# Date 2008-01-16 Time 04:15:07 PST -0800 (1200485707.25 s)
#phil __OFF__

Command line arguments: "../240.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27702
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 240

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 48.1033, 88.1178, 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: 3.40, per 1000 atoms: 1.20


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0676 1.96097
Completeness in resolution range: 0.908286
Completeness with d_max=infinity: 0.905598

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0676
                             d_min =   1.9610

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0676 1.96097
Completeness in resolution range: 0.908286
Completeness with d_max=infinity: 0.905598

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0680 -  4.1972 [2257/2285]  2027   230  10.2%
  bin  2:  4.1972 -  3.3434 [2184/2207]  1964   220  10.1%
  bin  3:  3.3434 -  2.9243 [2152/2177]  1946   206   9.6%
  bin  4:  2.9243 -  2.6585 [2105/2132]  1889   216  10.3%
  bin  5:  2.6585 -  2.4689 [2105/2138]  1891   214  10.2%
  bin  6:  2.4689 -  2.3239 [2113/2141]  1906   207   9.8%
  bin  7:  2.3239 -  2.2078 [2081/2117]  1879   202   9.7%
  bin  8:  2.2078 -  2.1120 [2099/2141]  1887   212  10.1%
  bin  9:  2.1120 -  2.0309 [1951/2112]  1759   192   9.8%
  bin 10:  2.0309 -  1.9610 [ 542/2117]   482    60  11.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_240/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:
        1.17 -     1.91: 11
        1.91 -     2.66: 99
        2.66 -     3.41: 4364
        3.41 -     4.15: 9275
        4.15 -     4.90: 14326
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.167 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.320 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.418 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.620 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.650 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28070 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_240/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_240/model_refine_001.geo

CPU time processing inputs: 9.29


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 48.10325 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4994   r_free= 0.4985   ksol= 0.00   Bsol= 0.00   scale= 0.858    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.303827                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.6819 0.99   1471  161 0.4026 0.4173      6.6202      6.6418|
|  2:  4.6819 -  3.7348 0.99   1415  156 0.4538 0.4716       6.875      6.9014|
|  3:  3.7348 -  3.2682 0.99   1377  158 0.4913 0.4831       6.708      6.6953|
|  4:  3.2682 -  2.9719 0.98   1383  145 0.5012 0.4682      6.5261       6.508|
|  5:  2.9719 -  2.7603 0.99   1372  157 0.5272 0.5237      6.3708      6.3965|
|  6:  2.7603 -  2.5984 0.99   1370  151 0.5308 0.5374      6.2826      6.1907|
|  7:  2.5984 -  2.4689 0.98   1329  158 0.5241 0.4632      6.2291      6.1531|
|  8:  2.4689 -  2.3618 0.98   1374  144 0.5470 0.5421        6.17      6.1995|
|  9:  2.3618 -  2.2712 0.99   1343  145 0.5476 0.5364       6.116      6.1888|
| 10:  2.2712 -  2.1931 0.99   1349  147 0.5288 0.5428      6.0832       6.093|
| 11:  2.1931 -  2.1247 0.97   1334  157 0.5442 0.5588      6.0078      6.0287|
| 12:  2.1247 -  2.0641 0.98   1331  149 0.5347 0.5190      5.9517      5.9368|
| 13:  2.0641 -  2.0099 0.71    959  104 0.5287 0.5951      5.8681       5.824|
| 14:  2.0099 -  1.9610 0.16    223   27 0.4872 0.4293      5.9187      5.7118|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.6819  1471   161  0.66  38.04   0.80     0.68      85212.44|
|  2:  4.6819 -  3.7348  1415   156  0.64  40.29   0.88     0.73     129725.82|
|  3:  3.7348 -  3.2682  1377   158  0.51  50.94   0.86     0.69     137687.23|
|  4:  3.2682 -  2.9719  1383   145  0.42  58.47   0.86     0.59     117395.44|
|  5:  2.9719 -  2.7603  1372   157  0.34  64.43   0.84     0.50      92013.68|
|  6:  2.7603 -  2.5984  1370   151  0.32  65.84   0.87     0.47      76564.22|
|  7:  2.5984 -  2.4689  1329   158  0.30  67.21   0.88     0.43      70260.06|
|  8:  2.4689 -  2.3618  1374   144  0.28  68.71   0.86     0.42      63042.83|
|  9:  2.3618 -  2.2712  1343   145  0.26  70.67   0.89     0.41      61255.49|
| 10:  2.2712 -  2.1931  1349   147  0.27  69.69   0.89     0.41      53701.94|
| 11:  2.1931 -  2.1247  1334   157  0.21  74.10   0.88     0.35      53136.69|
| 12:  2.1247 -  2.0641  1331   149  0.16  77.75   0.90     0.27      50246.80|
| 13:  2.0641 -  2.0099   959   104  0.13  80.45   0.91     0.22      44785.72|
| 14:  2.0099 -  1.9610   223    27  0.20  74.95   1.00     0.24      32120.34|
|alpha:            min =        0.22 max =            0.73 mean =         0.48|
|beta:             min =    32120.34 max =       137687.23 mean =     80237.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.04|
|phase err.(test): min =        0.00 max =           89.98 mean =        63.17|
|-----------------------------------------------------------------------------|

============================== 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 = 24.693291             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.079   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.327223              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.698   (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 |  1.167 -  1.540:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.540 -  1.913:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.913 -  2.287:       14 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.287 -  2.660:       85 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.660 -  3.033:     2062 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.033 -  3.407:     2302 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.407 -  3.780:     3950 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.780 -  4.153:     5325 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.153 -  4.527:     6371 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.527 -  4.900:     7955 |
|-----------------------------------------------------------------------------|
|-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 |        0.202 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.167 |       0.737 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.002)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4994   r_free= 0.4985   ksol= 0.00   Bsol= 0.00   scale= 0.858    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.303827                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4935   r_free= 0.4893   ksol= 0.28   Bsol= 20.00   scale= 0.903   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,3.26,1.90,0.00,0.00,0.00); trace/3= 1.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.301361                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.961472             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.442   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.022080              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.258   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4935      final r-factor (work) = 0.3862          |
| start r-factor (free) = 0.4893      final r-factor (free) = 0.4191          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 63.0715 = 19.96 * 0.50 * 6.2991 + 1.00 * 0.2019                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 62.1374 = 19.96 * 0.50 * 6.2055 + 1.00 * 0.2018                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3862      final r-factor (work) = 0.3462          |
| start r-factor (free) = 0.4191      final r-factor (free) = 0.4248          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5541 = 2.02 * 1.00 * 6.2055 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3762 = 2.02 * 1.00 * 6.1071 + 1.00 * 0.0272                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.002)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.11  20.68    None  None   None       |
|    all(noH): 2823   0      0.00    105.11  20.68    None  None   None       |
|    Sol.    : 438    0      0.00    105.11  40.81    None  None   None       |
|    Mac.    : 2385   0      0.00    103.80  16.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.512:  946   |   5:    52.557 -  63.069:  111        |
|      1:    10.512 -  21.023:  796   |   6:    63.069 -  73.580:   48        |
|      2:    21.023 -  31.535:  469   |   7:    73.580 -  84.092:   21        |
|      3:    31.535 -  42.046:  272   |   8:    84.092 -  94.603:    5        |
|      4:    42.046 -  52.557:  152   |   9:    94.603 - 105.115:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3462 r_free = 0.4248             target_work(ml) = 6.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3460 r_free = 0.4245             target_work(ml) = 6.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3460   r_free= 0.4245   ksol= 0.28   Bsol= 20.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,3.26,1.90,0.00,0.00,0.00); trace/3= 1.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.110788                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3445   r_free= 0.4216   ksol= 0.31   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,2.27,1.56,0.00,0.00,0.00); trace/3= 0.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.109690                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.131783             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.513   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.457836              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.483  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3445      final r-factor (work) = 0.2896          |
| start r-factor (free) = 0.4216      final r-factor (free) = 0.3574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.2046 = 11.13 * 0.50 * 6.1091 + 1.00 * 0.2019                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.7812 = 11.13 * 0.50 * 6.0519 + 1.00 * 0.0969                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2896      final r-factor (work) = 0.2695          |
| start r-factor (free) = 0.3574      final r-factor (free) = 0.3478          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8503 = 1.46 * 1.00 * 6.0519 + 1.00 * 0.0276                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6792 = 1.46 * 1.00 * 5.9385 + 1.00 * 0.0218                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.002)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.03  20.31    None  None   None       |
|    all(noH): 2823   0      0.00    109.03  20.31    None  None   None       |
|    Sol.    : 438    0      0.00    109.03  42.09    None  None   None       |
|    Mac.    : 2385   0      0.00    106.91  16.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.903: 1029   |   5:    54.515 -  65.418:   83        |
|      1:    10.903 -  21.806:  858   |   6:    65.418 -  76.321:   49        |
|      2:    21.806 -  32.709:  390   |   7:    76.321 -  87.224:   23        |
|      3:    32.709 -  43.612:  235   |   8:    87.224 -  98.127:   12        |
|      4:    43.612 -  54.515:  141   |   9:    98.127 - 109.030:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2695 r_free = 0.3478             target_work(ml) = 5.928         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2693 r_free = 0.3476             target_work(ml) = 5.928         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2693   r_free= 0.3476   ksol= 0.31   Bsol= 50.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,2.27,1.56,0.00,0.00,0.00); trace/3= 0.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.928093                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2697   r_free= 0.3477   ksol= 0.32   Bsol= 59.46   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,1.23,0.90,0.00,0.00,0.00); trace/3= 0.13                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.929535                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.747710              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.807   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.302716              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.364  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2697      final r-factor (work) = 0.2203          |
| start r-factor (free) = 0.3477      final r-factor (free) = 0.2827          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1038 = 7.75 * 0.50 * 5.9390 + 1.00 * 0.0969                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.7777 = 7.75 * 0.50 * 5.8581 + 1.00 * 0.0843                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2203      final r-factor (work) = 0.1971          |
| start r-factor (free) = 0.2827      final r-factor (free) = 0.2643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.5113 = 2.30 * 1.00 * 5.8581 + 1.00 * 0.0218                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1271 = 2.30 * 1.00 * 5.6918 + 1.00 * 0.0205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.002)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.66  20.18    None  None   None       |
|    all(noH): 2823   0      0.00    115.66  20.18    None  None   None       |
|    Sol.    : 438    0      3.54    115.66  49.05    None  None   None       |
|    Mac.    : 2385   0      0.00    109.83  14.87    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 -  11.566: 1255   |   5:    57.829 -  69.395:   84        |
|      1:    11.566 -  23.132:  833   |   6:    69.395 -  80.961:   54        |
|      2:    23.132 -  34.697:  259   |   7:    80.961 -  92.526:   34        |
|      3:    34.697 -  46.263:  153   |   8:    92.526 - 104.092:   15        |
|      4:    46.263 -  57.829:  125   |   9:   104.092 - 115.658:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1971 r_free = 0.2643             target_work(ml) = 5.655         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1971 r_free = 0.2642             target_work(ml) = 5.655         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1971   r_free= 0.2642   ksol= 0.32   Bsol= 59.46   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,1.23,0.90,0.00,0.00,0.00); trace/3= 0.13                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.654560                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1967   r_free= 0.2635   ksol= 0.34   Bsol= 75.22   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,0.04,0.25,0.00,0.00,0.00); trace/3= -0.62                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.653460                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.180217              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.537  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.246163              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.929  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1967      final r-factor (work) = 0.1647          |
| start r-factor (free) = 0.2635      final r-factor (free) = 0.2222          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9850 = 4.18 * 0.50 * 5.6938 + 1.00 * 0.0843                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7441 = 4.18 * 0.50 * 5.5861 + 1.00 * 0.0686                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1647      final r-factor (work) = 0.1559          |
| start r-factor (free) = 0.2222      final r-factor (free) = 0.2033          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3954 = 0.25 * 1.00 * 5.5861 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3590 = 0.25 * 1.00 * 5.4705 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.002)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.40    109.40  18.61    None  None   None       |
|    all(noH): 2823   0      1.40    109.40  18.61    None  None   None       |
|    Sol.    : 438    0      5.51    109.40  46.02    None  None   None       |
|    Mac.    : 2385   0      1.40    106.11  13.57    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:     1.399 -  12.198: 1454   |   5:    55.397 -  66.197:   70        |
|      1:    12.198 -  22.998:  776   |   6:    66.197 -  76.997:   42        |
|      2:    22.998 -  33.798:  175   |   7:    76.997 -  87.797:   32        |
|      3:    33.798 -  44.598:  122   |   8:    87.797 -  98.596:   14        |
|      4:    44.598 -  55.397:  129   |   9:    98.596 - 109.396:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1559 r_free = 0.2033             target_work(ml) = 5.426         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1556 r_free = 0.2028             target_work(ml) = 5.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1556   r_free= 0.2028   ksol= 0.34   Bsol= 75.22   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,0.04,0.25,0.00,0.00,0.00); trace/3= -0.62                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.424496                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1559   r_free= 0.2023   ksol= 0.34   Bsol= 73.42   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-0.73,-0.28,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.425617                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.964755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.954  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.754784              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.384  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1559      final r-factor (work) = 0.1370          |
| start r-factor (free) = 0.2023      final r-factor (free) = 0.1835          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1800 = 2.96 * 0.50 * 5.4719 + 1.00 * 0.0686                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0308 = 2.96 * 0.50 * 5.3711 + 1.00 * 0.0688                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1370      final r-factor (work) = 0.1318          |
| start r-factor (free) = 0.1835      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0662 = 0.75 * 1.00 * 5.3711 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0170 = 0.75 * 1.00 * 5.3048 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.002)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    111.13  18.38    None  None   None       |
|    all(noH): 2823   0      1.35    111.13  18.38    None  None   None       |
|    Sol.    : 438    0      2.90    111.13  46.92    None  None   None       |
|    Mac.    : 2385   0      1.35    107.69  13.15    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:     1.348 -  12.326: 1507   |   5:    56.240 -  67.219:   76        |
|      1:    12.326 -  23.305:  754   |   6:    67.219 -  78.197:   54        |
|      2:    23.305 -  34.283:  170   |   7:    78.197 -  89.176:   28        |
|      3:    34.283 -  45.262:  103   |   8:    89.176 - 100.154:   16        |
|      4:    45.262 -  56.240:  111   |   9:   100.154 - 111.133:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1318 r_free = 0.1827             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1318 r_free = 0.1827             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1827   ksol= 0.34   Bsol= 73.42   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-0.73,-0.28,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.299707                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.6819 0.99   1471  161 0.1022 0.1404      5.4506      5.6675|
|  2:  4.6819 -  3.7348 0.99   1415  156 0.0917 0.1091      5.5033      5.6724|
|  3:  3.7348 -  3.2682 0.99   1377  158 0.1233 0.1773       5.601      5.9532|
|  4:  3.2682 -  2.9719 0.98   1383  145 0.1506 0.1949      5.5946      5.7737|
|  5:  2.9719 -  2.7603 0.99   1372  157 0.1633 0.2024      5.5124      5.6997|
|  6:  2.7603 -  2.5984 0.99   1370  151 0.1526 0.2365      5.3798      5.6013|
|  7:  2.5984 -  2.4689 0.98   1329  158 0.1476 0.1878      5.3191      5.4941|
|  8:  2.4689 -  2.3618 0.98   1374  144 0.1479 0.2252      5.2638      5.5296|
|  9:  2.3618 -  2.2712 0.99   1343  145 0.1378 0.1973      5.1755      5.3942|
| 10:  2.2712 -  2.1931 0.99   1349  147 0.1428 0.2138      5.1197      5.3292|
| 11:  2.1931 -  2.1247 0.97   1334  157 0.1344 0.2005      5.0401       5.373|
| 12:  2.1247 -  2.0641 0.98   1331  149 0.1308 0.1666      4.9621      5.1351|
| 13:  2.0641 -  2.0099 0.71    959  104 0.1277 0.2072      4.8747      5.1603|
| 14:  2.0099 -  1.9610 0.16    223   27 0.1201 0.2046      4.8617      5.0243|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.6819  1471   161  0.93  10.29   0.96     0.93       8618.49|
|  2:  4.6819 -  3.7348  1415   156  0.95   9.20   1.01     1.00      10737.77|
|  3:  3.7348 -  3.2682  1377   158  0.92  13.34   1.03     1.03      13116.31|
|  4:  3.2682 -  2.9719  1383   145  0.89  17.66   1.01     1.00      13970.26|
|  5:  2.9719 -  2.7603  1372   157  0.87  19.67   1.01     0.99      12561.91|
|  6:  2.7603 -  2.5984  1370   151  0.86  20.13   0.98     0.95      10076.11|
|  7:  2.5984 -  2.4689  1329   158  0.87  19.61   1.00     0.97       9040.27|
|  8:  2.4689 -  2.3618  1374   144  0.86  20.34   1.00     0.95       8128.75|
|  9:  2.3618 -  2.2712  1343   145  0.87  19.42   0.99     0.92       6837.17|
| 10:  2.2712 -  2.1931  1349   147  0.87  19.58   1.00     0.96       6266.54|
| 11:  2.1931 -  2.1247  1334   157  0.88  19.21   0.99     0.94       5458.46|
| 12:  2.1247 -  2.0641  1331   149  0.88  18.28   0.99     0.99       4658.61|
| 13:  2.0641 -  2.0099   959   104  0.88  18.86   0.99     0.97       4081.01|
| 14:  2.0099 -  1.9610   223    27  0.90  16.48   0.96     0.90       3592.59|
|alpha:            min =        0.90 max =            1.03 mean =         0.97|
|beta:             min =     3592.59 max =        13970.26 mean =      8809.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.85 mean =        17.23|
|phase err.(test): min =        0.00 max =           89.95 mean =        16.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1323   r_free= 0.1826   ksol= 0.33   Bsol= 73.38   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.04,-0.33,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.300210                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1323   r_free= 0.1826   ksol= 0.33   Bsol= 73.38   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.04,-0.33,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.300210                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.6819 0.99   1471  161 0.1042 0.1397      5.4518       5.658|
|  2:  4.6819 -  3.7348 0.99   1415  156 0.0928 0.1087      5.5066      5.6763|
|  3:  3.7348 -  3.2682 0.99   1377  158 0.1235 0.1764      5.6027      5.9521|
|  4:  3.2682 -  2.9719 0.98   1383  145 0.1510 0.1949       5.596      5.7741|
|  5:  2.9719 -  2.7603 0.99   1372  157 0.1633 0.2024      5.5128      5.6987|
|  6:  2.7603 -  2.5984 0.99   1370  151 0.1525 0.2362      5.3792      5.5993|
|  7:  2.5984 -  2.4689 0.98   1329  158 0.1475 0.1883      5.3184      5.4954|
|  8:  2.4689 -  2.3618 0.98   1374  144 0.1477 0.2251      5.2636      5.5307|
|  9:  2.3618 -  2.2712 0.99   1343  145 0.1378 0.1976      5.1753      5.3939|
| 10:  2.2712 -  2.1931 0.99   1349  147 0.1426 0.2141      5.1193      5.3303|
| 11:  2.1931 -  2.1247 0.97   1334  157 0.1344 0.2004      5.0394      5.3724|
| 12:  2.1247 -  2.0641 0.98   1331  149 0.1309 0.1667      4.9626       5.136|
| 13:  2.0641 -  2.0099 0.71    959  104 0.1279 0.2071      4.8749      5.1584|
| 14:  2.0099 -  1.9610 0.16    223   27 0.1200 0.2046      4.8624      5.0265|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.6819  1471   161  0.93  10.29   0.96     0.93       8506.98|
|  2:  4.6819 -  3.7348  1415   156  0.95   9.17   1.01     1.00      10676.25|
|  3:  3.7348 -  3.2682  1377   158  0.92  13.33   1.03     1.03      13119.40|
|  4:  3.2682 -  2.9719  1383   145  0.89  17.68   1.01     1.00      13993.33|
|  5:  2.9719 -  2.7603  1372   157  0.87  19.65   1.01     0.99      12552.68|
|  6:  2.7603 -  2.5984  1370   151  0.86  20.10   0.98     0.95      10069.36|
|  7:  2.5984 -  2.4689  1329   158  0.87  19.60   1.00     0.96       9031.84|
|  8:  2.4689 -  2.3618  1374   144  0.86  20.35   1.00     0.94       8139.57|
|  9:  2.3618 -  2.2712  1343   145  0.87  19.42   0.98     0.91       6845.06|
| 10:  2.2712 -  2.1931  1349   147  0.87  19.59   0.99     0.95       6272.10|
| 11:  2.1931 -  2.1247  1334   157  0.88  19.21   0.98     0.93       5458.51|
| 12:  2.1247 -  2.0641  1331   149  0.88  18.27   0.98     0.98       4658.91|
| 13:  2.0641 -  2.0099   959   104  0.88  18.85   0.98     0.96       4075.75|
| 14:  2.0099 -  1.9610   223    27  0.90  16.49   0.96     0.89       3591.37|
|alpha:            min =        0.89 max =            1.03 mean =         0.96|
|beta:             min =     3591.37 max =        13993.33 mean =      8796.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.91 mean =        17.22|
|phase err.(test): min =        0.00 max =           89.83 mean =        16.62|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.002)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    111.09  18.34    None  None   None       |
|    all(noH): 2823   0      1.30    111.09  18.34    None  None   None       |
|    Sol.    : 438    0      2.85    111.09  46.87    None  None   None       |
|    Mac.    : 2385   0      1.30    107.64  13.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.300 -  12.279: 1507   |   5:    56.193 -  67.171:   76        |
|      1:    12.279 -  23.257:  754   |   6:    67.171 -  78.150:   54        |
|      2:    23.257 -  34.236:  170   |   7:    78.150 -  89.128:   28        |
|      3:    34.236 -  45.214:  103   |   8:    89.128 - 100.107:   16        |
|      4:    45.214 -  56.193:  111   |   9:   100.107 - 111.085:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.672 - 4.933
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 316
   mapped sites are within: 0.746 - 4.933

peak=    9.253 closest distance to " O  BHOH Z  74 " =    1.233
peak=    8.655 closest distance to " O   HOH Z 203 " =    1.244
peak=    7.550 closest distance to " O   HOH Z 255 " =    1.425
peak=    7.464 closest distance to " O   HOH Z 178 " =    1.274
peak=    7.010 closest distance to " O   HOH Z 117 " =    1.856
peak=    6.761 closest distance to " O   GLN A  11 " =    1.113
peak=    5.840 closest distance to " O   HOH Z 248 " =    1.672
peak=    5.518 closest distance to " O   HOH Z 124 " =    1.245
peak=    5.418 closest distance to " O   HOH Z 210 " =    1.430
peak=    5.400 closest distance to " O   HOH Z  54 " =    1.737
peak=    5.321 closest distance to " O   HOH Z 404 " =    1.380
peak=    5.119 closest distance to " O   HOH Z  49 " =    1.650
peak=    5.111 closest distance to " O   HOH Z  65 " =    1.160
peak=    4.975 closest distance to " CD2 TRP A 179 " =    1.339
peak=    4.950 closest distance to " O   HOH Z  67 " =    1.248
peak=    4.887 closest distance to " O   HOH Z  69 " =    1.675
peak=    4.861 closest distance to " CA  TYR A  30 " =    0.960
peak=    4.772 closest distance to " O   HOH Z 403 " =    2.177
peak=    4.741 closest distance to " CZ3 TRP A 266 " =    1.085
peak=    4.718 closest distance to " O   HOH Z 394 " =    1.787
peak=    4.568 closest distance to " O   HOH Z 272 " =    1.551
peak=    4.495 closest distance to " O   HOH Z 132 " =    2.731
peak=    4.481 closest distance to " CG  PRO A 280 " =    0.847
peak=    4.480 closest distance to " O   HOH Z 113 " =    1.864
peak=    4.437 closest distance to " CG  PRO A  54 " =    1.339
peak=    4.427 closest distance to " CB  ARG A 275 " =    0.861
peak=    4.410 closest distance to " OE1 GLN A  55 " =    1.568
peak=    4.387 closest distance to " O  BHOH Z 338 " =    1.190
peak=    4.383 closest distance to " O   HOH Z 433 " =    1.864
peak=    4.370 closest distance to " O   HOH Z 412 " =    3.485
peak=    4.366 closest distance to " O   HOH Z 102 " =    1.538
peak=    4.360 closest distance to " O   HOH Z  43 " =    2.326
peak=    4.351 closest distance to " O   HOH Z 425 " =    1.548
peak=    4.333 closest distance to " O   HOH Z 277 " =    1.405
peak=    4.282 closest distance to " O   HOH Z 186 " =    2.192
peak=    4.262 closest distance to " O   HOH Z 144 " =    1.899
peak=    4.255 closest distance to " O   HOH Z 116 " =    1.485
peak=    4.249 closest distance to " O   HOH Z 130 " =    2.387
peak=    4.249 closest distance to " CG2BVAL A  41 " =    0.839
peak=    4.240 closest distance to " CA  ARG A  36 " =    1.068
peak=    4.235 closest distance to " CB  GLN A 223 " =    1.416
peak=    4.214 closest distance to " O   HOH Z 128 " =    1.580
peak=    4.214 closest distance to " O   HOH Z 261 " =    2.438
peak=    4.197 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.178 closest distance to " CG  PRO A  90 " =    1.341
peak=    4.166 closest distance to " O   HOH Z 431 " =    1.280
peak=    4.163 closest distance to " CD  ARG A  36 " =    1.082
peak=    4.158 closest distance to " CG  GLN A  11 " =    1.185
peak=    4.154 closest distance to " O   HOH Z 189 " =    2.913
peak=    4.140 closest distance to " CB  SER A  63 " =    1.249
peak=    4.136 closest distance to " O   HOH Z 134 " =    2.020
peak=    4.130 closest distance to " O   HOH Z  40 " =    2.056
peak=    4.127 closest distance to " O   HOH Z 406 " =    1.798
peak=    4.121 closest distance to " O   HOH Z 176 " =    1.702
peak=    4.103 closest distance to " NH2 ARG A 156 " =    1.131
peak=    4.095 closest distance to " CG2 VAL A 197 " =    1.221
peak=    4.084 closest distance to " O   HOH Z 193 " =    1.411
peak=    4.082 closest distance to " O   HOH Z  63 " =    1.994
peak=    4.054 closest distance to " O   HOH Z 234 " =    3.533
peak=    4.044 closest distance to " O   HOH Z  80 " =    2.207
peak=    4.011 closest distance to " CZ  PHE A 218 " =    1.210
peak=    4.009 closest distance to " O   HOH Z 340 " =    1.443
peak=    3.991 closest distance to " O   HOH Z  97 " =    1.307
peak=    3.990 closest distance to " O   HOH Z 414 " =    1.639
peak=    3.974 closest distance to " O   HOH Z  39 " =    1.385
peak=    3.966 closest distance to " O   HOH Z 298 " =    2.001
peak=    3.944 closest distance to " CA  ALA A 100 " =    1.122
peak=    3.933 closest distance to " CB  SER A  62 " =    1.003
peak=    3.918 closest distance to " O   ALA A 165 " =    1.351
peak=    3.914 closest distance to " CG2AVAL A 121 " =    2.071
peak=    3.910 closest distance to " CB  ASN A  39 " =    0.765
peak=    3.910 closest distance to " O   HOH Z 362 " =    3.331
peak=    3.910 closest distance to " CB  TRP A 179 " =    1.283
peak=    3.905 closest distance to " O   HOH Z 264 " =    1.181
peak=    3.900 closest distance to " O   HOH Z 214 " =    1.380
peak=    3.892 closest distance to " CG  GLN A  58 " =    1.078
peak=    3.887 closest distance to " O   HOH Z 126 " =    1.593
peak=    3.882 closest distance to " CG2BVAL A 121 " =    0.798
peak=    3.873 closest distance to " O   HOH Z 299 " =    3.946
peak=    3.863 closest distance to " O   HOH Z 184 " =    1.558
peak=    3.853 closest distance to " CB  SER A  26 " =    1.801
peak=    3.851 closest distance to " ND2 ASN A 249 " =    2.167
peak=    3.848 closest distance to " NZ  LYS A 117 " =    3.010
peak=    3.843 closest distance to " O   HOH Z 417 " =    1.410
peak=    3.840 closest distance to " O   HOH Z   9 " =    1.297
peak=    3.829 closest distance to " CG AARG A 275 " =    1.114
peak=    3.827 closest distance to " O   HOH Z 147 " =    1.397
peak=    3.827 closest distance to " CD  ARG A 159 " =    0.810
peak=    3.816 closest distance to " N   SER A 164 " =    1.002
peak=    3.816 closest distance to " O   HOH Z 213 " =    1.807
peak=    3.802 closest distance to " CB  ASN A 285 " =    0.922
peak=    3.786 closest distance to " CB  ASN A 148 " =    1.441
peak=    3.785 closest distance to " CA  THR A 246 " =    1.049
peak=    3.775 closest distance to " O   HOH Z 146 " =    1.300
peak=    3.766 closest distance to " CB  THR A  52 " =    0.871
peak=    3.754 closest distance to " NE2 GLN A  11 " =    1.179
peak=    3.742 closest distance to " O   HOH Z 369 " =    2.058
peak=    3.736 closest distance to " CA  GLU A 152 " =    0.928
peak=    3.735 closest distance to " O   PRO A 198 " =    1.544
peak=    3.727 closest distance to " CZ  PHE A  38 " =    1.075
peak=    3.717 closest distance to " O   HOH Z 437 " =    2.158
peak=    3.715 closest distance to " CA  ARG A 195 " =    1.164
peak=    3.713 closest distance to " CB  GLU A 128 " =    1.094
peak=    3.710 closest distance to " N   ALA A   1 " =    2.270
peak=    3.709 closest distance to " O   SER A  87 " =    2.172
peak=    3.706 closest distance to " O   HOH Z  78 " =    1.718
peak=    3.698 closest distance to " O   HOH Z 346 " =    1.524
peak=    3.695 closest distance to " O   HOH Z 193 " =    1.538
peak=    3.691 closest distance to " CD  ARG A 195 " =    1.159
peak=    3.690 closest distance to " O   HOH Z 278 " =    0.951
peak=    3.687 closest distance to " CB  SER A 141 " =    1.189
peak=    3.672 closest distance to " O   HOH Z  35 " =    1.948
peak=    3.672 closest distance to " OD1 ASN A 301 " =    1.131
peak=    3.665 closest distance to " O   HOH Z 402 " =    1.605
peak=    3.654 closest distance to " O   HOH Z 251 " =    1.648
peak=    3.643 closest distance to " CB  ARG A 190 " =    1.872
peak=    3.642 closest distance to " CA  VAL A 112 " =    1.167
peak=    3.638 closest distance to " O   HOH Z 297 " =    1.164
peak=    3.637 closest distance to " CB  MET A 105 " =    0.975
peak=    3.630 closest distance to " CD  PRO A  54 " =    1.106
peak=    3.619 closest distance to " CD  LYS A 166 " =    1.583
peak=    3.617 closest distance to " O   HOH Z  76 " =    1.063
peak=    3.611 closest distance to " O   HOH Z 331 " =    1.354
peak=    3.610 closest distance to " O   HOH Z 209 " =    2.132
peak=    3.607 closest distance to " CG1 ILE A  33 " =    1.301
peak=    3.594 closest distance to " CB  PRO A  54 " =    1.009
peak=    3.593 closest distance to " O   ASN A  74 " =    1.856
peak=    3.593 closest distance to " O   HOH Z 247 " =    1.458
peak=    3.591 closest distance to " O   HOH Z 401 " =    1.074
peak=    3.590 closest distance to " O   HOH Z  63 " =    2.069
peak=    3.583 closest distance to " CB  GLU A 152 " =    1.041
peak=    3.583 closest distance to " OE1 GLU A   2 " =    1.296
peak=    3.580 closest distance to " CE1 TYR A 186 " =    1.216
peak=    3.566 closest distance to " O   HOH Z 298 " =    4.524
peak=    3.564 closest distance to " CB  ASP A 191 " =    1.242
peak=    3.563 closest distance to " O   HOH Z  85 " =    1.388
peak=    3.562 closest distance to " O   HOH Z 358 " =    1.315
peak=    3.557 closest distance to " O   HOH Z 427 " =    3.165
peak=    3.556 closest distance to " O   HOH Z  26 " =    1.076
peak=    3.552 closest distance to " CD  LYS A 119 " =    1.713
peak=    3.548 closest distance to " CA  THR A  82 " =    1.698
peak=    3.539 closest distance to " CG2 THR A 220 " =    0.950
peak=    3.537 closest distance to " CB  GLN A 194 " =    0.935
peak=    3.534 closest distance to " O   HOH Z 209 " =    2.512
peak=    3.531 closest distance to " CA  SER A  12 " =    1.411
peak=    3.531 closest distance to " O   HOH Z 196 " =    1.414
peak=    3.527 closest distance to " O   HOH Z  88 " =    3.557
peak=    3.517 closest distance to " O   HOH Z  68 " =    1.866
peak=    3.504 closest distance to " O   HOH Z 195 " =    1.154
peak=    3.504 closest distance to " CB  PHE A 204 " =    0.834
peak=    3.497 closest distance to " N   THR A  52 " =    1.125
peak=    3.492 closest distance to " O   THR A 220 " =    1.119
peak=    3.491 closest distance to " O   GLY A  91 " =    1.179
peak=    3.489 closest distance to " CZ3 TRP A  85 " =    1.111
peak=    3.470 closest distance to " O   HOH Z 345 " =    1.693
peak=    3.465 closest distance to " O   HOH Z 141 " =    1.859
peak=    3.465 closest distance to " NE2 GLN A  58 " =    3.172
peak=    3.454 closest distance to " CG  PRO A 243 " =    1.103
peak=    3.448 closest distance to " O   HOH Z 423 " =    2.210
peak=    3.444 closest distance to " CB  ARG A  79 " =    0.867
peak=    3.443 closest distance to " O   HOH Z 154 " =    2.301
peak=    3.442 closest distance to " CE  LYS A  76 " =    0.854
peak=    3.440 closest distance to " O   HOH Z 130 " =    1.169
peak=    3.431 closest distance to " OG  SER A 245 " =    1.419
peak=    3.425 closest distance to " O   HOH Z 287 " =    1.510
peak=    3.423 closest distance to " CB  PHE A  16 " =    1.242
peak=    3.419 closest distance to " O   HOH Z 422 " =    3.000
peak=    3.411 closest distance to " N   HIS A 108 " =    1.730
peak=    3.410 closest distance to " O   HOH Z 365 " =    2.439
peak=    3.408 closest distance to " CD1 ILE A 199 " =    1.378
peak=    3.399 closest distance to " CB  MET A  40 " =    1.064
peak=    3.398 closest distance to " CA  ALA A 160 " =    0.921
peak=    3.397 closest distance to " O   HOH Z 423 " =    1.893
peak=    3.388 closest distance to " O   HOH Z 132 " =    2.242
peak=    3.388 closest distance to " CB  ALA A 114 " =    0.747
peak=    3.387 closest distance to " CG  LYS A  76 " =    1.146
peak=    3.382 closest distance to " O   HOH Z 369 " =    1.493
peak=    3.381 closest distance to " CG  ARG A 138 " =    1.366
peak=    3.377 closest distance to " O   HOH Z 111 " =    1.521
peak=    3.377 closest distance to " CD1 LEU A  96 " =    0.844
peak=    3.372 closest distance to " O   HOH Z 435 " =    1.901
peak=    3.369 closest distance to " CA  ALA A  51 " =    1.033
peak=    3.367 closest distance to " O   HOH Z 250 " =    2.611
peak=    3.366 closest distance to " ND2 ASN A 187 " =    1.488
peak=    3.364 closest distance to " O   HOH Z 272 " =    2.040
peak=    3.360 closest distance to " CB  LEU A   5 " =    1.168
peak=    3.353 closest distance to " O   HOH Z 279 " =    2.116
peak=    3.352 closest distance to " CB  LEU A  83 " =    0.793
peak=    3.347 closest distance to " O   THR A 251 " =    1.317
peak=    3.346 closest distance to " N   GLY A 111 " =    1.261
peak=    3.344 closest distance to " OG BSER A 164 " =    2.139
peak=    3.342 closest distance to " O   HOH Z 214 " =    2.365
peak=    3.341 closest distance to " CB  TRP A 179 " =    1.780
peak=    3.336 closest distance to " O   HOH Z 336 " =    1.927
peak=    3.333 closest distance to " O   HOH Z  85 " =    2.109
peak=    3.331 closest distance to " CA  GLY A 196 " =    0.980
peak=    3.331 closest distance to " ND2 ASN A 249 " =    0.932
peak=    3.330 closest distance to " CA  ALA A 158 " =    1.528
peak=    3.330 closest distance to " CA  ASP A 149 " =    1.217
peak=    3.328 closest distance to " CB  VAL A 265 " =    1.113
peak=    3.328 closest distance to " OD1 ASN A 217 " =    1.492
peak=    3.327 closest distance to " CD2 TYR A  68 " =    0.746
peak=    3.322 closest distance to " O   HOH Z 163 " =    1.505
peak=    3.322 closest distance to " OG BSER A 258 " =    2.742
peak=    3.321 closest distance to " CG  MET A 188 " =    0.931
peak=    3.317 closest distance to " O   HOH Z  59 " =    1.739
peak=    3.316 closest distance to " O   HOH Z 250 " =    1.442
peak=    3.313 closest distance to " CA  TYR A 116 " =    1.433
peak=    3.309 closest distance to " CB  GLU A 277 " =    3.816
peak=    3.309 closest distance to " CA  ASN A 217 " =    1.309
peak=    3.307 closest distance to " CB  TYR A 116 " =    1.151
peak=    3.295 closest distance to " O   HOH Z 126 " =    2.245
peak=    3.292 closest distance to " O   HOH Z 258 " =    1.547
peak=    3.290 closest distance to " O   HOH Z 284 " =    2.894
peak=    3.288 closest distance to " CB  SER A  32 " =    1.238
peak=    3.283 closest distance to " O   HOH Z  48 " =    1.639
peak=    3.279 closest distance to " O   HOH Z 139 " =    4.737
peak=    3.277 closest distance to " O   HOH Z 394 " =    3.692
peak=    3.277 closest distance to " NH2AARG A 275 " =    2.489
peak=    3.275 closest distance to " CB  ALA A 248 " =    1.436
peak=    3.275 closest distance to " CA  ARG A 139 " =    1.520
peak=    3.272 closest distance to " CD  ARG A 269 " =    0.961
peak=    3.271 closest distance to " CG1 ILE A  20 " =    1.334
peak=    3.266 closest distance to " O   HOH Z 240 " =    2.622
peak=    3.260 closest distance to " O   HOH Z 350 " =    2.005
peak=    3.259 closest distance to " O   HOH Z 185 " =    1.720
peak=    3.257 closest distance to " O   HOH Z 366 " =    2.363
peak=    3.256 closest distance to " O   ASP A 200 " =    1.522
peak=    3.255 closest distance to " O   HOH Z 299 " =    4.486
peak=    3.251 closest distance to " CB  ASP A 140 " =    0.983
peak=    3.245 closest distance to " CD1 LEU A 167 " =    1.027
peak=    3.243 closest distance to " O   THR A 182 " =    1.598
peak=    3.243 closest distance to " CA  ASP A 140 " =    1.588
peak=    3.241 closest distance to " CG  GLN A  77 " =    0.793
peak=    3.240 closest distance to " CG  PRO A 198 " =    1.284
peak=    3.237 closest distance to " O   HOH Z 139 " =    1.295
peak=    3.236 closest distance to " O   HOH Z 282 " =    2.243
peak=    3.232 closest distance to " CA  ASP A 162 " =    1.174
peak=    3.230 closest distance to " O   HOH Z 301 " =    1.395
peak=    3.225 closest distance to " O   HOH Z 238 " =    3.670
peak=    3.222 closest distance to " CA  ALA A 299 " =    1.176
peak=    3.220 closest distance to " CA  ALA A   9 " =    1.089
peak=    3.218 closest distance to " O   HOH Z 313 " =    1.820
peak=    3.217 closest distance to " OE1 GLN A 223 " =    3.289
peak=    3.215 closest distance to " O   HOH Z 154 " =    1.467
peak=    3.215 closest distance to " O   HOH Z  18 " =    1.774
peak=    3.214 closest distance to " CA  GLN A  73 " =    1.421
peak=    3.213 closest distance to " CB  GLU A  46 " =    1.159
peak=    3.213 closest distance to " O   HOH Z 316 " =    2.965
peak=    3.206 closest distance to " O   HOH Z 359 " =    1.589
peak=    3.204 closest distance to " CB  ASN A 187 " =    1.340
peak=    3.199 closest distance to " CD2 LEU A 297 " =    1.170
peak=    3.198 closest distance to " CB  PRO A 243 " =    1.329
peak=    3.196 closest distance to " O   HOH Z 343 " =    2.618
peak=    3.195 closest distance to " ND2 ASN A 301 " =    1.553
peak=    3.191 closest distance to " NZ  LYS A 117 " =    0.795
peak=    3.190 closest distance to " OG  SER A  62 " =    2.757
peak=    3.189 closest distance to " O   HOH Z 357 " =    2.206
peak=    3.185 closest distance to " CB  GLN A  58 " =    1.074
peak=    3.183 closest distance to " CA  SER A  32 " =    1.611
peak=    3.183 closest distance to " O   HOH Z 407 " =    1.732
peak=    3.180 closest distance to " N   ALA A   1 " =    1.117
peak=    3.178 closest distance to " OG BSER A  99 " =    2.882
peak=    3.178 closest distance to " CB  ASP A 124 " =    0.917
peak=    3.177 closest distance to " NH2BARG A 145 " =    2.090
peak=    3.176 closest distance to " O   HOH Z 371 " =    2.327
peak=    3.174 closest distance to " OE1 GLN A  73 " =    1.253
peak=    3.173 closest distance to " O   HOH Z 313 " =    1.979
peak=    3.171 closest distance to " CB  ASN A 142 " =    1.066
peak=    3.171 closest distance to " CD  ARG A  79 " =    2.501
peak=    3.170 closest distance to " NH2 ARG A  36 " =    1.148
peak=    3.169 closest distance to " CA  ASP A 191 " =    0.997
peak=    3.168 closest distance to " CA  ARG A 156 " =    1.007
peak=    3.167 closest distance to " OE1 GLN A 223 " =    2.301
peak=    3.164 closest distance to " O   HOH Z 368 " =    2.113
peak=    3.162 closest distance to " CA  ALA A 129 " =    1.145
peak=    3.161 closest distance to " CA  SER A  87 " =    1.110
peak=    3.159 closest distance to " CB  SER A 245 " =    1.586
peak=    3.158 closest distance to " O   HOH Z 120 " =    2.573
peak=    3.158 closest distance to " CG2 THR A  29 " =    1.299
peak=    3.157 closest distance to " CB  SER A 273 " =    0.857
peak=    3.155 closest distance to " O   HOH Z 316 " =    3.196
peak=    3.155 closest distance to " CA  THR A 221 " =    1.082
peak=    3.155 closest distance to " O   TYR A 116 " =    1.443
peak=    3.154 closest distance to " O   HOH Z  15 " =    2.154
peak=    3.151 closest distance to " CA  ALA A 154 " =    1.121
peak=    3.150 closest distance to " NH1AARG A 145 " =    1.467
peak=    3.149 closest distance to " O   HOH Z 142 " =    1.645
peak=    3.146 closest distance to " O   HOH Z 189 " =    2.353
peak=    3.137 closest distance to " O   HOH Z  27 " =    1.074
peak=    3.136 closest distance to " O   HOH Z 207 " =    1.368
peak=    3.133 closest distance to " CB  GLU A  37 " =    0.853
peak=    3.127 closest distance to " O   HOH Z 236 " =    1.605
peak=    3.126 closest distance to " NH1 ARG A  36 " =    1.234
peak=    3.116 closest distance to " O   HOH Z 200 " =    3.271
peak=    3.115 closest distance to " CE1 HIS A  81 " =    1.621
peak=    3.114 closest distance to " CG  MET A 185 " =    1.194
peak=    3.104 closest distance to " O   HOH Z 303 " =    2.416
peak=    3.104 closest distance to " O   HOH Z  47 " =    2.340
peak=    3.100 closest distance to " CA  CYS A 260 " =    1.451
peak=    3.097 closest distance to " O   HOH Z 258 " =    2.019
peak=    3.096 closest distance to " CG2 ILE A 120 " =    1.271
peak=    3.094 closest distance to " O   HOH Z 435 " =    2.866
peak=    3.090 closest distance to " NH2AARG A 145 " =    1.101
peak=    3.088 closest distance to " O   GLU A   2 " =    1.545
peak=    3.082 closest distance to " O   HOH Z 199 " =    1.449
peak=    3.079 closest distance to " CA  LEU A  83 " =    1.363
peak=    3.075 closest distance to " O  BHOH Z 338 " =    1.975
peak=    3.073 closest distance to " O   HOH Z 128 " =    2.339
peak=    3.073 closest distance to " CB  ARG A 156 " =    0.998
peak=    3.060 closest distance to " O   HOH Z 163 " =    2.076
peak=    3.053 closest distance to " NE2 GLN A  58 " =    4.933
peak=    3.046 closest distance to " O   HOH Z  83 " =    1.629

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.702 - 5.937
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 213
   mapped sites are within: 0.702 - 5.937

peak=   -4.663 closest distance to " O   GLN A  11 " =    1.042
peak=   -4.503 closest distance to " CG  GLN A  11 " =    1.197
peak=   -4.448 closest distance to " O  BHOH Z  74 " =    0.842
peak=   -4.437 closest distance to " CD2 TYR A  30 " =    2.734
peak=   -4.386 closest distance to " O   HOH Z 150 " =    1.661
peak=   -4.334 closest distance to " O   PRO A 198 " =    1.328
peak=   -4.322 closest distance to " O   HOH Z 422 " =    1.096
peak=   -4.308 closest distance to " O   HOH Z   7 " =    1.044
peak=   -4.304 closest distance to " O   VAL A  67 " =    2.855
peak=   -4.299 closest distance to " CD  GLN A 223 " =    1.619
peak=   -4.218 closest distance to " O   HOH Z 166 " =    1.590
peak=   -4.216 closest distance to " O   HOH Z 155 " =    1.774
peak=   -4.205 closest distance to " CG  PRO A 243 " =    1.677
peak=   -4.171 closest distance to " CD2 LEU A 237 " =    2.382
peak=   -4.165 closest distance to " CG2 ILE A  20 " =    2.995
peak=   -4.122 closest distance to " CD  ARG A  14 " =    3.354
peak=   -4.112 closest distance to " CG  GLN A  58 " =    0.945
peak=   -4.059 closest distance to " CD1 PHE A  59 " =    2.013
peak=   -4.057 closest distance to " O   HOH Z  67 " =    1.210
peak=   -4.039 closest distance to " NE  ARG A 156 " =    2.005
peak=   -4.019 closest distance to " O   HOH Z 411 " =    5.552
peak=   -4.009 closest distance to " CG2 VAL A 189 " =    2.155
peak=   -3.988 closest distance to " CG  GLN A  58 " =    1.361
peak=   -3.986 closest distance to " CG  GLU A  53 " =    1.428
peak=   -3.950 closest distance to " NE2 GLN A 223 " =    1.194
peak=   -3.948 closest distance to " CD  ARG A  36 " =    1.013
peak=   -3.946 closest distance to " O   HOH Z 165 " =    1.787
peak=   -3.904 closest distance to " CZ2 TRP A  92 " =    2.840
peak=   -3.883 closest distance to " O   HOH Z  56 " =    1.013
peak=   -3.852 closest distance to " CD2 PHE A  61 " =    2.029
peak=   -3.811 closest distance to " CD2 TYR A 293 " =    1.828
peak=   -3.794 closest distance to " O   HOH Z 150 " =    1.565
peak=   -3.793 closest distance to " O   HOH Z 203 " =    1.518
peak=   -3.779 closest distance to " O   VAL A 174 " =    2.161
peak=   -3.768 closest distance to " CD1 LEU A 101 " =    2.473
peak=   -3.754 closest distance to " O   HOH Z 377 " =    2.146
peak=   -3.746 closest distance to " CD1 ILE A 109 " =    2.733
peak=   -3.746 closest distance to " CE2 PHE A  61 " =    2.763
peak=   -3.731 closest distance to " ND2BASN A 224 " =    2.000
peak=   -3.727 closest distance to " O   PHE A 218 " =    1.433
peak=   -3.725 closest distance to " CB  ALA A  43 " =    2.653
peak=   -3.718 closest distance to " O   HOH Z 166 " =    1.761
peak=   -3.707 closest distance to " O   HOH Z 278 " =    1.073
peak=   -3.705 closest distance to " C   HIS A 108 " =    1.083
peak=   -3.696 closest distance to " O   HOH Z 366 " =    1.476
peak=   -3.695 closest distance to " CA  GLY A 133 " =    1.941
peak=   -3.673 closest distance to " CE3 TRP A 150 " =    2.396
peak=   -3.656 closest distance to " O   HOH Z 374 " =    2.020
peak=   -3.650 closest distance to " O   HOH Z 124 " =    1.480
peak=   -3.643 closest distance to " CD1 TRP A 179 " =    1.183
peak=   -3.636 closest distance to " C   ASN A 285 " =    2.258
peak=   -3.630 closest distance to " O   HOH Z 120 " =    1.077
peak=   -3.617 closest distance to " OG BSER A 134 " =    1.416
peak=   -3.602 closest distance to " O   HOH Z 109 " =    3.642
peak=   -3.599 closest distance to " C   THR A 279 " =    1.176
peak=   -3.597 closest distance to " O   HOH Z 221 " =    1.082
peak=   -3.593 closest distance to " CG  GLN A 103 " =    2.355
peak=   -3.584 closest distance to " O   HOH Z 191 " =    5.937
peak=   -3.571 closest distance to " O   HOH Z 407 " =    1.398
peak=   -3.566 closest distance to " O   HOH Z 340 " =    1.490
peak=   -3.553 closest distance to " CA  ASP A 298 " =    1.178
peak=   -3.543 closest distance to " CH2 TRP A 150 " =    1.118
peak=   -3.541 closest distance to " NE2 GLN A  94 " =    1.862
peak=   -3.535 closest distance to " OD1 ASP A 171 " =    1.548
peak=   -3.529 closest distance to " O   HOH Z 274 " =    1.120
peak=   -3.521 closest distance to " N   ALA A  43 " =    2.682
peak=   -3.520 closest distance to " CG2BVAL A  41 " =    1.972
peak=   -3.514 closest distance to " O   HOH Z   6 " =    1.635
peak=   -3.510 closest distance to " O   HOH Z 203 " =    0.702
peak=   -3.510 closest distance to " O   HOH Z 171 " =    2.552
peak=   -3.507 closest distance to " O   HOH Z 138 " =    0.871
peak=   -3.499 closest distance to " CD  GLN A  73 " =    0.716
peak=   -3.498 closest distance to " OE2 GLU A 152 " =    1.418
peak=   -3.497 closest distance to " O   HOH Z 250 " =    1.751
peak=   -3.495 closest distance to " O   HOH Z 134 " =    2.689
peak=   -3.482 closest distance to " CB  SER A 141 " =    2.129
peak=   -3.473 closest distance to " O   HOH Z  60 " =    1.531
peak=   -3.472 closest distance to " O   HOH Z 205 " =    0.774
peak=   -3.470 closest distance to " CG  ARG A 259 " =    2.413
peak=   -3.469 closest distance to " CA  GLY A 241 " =    2.340
peak=   -3.468 closest distance to " O   HOH Z 156 " =    3.571
peak=   -3.463 closest distance to " OD2 ASP A 298 " =    0.979
peak=   -3.461 closest distance to " CA  SER A 276 " =    1.588
peak=   -3.461 closest distance to " CB  ASN A  45 " =    2.058
peak=   -3.459 closest distance to " O   HOH Z 197 " =    1.690
peak=   -3.457 closest distance to " O   HOH Z 196 " =    1.649
peak=   -3.456 closest distance to " O   HOH Z 330 " =    1.070
peak=   -3.455 closest distance to " SG ACYS A 201 " =    1.159
peak=   -3.453 closest distance to " CA  GLY A 203 " =    2.362
peak=   -3.451 closest distance to " CG  MET A 105 " =    0.964
peak=   -3.449 closest distance to " O   HOH Z 397 " =    1.067
peak=   -3.449 closest distance to " CZ  ARG A 156 " =    1.605
peak=   -3.442 closest distance to " O   SER A 271 " =    1.655
peak=   -3.442 closest distance to " CZ  TYR A 169 " =    2.015
peak=   -3.430 closest distance to " O   PRO A  54 " =    1.866
peak=   -3.427 closest distance to " O   PRO A 163 " =    2.178
peak=   -3.414 closest distance to " O   HOH Z 423 " =    4.147
peak=   -3.397 closest distance to " OD2 ASP A 171 " =    1.775
peak=   -3.381 closest distance to " CG1 VAL A 112 " =    2.535
peak=   -3.379 closest distance to " NE2 GLN A 278 " =    1.888
peak=   -3.378 closest distance to " O   HOH Z 109 " =    2.594
peak=   -3.377 closest distance to " CG1 VAL A 189 " =    2.425
peak=   -3.373 closest distance to " O   HOH Z  54 " =    1.829
peak=   -3.369 closest distance to " CD  LYS A 289 " =    2.390
peak=   -3.366 closest distance to " O   HOH Z 345 " =    2.814
peak=   -3.363 closest distance to " O   HOH Z 234 " =    4.115
peak=   -3.355 closest distance to " O   HOH Z 418 " =    1.250
peak=   -3.348 closest distance to " CE1 HIS A  81 " =    1.481
peak=   -3.348 closest distance to " CD2 HIS A 115 " =    0.933
peak=   -3.347 closest distance to " CA  PRO A 280 " =    0.994
peak=   -3.342 closest distance to " CG1AVAL A 121 " =    1.402
peak=   -3.342 closest distance to " OG  SER A  97 " =    2.185
peak=   -3.342 closest distance to " CB  ALA A 291 " =    2.480
peak=   -3.338 closest distance to " O   ASN A 110 " =    2.412
peak=   -3.335 closest distance to " CD1 ILE A 106 " =    2.191
peak=   -3.335 closest distance to " CA  GLY A 241 " =    3.321
peak=   -3.334 closest distance to " O   HOH Z 148 " =    3.716
peak=   -3.331 closest distance to " O   SER A 146 " =    1.122
peak=   -3.324 closest distance to " CB  PRO A 243 " =    2.772
peak=   -3.323 closest distance to " C   SER A 288 " =    1.127
peak=   -3.321 closest distance to " O   HOH Z 111 " =    4.095
peak=   -3.318 closest distance to " CB  ALA A 161 " =    2.570
peak=   -3.311 closest distance to " O   HOH Z 438 " =    2.992
peak=   -3.308 closest distance to " CA  ASN A 127 " =    1.096
peak=   -3.306 closest distance to " O   HOH Z 331 " =    1.103
peak=   -3.302 closest distance to " CZ  TYR A 172 " =    1.889
peak=   -3.300 closest distance to " O   SER A 273 " =    1.043
peak=   -3.296 closest distance to " N   SER A 134 " =    1.206
peak=   -3.287 closest distance to " O   HOH Z  35 " =    2.231
peak=   -3.285 closest distance to " CA  GLY A  57 " =    2.198
peak=   -3.279 closest distance to " ND2 ASN A  60 " =    2.188
peak=   -3.279 closest distance to " CG  LEU A 281 " =    2.024
peak=   -3.275 closest distance to " NZ  LYS A 117 " =    1.645
peak=   -3.270 closest distance to " CZ  PHE A  38 " =    2.219
peak=   -3.264 closest distance to " O   HOH Z  52 " =    1.918
peak=   -3.260 closest distance to " O   ARG A  79 " =    0.965
peak=   -3.257 closest distance to " O   HOH Z 388 " =    2.142
peak=   -3.256 closest distance to " CA  TRP A 150 " =    1.152
peak=   -3.254 closest distance to " CD  GLN A  88 " =    0.942
peak=   -3.244 closest distance to " O   HOH Z 102 " =    1.665
peak=   -3.231 closest distance to " CB  ALA A 131 " =    2.433
peak=   -3.230 closest distance to " O   HOH Z 392 " =    1.246
peak=   -3.225 closest distance to " O   HOH Z 438 " =    1.909
peak=   -3.221 closest distance to " CB  ALA A 248 " =    2.195
peak=   -3.216 closest distance to " SD  MET A 188 " =    1.333
peak=   -3.216 closest distance to " O   SER A 210 " =    1.674
peak=   -3.215 closest distance to " CD  ARG A  79 " =    1.262
peak=   -3.215 closest distance to " CB  ALA A  10 " =    2.199
peak=   -3.210 closest distance to " CG2 THR A  18 " =    2.790
peak=   -3.208 closest distance to " OD1 ASN A 110 " =    1.106
peak=   -3.205 closest distance to " O   HOH Z 152 " =    0.873
peak=   -3.205 closest distance to " CD1 LEU A  96 " =    2.295
peak=   -3.204 closest distance to " OD1 ASN A 301 " =    1.859
peak=   -3.202 closest distance to " O   HOH Z 195 " =    3.331
peak=   -3.202 closest distance to " OG  SER A   3 " =    1.850
peak=   -3.197 closest distance to " CA  VAL A 197 " =    1.024
peak=   -3.196 closest distance to " O   HOH Z 150 " =    0.867
peak=   -3.194 closest distance to " CB  TRP A  85 " =    2.598
peak=   -3.189 closest distance to " O   HOH Z 428 " =    1.607
peak=   -3.187 closest distance to " O   HOH Z 179 " =    2.114
peak=   -3.183 closest distance to " O   HOH Z  49 " =    0.718
peak=   -3.180 closest distance to " O   HOH Z 198 " =    1.445
peak=   -3.177 closest distance to " CG1AVAL A  41 " =    2.547
peak=   -3.176 closest distance to " NH2 ARG A  36 " =    1.162
peak=   -3.173 closest distance to " O   HOH Z  44 " =    1.798
peak=   -3.172 closest distance to " CD2 LEU A 237 " =    2.677
peak=   -3.172 closest distance to " CD  GLU A 128 " =    1.995
peak=   -3.170 closest distance to " O   HOH Z  64 " =    2.884
peak=   -3.167 closest distance to " CD1 ILE A 239 " =    2.475
peak=   -3.166 closest distance to " O   HOH Z 149 " =    1.763
peak=   -3.163 closest distance to " O   HOH Z 320 " =    1.478
peak=   -3.162 closest distance to " O   TYR A 186 " =    1.796
peak=   -3.159 closest distance to " NH2 ARG A  66 " =    2.139
peak=   -3.151 closest distance to " O   HOH Z 281 " =    2.348
peak=   -3.149 closest distance to " O   HOH Z 283 " =    1.956
peak=   -3.149 closest distance to " CG  LEU A  83 " =    2.025
peak=   -3.147 closest distance to " O   HOH Z 313 " =    1.376
peak=   -3.145 closest distance to " O   HOH Z 326 " =    5.135
peak=   -3.143 closest distance to " O   VAL A 257 " =    1.437
peak=   -3.142 closest distance to " CA  ASP A  65 " =    1.231
peak=   -3.140 closest distance to " O   HOH Z 434 " =    2.125
peak=   -3.139 closest distance to " N   LEU A 237 " =    2.044
peak=   -3.137 closest distance to " CG1 VAL A 265 " =    2.843
peak=   -3.136 closest distance to " CB  GLN A  58 " =    5.620
peak=   -3.134 closest distance to " O   HOH Z 178 " =    1.560
peak=   -3.132 closest distance to " CE  MET A 105 " =    2.028
peak=   -3.132 closest distance to " O   HOH Z  40 " =    2.449
peak=   -3.129 closest distance to " C   VAL A 265 " =    0.956
peak=   -3.125 closest distance to " O   HOH Z  38 " =    1.427
peak=   -3.123 closest distance to " ND2 ASN A  45 " =    1.884
peak=   -3.122 closest distance to " OD2 ASP A 270 " =    0.999
peak=   -3.120 closest distance to " O   HOH Z 198 " =    2.309
peak=   -3.119 closest distance to " O   HOH Z  41 " =    1.869
peak=   -3.117 closest distance to " O   HOH Z 336 " =    5.072
peak=   -3.114 closest distance to " O   HOH Z 145 " =    2.984
peak=   -3.112 closest distance to " CD1 LEU A   5 " =    2.288
peak=   -3.109 closest distance to " ND2 ASN A  60 " =    1.595
peak=   -3.109 closest distance to " O   HOH Z 136 " =    1.218
peak=   -3.108 closest distance to " O   HOH Z 108 " =    2.235
peak=   -3.106 closest distance to " O   HOH Z   2 " =    2.073
peak=   -3.099 closest distance to " O   HOH Z  10 " =    1.734
peak=   -3.098 closest distance to " O   ASP A 191 " =    2.044
peak=   -3.098 closest distance to " N   ALA A 226 " =    1.932
peak=   -3.094 closest distance to " CD1 ILE A 263 " =    1.963
peak=   -3.093 closest distance to " O   SER A   3 " =    0.946
peak=   -3.089 closest distance to " O   HOH Z 216 " =    1.613
peak=   -3.089 closest distance to " NE2 GLN A  88 " =    1.017
peak=   -3.081 closest distance to " CG  ASP A 162 " =    1.718
peak=   -3.079 closest distance to " CZ3 TRP A  70 " =    1.635
peak=   -3.071 closest distance to " O   GLU A 128 " =    1.351
peak=   -3.051 closest distance to " O   ASN A  45 " =    1.972
peak=   -3.034 closest distance to " O   HOH Z 141 " =    1.787
peak=   -3.026 closest distance to " O   HOH Z 423 " =    2.599

================= 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    :  0.4994 0.4985   6.303827e+00   6.296815e+00
   1_bss:  0.4935 0.4893   6.301361e+00   6.292840e+00
   1_xyz:  0.3862 0.4191   6.156496e+00   6.208631e+00
   1_adp:  0.3462 0.4248   6.111243e+00   6.219939e+00
   1_occ:  0.3460 0.4245   6.110788e+00   6.220224e+00
   2_bss:  0.3445 0.4216   6.109690e+00   6.218543e+00
   2_xyz:  0.2896 0.3574   5.962208e+00   6.112511e+00
   2_adp:  0.2695 0.3478   5.928377e+00   6.092955e+00
   2_occ:  0.2693 0.3476   5.928093e+00   6.092810e+00
   3_bss:  0.2697 0.3477   5.929535e+00   6.092993e+00
   3_xyz:  0.2203 0.2827   5.735837e+00   5.926554e+00
   3_adp:  0.1971 0.2643   5.655059e+00   5.866304e+00
   3_occ:  0.1971 0.2642   5.654560e+00   5.865995e+00
   4_bss:  0.1967 0.2635   5.653460e+00   5.864927e+00
   4_xyz:  0.1647 0.2222   5.487194e+00   5.714846e+00
   4_adp:  0.1559 0.2033   5.425655e+00   5.629623e+00
   4_occ:  0.1556 0.2028   5.424496e+00   5.628591e+00
   5_bss:  0.1559 0.2023   5.425617e+00   5.628642e+00
   5_xyz:  0.1370 0.1835   5.323245e+00   5.540762e+00
   5_adp:  0.1318 0.1827   5.299763e+00   5.526727e+00
   5_occ:  0.1318 0.1827   5.299707e+00   5.526640e+00
   5_bss:  0.1323 0.1826   5.300210e+00   5.526083e+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:  0.282  20.000  -2.074   3.260   1.902   0.000   0.000   0.000
   1_xyz:  0.282  20.000  -2.074   3.260   1.902   0.000   0.000   0.000
   1_adp:  0.282  20.000  -2.074   3.260   1.902   0.000   0.000   0.000
   1_occ:  0.282  20.000  -2.074   3.260   1.902   0.000   0.000   0.000
   2_bss:  0.311  50.000  -1.024   2.275   1.564   0.000   0.000   0.000
   2_xyz:  0.311  50.000  -1.024   2.275   1.564   0.000   0.000   0.000
   2_adp:  0.311  50.000  -1.024   2.275   1.564   0.000   0.000   0.000
   2_occ:  0.311  50.000  -1.024   2.275   1.564   0.000   0.000   0.000
   3_bss:  0.324  59.460  -1.745   1.226   0.896   0.000   0.000   0.000
   3_xyz:  0.324  59.460  -1.745   1.226   0.896   0.000   0.000   0.000
   3_adp:  0.324  59.460  -1.745   1.226   0.896   0.000   0.000   0.000
   3_occ:  0.324  59.460  -1.745   1.226   0.896   0.000   0.000   0.000
   4_bss:  0.335  75.224  -2.146   0.043   0.247   0.000   0.000   0.000
   4_xyz:  0.335  75.224  -2.146   0.043   0.247   0.000   0.000   0.000
   4_adp:  0.335  75.224  -2.146   0.043   0.247   0.000   0.000   0.000
   4_occ:  0.335  75.224  -2.146   0.043   0.247   0.000   0.000   0.000
   5_bss:  0.336  73.425  -2.716  -0.732  -0.280  -0.000  -0.000  -0.000
   5_xyz:  0.336  73.425  -2.716  -0.732  -0.280  -0.000  -0.000  -0.000
   5_adp:  0.336  73.425  -2.716  -0.732  -0.280  -0.000  -0.000  -0.000
   5_occ:  0.336  73.425  -2.716  -0.732  -0.280  -0.000  -0.000  -0.000
   5_bss:  0.333  73.377  -2.781  -1.043  -0.329  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.054 0.3539  0.4808    80230.260
   1_bss:  61.910 0.3678  0.5211    78021.016
   1_xyz:  48.838 0.5346  0.7410    53726.086
   1_adp:  49.698 0.5232  0.7345    55475.649
   1_occ:  49.710 0.5230  0.7328    55449.648
   2_bss:  49.318 0.5278  0.7398    54710.791
   2_xyz:  39.924 0.6424  0.8854    37503.480
   2_adp:  38.514 0.6595  0.8878    35563.082
   2_occ:  38.503 0.6596  0.8876    35520.490
   3_bss:  38.504 0.6597  0.8638    35578.027
   3_xyz:  30.020 0.7558  0.9585    21601.893
   3_adp:  27.154 0.7879  0.9623    18531.221
   3_occ:  27.136 0.7881  0.9624    18506.526
   4_bss:  27.017 0.7893  0.9396    18368.378
   4_xyz:  21.988 0.8411  0.9736    12608.218
   4_adp:  19.570 0.8660  0.9840    10779.742
   4_occ:  19.539 0.8663  0.9842    10748.080
   5_bss:  19.522 0.8665  0.9634    10745.916
   5_xyz:  17.440 0.8858  0.9730     8891.948
   5_adp:  17.166 0.8883  0.9686     8806.382
   5_occ:  17.169 0.8883  0.9684     8808.403
   5_bss:  17.162 0.8883  0.9625     8795.922
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.0194e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.0194e-01
   1_xyz:   1.864  0.017  0.118 16.346  0.008  4.104   2.0184e-01
   1_adp:   1.864  0.017  0.118 16.346  0.008  4.104   2.0184e-01
   1_occ:   1.864  0.017  0.118 16.346  0.008  4.104   2.0184e-01
   2_bss:   1.864  0.017  0.118 16.346  0.008  4.104   2.0184e-01
   2_xyz:   1.320  0.010  0.086 15.181  0.005  4.126   9.6898e-02
   2_adp:   1.320  0.010  0.086 15.181  0.005  4.126   9.6898e-02
   2_occ:   1.320  0.010  0.086 15.181  0.005  4.126   9.6898e-02
   3_bss:   1.320  0.010  0.086 15.181  0.005  4.126   9.6898e-02
   3_xyz:   1.226  0.009  0.079 14.702  0.005  4.112   8.4254e-02
   3_adp:   1.226  0.009  0.079 14.702  0.005  4.112   8.4254e-02
   3_occ:   1.226  0.009  0.079 14.702  0.005  4.112   8.4254e-02
   4_bss:   1.226  0.009  0.079 14.702  0.005  4.112   8.4254e-02
   4_xyz:   1.099  0.008  0.077 14.431  0.004  4.110   6.8562e-02
   4_adp:   1.099  0.008  0.077 14.431  0.004  4.110   6.8562e-02
   4_occ:   1.099  0.008  0.077 14.431  0.004  4.110   6.8562e-02
   5_bss:   1.099  0.008  0.077 14.431  0.004  4.110   6.8562e-02
   5_xyz:   1.110  0.009  0.079 14.470  0.004  4.120   6.8798e-02
   5_adp:   1.110  0.009  0.079 14.470  0.004  4.120   6.8798e-02
   5_occ:   1.110  0.009  0.079 14.470  0.004  4.120   6.8798e-02
   5_bss:   1.110  0.009  0.079 14.470  0.004  4.120   6.8798e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.167   2.4502e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.167   2.4502e-01
   1_xyz:  10.841  0.152  0.464 83.250  0.036  1.884   2.5804e-01
   1_adp:  10.841  0.152  0.464 83.250  0.036  1.884   2.5804e-01
   1_occ:  10.841  0.152  0.464 83.250  0.036  1.884   2.5804e-01
   2_bss:  10.841  0.152  0.464 83.250  0.036  1.884   2.5804e-01
   2_xyz:   7.819  0.052  0.316 86.543  0.026  2.136   1.2592e-01
   2_adp:   7.819  0.052  0.316 86.543  0.026  2.136   1.2592e-01
   2_occ:   7.819  0.052  0.316 86.543  0.026  2.136   1.2592e-01
   3_bss:   7.819  0.052  0.316 86.543  0.026  2.136   1.2592e-01
   3_xyz:   7.458  0.060  0.223 80.140  0.043  2.209   5.9298e-02
   3_adp:   7.458  0.060  0.223 80.140  0.043  2.209   5.9298e-02
   3_occ:   7.458  0.060  0.223 80.140  0.043  2.209   5.9298e-02
   4_bss:   7.458  0.060  0.223 80.140  0.043  2.209   5.9298e-02
   4_xyz:   7.718  0.053  0.213 80.035  0.032  2.312   6.0574e-02
   4_adp:   7.718  0.053  0.213 80.035  0.032  2.312   6.0574e-02
   4_occ:   7.718  0.053  0.213 80.035  0.032  2.312   6.0574e-02
   5_bss:   7.718  0.053  0.213 80.035  0.032  2.312   6.0574e-02
   5_xyz:   7.992  0.048  0.263 81.258  0.032  2.327   4.7202e-02
   5_adp:   7.992  0.048  0.263 81.258  0.032  2.327   4.7202e-02
   5_occ:   7.992  0.048  0.263 81.258  0.032  2.327   4.7202e-02
   5_bss:   7.992  0.048  0.263 81.258  0.032  2.327   4.7202e-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: 105.11   0.00  20.68 103.80   0.00  16.98 105.11   0.00  40.81
   1_occ: 105.11   0.00  20.68 103.80   0.00  16.98 105.11   0.00  40.81
   2_bss: 105.11   0.00  20.68 103.80   0.00  16.98 105.11   0.00  40.81
   2_xyz: 105.11   0.00  20.68 103.80   0.00  16.98 105.11   0.00  40.81
   2_adp: 109.03   0.00  20.31 106.91   0.00  16.32 109.03   0.00  42.09
   2_occ: 109.03   0.00  20.31 106.91   0.00  16.32 109.03   0.00  42.09
   3_bss: 109.03   0.00  20.31 106.91   0.00  16.32 109.03   0.00  42.09
   3_xyz: 109.03   0.00  20.31 106.91   0.00  16.32 109.03   0.00  42.09
   3_adp: 115.66   0.00  20.18 109.83   0.00  14.87 115.66   3.54  49.05
   3_occ: 115.66   0.00  20.18 109.83   0.00  14.87 115.66   3.54  49.05
   4_bss: 115.66   0.00  20.18 109.83   0.00  14.87 115.66   3.54  49.05
   4_xyz: 115.66   0.00  20.18 109.83   0.00  14.87 115.66   3.54  49.05
   4_adp: 109.40   1.40  18.61 106.11   1.40  13.57 109.40   5.51  46.02
   4_occ: 109.40   1.40  18.61 106.11   1.40  13.57 109.40   5.51  46.02
   5_bss: 109.40   1.40  18.61 106.11   1.40  13.57 109.40   5.51  46.02
   5_xyz: 109.40   1.40  18.61 106.11   1.40  13.57 109.40   5.51  46.02
   5_adp: 111.13   1.35  18.38 107.69   1.35  13.15 111.13   2.90  46.92
   5_occ: 111.13   1.35  18.38 107.69   1.35  13.15 111.13   2.90  46.92
   5_bss: 111.09   1.30  18.34 107.64   1.30  13.10 111.09   2.85  46.87
------------------------------------------------------------------------
 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:    2.721    0.012    0.475
   1_adp:    2.721    0.012    0.475
   1_occ:    2.721    0.012    0.475
   2_bss:    2.721    0.012    0.475
   2_xyz:    2.606    0.043    0.624
   2_adp:    2.606    0.043    0.624
   2_occ:    2.606    0.043    0.624
   3_bss:    2.606    0.043    0.624
   3_xyz:    2.637    0.070    0.801
   3_adp:    2.637    0.070    0.801
   3_occ:    2.637    0.070    0.801
   4_bss:    2.637    0.070    0.801
   4_xyz:    2.596    0.081    0.873
   4_adp:    2.596    0.081    0.873
   4_occ:    2.596    0.081    0.873
   5_bss:    2.596    0.081    0.873
   5_xyz:    2.537    0.049    0.925
   5_adp:    2.537    0.049    0.925
   5_occ:    2.537    0.049    0.925
   5_bss:    2.537    0.049    0.925
------------------------------------------------------------------------

CPU time actual refinement: 359.11


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_240/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_240/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_240/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_240/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_240/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 358.96 
  Macro-tasks:
    bulk solvent and scale       = 51.75  
    individual site refinement   = 139.92 
    weights calculation          = 30.32  
    collect and process          = 6.52   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 228.64 
  Micro-tasks:
    mask                            = 2.93   
    f_calc                          = 112.72 
    alpha_beta                      = 8.35   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 120.27 
    fmodel                         = 8.42   
    r_factors                      = 0.33   
    phase_errors                   = 10.21  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 264.63 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.124 micro seconds
Total CPU time: 6.21 minutes
from_scatterers_fft:    649 calls, 112.34 s
gradients_fft:          594 calls, 107.53 s

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

# Date 2008-01-16 Time 04:21:19 PST -0800 (1200486079.13 s)
Start R-work = 0.4994, R-free = 0.4985 (no bulk solvent and anisotropic scale)
Final R-work = 0.1526, R-free = 0.1993 (no bulk solvent and anisotropic scale)

Start R-work = 0.4935, R-free = 0.4893
Final R-work = 0.1323, R-free = 0.1826