151 " =    1.018
peak=    3.818 closest distance to " O   HOH Z 193 " =    1.858
peak=    3.818 closest distance to " O   HOH Z 135 " =    1.719
peak=    3.810 closest distance to " O   HOH Z 368 " =    3.691
peak=    3.810 closest distance to " O   HOH Z  30 " =    1.752
peak=    3.802 closest distance to " CB  ARG A 139 " =    1.050
peak=    3.790 closest distance to " CB  VAL A 265 " =    1.323
peak=    3.786 closest distance to " O   HOH Z 175 " =    2.193
peak=    3.781 closest distance to " O   HOH Z  10 " =    1.781
peak=    3.779 closest distance to " CB  TRP A 266 " =    1.027
peak=    3.776 closest distance to " CZ  PHE A 218 " =    1.062
peak=    3.772 closest distance to " O   HOH Z 195 " =    1.351
peak=    3.769 closest distance to " OD1 ASN A  69 " =    2.634
peak=    3.769 closest distance to " O   HOH Z 394 " =    1.680
peak=    3.760 closest distance to " CB  ARG A  79 " =    1.292
peak=    3.756 closest distance to " CA  GLY A 241 " =    3.756
peak=    3.751 closest distance to " O   HOH Z 403 " =    1.396
peak=    3.745 closest distance to " O   HOH Z 258 " =    2.163
peak=    3.743 closest distance to " O   HOH Z 365 " =    2.682
peak=    3.741 closest distance to " CB  THR A 157 " =    1.165
peak=    3.735 closest distance to " CG  PRO A 280 " =    0.719
peak=    3.734 closest distance to " O   HOH Z  44 " =    2.785
peak=    3.729 closest distance to " O   ASN A 209 " =    1.413
peak=    3.724 closest distance to " CG1 ILE A  33 " =    1.235
peak=    3.715 closest distance to " CB  ASN A  39 " =    0.905
peak=    3.709 closest distance to " O   HOH Z 171 " =    2.861
peak=    3.705 closest distance to " CB  TYR A 169 " =    0.785
peak=    3.703 closest distance to " O   HOH Z 115 " =    1.687
peak=    3.703 closest distance to " O   HOH Z 352 " =    1.682
peak=    3.693 closest distance to " O   HOH Z  68 " =    2.075
peak=    3.690 closest distance to " CD  ARG A  66 " =    2.190
peak=    3.678 closest distance to " CA  THR A 264 " =    0.838
peak=    3.672 closest distance to " CD BLYS A 290 " =    1.032
peak=    3.670 closest distance to " O   HOH Z 180 " =    2.096
peak=    3.669 closest distance to " O   HOH Z 405 " =    1.492
peak=    3.663 closest distance to " O   HOH Z  40 " =    2.208
peak=    3.658 closest distance to " CB  LEU A 143 " =    1.117
peak=    3.651 closest distance to " NE AARG A 275 " =    1.463
peak=    3.647 closest distance to " O   HOH Z 116 " =    2.999
peak=    3.644 closest distance to " O   HOH Z 144 " =    2.269
peak=    3.624 closest distance to " CB  SER A 212 " =    1.207
peak=    3.623 closest distance to " O   HOH Z  20 " =    1.731
peak=    3.616 closest distance to " CB  VAL A 202 " =    1.662
peak=    3.616 closest distance to " CB  GLU A 277 " =    3.594
peak=    3.614 closest distance to " O   HOH Z 250 " =    1.418
peak=    3.613 closest distance to " O   HOH Z 126 " =    1.459
peak=    3.610 closest distance to " CB  TYR A 169 " =    0.883
peak=    3.603 closest distance to " O   HOH Z 302 " =    1.702
peak=    3.598 closest distance to " O   HOH Z 234 " =    3.812
peak=    3.596 closest distance to " O   HOH Z 158 " =    2.794
peak=    3.590 closest distance to " OD2 ASP A 286 " =    2.807
peak=    3.587 closest distance to " O   HOH Z 128 " =    2.201
peak=    3.586 closest distance to " CA  ALA A 233 " =    1.153
peak=    3.585 closest distance to " CE  LYS A  76 " =    0.835
peak=    3.583 closest distance to " O   HOH Z 362 " =    1.953
peak=    3.583 closest distance to " CB  ASP A 124 " =    0.723
peak=    3.582 closest distance to " O   HOH Z 371 " =    2.712
peak=    3.577 closest distance to " CG  PRO A 243 " =    1.076
peak=    3.577 closest distance to " O   HOH Z 272 " =    2.101
peak=    3.576 closest distance to " CD1 LEU A 300 " =    1.218
peak=    3.555 closest distance to " O   HOH Z  44 " =    1.672
peak=    3.552 closest distance to " O   HOH Z  21 " =    1.684
peak=    3.548 closest distance to " O   HOH Z  88 " =    3.927
peak=    3.538 closest distance to " NH1AARG A 145 " =    1.178
peak=    3.534 closest distance to " O   TYR A 116 " =    1.336
peak=    3.532 closest distance to " O   HOH Z 327 " =    1.760
peak=    3.530 closest distance to " CA  SER A  87 " =    1.026
peak=    3.528 closest distance to " O   HOH Z 389 " =    1.961
peak=    3.527 closest distance to " NE2 GLN A  73 " =    3.752
peak=    3.527 closest distance to " CB  ILE A 120 " =    1.322
peak=    3.524 closest distance to " O   HOH Z 145 " =    1.480
peak=    3.524 closest distance to " O   HOH Z 281 " =    4.686
peak=    3.512 closest distance to " CB  TRP A 179 " =    1.492
peak=    3.512 closest distance to " O   HOH Z 313 " =    1.623
peak=    3.510 closest distance to " O   HOH Z  88 " =    3.078
peak=    3.507 closest distance to " O   HOH Z 425 " =    1.996
peak=    3.506 closest distance to " CB  ALA A 114 " =    1.425
peak=    3.506 closest distance to " CB  ASN A 142 " =    0.944
peak=    3.505 closest distance to " O   HOH Z  58 " =    1.739
peak=    3.503 closest distance to " N   ALA A   1 " =    2.002
peak=    3.503 closest distance to " O   HOH Z 214 " =    1.980
peak=    3.495 closest distance to " OG  SER A  62 " =    3.021
peak=    3.495 closest distance to " CD  PRO A 243 " =    1.748
peak=    3.493 closest distance to " O   HOH Z 207 " =    2.242
peak=    3.492 closest distance to " O   HOH Z 373 " =    1.508
peak=    3.490 closest distance to " CB  LYS A 117 " =    1.242
peak=    3.490 closest distance to " CA  ALA A 299 " =    0.874
peak=    3.481 closest distance to " O   HOH Z   3 " =    1.971
peak=    3.479 closest distance to " N   SER A  97 " =    0.888
peak=    3.478 closest distance to " O   HOH Z 128 " =    1.981
peak=    3.477 closest distance to " CA  ASN A 215 " =    1.130
peak=    3.470 closest distance to " O   HOH Z  59 " =    2.034
peak=    3.458 closest distance to " CB  SER A 276 " =    1.167
peak=    3.458 closest distance to " O   HOH Z 368 " =    1.894
peak=    3.456 closest distance to " OG  SER A  62 " =    3.044
peak=    3.455 closest distance to " N   TYR A  15 " =    0.913
peak=    3.453 closest distance to " O   HOH Z 108 " =    2.140
peak=    3.452 closest distance to " CB  GLN A  88 " =    1.286
peak=    3.452 closest distance to " CA  TYR A  30 " =    1.049
peak=    3.447 closest distance to " O   HOH Z 188 " =    2.018
peak=    3.442 closest distance to " CA  TYR A 116 " =    1.347
peak=    3.439 closest distance to " CA  LEU A 101 " =    1.594
peak=    3.438 closest distance to " N   CYS A 260 " =    0.770
peak=    3.435 closest distance to " CA  MET A 105 " =    0.906
peak=    3.430 closest distance to " CD  LYS A 166 " =    1.328
peak=    3.430 closest distance to " CD1 LEU A 255 " =    1.778
peak=    3.429 closest distance to " O   HOH Z 289 " =    1.643
peak=    3.427 closest distance to " CA  ILE A 234 " =    1.021
peak=    3.425 closest distance to " O   HOH Z 119 " =    1.598
peak=    3.418 closest distance to " CA  ALA A 154 " =    0.948
peak=    3.418 closest distance to " O   HOH Z 305 " =    3.664
peak=    3.417 closest distance to " O   HOH Z 184 " =    1.717
peak=    3.417 closest distance to " O   HOH Z 109 " =    2.496
peak=    3.416 closest distance to " CA  ALA A 160 " =    0.897
peak=    3.414 closest distance to " OE2 GLU A  53 " =    2.023
peak=    3.414 closest distance to " O   HOH Z 147 " =    1.745
peak=    3.412 closest distance to " O   HOH Z 422 " =    2.749
peak=    3.409 closest distance to " O   HOH Z 295 " =    1.595
peak=    3.408 closest distance to " O   HOH Z 432 " =    1.833
peak=    3.402 closest distance to " CB  TYR A 116 " =    0.888
peak=    3.397 closest distance to " O   HOH Z 343 " =    3.428
peak=    3.395 closest distance to " O   HOH Z  97 " =    2.125
peak=    3.394 closest distance to " N   ASN A 127 " =    1.381
peak=    3.389 closest distance to " N   GLN A 278 " =    1.172
peak=    3.379 closest distance to " CE3 TRP A 274 " =    1.295
peak=    3.374 closest distance to " O   HOH Z 217 " =    1.621
peak=    3.370 closest distance to " O   HOH Z 122 " =    1.624
peak=    3.361 closest distance to " O   HOH Z 213 " =    2.030
peak=    3.359 closest distance to " O   HOH Z 225 " =    1.459
peak=    3.358 closest distance to " O   HOH Z 172 " =    2.677
peak=    3.351 closest distance to " OD1BASN A 224 " =    2.284
peak=    3.350 closest distance to " O   HOH Z 146 " =    1.721
peak=    3.349 closest distance to " NE  ARG A  66 " =    3.702
peak=    3.348 closest distance to " O   HOH Z 371 " =    1.954
peak=    3.343 closest distance to " O   MET A 105 " =    1.769
peak=    3.341 closest distance to " O   HOH Z  51 " =    1.713
peak=    3.339 closest distance to " O   HOH Z 158 " =    1.752
peak=    3.339 closest distance to " NH1 ARG A  14 " =    0.976
peak=    3.339 closest distance to " CB  ALA A  43 " =    0.828
peak=    3.332 closest distance to " CG  MET A 113 " =    1.289
peak=    3.332 closest distance to " CB  GLU A 152 " =    0.952
peak=    3.330 closest distance to " OG BSER A  99 " =    2.282
peak=    3.329 closest distance to " CA  ALA A  21 " =    1.224
peak=    3.324 closest distance to " O   HOH Z 219 " =    2.188
peak=    3.322 closest distance to " CA  GLY A 267 " =    1.255
peak=    3.320 closest distance to " O   HOH Z  55 " =    2.013
peak=    3.316 closest distance to " N   GLU A   2 " =    1.380
peak=    3.305 closest distance to " CB  GLU A 236 " =    1.255
peak=    3.305 closest distance to " CA  ALA A 291 " =    0.895
peak=    3.301 closest distance to " CD1 ILE A  33 " =    1.665
peak=    3.297 closest distance to " CA  SER A  95 " =    1.056
peak=    3.293 closest distance to " CZ3 TRP A 123 " =    1.409
peak=    3.291 closest distance to " O   HOH Z 148 " =    3.357
peak=    3.285 closest distance to " CB  GLU A  46 " =    0.956
peak=    3.285 closest distance to " NH2 ARG A 219 " =    1.811
peak=    3.282 closest distance to " CA  ARG A 195 " =    1.284
peak=    3.279 closest distance to " CB  PRO A 243 " =    1.159
peak=    3.278 closest distance to " O   HOH Z 409 " =    2.192
peak=    3.275 closest distance to " CB  SER A  62 " =    1.126
peak=    3.272 closest distance to " O   HOH Z  59 " =    1.619
peak=    3.271 closest distance to " O   HOH Z  17 " =    1.756
peak=    3.269 closest distance to " CB  THR A  82 " =    1.276
peak=    3.268 closest distance to " CA  ARG A 102 " =    1.182
peak=    3.267 closest distance to " O   HOH Z 227 " =    1.793
peak=    3.266 closest distance to " CB  TRP A 150 " =    1.118
peak=    3.266 closest distance to " OG BSER A 134 " =    3.214
peak=    3.261 closest distance to " CA  ASN A 217 " =    1.130
peak=    3.259 closest distance to " O   HOH Z 310 " =    2.392
peak=    3.258 closest distance to " O   HOH Z 113 " =    1.889
peak=    3.257 closest distance to " O   HOH Z 193 " =    2.097
peak=    3.253 closest distance to " O   HOH Z 426 " =    1.826
peak=    3.252 closest distance to " CA  MET A  40 " =    1.081
peak=    3.252 closest distance to " O   HOH Z 181 " =    2.120
peak=    3.250 closest distance to " CZ  PHE A 192 " =    0.935
peak=    3.250 closest distance to " O   HOH Z 271 " =    2.483
peak=    3.248 closest distance to " O   HOH Z 207 " =    1.752
peak=    3.248 closest distance to " OG BSER A 164 " =    2.307
peak=    3.246 closest distance to " CD  ARG A 138 " =    0.770
peak=    3.245 closest distance to " NE2 GLN A  58 " =    3.737
peak=    3.241 closest distance to " CG1BVAL A  72 " =    1.470
peak=    3.241 closest distance to " O   ASN A  74 " =    1.579
peak=    3.238 closest distance to " O   HOH Z 374 " =    2.690
peak=    3.236 closest distance to " O   HOH Z 414 " =    1.258
peak=    3.235 closest distance to " O   HOH Z 189 " =    2.262
peak=    3.233 closest distance to " CA  GLY A 136 " =    0.996
peak=    3.228 closest distance to " O   THR A 220 " =    1.483
peak=    3.228 closest distance to " O   HOH Z 132 " =    3.625
peak=    3.227 closest distance to " O   HOH Z 286 " =    2.322
peak=    3.226 closest distance to " O   HOH Z 227 " =    1.927
peak=    3.225 closest distance to " NH2BARG A 145 " =    2.105
peak=    3.225 closest distance to " CB  ALA A  34 " =    1.190
peak=    3.223 closest distance to " N   SER A 134 " =    1.366
peak=    3.223 closest distance to " CG  GLN A  88 " =    1.094
peak=    3.216 closest distance to " O   HOH Z  66 " =    2.117
peak=    3.210 closest distance to " O   HOH Z 393 " =    1.200
peak=    3.207 closest distance to " OG  SER A  22 " =    2.904
peak=    3.204 closest distance to " CB  THR A 235 " =    1.033
peak=    3.203 closest distance to " CD2 TRP A 179 " =    1.233
peak=    3.202 closest distance to " ND1 HIS A  81 " =    1.674
peak=    3.201 closest distance to " CA  ALA A 158 " =    1.085
peak=    3.200 closest distance to " O   HOH Z 344 " =    3.187
peak=    3.197 closest distance to " CG  GLN A 278 " =    1.353
peak=    3.193 closest distance to " CG1 VAL A 153 " =    0.917
peak=    3.193 closest distance to " CA  GLU A  46 " =    0.792
peak=    3.192 closest distance to " CA  ALA A  51 " =    1.007
peak=    3.188 closest distance to " O   HOH Z 284 " =    3.118
peak=    3.186 closest distance to " N   ARG A 156 " =    1.315
peak=    3.185 closest distance to " CD1 ILE A 263 " =    1.301
peak=    3.183 closest distance to " CB  ARG A 138 " =    0.939
peak=    3.182 closest distance to " O   HOH Z 273 " =    2.865
peak=    3.181 closest distance to " NE2 GLN A 278 " =    3.689
peak=    3.181 closest distance to " O   HOH Z 110 " =    1.528
peak=    3.179 closest distance to " CB  ASP A 140 " =    0.799
peak=    3.178 closest distance to " O   HOH Z 244 " =    1.647
peak=    3.173 closest distance to " O   HOH Z 213 " =    1.928
peak=    3.172 closest distance to " N   SER A 146 " =    1.666
peak=    3.169 closest distance to " CB  ALA A  10 " =    0.866
peak=    3.168 closest distance to " CD2 LEU A 297 " =    1.004
peak=    3.168 closest distance to " NH1BARG A 145 " =    1.292
peak=    3.166 closest distance to " CB  ALA A 291 " =    1.357
peak=    3.160 closest distance to " CB  ALA A 180 " =    1.388
peak=    3.153 closest distance to " CD2 PHE A  59 " =    1.648
peak=    3.152 closest distance to " O   HOH Z  85 " =    2.050
peak=    3.151 closest distance to " O   HOH Z  59 " =    2.442
peak=    3.151 closest distance to " SD  MET A  93 " =    1.286
peak=    3.149 closest distance to " O   HOH Z 329 " =    3.849
peak=    3.147 closest distance to " CE3 TRP A  85 " =    0.866
peak=    3.141 closest distance to " CG  GLU A 277 " =    1.969
peak=    3.137 closest distance to " O   HOH Z 286 " =    2.412
peak=    3.133 closest distance to " O   HOH Z 128 " =    2.027
peak=    3.133 closest distance to " O   HOH Z 407 " =    2.099
peak=    3.132 closest distance to " CA  TYR A 186 " =    1.537
peak=    3.127 closest distance to " NH2AARG A 190 " =    1.520
peak=    3.123 closest distance to " CG BARG A 275 " =    1.439
peak=    3.120 closest distance to " CB  ALA A 114 " =    1.071
peak=    3.120 closest distance to " O   HOH Z 288 " =    2.025
peak=    3.115 closest distance to " O   HOH Z 133 " =    1.578
peak=    3.106 closest distance to " CB  LEU A 300 " =    0.944
peak=    3.105 closest distance to " CB  PHE A 204 " =    0.747
peak=    3.105 closest distance to " O   HOH Z 116 " =    1.697
peak=    3.104 closest distance to " O   HOH Z 154 " =    1.979
peak=    3.103 closest distance to " O   HOH Z 266 " =    3.432
peak=    3.102 closest distance to " CB  GLU A 152 " =    1.337
peak=    3.087 closest distance to " O   HOH Z 282 " =    1.367
peak=    3.086 closest distance to " O   GLY A 302 " =    1.591
peak=    3.080 closest distance to " O   HOH Z 130 " =    2.134
peak=    3.078 closest distance to " C   GLU A 277 " =    1.381
peak=    3.073 closest distance to " O   HOH Z 386 " =    2.630
peak=    3.070 closest distance to " CD2 TYR A 186 " =    1.010
peak=    3.007 closest distance to " CB  VAL A 265 " =    2.096
peak=    3.004 closest distance to " CB  GLU A 277 " =    3.825

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.620 - 5.678
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.708 - 5.678

peak=   -4.560 closest distance to " CB  PRO A 243 " =    2.510
peak=   -4.555 closest distance to " O   HOH Z 377 " =    1.817
peak=   -4.432 closest distance to " O   PRO A 198 " =    1.317
peak=   -4.293 closest distance to " CD  ARG A  14 " =    3.346
peak=   -4.237 closest distance to " O   HOH Z  65 " =    1.061
peak=   -4.194 closest distance to " O   HOH Z 407 " =    3.278
peak=   -4.187 closest distance to " O   HOH Z 266 " =    4.825
peak=   -4.162 closest distance to " O   HOH Z 185 " =    2.053
peak=   -4.160 closest distance to " CA  GLY A  98 " =    1.834
peak=   -4.153 closest distance to " CZ3 TRP A 179 " =    1.101
peak=   -4.083 closest distance to " CD  ARG A 156 " =    2.073
peak=   -4.068 closest distance to " O   HOH Z 231 " =    1.938
peak=   -4.064 closest distance to " O   HOH Z 290 " =    1.138
peak=   -4.061 closest distance to " O   SER A 135 " =    1.450
peak=   -4.046 closest distance to " O   HOH Z 351 " =    1.610
peak=   -3.976 closest distance to " CD1 LEU A 255 " =    2.991
peak=   -3.941 closest distance to " OG BSER A 134 " =    1.337
peak=   -3.924 closest distance to " C   ALA A 158 " =    1.528
peak=   -3.903 closest distance to " CB  ALA A  43 " =    2.433
peak=   -3.838 closest distance to " O   HOH Z 316 " =    1.893
peak=   -3.787 closest distance to " O   HOH Z 313 " =    1.711
peak=   -3.787 closest distance to " N   THR A 157 " =    1.558
peak=   -3.762 closest distance to " CG  MET A 105 " =    0.936
peak=   -3.743 closest distance to " O   VAL A  67 " =    2.569
peak=   -3.742 closest distance to " O   HOH Z 372 " =    2.437
peak=   -3.735 closest distance to " CB  ALA A 248 " =    1.994
peak=   -3.720 closest distance to " OG  SER A  87 " =    1.292
peak=   -3.714 closest distance to " CB  ASP A  27 " =    2.376
peak=   -3.711 closest distance to " O   PRO A 243 " =    2.342
peak=   -3.685 closest distance to " O   HOH Z 231 " =    0.920
peak=   -3.683 closest distance to " O   SER A  22 " =    2.661
peak=   -3.680 closest distance to " O   HOH Z  38 " =    1.483
peak=   -3.679 closest distance to " CG  GLN A 223 " =    2.194
peak=   -3.649 closest distance to " CB  ASN A  39 " =    2.274
peak=   -3.636 closest distance to " O   HOH Z 389 " =    2.015
peak=   -3.625 closest distance to " O   HOH Z  13 " =    1.706
peak=   -3.623 closest distance to " O   HOH Z  52 " =    1.184
peak=   -3.618 closest distance to " O   HOH Z   1 " =    1.421
peak=   -3.608 closest distance to " CA  GLY A 203 " =    2.287
peak=   -3.603 closest distance to " CD2 LEU A 237 " =    2.841
peak=   -3.599 closest distance to " ND2 ASN A 249 " =    2.257
peak=   -3.588 closest distance to " CA  GLY A 241 " =    2.223
peak=   -3.584 closest distance to " O   HOH Z 298 " =    1.096
peak=   -3.581 closest distance to " O   HOH Z 152 " =    5.001
peak=   -3.580 closest distance to " CG1 VAL A 112 " =    3.013
peak=   -3.554 closest distance to " O   HOH Z 198 " =    1.998
peak=   -3.549 closest distance to " O   HOH Z  51 " =    0.959
peak=   -3.544 closest distance to " C   HIS A 108 " =    1.141
peak=   -3.536 closest distance to " O   HOH Z 298 " =    2.529
peak=   -3.535 closest distance to " O   ILE A  49 " =    1.692
peak=   -3.531 closest distance to " CB  ALA A   9 " =    2.426
peak=   -3.527 closest distance to " O   HOH Z 166 " =    1.256
peak=   -3.527 closest distance to " NH2 ARG A  79 " =    1.991
peak=   -3.523 closest distance to " C   LEU A 143 " =    1.296
peak=   -3.498 closest distance to " C   LEU A 222 " =    0.708
peak=   -3.494 closest distance to " CG1 VAL A 197 " =    2.249
peak=   -3.488 closest distance to " O   PRO A 163 " =    1.885
peak=   -3.488 closest distance to " O   HOH Z 385 " =    2.065
peak=   -3.485 closest distance to " CD2 TYR A 293 " =    1.901
peak=   -3.485 closest distance to " O   HOH Z  11 " =    1.863
peak=   -3.477 closest distance to " OD1 ASN A 187 " =    1.670
peak=   -3.474 closest distance to " CG  PHE A 283 " =    2.658
peak=   -3.472 closest distance to " CB  ALA A 291 " =    2.199
peak=   -3.470 closest distance to " N   ASP A 171 " =    2.424
peak=   -3.469 closest distance to " O   HOH Z 384 " =    2.920
peak=   -3.467 closest distance to " O   HOH Z 191 " =    5.394
peak=   -3.467 closest distance to " CG  GLN A  88 " =    0.832
peak=   -3.466 closest distance to " N   GLN A  58 " =    1.668
peak=   -3.466 closest distance to " CB  TRP A  85 " =    2.480
peak=   -3.466 closest distance to " CE2 TYR A  30 " =    2.618
peak=   -3.464 closest distance to " CE  MET A 105 " =    2.436
peak=   -3.459 closest distance to " CB  CYS A 254 " =    2.063
peak=   -3.455 closest distance to " O   VAL A 189 " =    2.417
peak=   -3.451 closest distance to " O   HOH Z  90 " =    2.705
peak=   -3.448 closest distance to " ND2 ASN A  45 " =    1.158
peak=   -3.444 closest distance to " CE  MET A  93 " =    1.132
peak=   -3.441 closest distance to " N   ALA A  43 " =    2.460
peak=   -3.437 closest distance to " OD1 ASN A 148 " =    1.550
peak=   -3.433 closest distance to " O   HOH Z 282 " =    4.579
peak=   -3.428 closest distance to " ND2 ASN A 285 " =    2.077
peak=   -3.427 closest distance to " O   PHE A 218 " =    1.331
peak=   -3.424 closest distance to " CG  PRO A 163 " =    2.427
peak=   -3.422 closest distance to " O   HOH Z 317 " =    1.478
peak=   -3.419 closest distance to " O   HOH Z 211 " =    1.478
peak=   -3.415 closest distance to " CD2 LEU A 143 " =    2.559
peak=   -3.412 closest distance to " O   HOH Z 168 " =    1.775
peak=   -3.411 closest distance to " O   PRO A 198 " =    1.301
peak=   -3.409 closest distance to " OG BSER A 134 " =    1.664
peak=   -3.408 closest distance to " CG2 THR A  18 " =    2.789
peak=   -3.400 closest distance to " CB  PRO A  54 " =    2.421
peak=   -3.399 closest distance to " CE2 PHE A 218 " =    2.412
peak=   -3.398 closest distance to " O   HOH Z  39 " =    1.164
peak=   -3.398 closest distance to " O   HOH Z  60 " =    2.126
peak=   -3.397 closest distance to " O   HOH Z 111 " =    1.884
peak=   -3.395 closest distance to " O   HOH Z 281 " =    2.841
peak=   -3.395 closest distance to " ND2 ASN A  45 " =    1.968
peak=   -3.394 closest distance to " O   HOH Z 140 " =    1.479
peak=   -3.392 closest distance to " O   HOH Z 131 " =    4.157
peak=   -3.391 closest distance to " OE1 GLN A  88 " =    1.242
peak=   -3.379 closest distance to " O   ALA A 180 " =    1.226
peak=   -3.372 closest distance to " O   HOH Z 102 " =    1.593
peak=   -3.371 closest distance to " CZ  PHE A  59 " =    1.520
peak=   -3.366 closest distance to " CE1 TYR A 169 " =    2.553
peak=   -3.361 closest distance to " C   ALA A 114 " =    2.209
peak=   -3.350 closest distance to " OG  SER A  97 " =    2.172
peak=   -3.348 closest distance to " O   HOH Z  43 " =    1.734
peak=   -3.347 closest distance to " CA  GLY A 133 " =    2.001
peak=   -3.347 closest distance to " O   HOH Z 218 " =    3.523
peak=   -3.339 closest distance to " O   ASP A 162 " =    2.217
peak=   -3.339 closest distance to " O   HOH Z 377 " =    1.138
peak=   -3.337 closest distance to " CD  ARG A 139 " =    1.633
peak=   -3.336 closest distance to " CD  LYS A 289 " =    2.364
peak=   -3.330 closest distance to " CG  GLN A 240 " =    2.410
peak=   -3.328 closest distance to " CG  ASN A  39 " =    1.706
peak=   -3.320 closest distance to " O   HOH Z 292 " =    1.397
peak=   -3.317 closest distance to " CB  PHE A 192 " =    1.784
peak=   -3.313 closest distance to " CE3 TRP A 274 " =    2.485
peak=   -3.305 closest distance to " O   HOH Z  28 " =    1.750
peak=   -3.304 closest distance to " O   HOH Z 352 " =    2.213
peak=   -3.303 closest distance to " OG  SER A 245 " =    1.261
peak=   -3.300 closest distance to " CE3 TRP A 123 " =    1.395
peak=   -3.297 closest distance to " O   HOH Z 198 " =    1.696
peak=   -3.296 closest distance to " O   HOH Z 348 " =    1.782
peak=   -3.294 closest distance to " ND2 ASN A 187 " =    1.397
peak=   -3.294 closest distance to " OD2 ASP A 191 " =    1.480
peak=   -3.289 closest distance to " NH1AARG A 275 " =    1.916
peak=   -3.285 closest distance to " OXT GLY A 302 " =    3.189
peak=   -3.278 closest distance to " O   HOH Z 243 " =    1.936
peak=   -3.275 closest distance to " O   GLY A  17 " =    1.156
peak=   -3.274 closest distance to " CD  GLN A  58 " =    0.931
peak=   -3.273 closest distance to " CD1 ILE A 239 " =    2.296
peak=   -3.272 closest distance to " NH2AARG A 275 " =    5.507
peak=   -3.270 closest distance to " OD2 ASP A 171 " =    1.743
peak=   -3.269 closest distance to " N   ASP A 270 " =    1.358
peak=   -3.266 closest distance to " ND2BASN A 224 " =    1.556
peak=   -3.261 closest distance to " C   ASN A 187 " =    1.842
peak=   -3.253 closest distance to " CB  ALA A 114 " =    2.535
peak=   -3.251 closest distance to " O   HOH Z  49 " =    1.301
peak=   -3.245 closest distance to " CB  ASP A 132 " =    2.354
peak=   -3.245 closest distance to " O   HOH Z 134 " =    1.723
peak=   -3.244 closest distance to " CG  ASP A 231 " =    0.750
peak=   -3.240 closest distance to " OD1 ASP A 171 " =    1.555
peak=   -3.239 closest distance to " O   HOH Z 318 " =    1.723
peak=   -3.236 closest distance to " ND2 ASN A  45 " =    1.406
peak=   -3.235 closest distance to " O   HOH Z 427 " =    1.708
peak=   -3.234 closest distance to " O   HOH Z 118 " =    1.358
peak=   -3.233 closest distance to " CG1 VAL A 250 " =    2.650
peak=   -3.233 closest distance to " OD2 ASP A 171 " =    2.024
peak=   -3.233 closest distance to " CB  TYR A  15 " =    2.147
peak=   -3.227 closest distance to " O   HOH Z 345 " =    2.269
peak=   -3.222 closest distance to " O   ASN A 301 " =    1.414
peak=   -3.217 closest distance to " CB  PRO A 163 " =    2.451
peak=   -3.216 closest distance to " O   HOH Z 414 " =    1.838
peak=   -3.216 closest distance to " OD2 ASP A  27 " =    1.700
peak=   -3.212 closest distance to " NE  ARG A  36 " =    2.028
peak=   -3.208 closest distance to " CG2 THR A 178 " =    2.177
peak=   -3.204 closest distance to " O   HOH Z 417 " =    2.171
peak=   -3.203 closest distance to " CB  ALA A 248 " =    2.375
peak=   -3.203 closest distance to " CE  LYS A  76 " =    2.883
peak=   -3.201 closest distance to " C   GLU A 236 " =    0.815
peak=   -3.186 closest distance to " CA  GLY A  57 " =    2.063
peak=   -3.184 closest distance to " C   ALA A 242 " =    2.129
peak=   -3.183 closest distance to " O   ARG A 145 " =    1.396
peak=   -3.182 closest distance to " CE BMET A  47 " =    1.423
peak=   -3.180 closest distance to " O   HOH Z 253 " =    3.969
peak=   -3.172 closest distance to " N   ALA A   1 " =    1.710
peak=   -3.172 closest distance to " O   HOH Z 250 " =    1.398
peak=   -3.171 closest distance to " C   LYS A  76 " =    1.523
peak=   -3.166 closest distance to " O   HOH Z 166 " =    1.634
peak=   -3.165 closest distance to " CZ BARG A 275 " =    1.604
peak=   -3.161 closest distance to " O   VAL A  67 " =    2.798
peak=   -3.159 closest distance to " O   GLN A 240 " =    2.053
peak=   -3.158 closest distance to " OE2 GLU A 152 " =    1.040
peak=   -3.158 closest distance to " SD BMET A  47 " =    0.874
peak=   -3.156 closest distance to " CG1 VAL A  78 " =    2.541
peak=   -3.153 closest distance to " O   HOH Z 359 " =    3.209
peak=   -3.152 closest distance to " O   ALA A  10 " =    1.667
peak=   -3.149 closest distance to " OH  TYR A 247 " =    1.780
peak=   -3.146 closest distance to " O   ALA A   1 " =    1.142
peak=   -3.145 closest distance to " ND2 ASN A 215 " =    2.249
peak=   -3.140 closest distance to " O   HOH Z 426 " =    2.295
peak=   -3.139 closest distance to " CG2 ILE A  49 " =    2.700
peak=   -3.137 closest distance to " CG  ARG A 269 " =    2.552
peak=   -3.136 closest distance to " OE1 GLN A  58 " =    3.048
peak=   -3.135 closest distance to " O   HOH Z 147 " =    1.425
peak=   -3.134 closest distance to " O   HOH Z  73 " =    2.249
peak=   -3.134 closest distance to " O   HOH Z 111 " =    1.135
peak=   -3.127 closest distance to " O   HOH Z 412 " =    4.407
peak=   -3.115 closest distance to " O   HOH Z 222 " =    1.015
peak=   -3.105 closest distance to " O   HOH Z 281 " =    3.070
peak=   -3.105 closest distance to " O   HOH Z 346 " =    1.655
peak=   -3.101 closest distance to " O   GLY A  80 " =    2.358
peak=   -3.098 closest distance to " O   HOH Z 409 " =    5.678
peak=   -3.097 closest distance to " O   HOH Z 256 " =    1.496
peak=   -3.089 closest distance to " O   HOH Z  25 " =    2.093
peak=   -3.088 closest distance to " O   SER A  62 " =    2.193
peak=   -3.077 closest distance to " O   HOH Z 432 " =    3.670
peak=   -3.073 closest distance to " CD2 PHE A  61 " =    2.077
peak=   -3.068 closest distance to " CG  TRP A 266 " =    1.712
peak=   -3.045 closest distance to " NH2 ARG A 219 " =    1.843
peak=   -3.040 closest distance to " C   MET A 188 " =    1.588
peak=   -3.031 closest distance to " N   VAL A  72 " =    1.390
peak=   -3.018 closest distance to " CE1 PHE A  59 " =    2.182

================= 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    :  0.4198 0.4178   6.232694e+00   6.228414e+00
   1_bss:  0.4090 0.4090   6.221844e+00   6.215472e+00
   1_xyz:  0.2924 0.3311   5.968546e+00   6.036718e+00
   1_adp:  0.2677 0.3443   5.923979e+00   6.067460e+00
   1_occ:  0.2673 0.3441   5.922892e+00   6.066864e+00
   2_bss:  0.2659 0.3403   5.917779e+00   6.060970e+00
   2_xyz:  0.2018 0.2613   5.665922e+00   5.849315e+00
   2_adp:  0.1848 0.2412   5.591481e+00   5.783646e+00
   2_occ:  0.1847 0.2409   5.591379e+00   5.783949e+00
   3_bss:  0.1844 0.2397   5.588441e+00   5.779880e+00
   3_xyz:  0.1469 0.1966   5.380019e+00   5.598547e+00
   3_adp:  0.1384 0.1883   5.331459e+00   5.553598e+00
   3_occ:  0.1383 0.1881   5.331180e+00   5.553183e+00
   4_bss:  0.1385 0.1877   5.329644e+00   5.550893e+00
   4_xyz:  0.1216 0.1691   5.215350e+00   5.449579e+00
   4_adp:  0.1179 0.1658   5.192361e+00   5.431214e+00
   4_occ:  0.1178 0.1659   5.192310e+00   5.431235e+00
   5_bss:  0.1178 0.1659   5.191999e+00   5.431016e+00
   5_xyz:  0.1130 0.1600   5.159801e+00   5.405660e+00
   5_adp:  0.1121 0.1584   5.153239e+00   5.398787e+00
   5_occ:  0.1121 0.1585   5.153281e+00   5.399010e+00
   5_bss:  0.1122 0.1579   5.152088e+00   5.396071e+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:  0.346  50.000  -0.502   2.860  -1.912   0.000  -0.000  -0.000
   1_xyz:  0.346  50.000  -0.502   2.860  -1.912   0.000  -0.000  -0.000
   1_adp:  0.346  50.000  -0.502   2.860  -1.912   0.000  -0.000  -0.000
   1_occ:  0.346  50.000  -0.502   2.860  -1.912   0.000  -0.000  -0.000
   2_bss:  0.331  66.689  -1.242  -0.297  -1.235  -0.000  -0.000  -0.000
   2_xyz:  0.331  66.689  -1.242  -0.297  -1.235  -0.000  -0.000  -0.000
   2_adp:  0.331  66.689  -1.242  -0.297  -1.235  -0.000  -0.000  -0.000
   2_occ:  0.331  66.689  -1.242  -0.297  -1.235  -0.000  -0.000  -0.000
   3_bss:  0.334  59.894  -1.627  -1.570  -0.972  -0.000  -0.000  -0.000
   3_xyz:  0.334  59.894  -1.627  -1.570  -0.972  -0.000  -0.000  -0.000
   3_adp:  0.334  59.894  -1.627  -1.570  -0.972  -0.000  -0.000  -0.000
   3_occ:  0.334  59.894  -1.627  -1.570  -0.972  -0.000  -0.000  -0.000
   4_bss:  0.329  59.894  -2.044  -2.455  -1.276  -0.000  -0.000  -0.000
   4_xyz:  0.329  59.894  -2.044  -2.455  -1.276  -0.000  -0.000  -0.000
   4_adp:  0.329  59.894  -2.044  -2.455  -1.276  -0.000  -0.000  -0.000
   4_occ:  0.329  59.894  -2.044  -2.455  -1.276  -0.000  -0.000  -0.000
   5_bss:  0.320  53.860  -2.047  -2.586  -1.228  -0.000  -0.000  -0.000
   5_xyz:  0.320  53.860  -2.047  -2.586  -1.228  -0.000  -0.000  -0.000
   5_adp:  0.320  53.860  -2.047  -2.586  -1.228  -0.000  -0.000  -0.000
   5_occ:  0.320  53.860  -2.047  -2.586  -1.228  -0.000  -0.000  -0.000
   5_bss:  0.320  53.860  -1.999  -2.606  -1.135  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.605 0.5264  0.7060    57323.930
   1_bss:  49.015 0.5324  0.7209    55087.192
   1_xyz:  34.527 0.7079  0.9118    30236.895
   1_adp:  36.737 0.6808  0.8846    32870.534
   1_occ:  36.736 0.6808  0.8836    32803.434
   2_bss:  36.111 0.6879  0.8611    31916.121
   2_xyz:  26.401 0.7956  0.9613    17635.037
   2_adp:  23.769 0.8241  0.9736    15038.800
   2_occ:  23.782 0.8240  0.9731    15047.753
   3_bss:  23.630 0.8254  0.9582    14856.207
   3_xyz:  18.871 0.8718  0.9892     9839.481
   3_adp:  17.722 0.8831  0.9899     9078.442
   3_occ:  17.717 0.8831  0.9897     9069.025
   4_bss:  17.654 0.8836  0.9716     9009.268
   4_xyz:  15.449 0.9027  0.9812     7242.119
   4_adp:  14.964 0.9071  0.9787     6970.267
   4_occ:  14.966 0.9070  0.9785     6968.063
   5_bss:  14.967 0.9070  0.9774     6962.610
   5_xyz:  14.391 0.9119  0.9787     6576.657
   5_adp:  14.204 0.9135  0.9745     6476.449
   5_occ:  14.209 0.9135  0.9744     6476.940
   5_bss:  14.169 0.9137  0.9760     6413.292
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7175e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7175e-01
   1_xyz:   1.460  0.011  0.101 15.846  0.006  4.108   1.1654e-01
   1_adp:   1.460  0.011  0.101 15.846  0.006  4.108   1.1654e-01
   1_occ:   1.460  0.011  0.101 15.846  0.006  4.108   1.1654e-01
   2_bss:   1.460  0.011  0.101 15.846  0.006  4.108   1.1654e-01
   2_xyz:   1.107  0.008  0.077 14.443  0.004  4.108   6.7434e-02
   2_adp:   1.107  0.008  0.077 14.443  0.004  4.108   6.7434e-02
   2_occ:   1.107  0.008  0.077 14.443  0.004  4.108   6.7434e-02
   3_bss:   1.107  0.008  0.077 14.443  0.004  4.108   6.7434e-02
   3_xyz:   0.923  0.006  0.065 14.176  0.003  4.113   5.3582e-02
   3_adp:   0.923  0.006  0.065 14.176  0.003  4.113   5.3582e-02
   3_occ:   0.923  0.006  0.065 14.176  0.003  4.113   5.3582e-02
   4_bss:   0.923  0.006  0.065 14.176  0.003  4.113   5.3582e-02
   4_xyz:   0.979  0.007  0.073 14.326  0.004  4.119   5.8149e-02
   4_adp:   0.979  0.007  0.073 14.326  0.004  4.119   5.8149e-02
   4_occ:   0.979  0.007  0.073 14.326  0.004  4.119   5.8149e-02
   5_bss:   0.979  0.007  0.073 14.326  0.004  4.119   5.8149e-02
   5_xyz:   0.993  0.007  0.073 14.442  0.004  4.110   5.8762e-02
   5_adp:   0.993  0.007  0.073 14.442  0.004  4.110   5.8762e-02
   5_occ:   0.993  0.007  0.073 14.442  0.004  4.110   5.8762e-02
   5_bss:   0.993  0.007  0.073 14.442  0.004  4.110   5.8762e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.775   2.4072e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.775   2.4072e-01
   1_xyz:   8.755  0.077  0.371 88.484  0.045  2.067   9.8575e-02
   1_adp:   8.755  0.077  0.371 88.484  0.045  2.067   9.8575e-02
   1_occ:   8.755  0.077  0.371 88.484  0.045  2.067   9.8575e-02
   2_bss:   8.755  0.077  0.371 88.484  0.045  2.067   9.8575e-02
   2_xyz:   6.820  0.038  0.241 84.912  0.038  2.273   6.2147e-02
   2_adp:   6.820  0.038  0.241 84.912  0.038  2.273   6.2147e-02
   2_occ:   6.820  0.038  0.241 84.912  0.038  2.273   6.2147e-02
   3_bss:   6.820  0.038  0.241 84.912  0.038  2.273   6.2147e-02
   3_xyz:   7.656  0.052  0.222 84.400  0.019  2.309   1.0910e-01
   3_adp:   7.656  0.052  0.222 84.400  0.019  2.309   1.0910e-01
   3_occ:   7.656  0.052  0.222 84.400  0.019  2.309   1.0910e-01
   4_bss:   7.656  0.052  0.222 84.400  0.019  2.309   1.0910e-01
   4_xyz:   7.954  0.046  0.223 83.889  0.033  2.309   8.1493e-02
   4_adp:   7.954  0.046  0.223 83.889  0.033  2.309   8.1493e-02
   4_occ:   7.954  0.046  0.223 83.889  0.033  2.309   8.1493e-02
   5_bss:   7.954  0.046  0.223 83.889  0.033  2.309   8.1493e-02
   5_xyz:   8.148  0.045  0.229 84.542  0.030  2.283   4.2636e-02
   5_adp:   8.148  0.045  0.229 84.542  0.030  2.283   4.2636e-02
   5_occ:   8.148  0.045  0.229 84.542  0.030  2.283   4.2636e-02
   5_bss:   8.148  0.045  0.229 84.542  0.030  2.283   4.2636e-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: 102.55   0.00  18.16  67.14   0.00  14.19 102.55   2.92  39.79
   1_occ: 102.55   0.00  18.16  67.14   0.00  14.19 102.55   2.92  39.79
   2_bss: 102.55   0.00  18.16  67.14   0.00  14.19 102.55   2.92  39.79
   2_xyz: 102.55   0.00  18.16  67.14   0.00  14.19 102.55   2.92  39.79
   2_adp: 100.66   0.00  17.82  79.44   0.00  13.53 100.66   5.27  41.18
   2_occ: 100.66   0.00  17.82  79.44   0.00  13.53 100.66   5.27  41.18
   3_bss: 100.66   0.00  17.82  79.44   0.00  13.53 100.66   5.27  41.18
   3_xyz: 100.66   0.00  17.82  79.44   0.00  13.53 100.66   5.27  41.18
   3_adp:  97.59   0.72  17.50  81.73   0.72  13.04  97.59   5.12  41.83
   3_occ:  97.59   0.72  17.50  81.73   0.72  13.04  97.59   5.12  41.83
   4_bss:  97.59   0.72  17.50  81.73   0.72  13.04  97.59   5.12  41.83
   4_xyz:  97.59   0.72  17.50  81.73   0.72  13.04  97.59   5.12  41.83
   4_adp:  96.03   0.00  17.47  91.05   0.00  12.93  96.03   3.75  42.20
   4_occ:  96.03   0.00  17.47  91.05   0.00  12.93  96.03   3.75  42.20
   5_bss:  96.03   0.00  17.47  91.05   0.00  12.93  96.03   3.75  42.20
   5_xyz:  96.03   0.00  17.47  91.05   0.00  12.93  96.03   3.75  42.20
   5_adp:  95.86   0.09  17.13  95.86   0.09  12.78  92.01   4.74  40.81
   5_occ:  95.86   0.09  17.13  95.86   0.09  12.78  92.01   4.74  40.81
   5_bss:  95.86   0.09  17.13  95.86   0.09  12.78  92.01   4.74  40.81
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.667    0.026    0.392
   1_adp:    1.667    0.026    0.392
   1_occ:    1.667    0.026    0.392
   2_bss:    1.667    0.026    0.392
   2_xyz:    1.335    0.047    0.511
   2_adp:    1.335    0.047    0.511
   2_occ:    1.335    0.047    0.511
   3_bss:    1.335    0.047    0.511
   3_xyz:    1.289    0.050    0.611
   3_adp:    1.289    0.050    0.611
   3_occ:    1.289    0.050    0.611
   4_bss:    1.289    0.050    0.611
   4_xyz:    1.313    0.061    0.651
   4_adp:    1.313    0.061    0.651
   4_occ:    1.313    0.061    0.651
   5_bss:    1.313    0.061    0.651
   5_xyz:    1.421    0.064    0.668
   5_adp:    1.421    0.064    0.668
   5_occ:    1.421    0.064    0.668
   5_bss:    1.421    0.064    0.668
------------------------------------------------------------------------

CPU time actual refinement: 336.93


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_984/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_984/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_984/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_984/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_984/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.77 
  Macro-tasks:
    bulk solvent and scale       = 37.17  
    individual site refinement   = 138.10 
    weights calculation          = 31.02  
    collect and process          = 6.80   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 213.21 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 109.69 
    alpha_beta                      = 8.60   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 115.95 
    fmodel                         = 6.63   
    r_factors                      = 0.15   
    phase_errors                   = 10.51  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 255.40 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.889 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    605 calls, 109.19 s
gradients_fft:          550 calls, 103.36 s

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

# Date 2008-01-16 Time 06:07:53 PST -0800 (1200492473.10 s)
Start R-work = 0.4198, R-free = 0.4178 (no bulk solvent and anisotropic scale)
Final R-work = 0.1358, R-free = 0.1779 (no bulk solvent and anisotropic scale)

Start R-work = 0.4090, R-free = 0.4090
Final R-work = 0.1122, R-free = 0.1579