# Date 2008-01-16 Time 06:19:06 PST -0800 (1200493146.10 s)
#phil __OFF__

Command line arguments: "../1099.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31723
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1099

-------------------------------------------------------------------------------
  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: (71.655, 45.7567, 88.5498, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (71.655, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 1.95472
Completeness in resolution range: 0.903635
Completeness with d_max=infinity: 0.901141

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3141
                             d_min =   1.9547

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: (71.655, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 1.95472
Completeness in resolution range: 0.903635
Completeness with d_max=infinity: 0.901141

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3145 -  4.1854 [2278/2305]  2049   229  10.1%
  bin  2:  4.1854 -  3.3333 [2188/2208]  1976   212   9.7%
  bin  3:  3.3333 -  2.9153 [2160/2179]  1936   224  10.4%
  bin  4:  2.9153 -  2.6502 [2122/2152]  1906   216  10.2%
  bin  5:  2.6502 -  2.4611 [2148/2167]  1926   222  10.3%
  bin  6:  2.4611 -  2.3165 [2095/2120]  1896   199   9.5%
  bin  7:  2.3165 -  2.2008 [2137/2165]  1917   220  10.3%
  bin  8:  2.2008 -  2.1053 [2091/2127]  1889   202   9.7%
  bin  9:  2.1053 -  2.0244 [1896/2131]  1715   181   9.5%
  bin 10:  2.0244 -  1.9547 [ 474/2124]   420    54  11.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1099/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:
        1.68 -     2.32: 26
        2.32 -     2.97: 1782
        2.97 -     3.61: 4539
        3.61 -     4.26: 9101
        4.26 -     4.90: 12673
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.854 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28116 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_1099/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1099/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 71.655 45.75675 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5087   r_free= 0.5139   ksol= 0.00   Bsol= 0.00   scale= 0.849    |
|                                                                             |
| 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:   1.03 A                  |
| x-ray target function (ml) for work reflections: 6.315221                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.6694 0.99   1482  166 0.4295 0.4104      6.6755      6.6475|
|  2:  4.6694 -  3.7238 0.99   1416  157 0.4679 0.4692      6.8883      6.9084|
|  3:  3.7238 -  3.2583 0.99   1395  153 0.4834 0.4646      6.7013      6.6845|
|  4:  3.2583 -  2.9627 0.99   1393  158 0.5155 0.5547      6.5547      6.5512|
|  5:  2.9627 -  2.7517 0.99   1378  157 0.5399 0.5720      6.3787      6.3873|
|  6:  2.7517 -  2.5903 0.99   1368  146 0.5414 0.5267      6.3063      6.2408|
|  7:  2.5903 -  2.4611 0.99   1361  166 0.5504 0.5319      6.2381      6.1907|
|  8:  2.4611 -  2.3543 0.98   1368  138 0.5430 0.6047      6.1616      6.1716|
|  9:  2.3543 -  2.2640 0.98   1349  155 0.5491 0.5738      6.1387       6.188|
| 10:  2.2640 -  2.1861 1.00   1363  150 0.5449 0.5182      6.0688        6.05|
| 11:  2.1861 -  2.1179 0.98   1330  147 0.5192 0.5392       6.007      6.0348|
| 12:  2.1179 -  2.0575 0.98   1361  148 0.5436 0.5554      5.9265      5.9203|
| 13:  2.0575 -  2.0035 0.64    866   99 0.5302 0.4861      5.8921      5.7752|
| 14:  2.0035 -  1.9547 0.14    200   19 0.4925 0.4173      5.8226      5.9761|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.6694  1482   166  0.67  37.07   0.78     0.72      85114.83|
|  2:  4.6694 -  3.7238  1416   157  0.61  43.04   0.86     0.71     147809.44|
|  3:  3.7238 -  3.2583  1395   153  0.42  58.12   0.87     0.59     163972.41|
|  4:  3.2583 -  2.9627  1393   158  0.25  71.48   0.85     0.37     154397.80|
|  5:  2.9627 -  2.7517  1378   157  0.18  76.81   0.83     0.28     113149.23|
|  6:  2.7517 -  2.5903  1368   146  0.13  80.19   0.86     0.20      96071.38|
|  7:  2.5903 -  2.4611  1361   166  0.15  78.56   0.86     0.23      80199.91|
|  8:  2.4611 -  2.3543  1368   138  0.11  81.45   0.86     0.17      72426.01|
|  9:  2.3543 -  2.2640  1349   155  0.14  79.83   0.89     0.21      66327.37|
| 10:  2.2640 -  2.1861  1363   150  0.14  79.89   0.88     0.21      59475.00|
| 11:  2.1861 -  2.1179  1330   147  0.19  75.92   0.93     0.31      55298.83|
| 12:  2.1179 -  2.0575  1361   148  0.21  74.08   0.86     0.36      47391.23|
| 13:  2.0575 -  2.0035   866    99  0.27  70.27   0.94     0.44      40029.45|
| 14:  2.0035 -  1.9547   200    19  0.34  65.01   1.03     0.49      30734.35|
|alpha:            min =        0.17 max =            0.72 mean =         0.37|
|beta:             min =    30734.35 max =       163972.41 mean =     92128.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.27|
|phase err.(work): min =        0.00 max =           90.00 mean =        69.35|
|phase err.(test): min =        0.00 max =           89.99 mean =        69.68|
|-----------------------------------------------------------------------------|

============================== 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 = 21.672285             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.976   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.413662              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.726   (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 |  1.681 -  2.003:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       80 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1702 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1898 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2641 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4705 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4396 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5764 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6909 |
|-----------------------------------------------------------------------------|
|-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 |        0.184 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.479 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.996)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5087   r_free= 0.5139   ksol= 0.00   Bsol= 0.00   scale= 0.849    |
|                                                                             |
| 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:   1.03 A                  |
| x-ray target function (ml) for work reflections: 6.315221                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5020   r_free= 0.5112   ksol= 0.30   Bsol= 50.00   scale= 0.882   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.36,2.47,-0.00,0.00,0.00); trace/3= 0.35                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.03 A                  |
| x-ray target function (ml) for work reflections: 6.315252                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.086727             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.773   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.195036              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.075   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5020      final r-factor (work) = 0.4488          |
| start r-factor (free) = 0.5112      final r-factor (free) = 0.4902          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.0871 = 17.09 * 0.50 * 6.3094 + 1.00 * 0.1839                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.6594 = 17.09 * 0.50 * 6.2661 + 1.00 * 0.1261                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4488      final r-factor (work) = 0.4184          |
| start r-factor (free) = 0.4902      final r-factor (free) = 0.4979          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7603 = 2.20 * 1.00 * 6.2661 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.6923 = 2.20 * 1.00 * 6.2275 + 1.00 * 0.0228                              |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.996)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.60   21.32    None  None   None       |
|    all(noH): 2823   0      0.00    92.60   21.32    None  None   None       |
|    Sol.    : 438    0      0.00    86.38   33.85    None  None   None       |
|    Mac.    : 2385   0      0.00    92.60   19.02    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 -   9.260:  565   |   5:    46.301 -  55.562:  107        |
|      1:     9.260 -  18.521:  845   |   6:    55.562 -  64.822:   56        |
|      2:    18.521 -  27.781:  644   |   7:    64.822 -  74.082:   26        |
|      3:    27.781 -  37.041:  377   |   8:    74.082 -  83.342:    3        |
|      4:    37.041 -  46.301:  195   |   9:    83.342 -  92.603:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4184 r_free = 0.4979             target_work(ml) = 6.230         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4180 r_free = 0.4985             target_work(ml) = 6.230         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4180   r_free= 0.4985   ksol= 0.30   Bsol= 50.00   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.36,2.47,-0.00,0.00,0.00); trace/3= 0.35                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.229737                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4188   r_free= 0.4980   ksol= 0.36   Bsol= 92.12   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,-0.25,1.99,-0.00,0.00,0.00); trace/3= 0.50                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.232064                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.908777             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.200  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.107031              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.345  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4188      final r-factor (work) = 0.3706          |
| start r-factor (free) = 0.4980      final r-factor (free) = 0.4559          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 74.5984 = 23.91 * 0.50 * 6.2297 + 1.00 * 0.1261                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 74.1937 = 23.91 * 0.50 * 6.1956 + 1.00 * 0.1285                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3706      final r-factor (work) = 0.3537          |
| start r-factor (free) = 0.4559      final r-factor (free) = 0.4510          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8813 = 1.11 * 1.00 * 6.1956 + 1.00 * 0.0226                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8036 = 1.11 * 1.00 * 6.1313 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.996)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.25   21.00    None  None   None       |
|    all(noH): 2823   0      0.00    89.25   21.00    None  None   None       |
|    Sol.    : 438    0      0.00    81.07   34.04    None  None   None       |
|    Mac.    : 2385   0      0.00    89.25   18.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.925:  543   |   5:    44.627 -  53.553:   97        |
|      1:     8.925 -  17.851:  859   |   6:    53.553 -  62.478:   63        |
|      2:    17.851 -  26.776:  629   |   7:    62.478 -  71.403:   29        |
|      3:    26.776 -  35.702:  393   |   8:    71.403 -  80.329:    5        |
|      4:    35.702 -  44.627:  201   |   9:    80.329 -  89.254:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3537 r_free = 0.4510             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3535 r_free = 0.4509             target_work(ml) = 6.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3535   r_free= 0.4509   ksol= 0.36   Bsol= 92.12   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,-0.25,1.99,-0.00,0.00,0.00); trace/3= 0.50                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.126349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3538   r_free= 0.4501   ksol= 0.38   Bsol= 104.57   scale= 1.019  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.78,1.25,-0.00,0.00,0.00); trace/3= 0.06                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.125966                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.268257             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.161  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 10.989247             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.550  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3538      final r-factor (work) = 0.2996          |
| start r-factor (free) = 0.4501      final r-factor (free) = 0.3789          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.0057 = 16.27 * 0.50 * 6.1318 + 1.00 * 0.1285                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.5706 = 16.27 * 0.50 * 6.0806 + 1.00 * 0.1100                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2996      final r-factor (work) = 0.2681          |
| start r-factor (free) = 0.3789      final r-factor (free) = 0.3709          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 66.8375 = 10.99 * 1.00 * 6.0806 + 1.00 * 0.0161                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 65.4733 = 10.99 * 1.00 * 5.9546 + 1.00 * 0.0365                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.996)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    132.41  23.88    None  None   None       |
|    all(noH): 2823   0      0.00    132.41  23.88    None  None   None       |
|    Sol.    : 438    0      0.00    132.41  50.12    None  None   None       |
|    Mac.    : 2385   0      0.00    122.83  19.06    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 -  13.241: 1182   |   5:    66.207 -  79.448:  101        |
|      1:    13.241 -  26.483:  721   |   6:    79.448 -  92.690:   44        |
|      2:    26.483 -  39.724:  368   |   7:    92.690 - 105.931:   26        |
|      3:    39.724 -  52.965:  236   |   8:   105.931 - 119.172:   12        |
|      4:    52.965 -  66.207:  128   |   9:   119.172 - 132.414:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2681 r_free = 0.3709             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2680 r_free = 0.3708             target_work(ml) = 5.939         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2680   r_free= 0.3708   ksol= 0.38   Bsol= 104.57   scale= 1.042  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.78,1.25,-0.00,0.00,0.00); trace/3= 0.06                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.939251                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2685   r_free= 0.3699   ksol= 0.38   Bsol= 121.02   scale= 1.040  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.27,-0.92,1.33,-0.00,0.00,0.00); trace/3= 0.05                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.937129                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.098171             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.005  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.481639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.029  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2685      final r-factor (work) = 0.2323          |
| start r-factor (free) = 0.3699      final r-factor (free) = 0.3235          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1754 = 10.10 * 0.50 * 5.9546 + 1.00 * 0.1100                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8281 = 10.10 * 0.50 * 5.8909 + 1.00 * 0.0844                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2323      final r-factor (work) = 0.2149          |
| start r-factor (free) = 0.3235      final r-factor (free) = 0.2859          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8741 = 0.48 * 1.00 * 5.8909 + 1.00 * 0.0368                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8055 = 0.48 * 1.00 * 5.7891 + 1.00 * 0.0172                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.996)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.96  20.26    None  None   None       |
|    all(noH): 2823   0      0.00    111.96  20.26    None  None   None       |
|    Sol.    : 438    0      2.26    111.96  47.53    None  None   None       |
|    Mac.    : 2385   0      0.00    109.48  15.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.196: 1113   |   5:    55.980 -  67.176:   87        |
|      1:    11.196 -  22.392:  907   |   6:    67.176 -  78.372:   37        |
|      2:    22.392 -  33.588:  301   |   7:    78.372 -  89.568:   33        |
|      3:    33.588 -  44.784:  188   |   8:    89.568 - 100.764:    9        |
|      4:    44.784 -  55.980:  139   |   9:   100.764 - 111.960:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2149 r_free = 0.2859             target_work(ml) = 5.728         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2147 r_free = 0.2854             target_work(ml) = 5.727         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2147   r_free= 0.2854   ksol= 0.38   Bsol= 121.02   scale= 1.042  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.27,-0.92,1.33,-0.00,0.00,0.00); trace/3= 0.05                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.726859                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2142   r_free= 0.2841   ksol= 0.34   Bsol= 82.35   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,-2.10,0.24,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.723527                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.961911              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.496  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.490153              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.501   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2142      final r-factor (work) = 0.1716          |
| start r-factor (free) = 0.2841      final r-factor (free) = 0.2340          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2362 = 6.96 * 0.50 * 5.7891 + 1.00 * 0.0845                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7278 = 6.96 * 0.50 * 5.6435 + 1.00 * 0.0832                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1716      final r-factor (work) = 0.1565          |
| start r-factor (free) = 0.2340      final r-factor (free) = 0.2167          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7807 = 0.49 * 1.00 * 5.6435 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7049 = 0.49 * 1.00 * 5.4924 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.996)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.63  19.23    None  None   None       |
|    all(noH): 2823   0      0.00    111.63  19.23    None  None   None       |
|    Sol.    : 438    0      3.89    110.95  48.70    None  None   None       |
|    Mac.    : 2385   0      0.00    111.63  13.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.163: 1224   |   5:    55.817 -  66.980:  108        |
|      1:    11.163 -  22.327:  951   |   6:    66.980 -  78.143:   58        |
|      2:    22.327 -  33.490:  208   |   7:    78.143 -  89.307:   21        |
|      3:    33.490 -  44.653:  128   |   8:    89.307 - 100.470:   10        |
|      4:    44.653 -  55.817:  109   |   9:   100.470 - 111.633:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1565 r_free = 0.2167             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1564 r_free = 0.2164             target_work(ml) = 5.449         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1564   r_free= 0.2164   ksol= 0.34   Bsol= 82.35   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,-2.10,0.24,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.448601                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.6694 0.99   1482  166 0.1018 0.1529      5.4648      5.7433|
|  2:  4.6694 -  3.7238 0.99   1416  157 0.1015 0.1519      5.6223      5.9715|
|  3:  3.7238 -  3.2583 0.99   1395  153 0.1476 0.2150      5.7541      6.0736|
|  4:  3.2583 -  2.9627 0.99   1393  158 0.1818 0.2352      5.7717      5.9557|
|  5:  2.9627 -  2.7517 0.99   1378  157 0.1884 0.2466       5.644      5.8217|
|  6:  2.7517 -  2.5903 0.99   1368  146 0.1792 0.2629      5.5204      5.7346|
|  7:  2.5903 -  2.4611 0.99   1361  166 0.1780 0.2339      5.4436      5.6407|
|  8:  2.4611 -  2.3543 0.98   1368  138 0.1822 0.2609      5.4202      5.6486|
|  9:  2.3543 -  2.2640 0.98   1349  155 0.1786 0.2391      5.3647      5.5849|
| 10:  2.2640 -  2.1861 1.00   1363  150 0.1685 0.2342      5.2819      5.4643|
| 11:  2.1861 -  2.1179 0.98   1330  147 0.1654 0.2424      5.2137      5.5469|
| 12:  2.1179 -  2.0575 0.98   1361  148 0.1702 0.2409      5.1467      5.3479|
| 13:  2.0575 -  2.0035 0.64    866   99 0.1586 0.2175      5.0834      5.2051|
| 14:  2.0035 -  1.9547 0.14    200   19 0.1557 0.2301      5.0088      5.4766|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.6694  1482   166  0.92  11.29   0.96     0.93       9537.69|
|  2:  4.6694 -  3.7238  1416   157  0.93  11.47   1.04     1.02      14373.54|
|  3:  3.7238 -  3.2583  1395   153  0.88  17.44   1.06     1.05      19047.02|
|  4:  3.2583 -  2.9627  1393   158  0.83  22.90   1.03     0.99      21780.19|
|  5:  2.9627 -  2.7517  1378   157  0.82  24.09   1.03     1.00      17464.63|
|  6:  2.7517 -  2.5903  1368   146  0.82  24.59   1.01     0.95      13906.55|
|  7:  2.5903 -  2.4611  1361   166  0.83  23.68   1.03     0.98      11797.89|
|  8:  2.4611 -  2.3543  1368   138  0.83  24.06   1.03     0.97      11282.25|
|  9:  2.3543 -  2.2640  1349   155  0.82  24.88   1.02     0.95      10190.81|
| 10:  2.2640 -  2.1861  1363   150  0.82  24.22   1.03     1.00       9082.95|
| 11:  2.1861 -  2.1179  1330   147  0.84  22.93   1.02     0.94       7748.12|
| 12:  2.1179 -  2.0575  1361   148  0.82  24.66   1.02     1.00       7197.37|
| 13:  2.0575 -  2.0035   866    99  0.84  23.32   1.03     0.99       6289.90|
| 14:  2.0035 -  1.9547   200    19  0.88  19.29   0.99     0.98       4981.76|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     4981.76 max =        21780.19 mean =     12402.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.95 mean =        21.32|
|phase err.(test): min =        0.00 max =           89.59 mean =        20.31|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1564   r_free= 0.2149   ksol= 0.33   Bsol= 66.51   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.81,-0.43,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.444160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1564   r_free= 0.2149   ksol= 0.33   Bsol= 66.51   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.81,-0.43,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.444160                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.6694 0.99   1482  166 0.1026 0.1427      5.4307      5.6832|
|  2:  4.6694 -  3.7238 0.99   1416  157 0.1017 0.1506      5.6031      5.9681|
|  3:  3.7238 -  3.2583 0.99   1395  153 0.1478 0.2148      5.7523      6.0725|
|  4:  3.2583 -  2.9627 0.99   1393  158 0.1818 0.2341      5.7709       5.952|
|  5:  2.9627 -  2.7517 0.99   1378  157 0.1886 0.2464      5.6448       5.823|
|  6:  2.7517 -  2.5903 0.99   1368  146 0.1793 0.2635      5.5207      5.7368|
|  7:  2.5903 -  2.4611 0.99   1361  166 0.1781 0.2339      5.4444      5.6411|
|  8:  2.4611 -  2.3543 0.98   1368  138 0.1821 0.2612      5.4204      5.6498|
|  9:  2.3543 -  2.2640 0.98   1349  155 0.1786 0.2388      5.3642      5.5833|
| 10:  2.2640 -  2.1861 1.00   1363  150 0.1686 0.2343      5.2822      5.4656|
| 11:  2.1861 -  2.1179 0.98   1330  147 0.1653 0.2425      5.2128      5.5455|
| 12:  2.1179 -  2.0575 0.98   1361  148 0.1702 0.2410      5.1476      5.3494|
| 13:  2.0575 -  2.0035 0.64    866   99 0.1586 0.2173      5.0837      5.2047|
| 14:  2.0035 -  1.9547 0.14    200   19 0.1557 0.2298      5.0091      5.4754|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.6694  1482   166  0.93  10.23   0.95     0.93       8198.36|
|  2:  4.6694 -  3.7238  1416   157  0.93  10.83   1.03     1.02      13190.80|
|  3:  3.7238 -  3.2583  1395   153  0.89  17.30   1.04     1.04      18768.11|
|  4:  3.2583 -  2.9627  1393   158  0.84  22.79   1.02     0.98      21620.40|
|  5:  2.9627 -  2.7517  1378   157  0.82  24.06   1.01     0.99      17462.95|
|  6:  2.7517 -  2.5903  1368   146  0.82  24.57   0.98     0.93      13908.14|
|  7:  2.5903 -  2.4611  1361   166  0.83  23.69   1.01     0.96      11829.04|
|  8:  2.4611 -  2.3543  1368   138  0.83  24.06   1.00     0.95      11296.94|
|  9:  2.3543 -  2.2640  1349   155  0.82  24.85   0.99     0.92      10191.19|
| 10:  2.2640 -  2.1861  1363   150  0.82  24.19   1.00     0.97       9081.99|
| 11:  2.1861 -  2.1179  1330   147  0.84  22.91   0.98     0.91       7751.01|
| 12:  2.1179 -  2.0575  1361   148  0.82  24.65   0.98     0.96       7207.64|
| 13:  2.0575 -  2.0035   866    99  0.84  23.30   0.99     0.96       6293.14|
| 14:  2.0035 -  1.9547   200    19  0.88  19.22   0.95     0.94       4967.06|
|alpha:            min =        0.91 max =            1.04 mean =         0.96|
|beta:             min =     4967.06 max =        21620.40 mean =     12164.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.97 mean =        21.15|
|phase err.(test): min =        0.00 max =           89.55 mean =        20.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.996)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.64  19.24    None  None   None       |
|    all(noH): 2823   0      0.00    111.64  19.24    None  None   None       |
|    Sol.    : 438    0      3.89    110.96  48.71    None  None   None       |
|    Mac.    : 2385   0      0.00    111.64  13.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.166: 1224   |   5:    55.820 -  66.983:  108        |
|      1:    11.166 -  22.330:  951   |   6:    66.983 -  78.146:   58        |
|      2:    22.330 -  33.493:  208   |   7:    78.146 -  89.309:   21        |
|      3:    33.493 -  44.656:  128   |   8:    89.309 - 100.473:   10        |
|      4:    44.656 -  55.820:  109   |   9:   100.473 - 111.636:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.630 - 5.763
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 337
   mapped sites are within: 0.734 - 5.763

peak=    7.728 closest distance to " O   HOH Z 103 " =    1.308
peak=    6.764 closest distance to " O   HOH Z 396 " =    1.205
peak=    6.577 closest distance to " O   HOH Z  41 " =    1.298
peak=    6.191 closest distance to " O   HOH Z 385 " =    1.694
peak=    6.100 closest distance to " O   HOH Z 131 " =    2.058
peak=    5.751 closest distance to " O   HOH Z 381 " =    1.362
peak=    5.720 closest distance to " O   HOH Z 431 " =    2.236
peak=    5.719 closest distance to " O   HOH Z  13 " =    1.434
peak=    5.614 closest distance to " CB  ASN A  60 " =    0.949
peak=    5.562 closest distance to " O   HOH Z 390 " =    1.339
peak=    5.387 closest distance to " O   PRO A  54 " =    1.022
peak=    5.230 closest distance to " O   HOH Z 245 " =    1.457
peak=    5.183 closest distance to " O   HOH Z 424 " =    2.099
peak=    5.118 closest distance to " O   HOH Z 117 " =    1.269
peak=    5.080 closest distance to " CG  PRO A  90 " =    1.414
peak=    5.072 closest distance to " O   HOH Z 144 " =    1.969
peak=    5.058 closest distance to " NH1AARG A 145 " =    1.274
peak=    5.040 closest distance to " O   PHE A  59 " =    0.969
peak=    4.995 closest distance to " O   HOH Z  66 " =    1.525
peak=    4.922 closest distance to " O   HOH Z 130 " =    1.264
peak=    4.900 closest distance to " N   SER A  63 " =    0.846
peak=    4.886 closest distance to " O   HOH Z 182 " =    1.658
peak=    4.864 closest distance to " O   HOH Z  63 " =    1.602
peak=    4.841 closest distance to " O   HOH Z 295 " =    1.828
peak=    4.840 closest distance to " O   HOH Z  70 " =    1.582
peak=    4.806 closest distance to " O   HOH Z 147 " =    1.521
peak=    4.796 closest distance to " O   HOH Z 403 " =    1.776
peak=    4.784 closest distance to " O   HOH Z 287 " =    1.981
peak=    4.775 closest distance to " O   HOH Z 359 " =    2.003
peak=    4.751 closest distance to " OG BSER A  12 " =    0.989
peak=    4.750 closest distance to " NE2 GLN A 103 " =    1.002
peak=    4.747 closest distance to " O   HOH Z  46 " =    1.779
peak=    4.725 closest distance to " CE3 TRP A 274 " =    1.441
peak=    4.720 closest distance to " O   HOH Z  29 " =    1.716
peak=    4.610 closest distance to " O   HOH Z  65 " =    2.208
peak=    4.584 closest distance to " O   HOH Z  67 " =    1.861
peak=    4.506 closest distance to " O   HOH Z 181 " =    1.616
peak=    4.468 closest distance to " O   HOH Z 427 " =    1.490
peak=    4.457 closest distance to " O   HOH Z  11 " =    1.362
peak=    4.453 closest distance to " O   HOH Z 120 " =    1.158
peak=    4.430 closest distance to " O   HOH Z 119 " =    1.237
peak=    4.393 closest distance to " O   HOH Z 255 " =    1.083
peak=    4.384 closest distance to " O   HOH Z 179 " =    1.070
peak=    4.349 closest distance to " O   HOH Z 375 " =    1.255
peak=    4.345 closest distance to " CB  PRO A  54 " =    1.273
peak=    4.344 closest distance to " O   PRO A 198 " =    1.417
peak=    4.324 closest distance to " O   ASN A 285 " =    0.994
peak=    4.322 closest distance to " O   HOH Z 131 " =    1.676
peak=    4.316 closest distance to " OG ASER A 258 " =    3.032
peak=    4.312 closest distance to " O   HOH Z  49 " =    2.154
peak=    4.310 closest distance to " O   HOH Z 410 " =    1.651
peak=    4.282 closest distance to " O   HOH Z 417 " =    2.802
peak=    4.215 closest distance to " O   HOH Z 422 " =    1.182
peak=    4.196 closest distance to " O   HOH Z 399 " =    0.820
peak=    4.194 closest distance to " C   HIS A 115 " =    1.012
peak=    4.175 closest distance to " O   HOH Z 280 " =    1.587
peak=    4.173 closest distance to " CB  SER A  63 " =    1.480
peak=    4.168 closest distance to " N   PHE A  59 " =    0.995
peak=    4.155 closest distance to " O   HOH Z 105 " =    1.399
peak=    4.118 closest distance to " NE2 GLN A  11 " =    1.252
peak=    4.112 closest distance to " O   HOH Z 102 " =    1.257
peak=    4.108 closest distance to " O   HOH Z 186 " =    1.502
peak=    4.107 closest distance to " O   HOH Z  30 " =    1.656
peak=    4.107 closest distance to " CB  ASN A 148 " =    1.250
peak=    4.086 closest distance to " O   HOH Z 411 " =    3.221
peak=    4.082 closest distance to " O   HOH Z 244 " =    1.695
peak=    4.067 closest distance to " O   HOH Z  97 " =    1.704
peak=    4.059 closest distance to " N   TYR A  15 " =    1.184
peak=    4.058 closest distance to " CB  PHE A  61 " =    1.170
peak=    4.047 closest distance to " O   HOH Z  72 " =    1.147
peak=    4.039 closest distance to " O   HOH Z 360 " =    1.227
peak=    4.038 closest distance to " O   HOH Z 225 " =    2.049
peak=    4.017 closest distance to " N   ALA A 165 " =    1.403
peak=    4.016 closest distance to " CB  MET A  40 " =    1.059
peak=    4.014 closest distance to " CZ3 TRP A 266 " =    1.150
peak=    4.014 closest distance to " O   HOH Z 303 " =    1.381
peak=    4.011 closest distance to " CB  GLN A 223 " =    1.707
peak=    4.004 closest distance to " O   HOH Z 126 " =    1.732
peak=    4.001 closest distance to " O   HOH Z 374 " =    1.269
peak=    3.987 closest distance to " CG  PRO A  54 " =    1.547
peak=    3.982 closest distance to " O   HOH Z 222 " =    2.081
peak=    3.982 closest distance to " O   HOH Z 427 " =    2.266
peak=    3.968 closest distance to " CE  MET A  93 " =    1.628
peak=    3.966 closest distance to " O   HOH Z 415 " =    1.234
peak=    3.947 closest distance to " CB  SER A 216 " =    1.184
peak=    3.937 closest distance to " CB  ARG A 275 " =    1.082
peak=    3.927 closest distance to " CD  ARG A 195 " =    3.459
peak=    3.925 closest distance to " N   GLN A 278 " =    1.282
peak=    3.914 closest distance to " C   GLN A  73 " =    1.273
peak=    3.912 closest distance to " N   PHE A 130 " =    1.370
peak=    3.911 closest distance to " O   HOH Z 127 " =    1.065
peak=    3.908 closest distance to " C   ASN A 209 " =    1.730
peak=    3.890 closest distance to " CB  PRO A  90 " =    1.144
peak=    3.886 closest distance to " NZ  LYS A 119 " =    2.466
peak=    3.883 closest distance to " NH2 ARG A  56 " =    1.133
peak=    3.882 closest distance to " O   HOH Z 237 " =    0.982
peak=    3.877 closest distance to " O   HOH Z 217 " =    2.619
peak=    3.876 closest distance to " O   HOH Z 419 " =    2.036
peak=    3.857 closest distance to " O   HOH Z 233 " =    1.273
peak=    3.850 closest distance to " CD  ARG A 159 " =    0.810
peak=    3.849 closest distance to " N   GLN A  73 " =    1.004
peak=    3.848 closest distance to " N   ALA A   1 " =    1.787
peak=    3.846 closest distance to " CB  TRP A 179 " =    1.355
peak=    3.834 closest distance to " O   HOH Z 248 " =    1.585
peak=    3.826 closest distance to " CG  GLN A  55 " =    0.919
peak=    3.814 closest distance to " O  BHOH Z  74 " =    1.189
peak=    3.814 closest distance to " CB  ASP A 124 " =    1.027
peak=    3.812 closest distance to " O   HOH Z  92 " =    1.507
peak=    3.811 closest distance to " O   HOH Z 155 " =    2.150
peak=    3.802 closest distance to " O   HOH Z 350 " =    1.394
peak=    3.796 closest distance to " O   HOH Z  88 " =    3.763
peak=    3.795 closest distance to " CG2 THR A 221 " =    1.142
peak=    3.789 closest distance to " CA  LEU A 282 " =    0.961
peak=    3.787 closest distance to " O   HOH Z 181 " =    2.350
peak=    3.785 closest distance to " O   HOH Z 124 " =    0.734
peak=    3.784 closest distance to " OE1 GLN A 240 " =    1.676
peak=    3.779 closest distance to " O   HOH Z  53 " =    2.287
peak=    3.769 closest distance to " O   HOH Z  21 " =    1.408
peak=    3.769 closest distance to " O   HOH Z  54 " =    1.420
peak=    3.767 closest distance to " O   HOH Z  69 " =    1.799
peak=    3.764 closest distance to " CB  ALA A 233 " =    1.235
peak=    3.757 closest distance to " CZ  PHE A 218 " =    1.218
peak=    3.751 closest distance to " CB  LEU A  83 " =    0.785
peak=    3.749 closest distance to " O   HOH Z 346 " =    1.284
peak=    3.748 closest distance to " CG2 ILE A 120 " =    1.162
peak=    3.746 closest distance to " O   HOH Z 296 " =    1.551
peak=    3.737 closest distance to " O   GLY A 302 " =    1.866
peak=    3.736 closest distance to " OG  SER A 276 " =    1.148
peak=    3.735 closest distance to " CB  SER A  99 " =    0.843
peak=    3.733 closest distance to " CD  LYS A 166 " =    1.623
peak=    3.729 closest distance to " CD2 PHE A  59 " =    2.106
peak=    3.721 closest distance to " O   GLN A  55 " =    1.228
peak=    3.720 closest distance to " CA  ASP A 162 " =    0.814
peak=    3.707 closest distance to " CB  ASN A  39 " =    0.871
peak=    3.699 closest distance to " O   HOH Z 213 " =    2.004
peak=    3.696 closest distance to " CB  ASP A 286 " =    1.767
peak=    3.695 closest distance to " NH2BARG A 190 " =    1.227
peak=    3.692 closest distance to " O   HOH Z  39 " =    1.483
peak=    3.690 closest distance to " ND2 ASN A  60 " =    2.676
peak=    3.689 closest distance to " CA  ALA A  51 " =    1.243
peak=    3.685 closest distance to " O   HOH Z  63 " =    2.218
peak=    3.678 closest distance to " CB  SER A 210 " =    1.256
peak=    3.678 closest distance to " O   ALA A 165 " =    1.480
peak=    3.671 closest distance to " O   HOH Z 257 " =    1.382
peak=    3.668 closest distance to " CB  VAL A 202 " =    1.570
peak=    3.665 closest distance to " N   ARG A 156 " =    1.417
peak=    3.662 closest distance to " CB  ALA A  43 " =    0.981
peak=    3.659 closest distance to " O   ASN A 142 " =    1.101
peak=    3.647 closest distance to " CG AASN A 224 " =    1.022
peak=    3.636 closest distance to " CA  VAL A 125 " =    1.137
peak=    3.629 closest distance to " O   HOH Z 424 " =    3.381
peak=    3.627 closest distance to " CG1 VAL A 296 " =    1.207
peak=    3.619 closest distance to " CG2 ILE A 239 " =    1.086
peak=    3.613 closest distance to " O   HOH Z 421 " =    2.894
peak=    3.604 closest distance to " CE2 PHE A  61 " =    0.825
peak=    3.593 closest distance to " CA  TYR A  30 " =    1.208
peak=    3.593 closest distance to " O   HOH Z  77 " =    1.474
peak=    3.592 closest distance to " O   HOH Z 313 " =    1.920
peak=    3.589 closest distance to " O   HOH Z 153 " =    3.408
peak=    3.587 closest distance to " CB  ARG A  66 " =    0.835
peak=    3.586 closest distance to " O   HOH Z 215 " =    1.959
peak=    3.583 closest distance to " O   HOH Z 180 " =    2.245
peak=    3.583 closest distance to " N   GLU A  53 " =    1.772
peak=    3.581 closest distance to " CG  PRO A 198 " =    1.327
peak=    3.577 closest distance to " CZ  PHE A  16 " =    0.881
peak=    3.560 closest distance to " CA  PRO A  54 " =    1.044
peak=    3.559 closest distance to " O   HOH Z 158 " =    1.739
peak=    3.557 closest distance to " CB  ALA A  10 " =    1.183
peak=    3.556 closest distance to " O   HOH Z  28 " =    1.219
peak=    3.549 closest distance to " O   HOH Z  52 " =    1.323
peak=    3.545 closest distance to " O   HOH Z 158 " =    2.944
peak=    3.544 closest distance to " O   HOH Z 170 " =    1.524
peak=    3.538 closest distance to " O   HOH Z  51 " =    2.261
peak=    3.538 closest distance to " CB  SER A  62 " =    1.351
peak=    3.535 closest distance to " N   SER A 210 " =    1.136
peak=    3.528 closest distance to " O   HOH Z 232 " =    2.339
peak=    3.527 closest distance to " CG1 VAL A 265 " =    1.062
peak=    3.522 closest distance to " CG2AVAL A 121 " =    1.728
peak=    3.522 closest distance to " CG2BVAL A  41 " =    1.112
peak=    3.522 closest distance to " O   HOH Z 132 " =    1.402
peak=    3.516 closest distance to " CE2 PHE A  16 " =    0.946
peak=    3.512 closest distance to " N   ASN A 142 " =    1.135
peak=    3.508 closest distance to " O   HOH Z  58 " =    2.186
peak=    3.507 closest distance to " CA  ILE A 234 " =    1.199
peak=    3.501 closest distance to " O   HOH Z  61 " =    1.459
peak=    3.485 closest distance to " O   HOH Z 362 " =    2.351
peak=    3.484 closest distance to " O   HOH Z 434 " =    1.779
peak=    3.482 closest distance to " O   HOH Z 368 " =    3.589
peak=    3.481 closest distance to " CD2 LEU A   5 " =    1.806
peak=    3.476 closest distance to " O   HOH Z 416 " =    1.547
peak=    3.475 closest distance to " ND2 ASN A 285 " =    1.123
peak=    3.474 closest distance to " O   HOH Z  17 " =    1.961
peak=    3.472 closest distance to " CB  SER A 288 " =    0.781
peak=    3.471 closest distance to " CE1 PHE A 225 " =    1.207
peak=    3.468 closest distance to " CG  LEU A 101 " =    1.018
peak=    3.468 closest distance to " O   HOH Z 239 " =    1.958
peak=    3.467 closest distance to " O   HOH Z   9 " =    2.826
peak=    3.459 closest distance to " CD  LYS A  76 " =    1.722
peak=    3.458 closest distance to " O   HOH Z  33 " =    1.873
peak=    3.457 closest distance to " ND2 ASN A 285 " =    0.749
peak=    3.454 closest distance to " CB  MET A 105 " =    1.420
peak=    3.453 closest distance to " CB  LYS A 290 " =    0.846
peak=    3.452 closest distance to " O   HOH Z 386 " =    1.896
peak=    3.450 closest distance to " OD1 ASN A  69 " =    1.188
peak=    3.446 closest distance to " O   MET A 105 " =    1.680
peak=    3.440 closest distance to " CG2 VAL A 257 " =    1.025
peak=    3.434 closest distance to " O   HOH Z 183 " =    1.488
peak=    3.430 closest distance to " CB  ALA A 184 " =    1.659
peak=    3.430 closest distance to " O   HOH Z  91 " =    2.489
peak=    3.424 closest distance to " CG  ASP A  27 " =    1.143
peak=    3.417 closest distance to " O   HOH Z 349 " =    1.854
peak=    3.416 closest distance to " O   HOH Z 128 " =    1.561
peak=    3.415 closest distance to " CA  TRP A  92 " =    1.330
peak=    3.414 closest distance to " CG  GLN A  58 " =    2.817
peak=    3.413 closest distance to " CG2 THR A 279 " =    1.217
peak=    3.409 closest distance to " CG2 THR A   4 " =    1.265
peak=    3.407 closest distance to " NE2 HIS A 207 " =    1.043
peak=    3.393 closest distance to " O   HOH Z 407 " =    2.206
peak=    3.393 closest distance to " O   HOH Z 139 " =    3.019
peak=    3.390 closest distance to " CA  ARG A  24 " =    1.076
peak=    3.384 closest distance to " C   VAL A  72 " =    1.110
peak=    3.377 closest distance to " O   HOH Z  76 " =    1.513
peak=    3.376 closest distance to " CG  GLN A  89 " =    1.531
peak=    3.374 closest distance to " CB  ASN A 110 " =    1.055
peak=    3.372 closest distance to " O   HOH Z  70 " =    1.402
peak=    3.361 closest distance to " O   HOH Z 293 " =    2.207
peak=    3.358 closest distance to " CA  GLU A 152 " =    1.101
peak=    3.357 closest distance to " O   HOH Z 437 " =    1.971
peak=    3.352 closest distance to " O   HOH Z 193 " =    1.480
peak=    3.351 closest distance to " C   LEU A  25 " =    1.091
peak=    3.346 closest distance to " CE  LYS A 119 " =    1.276
peak=    3.342 closest distance to " CB  ALA A 114 " =    0.976
peak=    3.338 closest distance to " O   HOH Z 296 " =    1.570
peak=    3.336 closest distance to " CB  GLU A 152 " =    1.233
peak=    3.336 closest distance to " O   HOH Z 298 " =    4.302
peak=    3.326 closest distance to " O   HOH Z 293 " =    1.322
peak=    3.325 closest distance to " CA  ARG A 195 " =    1.419
peak=    3.323 closest distance to " CD  ARG A  56 " =    0.983
peak=    3.323 closest distance to " CB  ILE A 263 " =    1.246
peak=    3.322 closest distance to " O   HOH Z 343 " =    2.559
peak=    3.320 closest distance to " CZ3 TRP A 123 " =    1.645
peak=    3.315 closest distance to " O   HOH Z 143 " =    1.258
peak=    3.315 closest distance to " OE1 GLN A  77 " =    1.558
peak=    3.309 closest distance to " O   HOH Z 369 " =    1.344
peak=    3.307 closest distance to " CB  SER A 276 " =    1.460
peak=    3.307 closest distance to " CG  LYS A 119 " =    0.985
peak=    3.306 closest distance to " O   HOH Z 412 " =    5.763
peak=    3.304 closest distance to " NZ  LYS A 166 " =    1.104
peak=    3.301 closest distance to " CD  ARG A 259 " =    1.368
peak=    3.298 closest distance to " CA  VAL A 153 " =    1.043
peak=    3.297 closest distance to " NZ ALYS A 290 " =    1.081
peak=    3.297 closest distance to " O   HOH Z 219 " =    2.238
peak=    3.296 closest distance to " CB  ILE A 120 " =    1.288
peak=    3.293 closest distance to " O   HOH Z  37 " =    1.188
peak=    3.289 closest distance to " CD2 LEU A 143 " =    1.184
peak=    3.287 closest distance to " O   HOH Z 380 " =    2.127
peak=    3.285 closest distance to " CG  ARG A 159 " =    1.058
peak=    3.280 closest distance to " CB  SER A 273 " =    1.262
peak=    3.279 closest distance to " OG ASER A 212 " =    1.408
peak=    3.275 closest distance to " O   HOH Z 351 " =    0.944
peak=    3.273 closest distance to " O   HOH Z 271 " =    1.860
peak=    3.268 closest distance to " CB  PHE A 225 " =    1.589
peak=    3.257 closest distance to " O   HOH Z 438 " =    2.798
peak=    3.257 closest distance to " O   ALA A 291 " =    1.620
peak=    3.256 closest distance to " O   HOH Z 393 " =    3.141
peak=    3.253 closest distance to " CG  ASN A 252 " =    1.445
peak=    3.253 closest distance to " CB  PRO A 163 " =    4.194
peak=    3.253 closest distance to " O   THR A 157 " =    2.022
peak=    3.252 closest distance to " CA  GLY A  57 " =    1.387
peak=    3.250 closest distance to " O   HOH Z 409 " =    4.651
peak=    3.243 closest distance to " O   ASN A  60 " =    1.122
peak=    3.229 closest distance to " O   HOH Z 199 " =    1.469
peak=    3.221 closest distance to " O   HOH Z 357 " =    2.279
peak=    3.218 closest distance to " CB  SER A   3 " =    1.150
peak=    3.216 closest distance to " O   HOH Z  57 " =    1.722
peak=    3.215 closest distance to " OG  SER A  32 " =    1.093
peak=    3.213 closest distance to " CD1 LEU A 228 " =    1.832
peak=    3.212 closest distance to " O   HOH Z 287 " =    2.017
peak=    3.211 closest distance to " NE2 GLN A  89 " =    1.555
peak=    3.205 closest distance to " O   THR A 251 " =    1.163
peak=    3.205 closest distance to " CA  ASN A  69 " =    0.865
peak=    3.201 closest distance to " NZ  LYS A  48 " =    2.092
peak=    3.200 closest distance to " CG  GLU A  53 " =    1.970
peak=    3.199 closest distance to " O   HOH Z   7 " =    2.559
peak=    3.199 closest distance to " OD1 ASP A 171 " =    1.136
peak=    3.197 closest distance to " O   SER A 206 " =    1.455
peak=    3.191 closest distance to " CA  ASN A  74 " =    1.719
peak=    3.186 closest distance to " O   HOH Z  29 " =    1.741
peak=    3.183 closest distance to " CD2 LEU A 261 " =    1.024
peak=    3.182 closest distance to " C   PHE A 208 " =    1.134
peak=    3.180 closest distance to " NE2 GLN A 183 " =    1.628
peak=    3.179 closest distance to " CG2 VAL A 268 " =    1.412
peak=    3.178 closest distance to " O   HOH Z 183 " =    1.664
peak=    3.174 closest distance to " O   HOH Z 153 " =    3.954
peak=    3.174 closest distance to " CB  ASP A 107 " =    1.066
peak=    3.174 closest distance to " CD  GLN A  55 " =    1.267
peak=    3.170 closest distance to " NH2 ARG A 269 " =    0.882
peak=    3.170 closest distance to " O   HOH Z 205 " =    0.990
peak=    3.165 closest distance to " CE AMET A  47 " =    1.579
peak=    3.164 closest distance to " CB  VAL A 296 " =    1.449
peak=    3.162 closest distance to " CB  TYR A  30 " =    1.370
peak=    3.162 closest distance to " O   HOH Z  68 " =    1.799
peak=    3.156 closest distance to " O   HOH Z 194 " =    1.746
peak=    3.152 closest distance to " OH  TYR A 169 " =    0.849
peak=    3.151 closest distance to " CD2 TRP A 179 " =    2.004
peak=    3.150 closest distance to " O   ALA A 158 " =    1.351
peak=    3.137 closest distance to " O   HOH Z  26 " =    1.837
peak=    3.123 closest distance to " O   HOH Z  69 " =    1.409
peak=    3.123 closest distance to " CG2 THR A 246 " =    1.972
peak=    3.123 closest distance to " NH1 ARG A  14 " =    0.869
peak=    3.115 closest distance to " CG  GLN A  58 " =    1.903
peak=    3.114 closest distance to " CA  ALA A   7 " =    1.012
peak=    3.114 closest distance to " CB  ALA A   1 " =    1.348
peak=    3.113 closest distance to " CB  ASN A 142 " =    0.886
peak=    3.104 closest distance to " O   HOH Z  55 " =    1.329
peak=    3.101 closest distance to " CB  ARG A  66 " =    0.831
peak=    3.100 closest distance to " N   PHE A 208 " =    1.181
peak=    3.098 closest distance to " O   HOH Z 276 " =    1.399
peak=    3.097 closest distance to " O   HOH Z 219 " =    2.313
peak=    3.091 closest distance to " N   GLU A   2 " =    1.473
peak=    3.090 closest distance to " O   HOH Z 352 " =    2.099
peak=    3.079 closest distance to " O   HOH Z 123 " =    1.315
peak=    3.073 closest distance to " O   HOH Z 425 " =    1.267
peak=    3.071 closest distance to " CB  ARG A 138 " =    1.723
peak=    3.067 closest distance to " O   HOH Z 422 " =    2.251
peak=    3.058 closest distance to " CA  VAL A 121 " =    1.075
peak=    3.044 closest distance to " CA  ILE A 263 " =    1.029
peak=    3.040 closest distance to " CB  GLN A  55 " =    1.066
peak=    3.035 closest distance to " O   HOH Z 258 " =    1.904
peak=    3.029 closest distance to " O   HOH Z  91 " =    2.348
peak=    3.029 closest distance to " C   THR A 178 " =    1.666
peak=    3.020 closest distance to " CB  PHE A  61 " =    0.998

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 224         
Filter by distance & map next to the model:
   mapped sites are within: 0.489 - 5.607
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 224
   mapped sites are within: 0.736 - 5.607

peak=   -4.981 closest distance to " C   PHE A  59 " =    0.946
peak=   -4.752 closest distance to " CB  PHE A  61 " =    1.047
peak=   -4.734 closest distance to " N   PRO A  54 " =    0.909
peak=   -4.651 closest distance to " O   HOH Z  27 " =    0.736
peak=   -4.484 closest distance to " O   HOH Z 313 " =    1.310
peak=   -4.444 closest distance to " O   HOH Z  28 " =    0.952
peak=   -4.345 closest distance to " O   HOH Z 181 " =    0.874
peak=   -4.301 closest distance to " CA  GLY A 133 " =    2.027
peak=   -4.253 closest distance to " CB  ALA A   9 " =    2.696
peak=   -4.248 closest distance to " O   HOH Z 100 " =    0.790
peak=   -4.231 closest distance to " O   VAL A 125 " =    2.386
peak=   -4.230 closest distance to " OE1 GLU A  44 " =    1.717
peak=   -4.211 closest distance to " O   HOH Z 257 " =    0.799
peak=   -4.158 closest distance to " O   GLY A 203 " =    2.371
peak=   -4.143 closest distance to " OG  SER A  97 " =    1.725
peak=   -4.136 closest distance to " CB  ASN A 285 " =    2.036
peak=   -4.119 closest distance to " OG  SER A  63 " =    1.140
peak=   -4.112 closest distance to " O   ASN A 285 " =    0.969
peak=   -4.090 closest distance to " NE1 TRP A 179 " =    1.047
peak=   -4.071 closest distance to " CD  GLN A  55 " =    1.211
peak=   -4.050 closest distance to " C   PHE A  61 " =    1.022
peak=   -4.032 closest distance to " CD1 TYR A 247 " =    2.564
peak=   -4.027 closest distance to " CD  GLN A  55 " =    0.840
peak=   -4.019 closest distance to " CG  GLN A  55 " =    1.097
peak=   -3.975 closest distance to " CG  GLN A  88 " =    1.007
peak=   -3.956 closest distance to " CD2 HIS A 207 " =    1.388
peak=   -3.907 closest distance to " O   THR A 178 " =    1.116
peak=   -3.906 closest distance to " CZ  PHE A  38 " =    2.363
peak=   -3.868 closest distance to " O   GLN A  58 " =    0.948
peak=   -3.862 closest distance to " N   ALA A  43 " =    2.757
peak=   -3.856 closest distance to " O   HOH Z 179 " =    1.130
peak=   -3.852 closest distance to " O   HOH Z 357 " =    1.217
peak=   -3.851 closest distance to " CA  ASN A 110 " =    0.998
peak=   -3.833 closest distance to " O   HOH Z 415 " =    1.359
peak=   -3.829 closest distance to " O   HOH Z 163 " =    1.415
peak=   -3.824 closest distance to " OE2 GLU A 152 " =    1.063
peak=   -3.809 closest distance to " O   HOH Z  37 " =    2.346
peak=   -3.779 closest distance to " OG  SER A  32 " =    1.821
peak=   -3.745 closest distance to " CA  SER A  63 " =    1.270
peak=   -3.739 closest distance to " CD2 LEU A 167 " =    1.879
peak=   -3.724 closest distance to " O   HOH Z  32 " =    1.654
peak=   -3.711 closest distance to " C   VAL A  72 " =    0.810
peak=   -3.700 closest distance to " CG  ARG A 259 " =    2.506
peak=   -3.692 closest distance to " O   SER A  99 " =    1.355
peak=   -3.688 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.674 closest distance to " NE2 GLN A 223 " =    1.425
peak=   -3.665 closest distance to " O   GLN A 240 " =    3.160
peak=   -3.647 closest distance to " CG2BVAL A  41 " =    1.396
peak=   -3.637 closest distance to " N   ALA A  19 " =    2.144
peak=   -3.631 closest distance to " O   ASN A  69 " =    0.906
peak=   -3.623 closest distance to " CB  ASP A 171 " =    2.374
peak=   -3.618 closest distance to " O   HOH Z  24 " =    1.138
peak=   -3.617 closest distance to " CD2 TYR A 293 " =    1.941
peak=   -3.612 closest distance to " OE1 GLN A  88 " =    0.866
peak=   -3.610 closest distance to " ND2 ASN A 285 " =    2.177
peak=   -3.608 closest distance to " O   HOH Z  10 " =    0.772
peak=   -3.597 closest distance to " CB  GLN A 144 " =    1.213
peak=   -3.596 closest distance to " O   HOH Z 389 " =    2.835
peak=   -3.588 closest distance to " O   HOH Z 216 " =    1.186
peak=   -3.584 closest distance to " C   ARG A 156 " =    1.285
peak=   -3.583 closest distance to " CB  ALA A  43 " =    2.559
peak=   -3.581 closest distance to " O   HOH Z  60 " =    1.397
peak=   -3.574 closest distance to " CD1 TYR A 214 " =    1.475
peak=   -3.573 closest distance to " O   HOH Z 119 " =    1.582
peak=   -3.571 closest distance to " CB  PRO A 243 " =    2.607
peak=   -3.561 closest distance to " O   HOH Z  67 " =    1.095
peak=   -3.554 closest distance to " O   HOH Z 385 " =    1.188
peak=   -3.553 closest distance to " CG1 VAL A 265 " =    2.554
peak=   -3.552 closest distance to " OG  SER A  32 " =    0.959
peak=   -3.550 closest distance to " O   HOH Z 131 " =    1.442
peak=   -3.549 closest distance to " O   HOH Z 417 " =    2.924
peak=   -3.541 closest distance to " CD  ARG A  14 " =    3.384
peak=   -3.535 closest distance to " O   HOH Z 102 " =    1.980
peak=   -3.522 closest distance to " CZ  ARG A  36 " =    1.633
peak=   -3.519 closest distance to " CG  ARG A 219 " =    2.223
peak=   -3.512 closest distance to " N   LEU A 282 " =    2.336
peak=   -3.507 closest distance to " O   HOH Z 103 " =    1.269
peak=   -3.505 closest distance to " O   ASN A 170 " =    1.982
peak=   -3.503 closest distance to " NE2 GLN A 194 " =    1.831
peak=   -3.497 closest distance to " O   HOH Z 438 " =    1.507
peak=   -3.497 closest distance to " O   HOH Z 358 " =    3.347
peak=   -3.486 closest distance to " NH2AARG A 275 " =    5.607
peak=   -3.480 closest distance to " O   HOH Z  54 " =    1.095
peak=   -3.477 closest distance to " O   HOH Z 348 " =    2.176
peak=   -3.460 closest distance to " CD  GLN A  77 " =    1.012
peak=   -3.458 closest distance to " O   VAL A 174 " =    2.325
peak=   -3.451 closest distance to " O   HOH Z 285 " =    1.474
peak=   -3.446 closest distance to " CD  ARG A 156 " =    1.983
peak=   -3.444 closest distance to " OG BSER A 134 " =    2.152
peak=   -3.434 closest distance to " O   GLY A  80 " =    2.608
peak=   -3.431 closest distance to " CB  ALA A 291 " =    2.198
peak=   -3.429 closest distance to " NE2 GLN A  77 " =    1.560
peak=   -3.426 closest distance to " O   HOH Z  37 " =    1.601
peak=   -3.415 closest distance to " CD1 ILE A 151 " =    2.847
peak=   -3.411 closest distance to " ND2 ASN A 285 " =    1.643
peak=   -3.411 closest distance to " O   HOH Z 404 " =    1.286
peak=   -3.410 closest distance to " CA  GLY A 241 " =    2.426
peak=   -3.409 closest distance to " O   TRP A  70 " =    1.366
peak=   -3.405 closest distance to " CB  ALA A 161 " =    1.578
peak=   -3.399 closest distance to " CG  TRP A 266 " =    1.546
peak=   -3.398 closest distance to " O   TRP A  92 " =    1.827
peak=   -3.395 closest distance to " O   PRO A 163 " =    1.822
peak=   -3.393 closest distance to " OG ASER A 134 " =    1.111
peak=   -3.390 closest distance to " O   HOH Z 111 " =    1.550
peak=   -3.386 closest distance to " O   HOH Z 345 " =    1.564
peak=   -3.385 closest distance to " N   TRP A 274 " =    1.330
peak=   -3.385 closest distance to " C   TYR A 172 " =    1.525
peak=   -3.379 closest distance to " CG  GLN A 122 " =    2.483
peak=   -3.377 closest distance to " O   HOH Z 368 " =    1.660
peak=   -3.374 closest distance to " O   HOH Z 278 " =    1.104
peak=   -3.374 closest distance to " O   HOH Z 199 " =    1.335
peak=   -3.370 closest distance to " C   LEU A 101 " =    1.387
peak=   -3.364 closest distance to " O   HOH Z  33 " =    2.136
peak=   -3.361 closest distance to " CG  MET A 185 " =    2.738
peak=   -3.352 closest distance to " O   HOH Z 242 " =    1.566
peak=   -3.346 closest distance to " CD1 PHE A  59 " =    2.361
peak=   -3.344 closest distance to " ND2 ASN A 285 " =    2.225
peak=   -3.342 closest distance to " C   ILE A 239 " =    1.921
peak=   -3.341 closest distance to " CG2 ILE A 120 " =    0.860
peak=   -3.339 closest distance to " O   HOH Z 201 " =    1.503
peak=   -3.339 closest distance to " CB  ASP A  27 " =    2.534
peak=   -3.335 closest distance to " O   HOH Z 166 " =    1.809
peak=   -3.329 closest distance to " O   ALA A  10 " =    1.628
peak=   -3.321 closest distance to " O   HOH Z 426 " =    1.721
peak=   -3.320 closest distance to " N   GLN A 122 " =    1.358
peak=   -3.318 closest distance to " CD1 TRP A 274 " =    1.083
peak=   -3.318 closest distance to " OH  TYR A 247 " =    1.418
peak=   -3.315 closest distance to " CA  ILE A 120 " =    1.168
peak=   -3.309 closest distance to " O   HOH Z 244 " =    1.119
peak=   -3.303 closest distance to " O   HOH Z 257 " =    1.481
peak=   -3.303 closest distance to " CG  MET A 105 " =    0.914
peak=   -3.297 closest distance to " O   HOH Z 409 " =    2.261
peak=   -3.290 closest distance to " O   HOH Z 246 " =    1.398
peak=   -3.282 closest distance to " O   HOH Z 408 " =    1.921
peak=   -3.276 closest distance to " O   HOH Z  70 " =    1.875
peak=   -3.272 closest distance to " CH2 TRP A 179 " =    1.413
peak=   -3.269 closest distance to " N   ARG A  66 " =    1.150
peak=   -3.269 closest distance to " CD2 LEU A 237 " =    2.509
peak=   -3.267 closest distance to " O   HOH Z 389 " =    0.783
peak=   -3.264 closest distance to " CD1 ILE A  33 " =    2.331
peak=   -3.262 closest distance to " CG  GLU A 128 " =    1.881
peak=   -3.253 closest distance to " OD1 ASP A 107 " =    1.225
peak=   -3.250 closest distance to " OD2 ASP A 272 " =    1.849
peak=   -3.245 closest distance to " O   HOH Z  80 " =    4.431
peak=   -3.241 closest distance to " CD  LYS A 166 " =    2.644
peak=   -3.241 closest distance to " OE1 GLN A 223 " =    5.077
peak=   -3.240 closest distance to " O   HOH Z 359 " =    1.215
peak=   -3.238 closest distance to " O   PHE A 218 " =    1.750
peak=   -3.234 closest distance to " O   HOH Z 333 " =    0.982
peak=   -3.234 closest distance to " O   HOH Z 140 " =    0.968
peak=   -3.231 closest distance to " CE3 TRP A 274 " =    2.344
peak=   -3.227 closest distance to " CA  GLY A  57 " =    2.126
peak=   -3.227 closest distance to " O   HOH Z  49 " =    1.015
peak=   -3.221 closest distance to " C   ASP A  50 " =    1.616
peak=   -3.215 closest distance to " OG  SER A  32 " =    1.400
peak=   -3.214 closest distance to " O   HOH Z  21 " =    0.943
peak=   -3.205 closest distance to " CB  PRO A  54 " =    2.344
peak=   -3.205 closest distance to " NE2 GLN A 223 " =    1.372
peak=   -3.203 closest distance to " O   HOH Z 353 " =    4.249
peak=   -3.202 closest distance to " O   HOH Z 245 " =    1.639
peak=   -3.201 closest distance to " O   ASN A 187 " =    1.266
peak=   -3.197 closest distance to " O   HOH Z 241 " =    1.390
peak=   -3.197 closest distance to " OE1 GLN A 278 " =    1.226
peak=   -3.194 closest distance to " O   HOH Z 358 " =    1.195
peak=   -3.191 closest distance to " CB  SER A 210 " =    1.200
peak=   -3.189 closest distance to " CG  PHE A 130 " =    1.108
peak=   -3.188 closest distance to " O   ARG A  24 " =    2.514
peak=   -3.186 closest distance to " O   HOH Z 244 " =    1.644
peak=   -3.185 closest distance to " CA  GLY A 203 " =    2.506
peak=   -3.182 closest distance to " O   HOH Z  72 " =    1.342
peak=   -3.180 closest distance to " ND2 ASN A 209 " =    1.827
peak=   -3.179 closest distance to " O   SER A  22 " =    2.758
peak=   -3.173 closest distance to " O   HOH Z 255 " =    0.892
peak=   -3.172 closest distance to " O   SER A  87 " =    2.160
peak=   -3.168 closest distance to " O   ILE A 106 " =    2.147
peak=   -3.167 closest distance to " O   HOH Z 298 " =    4.045
peak=   -3.165 closest distance to " NH2BARG A 275 " =    1.521
peak=   -3.164 closest distance to " CB  LYS A 289 " =    2.918
peak=   -3.164 closest distance to " O   HOH Z 323 " =    1.885
peak=   -3.163 closest distance to " CG  GLN A  73 " =    1.436
peak=   -3.160 closest distance to " O   HOH Z  69 " =    1.154
peak=   -3.157 closest distance to " O   HOH Z  57 " =    1.442
peak=   -3.155 closest distance to " CG2 THR A 178 " =    2.036
peak=   -3.151 closest distance to " CB  ASP A 132 " =    2.478
peak=   -3.150 closest distance to " O   HOH Z 118 " =    0.877
peak=   -3.147 closest distance to " O   HOH Z 340 " =    1.205
peak=   -3.143 closest distance to " O   HOH Z 417 " =    2.260
peak=   -3.141 closest distance to " NH2 ARG A  56 " =    1.097
peak=   -3.137 closest distance to " CD2 TYR A 116 " =    2.172
peak=   -3.132 closest distance to " O   HOH Z 412 " =    1.962
peak=   -3.131 closest distance to " O   HOH Z  52 " =    0.784
peak=   -3.130 closest distance to " CZ  PHE A  16 " =    0.857
peak=   -3.129 closest distance to " CA  THR A 264 " =    1.223
peak=   -3.128 closest distance to " O   HOH Z 291 " =    1.049
peak=   -3.128 closest distance to " OG  SER A 245 " =    1.743
peak=   -3.126 closest distance to " CG1 VAL A 112 " =    2.846
peak=   -3.125 closest distance to " CA  MET A 113 " =    1.131
peak=   -3.125 closest distance to " O   HOH Z 381 " =    1.273
peak=   -3.122 closest distance to " O   HOH Z 211 " =    3.053
peak=   -3.110 closest distance to " O   HOH Z 210 " =    2.016
peak=   -3.103 closest distance to " CD  ARG A  66 " =    1.464
peak=   -3.102 closest distance to " O   HOH Z 298 " =    2.436
peak=   -3.095 closest distance to " CA  SER A  63 " =    0.807
peak=   -3.094 closest distance to " N   VAL A 202 " =    2.154
peak=   -3.074 closest distance to " CG2 THR A 221 " =    2.350
peak=   -3.073 closest distance to " CB  ALA A 104 " =    2.259
peak=   -3.073 closest distance to " C   SER A  62 " =    1.518
peak=   -3.072 closest distance to " C   LEU A 222 " =    1.559
peak=   -3.068 closest distance to " C   HIS A 108 " =    1.365
peak=   -3.060 closest distance to " NE2 GLN A 240 " =    1.389
peak=   -3.057 closest distance to " O   HOH Z 328 " =    1.031
peak=   -3.050 closest distance to " O   HOH Z 390 " =    2.526
peak=   -3.049 closest distance to " O   VAL A  67 " =    2.896
peak=   -3.039 closest distance to " CG  ARG A 219 " =    2.424
peak=   -3.007 closest distance to " O   HOH Z  70 " =    1.955
peak=   -3.005 closest distance to " CA  SER A  62 " =    1.246

================= 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    :  0.5087 0.5139   6.315221e+00   6.306525e+00
   1_bss:  0.5020 0.5112   6.315252e+00   6.305006e+00
   1_xyz:  0.4488 0.4902   6.252101e+00   6.284099e+00
   1_adp:  0.4184 0.4979   6.230191e+00   6.287122e+00
   1_occ:  0.4180 0.4985   6.229737e+00   6.287187e+00
   2_bss:  0.4188 0.4980   6.232064e+00   6.287582e+00
   2_xyz:  0.3706 0.4559   6.141685e+00   6.242937e+00
   2_adp:  0.3537 0.4510   6.126799e+00   6.237900e+00
   2_occ:  0.3535 0.4509   6.126349e+00   6.237900e+00
   3_bss:  0.3538 0.4501   6.125966e+00   6.237235e+00
   3_xyz:  0.2996 0.3789   5.993170e+00   6.141359e+00
   3_adp:  0.2681 0.3709   5.939778e+00   6.124383e+00
   3_occ:  0.2680 0.3708   5.939251e+00   6.124282e+00
   4_bss:  0.2685 0.3699   5.937129e+00   6.122892e+00
   4_xyz:  0.2323 0.3235   5.804928e+00   6.026119e+00
   4_adp:  0.2149 0.2859   5.728190e+00   5.931494e+00
   4_occ:  0.2147 0.2854   5.726859e+00   5.929986e+00
   5_bss:  0.2142 0.2841   5.723527e+00   5.926741e+00
   5_xyz:  0.1716 0.2340   5.526756e+00   5.759797e+00
   5_adp:  0.1565 0.2167   5.449858e+00   5.688154e+00
   5_occ:  0.1564 0.2164   5.448601e+00   5.686503e+00
   5_bss:  0.1564 0.2149   5.444160e+00   5.681081e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -1.047  -0.356   2.467  -0.000   0.000   0.000
   1_xyz:  0.300  50.000  -1.047  -0.356   2.467  -0.000   0.000   0.000
   1_adp:  0.300  50.000  -1.047  -0.356   2.467  -0.000   0.000   0.000
   1_occ:  0.300  50.000  -1.047  -0.356   2.467  -0.000   0.000   0.000
   2_bss:  0.364  92.120  -0.254  -0.247   1.994  -0.000   0.000   0.000
   2_xyz:  0.364  92.120  -0.254  -0.247   1.994  -0.000   0.000   0.000
   2_adp:  0.364  92.120  -0.254  -0.247   1.994  -0.000   0.000   0.000
   2_occ:  0.364  92.120  -0.254  -0.247   1.994  -0.000   0.000   0.000
   3_bss:  0.383 104.566  -0.278  -0.780   1.250  -0.000   0.000   0.000
   3_xyz:  0.383 104.566  -0.278  -0.780   1.250  -0.000   0.000   0.000
   3_adp:  0.383 104.566  -0.278  -0.780   1.250  -0.000   0.000   0.000
   3_occ:  0.383 104.566  -0.278  -0.780   1.250  -0.000   0.000   0.000
   4_bss:  0.375 121.021  -0.268  -0.919   1.331  -0.000   0.000   0.000
   4_xyz:  0.375 121.021  -0.268  -0.919   1.331  -0.000   0.000   0.000
   4_adp:  0.375 121.021  -0.268  -0.919   1.331  -0.000   0.000   0.000
   4_occ:  0.375 121.021  -0.268  -0.919   1.331  -0.000   0.000   0.000
   5_bss:  0.341  82.348  -1.348  -2.101   0.243  -0.000   0.000   0.000
   5_xyz:  0.341  82.348  -1.348  -2.101   0.243  -0.000   0.000   0.000
   5_adp:  0.341  82.348  -1.348  -2.101   0.243  -0.000   0.000   0.000
   5_occ:  0.341  82.348  -1.348  -2.101   0.243  -0.000   0.000   0.000
   5_bss:  0.327  66.506  -1.941  -2.810  -0.428  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  69.382 0.2706  0.3732    92145.580
   1_bss:  69.080 0.2739  0.3942    92144.546
   1_xyz:  62.758 0.3563  0.5071    81501.671
   1_adp:  63.333 0.3486  0.5191    83528.818
   1_occ:  63.273 0.3494  0.5203    83494.837
   2_bss:  63.271 0.3494  0.5226    83510.402
   2_xyz:  54.059 0.4676  0.6964    64097.447
   2_adp:  52.991 0.4813  0.7111    62334.741
   2_occ:  52.996 0.4811  0.7104    62283.703
   3_bss:  52.852 0.4828  0.7027    61921.455
   3_xyz:  42.900 0.6059  0.8636    42406.777
   3_adp:  41.018 0.6288  0.8535    39579.439
   3_occ:  40.994 0.6290  0.8533    39515.318
   4_bss:  40.896 0.6300  0.8532    39220.081
   4_xyz:  34.712 0.7019  0.9306    28524.729
   4_adp:  29.871 0.7582  0.9669    22500.499
   4_occ:  29.821 0.7586  0.9670    22384.541
   5_bss:  29.647 0.7602  0.9324    22081.438
   5_xyz:  23.511 0.8252  0.9771    14467.816
   5_adp:  21.268 0.8487  0.9828    12458.491
   5_occ:  21.219 0.8491  0.9829    12404.807
   5_bss:  21.046 0.8505  0.9617    12166.973
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8394e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8394e-01
   1_xyz:   1.482  0.011  0.096 15.984  0.006  4.105   1.2606e-01
   1_adp:   1.482  0.011  0.096 15.984  0.006  4.105   1.2606e-01
   1_occ:   1.482  0.011  0.096 15.984  0.006  4.105   1.2606e-01
   2_bss:   1.482  0.011  0.096 15.984  0.006  4.105   1.2606e-01
   2_xyz:   1.452  0.010  0.099 16.371  0.006  4.105   1.2846e-01
   2_adp:   1.452  0.010  0.099 16.371  0.006  4.105   1.2846e-01
   2_occ:   1.452  0.010  0.099 16.371  0.006  4.105   1.2846e-01
   3_bss:   1.452  0.010  0.099 16.371  0.006  4.105   1.2846e-01
   3_xyz:   1.351  0.010  0.096 15.798  0.005  4.105   1.1000e-01
   3_adp:   1.351  0.010  0.096 15.798  0.005  4.105   1.1000e-01
   3_occ:   1.351  0.010  0.096 15.798  0.005  4.105   1.1000e-01
   4_bss:   1.351  0.010  0.096 15.798  0.005  4.105   1.1000e-01
   4_xyz:   1.201  0.009  0.088 14.925  0.005  4.123   8.4372e-02
   4_adp:   1.201  0.009  0.088 14.925  0.005  4.123   8.4372e-02
   4_occ:   1.201  0.009  0.088 14.925  0.005  4.123   8.4372e-02
   5_bss:   1.201  0.009  0.088 14.925  0.005  4.123   8.4372e-02
   5_xyz:   1.185  0.010  0.084 14.652  0.004  4.123   8.3153e-02
   5_adp:   1.185  0.010  0.084 14.652  0.004  4.123   8.3153e-02
   5_occ:   1.185  0.010  0.084 14.652  0.004  4.123   8.3153e-02
   5_bss:   1.185  0.010  0.084 14.652  0.004  4.123   8.3153e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4296e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4296e-01
   1_xyz:   8.194  0.047  0.334 83.421  0.036  1.927   9.5247e-02
   1_adp:   8.194  0.047  0.334 83.421  0.036  1.927   9.5247e-02
   1_occ:   8.194  0.047  0.334 83.421  0.036  1.927   9.5247e-02
   2_bss:   8.194  0.047  0.334 83.421  0.036  1.927   9.5247e-02
   2_xyz:   8.330  0.052  0.286 79.498  0.065  1.841   8.8113e-02
   2_adp:   8.330  0.052  0.286 79.498  0.065  1.841   8.8113e-02
   2_occ:   8.330  0.052  0.286 79.498  0.065  1.841   8.8113e-02
   3_bss:   8.330  0.052  0.286 79.498  0.065  1.841   8.8113e-02
   3_xyz:   8.077  0.051  0.337 86.765  0.024  2.132   1.2457e-01
   3_adp:   8.077  0.051  0.337 86.765  0.024  2.132   1.2457e-01
   3_occ:   8.077  0.051  0.337 86.765  0.024  2.132   1.2457e-01
   4_bss:   8.077  0.051  0.337 86.765  0.024  2.132   1.2457e-01
   4_xyz:  10.456  0.068  0.288 88.366  0.043  2.239   7.8439e-02
   4_adp:  10.456  0.068  0.288 88.366  0.043  2.239   7.8439e-02
   4_occ:  10.456  0.068  0.288 88.366  0.043  2.239   7.8439e-02
   5_bss:  10.456  0.068  0.288 88.366  0.043  2.239   7.8439e-02
   5_xyz:   7.711  0.056  0.292 85.273  0.022  2.255   6.3872e-02
   5_adp:   7.711  0.056  0.292 85.273  0.022  2.255   6.3872e-02
   5_occ:   7.711  0.056  0.292 85.273  0.022  2.255   6.3872e-02
   5_bss:   7.711  0.056  0.292 85.273  0.022  2.255   6.3872e-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:  92.60   0.00  21.32  92.60   0.00  19.02  86.38   0.00  33.85
   1_occ:  92.60   0.00  21.32  92.60   0.00  19.02  86.38   0.00  33.85
   2_bss:  92.60   0.00  21.32  92.60   0.00  19.02  86.38   0.00  33.85
   2_xyz:  92.60   0.00  21.32  92.60   0.00  19.02  86.38   0.00  33.85
   2_adp:  89.25   0.00  21.00  89.25   0.00  18.61  81.07   0.00  34.04
   2_occ:  89.25   0.00  21.00  89.25   0.00  18.61  81.07   0.00  34.04
   3_bss:  89.25   0.00  21.00  89.25   0.00  18.61  81.07   0.00  34.04
   3_xyz:  89.25   0.00  21.00  89.25   0.00  18.61  81.07   0.00  34.04
   3_adp: 132.41   0.00  23.88 122.83   0.00  19.06 132.41   0.00  50.12
   3_occ: 132.41   0.00  23.88 122.83   0.00  19.06 132.41   0.00  50.12
   4_bss: 132.41   0.00  23.88 122.83   0.00  19.06 132.41   0.00  50.12
   4_xyz: 132.41   0.00  23.88 122.83   0.00  19.06 132.41   0.00  50.12
   4_adp: 111.96   0.00  20.26 109.48   0.00  15.25 111.96   2.26  47.53
   4_occ: 111.96   0.00  20.26 109.48   0.00  15.25 111.96   2.26  47.53
   5_bss: 111.96   0.00  20.26 109.48   0.00  15.25 111.96   2.26  47.53
   5_xyz: 111.96   0.00  20.26 109.48   0.00  15.25 111.96   2.26  47.53
   5_adp: 111.63   0.00  19.23 111.63   0.00  13.82 110.95   3.89  48.70
   5_occ: 111.63   0.00  19.23 111.63   0.00  13.82 110.95   3.89  48.70
   5_bss: 111.64   0.00  19.24 111.64   0.00  13.82 110.96   3.89  48.71
------------------------------------------------------------------------
 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:    1.649    0.017    0.296
   1_adp:    1.649    0.017    0.296
   1_occ:    1.649    0.017    0.296
   2_bss:    1.649    0.017    0.296
   2_xyz:    1.764    0.055    0.551
   2_adp:    1.764    0.055    0.551
   2_occ:    1.764    0.055    0.551
   3_bss:    1.764    0.055    0.551
   3_xyz:    1.709    0.088    0.763
   3_adp:    1.709    0.088    0.763
   3_occ:    1.709    0.088    0.763
   4_bss:    1.709    0.088    0.763
   4_xyz:    1.756    0.069    0.870
   4_adp:    1.756    0.069    0.870
   4_occ:    1.756    0.069    0.870
   5_bss:    1.756    0.069    0.870
   5_xyz:    1.863    0.095    0.964
   5_adp:    1.863    0.095    0.964
   5_occ:    1.863    0.095    0.964
   5_bss:    1.863    0.095    0.964
------------------------------------------------------------------------

CPU time actual refinement: 375.78


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1099/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_1099/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1099/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1099/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1099/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 375.63 
  Macro-tasks:
    bulk solvent and scale       = 60.45  
    individual site refinement   = 167.88 
    weights calculation          = 30.38  
    collect and process          = 6.24   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 265.06 
  Micro-tasks:
    mask                            = 3.15   
    f_calc                          = 115.84 
    alpha_beta                      = 8.37   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 127.35 
    fmodel                         = 9.44   
    r_factors                      = 0.44   
    phase_errors                   = 9.42   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 275.43 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.257 micro seconds
Total CPU time: 6.49 minutes
from_scatterers_fft:    587 calls, 115.59 s
gradients_fft:          532 calls, 113.90 s

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

# Date 2008-01-16 Time 06:25:35 PST -0800 (1200493535.55 s)
Start R-work = 0.5087, R-free = 0.5139 (no bulk solvent and anisotropic scale)
Final R-work = 0.1764, R-free = 0.2324 (no bulk solvent and anisotropic scale)

Start R-work = 0.5020, R-free = 0.5112
Final R-work = 0.1564, R-free = 0.2149