# Date 2008-01-16 Time 06:35:06 PST -0800 (1200494106.42 s)
#phil __OFF__

Command line arguments: "../1201.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23774
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1201

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 48.1033, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.97152
Completeness in resolution range: 0.917475
Completeness with d_max=infinity: 0.914775

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1461
                             d_min =   1.9715

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.97152
Completeness in resolution range: 0.917475
Completeness with d_max=infinity: 0.914775

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1465 -  4.2198 [2241/2270]  2018   223  10.0%
  bin  2:  4.2198 -  3.3614 [2147/2170]  1931   216  10.1%
  bin  3:  3.3614 -  2.9400 [2111/2136]  1898   213  10.1%
  bin  4:  2.9400 -  2.6728 [2104/2120]  1898   206   9.8%
  bin  5:  2.6728 -  2.4821 [2086/2130]  1880   206   9.9%
  bin  6:  2.4821 -  2.3364 [2081/2109]  1874   207   9.9%
  bin  7:  2.3364 -  2.2197 [2068/2104]  1855   213  10.3%
  bin  8:  2.2197 -  2.1234 [2057/2099]  1854   203   9.9%
  bin  9:  2.1234 -  2.0418 [2040/2106]  1834   206  10.1%
  bin 10:  2.0418 -  1.9715 [ 654/2107]   588    66  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1201/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: 0.13 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:
        1.33 -     2.04: 9
        2.04 -     2.76: 390
        2.76 -     3.47: 4519
        3.47 -     4.19: 9300
        4.19 -     4.90: 13792
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.329 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.389 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.416 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.579 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.690 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28005 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_1201/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1201/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 48.10325 85.09415 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: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4775   r_free= 0.4598   ksol= 0.00   Bsol= 0.00   scale= 0.873    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.287941                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7071 0.99   1456  165 0.3796 0.4034       6.575      6.5732|
|  2:  4.7071 -  3.7549 0.99   1394  151 0.4210 0.4066       6.863      6.8425|
|  3:  3.7549 -  3.2858 0.99   1372  152 0.4584 0.4192      6.6788      6.6397|
|  4:  3.2858 -  2.9879 0.99   1359  151 0.4777 0.4628      6.5178      6.5052|
|  5:  2.9879 -  2.7751 0.99   1353  152 0.4965 0.4945      6.3545      6.3532|
|  6:  2.7751 -  2.6124 0.99   1349  154 0.5216 0.4879      6.2834      6.1748|
|  7:  2.6124 -  2.4821 0.98   1342  139 0.5121 0.4386      6.2397      6.1839|
|  8:  2.4821 -  2.3745 0.98   1336  149 0.5182 0.5000      6.1486      6.1927|
|  9:  2.3745 -  2.2834 0.99   1334  154 0.5403 0.5101      6.1478      6.0844|
| 10:  2.2834 -  2.2049 0.98   1337  149 0.5091 0.4943      6.0665      6.1158|
| 11:  2.2049 -  2.1361 0.97   1314  140 0.5311 0.5262      6.0289      5.9831|
| 12:  2.1361 -  2.0752 0.99   1318  145 0.5100 0.5194      5.9255      5.9862|
| 13:  2.0752 -  2.0207 0.81   1084  130 0.5084 0.4281      5.8639      5.8033|
| 14:  2.0207 -  1.9715 0.20    282   28 0.5661 0.4839      5.7896      5.7726|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.7071  1456   165  0.68  35.76   0.81     0.72      78084.61|
|  2:  4.7071 -  3.7549  1394   151  0.69  36.28   0.89     0.77     106884.44|
|  3:  3.7549 -  3.2858  1372   152  0.58  45.70   0.88     0.74     115843.28|
|  4:  3.2858 -  2.9879  1359   151  0.49  52.83   0.88     0.67     103856.67|
|  5:  2.9879 -  2.7751  1353   152  0.41  58.89   0.85     0.59      83578.65|
|  6:  2.7751 -  2.6124  1349   154  0.41  59.07   0.88     0.58      67598.58|
|  7:  2.6124 -  2.4821  1342   139  0.42  58.51   0.90     0.58      59624.22|
|  8:  2.4821 -  2.3745  1336   149  0.40  59.94   0.86     0.58      55598.14|
|  9:  2.3745 -  2.2834  1334   154  0.39  60.84   0.90     0.58      51375.25|
| 10:  2.2834 -  2.2049  1337   149  0.39  61.08   0.91     0.57      48319.25|
| 11:  2.2049 -  2.1361  1314   140  0.35  63.59   0.90     0.53      45364.75|
| 12:  2.1361 -  2.0752  1318   145  0.33  65.50   0.91     0.52      42399.72|
| 13:  2.0752 -  2.0207  1084   130  0.35  64.03   0.93     0.53      34928.82|
| 14:  2.0207 -  1.9715   282    28  0.38  61.62   0.86     0.60      26694.08|
|alpha:            min =        0.52 max =            0.77 mean =         0.62|
|beta:             min =    26694.08 max =       115843.28 mean =     68936.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.28|
|phase err.(test): min =        0.00 max =           89.91 mean =        55.13|
|-----------------------------------------------------------------------------|

============================== 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 = 12.846424             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.882   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.748031              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.472   (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 |  1.329 -  1.686:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.686 -  2.043:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.043 -  2.400:       21 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.400 -  2.757:      369 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.757 -  3.114:     2240 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.114 -  3.471:     2279 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.471 -  3.829:     4322 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.829 -  4.186:     4978 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.186 -  4.543:     6202 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.543 -  4.900:     7590 |
|-----------------------------------------------------------------------------|
|-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 |        0.186 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.329 |       0.504 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.203)------------------------------------------|
|    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: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4775   r_free= 0.4598   ksol= 0.00   Bsol= 0.00   scale= 0.873    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.287941                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4709   r_free= 0.4510   ksol= 0.27   Bsol= 16.58   scale= 0.917   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,3.72,-0.56,0.00,-0.00,-0.00); trace/3= 0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.284271                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.680919             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.655   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.324185              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.286   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4709      final r-factor (work) = 0.3820          |
| start r-factor (free) = 0.4510      final r-factor (free) = 0.4177          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.7281 = 10.68 * 0.50 * 6.2807 + 1.00 * 0.1862                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.1425 = 10.68 * 0.50 * 6.1800 + 1.00 * 0.1386                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3820      final r-factor (work) = 0.3531          |
| start r-factor (free) = 0.4177      final r-factor (free) = 0.4218          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1896 = 1.32 * 1.00 * 6.1800 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1277 = 1.32 * 1.00 * 6.1183 + 1.00 * 0.0260                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.203)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.86  17.82    None  None   None       |
|    all(noH): 2823   0      0.00    110.86  17.82    None  None   None       |
|    Sol.    : 438    0      0.00    69.90   36.36    None  None   None       |
|    Mac.    : 2385   0      0.00    110.86  14.42    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 -  11.086: 1005   |   5:    55.428 -  66.514:   30        |
|      1:    11.086 -  22.171:  982   |   6:    66.514 -  77.599:    1        |
|      2:    22.171 -  33.257:  475   |   7:    77.599 -  88.685:    0        |
|      3:    33.257 -  44.343:  208   |   8:    88.685 -  99.771:    0        |
|      4:    44.343 -  55.428:  121   |   9:    99.771 - 110.856:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3531 r_free = 0.4218             target_work(ml) = 6.120         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3530 r_free = 0.4224             target_work(ml) = 6.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3530   r_free= 0.4224   ksol= 0.27   Bsol= 16.58   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,3.72,-0.56,0.00,-0.00,-0.00); trace/3= 0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.120000                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3529   r_free= 0.4194   ksol= 0.32   Bsol= 58.24   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,2.21,-0.40,0.00,-0.00,-0.00); trace/3= 0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.121059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.311002             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.778  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.128210              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.869  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3529      final r-factor (work) = 0.2802          |
| start r-factor (free) = 0.4194      final r-factor (free) = 0.3347          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.9270 = 14.31 * 0.50 * 6.1195 + 1.00 * 0.1388                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.3146 = 14.31 * 0.50 * 6.0336 + 1.00 * 0.1413                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2802      final r-factor (work) = 0.2525          |
| start r-factor (free) = 0.3347      final r-factor (free) = 0.3261          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8286 = 1.13 * 1.00 * 6.0336 + 1.00 * 0.0214                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6510 = 1.13 * 1.00 * 5.8793 + 1.00 * 0.0179                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.203)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.09   19.02    None  None   None       |
|    all(noH): 2823   0      0.00    92.09   19.02    None  None   None       |
|    Sol.    : 438    0      1.88    92.09   41.96    None  None   None       |
|    Mac.    : 2385   0      0.00    86.99   14.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.209:  925   |   5:    46.047 -  55.256:  102        |
|      1:     9.209 -  18.419:  866   |   6:    55.256 -  64.466:   76        |
|      2:    18.419 -  27.628:  405   |   7:    64.466 -  73.675:   43        |
|      3:    27.628 -  36.838:  237   |   8:    73.675 -  82.885:   20        |
|      4:    36.838 -  46.047:  140   |   9:    82.885 -  92.094:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2525 r_free = 0.3261             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2522 r_free = 0.3253             target_work(ml) = 5.869         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2522   r_free= 0.3253   ksol= 0.32   Bsol= 58.24   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,2.21,-0.40,0.00,-0.00,-0.00); trace/3= 0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.869357                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2523   r_free= 0.3242   ksol= 0.32   Bsol= 68.60   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,1.02,-0.56,0.00,-0.00,-0.00); trace/3= -0.06                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.867210                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.126660              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.046  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.329740              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.785  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2523      final r-factor (work) = 0.2090          |
| start r-factor (free) = 0.3242      final r-factor (free) = 0.2668          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2123 = 5.13 * 0.50 * 5.8793 + 1.00 * 0.1416                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9232 = 5.13 * 0.50 * 5.7950 + 1.00 * 0.0686                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2090      final r-factor (work) = 0.1944          |
| start r-factor (free) = 0.2668      final r-factor (free) = 0.2526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7238 = 1.33 * 1.00 * 5.7950 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5385 = 1.33 * 1.00 * 5.6561 + 1.00 * 0.0175                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.203)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.65  19.27    None  None   None       |
|    all(noH): 2823   0      0.00    108.65  19.27    None  None   None       |
|    Sol.    : 438    0      3.41    101.18  46.89    None  None   None       |
|    Mac.    : 2385   0      0.00    108.65  14.20    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 -  10.865: 1213   |   5:    54.326 -  65.191:   86        |
|      1:    10.865 -  21.730:  865   |   6:    65.191 -  76.056:   61        |
|      2:    21.730 -  32.596:  259   |   7:    76.056 -  86.921:   41        |
|      3:    32.596 -  43.461:  153   |   8:    86.921 -  97.787:   14        |
|      4:    43.461 -  54.326:  124   |   9:    97.787 - 108.652:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1944 r_free = 0.2526             target_work(ml) = 5.632         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1943 r_free = 0.2524             target_work(ml) = 5.631         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1943   r_free= 0.2524   ksol= 0.32   Bsol= 68.60   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,1.02,-0.56,0.00,-0.00,-0.00); trace/3= -0.06                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.631473                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1945   r_free= 0.2523   ksol= 0.33   Bsol= 76.75   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,0.13,-1.01,0.00,-0.00,-0.00); trace/3= -0.69                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.631507                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.661634              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.698   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.343847              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.772  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1945      final r-factor (work) = 0.1578          |
| start r-factor (free) = 0.2523      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2566 = 4.66 * 0.50 * 5.6581 + 1.00 * 0.0686                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9989 = 4.66 * 0.50 * 5.5444 + 1.00 * 0.0760                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1578      final r-factor (work) = 0.1468          |
| start r-factor (free) = 0.2085      final r-factor (free) = 0.1942          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9239 = 0.34 * 1.00 * 5.5444 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8743 = 0.34 * 1.00 * 5.4164 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.203)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.85    109.25  18.06    None  None   None       |
|    all(noH): 2823   0      0.85    109.25  18.06    None  None   None       |
|    Sol.    : 438    0      4.73    105.82  45.15    None  None   None       |
|    Mac.    : 2385   0      0.85    109.25  13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.852 -  11.692: 1415   |   5:    55.049 -  65.889:   83        |
|      1:    11.692 -  22.531:  806   |   6:    65.889 -  76.728:   48        |
|      2:    22.531 -  33.371:  201   |   7:    76.728 -  87.568:   28        |
|      3:    33.371 -  44.210:  114   |   8:    87.568 -  98.407:    8        |
|      4:    44.210 -  55.049:  114   |   9:    98.407 - 109.246:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1468 r_free = 0.1942             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1467 r_free = 0.1941             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1941   ksol= 0.33   Bsol= 76.75   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,0.13,-1.01,0.00,-0.00,-0.00); trace/3= -0.69                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.376960                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1472   r_free= 0.1948   ksol= 0.33   Bsol= 71.34   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-0.56,-1.13,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.379516                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.308516              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.321  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.246243              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.205  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1472      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.1948      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3296 = 2.31 * 0.50 * 5.4178 + 1.00 * 0.0760                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2301 = 2.31 * 0.50 * 5.3442 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1357      final r-factor (work) = 0.1334          |
| start r-factor (free) = 0.1830      final r-factor (free) = 0.1799          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3278 = 0.25 * 1.00 * 5.3442 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3164 = 0.25 * 1.00 * 5.3041 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.203)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    109.76  17.43    None  None   None       |
|    all(noH): 2823   0      1.04    109.76  17.43    None  None   None       |
|    Sol.    : 438    0      4.82    107.10  43.29    None  None   None       |
|    Mac.    : 2385   0      1.04    109.76  12.68    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:     1.036 -  11.909: 1497   |   5:    55.399 -  66.272:   68        |
|      1:    11.909 -  22.781:  778   |   6:    66.272 -  77.144:   50        |
|      2:    22.781 -  33.654:  170   |   7:    77.144 -  88.017:   18        |
|      3:    33.654 -  44.526:  124   |   8:    88.017 -  98.889:    3        |
|      4:    44.526 -  55.399:  109   |   9:    98.889 - 109.762:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1334 r_free = 0.1799             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1333 r_free = 0.1799             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1333   r_free= 0.1799   ksol= 0.33   Bsol= 71.34   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-0.56,-1.13,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.296722                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7071 0.99   1456  165 0.1029 0.1333      5.4221      5.5899|
|  2:  4.7071 -  3.7549 0.99   1394  151 0.0927 0.1141      5.4944      5.7009|
|  3:  3.7549 -  3.2858 0.99   1372  152 0.1221 0.1828       5.583      5.9464|
|  4:  3.2858 -  2.9879 0.99   1359  151 0.1539 0.1802      5.6181      5.7581|
|  5:  2.9879 -  2.7751 0.99   1353  152 0.1668 0.2078      5.5133      5.6656|
|  6:  2.7751 -  2.6124 0.99   1349  154 0.1549 0.2314       5.385      5.5856|
|  7:  2.6124 -  2.4821 0.98   1342  139 0.1499 0.1968      5.3201       5.521|
|  8:  2.4821 -  2.3745 0.98   1336  149 0.1495 0.1948      5.2319      5.4313|
|  9:  2.3745 -  2.2834 0.99   1334  154 0.1445 0.2107      5.1806      5.3995|
| 10:  2.2834 -  2.2049 0.98   1337  149 0.1371 0.1886      5.1153      5.3623|
| 11:  2.2049 -  2.1361 0.97   1314  140 0.1357 0.2024      5.0573       5.299|
| 12:  2.1361 -  2.0752 0.99   1318  145 0.1376 0.1981      5.0007      5.2445|
| 13:  2.0752 -  2.0207 0.81   1084  130 0.1381 0.2021      4.9236      5.1582|
| 14:  2.0207 -  1.9715 0.20    282   28 0.1381 0.1601      4.8079      5.0145|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.7071  1456   165  0.94   9.72   0.96     0.94       7892.47|
|  2:  4.7071 -  3.7549  1394   151  0.95   8.95   1.00     0.99       9976.12|
|  3:  3.7549 -  3.2858  1372   152  0.92  13.39   1.02     1.01      12713.51|
|  4:  3.2858 -  2.9879  1359   151  0.89  17.13   1.01     0.98      13891.91|
|  5:  2.9879 -  2.7751  1353   152  0.86  20.56   1.00     0.98      12357.34|
|  6:  2.7751 -  2.6124  1349   154  0.87  19.14   0.99     0.96       9676.78|
|  7:  2.6124 -  2.4821  1342   139  0.88  18.61   0.99     0.95       8308.69|
|  8:  2.4821 -  2.3745  1336   149  0.87  19.33   1.00     0.96       7442.81|
|  9:  2.3745 -  2.2834  1334   154  0.88  18.95   1.00     0.95       6539.71|
| 10:  2.2834 -  2.2049  1337   149  0.88  18.30   0.99     0.94       5910.64|
| 11:  2.2049 -  2.1361  1314   140  0.88  18.66   0.99     0.94       5418.84|
| 12:  2.1361 -  2.0752  1318   145  0.88  19.21   0.99     0.97       5165.47|
| 13:  2.0752 -  2.0207  1084   130  0.88  19.06   0.99     0.98       4376.38|
| 14:  2.0207 -  1.9715   282    28  0.86  19.80   0.98     0.94       3480.73|
|alpha:            min =        0.94 max =            1.01 mean =         0.96|
|beta:             min =     3480.73 max =        13891.91 mean =      8444.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.92 mean =        16.93|
|phase err.(test): min =        0.00 max =           89.89 mean =        16.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1333   r_free= 0.1799   ksol= 0.32   Bsol= 64.56   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-0.90,-1.24,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.296438                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1333   r_free= 0.1799   ksol= 0.32   Bsol= 64.56   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-0.90,-1.24,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.296438                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7071 0.99   1456  165 0.1027 0.1332      5.4208      5.5864|
|  2:  4.7071 -  3.7549 0.99   1394  151 0.0924 0.1132      5.4904      5.6935|
|  3:  3.7549 -  3.2858 0.99   1372  152 0.1219 0.1824      5.5809      5.9468|
|  4:  3.2858 -  2.9879 0.99   1359  151 0.1540 0.1799      5.6181      5.7569|
|  5:  2.9879 -  2.7751 0.99   1353  152 0.1671 0.2078       5.514      5.6661|
|  6:  2.7751 -  2.6124 0.99   1349  154 0.1549 0.2314      5.3856      5.5862|
|  7:  2.6124 -  2.4821 0.98   1342  139 0.1499 0.1969      5.3204      5.5206|
|  8:  2.4821 -  2.3745 0.98   1336  149 0.1495 0.1950      5.2326       5.433|
|  9:  2.3745 -  2.2834 0.99   1334  154 0.1444 0.2107      5.1807      5.3999|
| 10:  2.2834 -  2.2049 0.98   1337  149 0.1372 0.1890      5.1156      5.3633|
| 11:  2.2049 -  2.1361 0.97   1314  140 0.1357 0.2026      5.0571      5.2991|
| 12:  2.1361 -  2.0752 0.99   1318  145 0.1377 0.1985       5.002      5.2463|
| 13:  2.0752 -  2.0207 0.81   1084  130 0.1382 0.2019       4.924      5.1581|
| 14:  2.0207 -  1.9715 0.20    282   28 0.1382 0.1597      4.8078      5.0114|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.7071  1456   165  0.94   9.68   0.96     0.94       7861.82|
|  2:  4.7071 -  3.7549  1394   151  0.95   8.90   1.00     0.99       9887.42|
|  3:  3.7549 -  3.2858  1372   152  0.92  13.31   1.02     1.01      12596.34|
|  4:  3.2858 -  2.9879  1359   151  0.89  17.11   1.00     0.97      13867.70|
|  5:  2.9879 -  2.7751  1353   152  0.86  20.54   0.99     0.97      12344.69|
|  6:  2.7751 -  2.6124  1349   154  0.87  19.14   0.98     0.96       9681.96|
|  7:  2.6124 -  2.4821  1342   139  0.88  18.60   0.98     0.94       8314.62|
|  8:  2.4821 -  2.3745  1336   149  0.87  19.35   0.99     0.95       7457.97|
|  9:  2.3745 -  2.2834  1334   154  0.88  18.96   0.99     0.94       6555.00|
| 10:  2.2834 -  2.2049  1337   149  0.88  18.32   0.97     0.93       5922.28|
| 11:  2.2049 -  2.1361  1314   140  0.88  18.66   0.98     0.93       5423.59|
| 12:  2.1361 -  2.0752  1318   145  0.88  19.23   0.97     0.96       5178.71|
| 13:  2.0752 -  2.0207  1084   130  0.88  19.06   0.97     0.96       4378.27|
| 14:  2.0207 -  1.9715   282    28  0.86  19.79   0.97     0.93       3472.29|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3472.29 max =        13867.70 mean =      8427.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.92|
|phase err.(test): min =        0.00 max =           89.67 mean =        16.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.203)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.00    109.73  17.40    None  None   None       |
|    all(noH): 2823   0      1.00    109.73  17.40    None  None   None       |
|    Sol.    : 438    0      4.78    107.06  43.26    None  None   None       |
|    Mac.    : 2385   0      1.00    109.73  12.65    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:     1.000 -  11.873: 1497   |   5:    55.363 -  66.236:   68        |
|      1:    11.873 -  22.745:  778   |   6:    66.236 -  77.108:   50        |
|      2:    22.745 -  33.618:  170   |   7:    77.108 -  87.981:   18        |
|      3:    33.618 -  44.491:  124   |   8:    87.981 -  98.853:    3        |
|      4:    44.491 -  55.363:  109   |   9:    98.853 - 109.726:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 358         
Filter by distance & map next to the model:
   mapped sites are within: 0.706 - 5.619
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 354 from: 358
   mapped sites are within: 0.706 - 5.619

peak=    7.642 closest distance to " O   HOH Z  41 " =    1.215
peak=    6.281 closest distance to " O   HOH Z 400 " =    1.094
peak=    5.745 closest distance to " O   HOH Z 120 " =    1.138
peak=    5.409 closest distance to " O   HOH Z 210 " =    1.588
peak=    5.298 closest distance to " O   ARG A 275 " =    0.811
peak=    5.118 closest distance to " CB  GLN A 223 " =    1.469
peak=    5.109 closest distance to " CB  SER A  63 " =    1.346
peak=    5.021 closest distance to " O   HOH Z 111 " =    2.074
peak=    5.019 closest distance to " NH2BARG A 102 " =    1.094
peak=    4.962 closest distance to " CG  PRO A 280 " =    0.945
peak=    4.886 closest distance to " CG  PRO A  54 " =    1.257
peak=    4.868 closest distance to " O   PRO A 198 " =    1.599
peak=    4.858 closest distance to " CG  PRO A 213 " =    1.340
peak=    4.795 closest distance to " CG  PRO A 198 " =    1.299
peak=    4.784 closest distance to " O   HOH Z 126 " =    1.951
peak=    4.745 closest distance to " CA  TYR A  30 " =    1.069
peak=    4.723 closest distance to " O   HOH Z 134 " =    2.139
peak=    4.714 closest distance to " O   HOH Z  15 " =    2.016
peak=    4.659 closest distance to " CB  ARG A 275 " =    0.914
peak=    4.655 closest distance to " O   HOH Z 404 " =    1.589
peak=    4.604 closest distance to " O  BHOH Z 338 " =    1.036
peak=    4.591 closest distance to " O   HOH Z 272 " =    1.335
peak=    4.579 closest distance to " O   HOH Z 433 " =    2.003
peak=    4.485 closest distance to " O   HOH Z  61 " =    1.601
peak=    4.485 closest distance to " CG  PRO A  90 " =    1.276
peak=    4.427 closest distance to " NE2 HIS A 115 " =    1.091
peak=    4.425 closest distance to " O   HOH Z 132 " =    1.496
peak=    4.394 closest distance to " O   HOH Z 132 " =    1.802
peak=    4.372 closest distance to " O   HOH Z  47 " =    1.743
peak=    4.370 closest distance to " O   HOH Z 232 " =    2.220
peak=    4.365 closest distance to " O   HOH Z 350 " =    1.086
peak=    4.355 closest distance to " CG2BVAL A  41 " =    1.027
peak=    4.336 closest distance to " O   HOH Z 394 " =    1.670
peak=    4.319 closest distance to " CB  PRO A  54 " =    0.835
peak=    4.291 closest distance to " O   HOH Z 234 " =    3.707
peak=    4.289 closest distance to " O   HOH Z  68 " =    1.977
peak=    4.267 closest distance to " O   HOH Z   4 " =    1.267
peak=    4.230 closest distance to " O   HOH Z  80 " =    2.289
peak=    4.227 closest distance to " O   HOH Z 214 " =    1.390
peak=    4.223 closest distance to " OE1 GLN A  77 " =    0.943
peak=    4.221 closest distance to " CB  TRP A 179 " =    1.477
peak=    4.204 closest distance to " O   HOH Z 124 " =    1.325
peak=    4.189 closest distance to " O   HOH Z 411 " =    3.030
peak=    4.187 closest distance to " O   HOH Z 247 " =    1.515
peak=    4.184 closest distance to " O   HOH Z 406 " =    1.590
peak=    4.167 closest distance to " O   HOH Z 418 " =    1.802
peak=    4.113 closest distance to " CE  LYS A 119 " =    1.266
peak=    4.096 closest distance to " CA  ASP A 191 " =    0.881
peak=    4.083 closest distance to " CG  GLN A  77 " =    0.844
peak=    4.081 closest distance to " O   HOH Z 389 " =    1.882
peak=    4.047 closest distance to " O   HOH Z 196 " =    2.490
peak=    4.042 closest distance to " CB  ASN A 148 " =    1.303
peak=    4.037 closest distance to " CB  LEU A 228 " =    1.145
peak=    4.034 closest distance to " O   HOH Z  97 " =    1.924
peak=    4.028 closest distance to " O   HOH Z   7 " =    1.182
peak=    4.018 closest distance to " CG2 VAL A  78 " =    1.015
peak=    4.015 closest distance to " CG1 ILE A  33 " =    1.334
peak=    4.007 closest distance to " O   HOH Z 426 " =    1.279
peak=    4.000 closest distance to " CG2 THR A 221 " =    1.128
peak=    3.983 closest distance to " O   HOH Z  47 " =    1.703
peak=    3.973 closest distance to " O   HOH Z 118 " =    2.098
peak=    3.970 closest distance to " NH2 ARG A 156 " =    1.256
peak=    3.969 closest distance to " OE1 GLN A  88 " =    0.898
peak=    3.962 closest distance to " O   HOH Z  49 " =    0.976
peak=    3.960 closest distance to " CD  ARG A  66 " =    2.765
peak=    3.958 closest distance to " O   HOH Z 422 " =    1.134
peak=    3.957 closest distance to " CB  GLN A  73 " =    1.056
peak=    3.952 closest distance to " O   HOH Z 324 " =    1.608
peak=    3.951 closest distance to " O   HOH Z 271 " =    2.469
peak=    3.951 closest distance to " O   GLY A  91 " =    1.181
peak=    3.934 closest distance to " N   ILE A  33 " =    1.116
peak=    3.933 closest distance to " OE1 GLN A  11 " =    2.066
peak=    3.925 closest distance to " CB  GLU A 128 " =    1.137
peak=    3.907 closest distance to " CB  VAL A 202 " =    1.448
peak=    3.907 closest distance to " O   HOH Z  22 " =    2.367
peak=    3.902 closest distance to " O   HOH Z  78 " =    2.503
peak=    3.898 closest distance to " CA  GLY A 196 " =    0.999
peak=    3.895 closest distance to " O   HOH Z 369 " =    2.173
peak=    3.890 closest distance to " CZ  PHE A 218 " =    1.134
peak=    3.876 closest distance to " CA  GLU A 152 " =    0.943
peak=    3.874 closest distance to " CB  TRP A 266 " =    0.925
peak=    3.874 closest distance to " CG AARG A 275 " =    1.142
peak=    3.873 closest distance to " CG1 VAL A 153 " =    1.104
peak=    3.869 closest distance to " O   HOH Z 149 " =    2.120
peak=    3.867 closest distance to " CB  GLU A 152 " =    1.174
peak=    3.863 closest distance to " O   HOH Z 431 " =    1.395
peak=    3.854 closest distance to " O   HOH Z 298 " =    1.968
peak=    3.854 closest distance to " O   HOH Z 374 " =    2.723
peak=    3.846 closest distance to " CD2 LEU A 297 " =    1.073
peak=    3.846 closest distance to " O   HOH Z 142 " =    1.640
peak=    3.841 closest distance to " O   THR A 251 " =    1.304
peak=    3.835 closest distance to " CB  GLU A 277 " =    0.974
peak=    3.832 closest distance to " O   SER A 276 " =    1.164
peak=    3.829 closest distance to " N   ASN A  39 " =    1.250
peak=    3.822 closest distance to " O   HOH Z  44 " =    2.447
peak=    3.819 closest distance to " CB  PRO A 198 " =    0.973
peak=    3.819 closest distance to " O   HOH Z 215 " =    1.481
peak=    3.816 closest distance to " O   HOH Z 150 " =    1.880
peak=    3.802 closest distance to " NH1 ARG A 269 " =    0.806
peak=    3.799 closest distance to " O   HOH Z 327 " =    1.751
peak=    3.796 closest distance to " CB  PRO A  54 " =    1.304
peak=    3.795 closest distance to " CA  GLN A 223 " =    0.935
peak=    3.795 closest distance to " CB  GLN A 183 " =    1.290
peak=    3.792 closest distance to " O   HOH Z 343 " =    2.371
peak=    3.784 closest distance to " CB  GLN A 194 " =    0.935
peak=    3.780 closest distance to " O   HOH Z 133 " =    1.552
peak=    3.774 closest distance to " CB  ASN A 187 " =    1.202
peak=    3.774 closest distance to " CG2 VAL A 197 " =    1.328
peak=    3.773 closest distance to " CB  ASN A 285 " =    0.812
peak=    3.763 closest distance to " O   HOH Z 301 " =    1.598
peak=    3.757 closest distance to " O   HOH Z 425 " =    1.590
peak=    3.751 closest distance to " CD BLYS A 290 " =    1.020
peak=    3.751 closest distance to " CB  MET A 105 " =    1.185
peak=    3.746 closest distance to " O   HOH Z 104 " =    3.391
peak=    3.745 closest distance to " O   HOH Z 243 " =    1.064
peak=    3.744 closest distance to " O   HOH Z  78 " =    1.206
peak=    3.741 closest distance to " CB  ASP A 140 " =    0.782
peak=    3.735 closest distance to " CD  ARG A 159 " =    0.806
peak=    3.734 closest distance to " CB  GLN A  58 " =    1.023
peak=    3.730 closest distance to " OD1 ASN A 217 " =    1.629
peak=    3.729 closest distance to " O   HOH Z 316 " =    3.007
peak=    3.728 closest distance to " CD1 TRP A 274 " =    1.092
peak=    3.727 closest distance to " CD  ARG A 269 " =    0.847
peak=    3.722 closest distance to " O   HOH Z 112 " =    1.575
peak=    3.716 closest distance to " O   HOH Z  89 " =    3.609
peak=    3.712 closest distance to " O   HOH Z  40 " =    2.291
peak=    3.709 closest distance to " N   SER A 164 " =    1.038
peak=    3.708 closest distance to " O   HOH Z 203 " =    1.936
peak=    3.708 closest distance to " O   HOH Z 193 " =    1.972
peak=    3.698 closest distance to " O   HOH Z  11 " =    1.208
peak=    3.695 closest distance to " O   HOH Z 432 " =    1.986
peak=    3.694 closest distance to " CA  VAL A  41 " =    0.778
peak=    3.692 closest distance to " O   HOH Z 189 " =    2.387
peak=    3.691 closest distance to " O   HOH Z 182 " =    1.084
peak=    3.684 closest distance to " CB  SER A  62 " =    0.867
peak=    3.684 closest distance to " O   HOH Z 139 " =    4.522
peak=    3.682 closest distance to " CA  GLU A 277 " =    1.130
peak=    3.682 closest distance to " N   ARG A 275 " =    0.829
peak=    3.677 closest distance to " CB  SER A 141 " =    1.065
peak=    3.675 closest distance to " O   HOH Z 174 " =    1.455
peak=    3.671 closest distance to " O   HOH Z 265 " =    2.138
peak=    3.666 closest distance to " OG  SER A  97 " =    3.467
peak=    3.659 closest distance to " CB  SER A 276 " =    1.105
peak=    3.655 closest distance to " CB  ALA A 256 " =    1.328
peak=    3.654 closest distance to " O   HOH Z 387 " =    2.546
peak=    3.647 closest distance to " O   HOH Z 192 " =    1.494
peak=    3.644 closest distance to " O   HOH Z 108 " =    1.324
peak=    3.643 closest distance to " CG  PRO A 243 " =    1.191
peak=    3.622 closest distance to " O   HOH Z   1 " =    3.134
peak=    3.620 closest distance to " CA  LYS A  48 " =    1.383
peak=    3.619 closest distance to " CB  ARG A 190 " =    1.764
peak=    3.617 closest distance to " CB  ALA A 100 " =    1.578
peak=    3.615 closest distance to " O   HOH Z 437 " =    1.744
peak=    3.599 closest distance to " CB  TYR A 169 " =    0.889
peak=    3.589 closest distance to " CB  PHE A  61 " =    0.720
peak=    3.586 closest distance to " CG2 THR A 220 " =    0.792
peak=    3.585 closest distance to " CB  MET A  47 " =    1.009
peak=    3.582 closest distance to " O   HOH Z  54 " =    1.768
peak=    3.579 closest distance to " CA  ALA A  21 " =    1.476
peak=    3.577 closest distance to " CD1 LEU A 222 " =    0.885
peak=    3.576 closest distance to " O   HOH Z  48 " =    1.892
peak=    3.572 closest distance to " N   PHE A 130 " =    1.280
peak=    3.571 closest distance to " CG2AVAL A 121 " =    1.964
peak=    3.569 closest distance to " O   HOH Z 163 " =    1.796
peak=    3.560 closest distance to " O   HOH Z 119 " =    2.310
peak=    3.559 closest distance to " CB  PHE A  16 " =    1.317
peak=    3.543 closest distance to " CB  ARG A  79 " =    1.338
peak=    3.540 closest distance to " CD1 LEU A 300 " =    1.269
peak=    3.531 closest distance to " CB  SER A  26 " =    0.888
peak=    3.530 closest distance to " CD  LYS A 119 " =    1.290
peak=    3.517 closest distance to " O   HOH Z 336 " =    1.566
peak=    3.517 closest distance to " O   HOH Z 132 " =    2.315
peak=    3.516 closest distance to " O   HOH Z 207 " =    2.291
peak=    3.515 closest distance to " NZ  LYS A 117 " =    3.157
peak=    3.515 closest distance to " OG  SER A 276 " =    0.742
peak=    3.509 closest distance to " O   HOH Z  88 " =    1.595
peak=    3.505 closest distance to " CA  ARG A 156 " =    1.007
peak=    3.504 closest distance to " CB  ILE A 199 " =    0.995
peak=    3.497 closest distance to " CA  ARG A 195 " =    1.109
peak=    3.479 closest distance to " O   HOH Z 327 " =    2.426
peak=    3.479 closest distance to " O   HOH Z 292 " =    1.556
peak=    3.476 closest distance to " CB  TRP A 150 " =    0.998
peak=    3.475 closest distance to " O   HOH Z  39 " =    1.734
peak=    3.472 closest distance to " CA  TRP A 274 " =    1.034
peak=    3.472 closest distance to " O   HOH Z 217 " =    1.288
peak=    3.458 closest distance to " O   HOH Z 245 " =    1.381
peak=    3.456 closest distance to " O   HOH Z 395 " =    1.458
peak=    3.456 closest distance to " CD2 TRP A 179 " =    1.291
peak=    3.453 closest distance to " O   GLY A  23 " =    2.409
peak=    3.452 closest distance to " CA  ILE A 106 " =    0.845
peak=    3.446 closest distance to " CA  ASP A 124 " =    0.831
peak=    3.442 closest distance to " O   HOH Z 344 " =    3.451
peak=    3.440 closest distance to " CA  LEU A  83 " =    1.564
peak=    3.436 closest distance to " O   HOH Z 352 " =    1.508
peak=    3.432 closest distance to " OD1 ASN A  69 " =    2.279
peak=    3.431 closest distance to " O   HOH Z 227 " =    1.771
peak=    3.426 closest distance to " O   HOH Z 185 " =    1.869
peak=    3.424 closest distance to " O   HOH Z 372 " =    1.186
peak=    3.423 closest distance to " CA  ALA A 100 " =    1.177
peak=    3.421 closest distance to " CB  ALA A   1 " =    1.251
peak=    3.419 closest distance to " CB  SER A 273 " =    0.915
peak=    3.418 closest distance to " O   HOH Z  20 " =    2.047
peak=    3.416 closest distance to " CG2 THR A  42 " =    0.933
peak=    3.414 closest distance to " CB  ARG A 269 " =    0.958
peak=    3.408 closest distance to " O   HOH Z  50 " =    3.657
peak=    3.397 closest distance to " O   HOH Z  44 " =    1.710
peak=    3.396 closest distance to " O   HOH Z 272 " =    1.972
peak=    3.396 closest distance to " O   HOH Z  21 " =    1.869
peak=    3.395 closest distance to " O   HOH Z 420 " =    2.200
peak=    3.393 closest distance to " CB  GLN A  88 " =    1.130
peak=    3.389 closest distance to " O   HOH Z 145 " =    1.914
peak=    3.387 closest distance to " O   HOH Z 214 " =    2.178
peak=    3.384 closest distance to " O   HOH Z 403 " =    1.919
peak=    3.382 closest distance to " C   GLY A  80 " =    1.311
peak=    3.380 closest distance to " O   HOH Z 117 " =    1.131
peak=    3.379 closest distance to " O   HOH Z 240 " =    1.924
peak=    3.378 closest distance to " NE AARG A 275 " =    1.599
peak=    3.374 closest distance to " O   HOH Z  49 " =    2.205
peak=    3.372 closest distance to " O   HOH Z 174 " =    1.775
peak=    3.372 closest distance to " O   HOH Z 368 " =    1.961
peak=    3.370 closest distance to " CG  GLN A  77 " =    1.191
peak=    3.370 closest distance to " NZ  LYS A 166 " =    3.246
peak=    3.365 closest distance to " O   HOH Z 294 " =    1.717
peak=    3.365 closest distance to " CA  SER A  87 " =    0.894
peak=    3.364 closest distance to " O   HOH Z 373 " =    1.703
peak=    3.364 closest distance to " CG1 ILE A 120 " =    1.137
peak=    3.362 closest distance to " O   HOH Z 154 " =    1.311
peak=    3.355 closest distance to " CA  THR A 294 " =    1.728
peak=    3.353 closest distance to " ND1 HIS A  81 " =    1.431
peak=    3.349 closest distance to " C   VAL A 265 " =    1.172
peak=    3.348 closest distance to " N   LYS A 166 " =    0.833
peak=    3.347 closest distance to " O   HOH Z 418 " =    5.619
peak=    3.346 closest distance to " CA  ASN A 127 " =    1.052
peak=    3.338 closest distance to " OG  SER A 245 " =    1.623
peak=    3.336 closest distance to " O   ALA A 165 " =    1.347
peak=    3.336 closest distance to " O   HOH Z 162 " =    1.898
peak=    3.332 closest distance to " O   HOH Z 128 " =    2.277
peak=    3.325 closest distance to " CG2 ILE A  20 " =    1.208
peak=    3.320 closest distance to " CZ  PHE A 192 " =    0.986
peak=    3.318 closest distance to " OG  SER A  62 " =    3.234
peak=    3.317 closest distance to " O   HOH Z 127 " =    1.070
peak=    3.317 closest distance to " CA  ARG A 102 " =    1.279
peak=    3.316 closest distance to " CA  ALA A 299 " =    1.317
peak=    3.308 closest distance to " CB  LEU A 261 " =    1.178
peak=    3.305 closest distance to " O   HOH Z 184 " =    1.295
peak=    3.303 closest distance to " NH1 ARG A  56 " =    1.377
peak=    3.297 closest distance to " CB  ALA A 154 " =    1.144
peak=    3.296 closest distance to " CD2 LEU A 255 " =    1.316
peak=    3.293 closest distance to " CB  TRP A 123 " =    1.253
peak=    3.290 closest distance to " OD1 ASP A 238 " =    0.950
peak=    3.286 closest distance to " CD1 LEU A  96 " =    0.782
peak=    3.286 closest distance to " CA  ARG A 139 " =    1.472
peak=    3.284 closest distance to " O   HOH Z 362 " =    3.016
peak=    3.276 closest distance to " CB  MET A  40 " =    0.815
peak=    3.275 closest distance to " O   HOH Z 136 " =    1.332
peak=    3.272 closest distance to " CA  ALA A  51 " =    1.002
peak=    3.272 closest distance to " CD1 PHE A  59 " =    1.830
peak=    3.269 closest distance to " CA  ALA A 160 " =    1.055
peak=    3.268 closest distance to " O   HOH Z 139 " =    3.338
peak=    3.267 closest distance to " CB  SER A 216 " =    0.737
peak=    3.267 closest distance to " O   HOH Z 215 " =    2.153
peak=    3.266 closest distance to " O   HOH Z  88 " =    3.777
peak=    3.263 closest distance to " N   TYR A  15 " =    0.890
peak=    3.260 closest distance to " CG2 ILE A 151 " =    0.831
peak=    3.257 closest distance to " O   HOH Z 272 " =    2.203
peak=    3.255 closest distance to " O   HOH Z 116 " =    1.761
peak=    3.251 closest distance to " O   HOH Z 192 " =    2.419
peak=    3.250 closest distance to " CE BMET A  47 " =    1.422
peak=    3.249 closest distance to " CZ3 TRP A 274 " =    4.708
peak=    3.248 closest distance to " O   HOH Z 287 " =    1.798
peak=    3.238 closest distance to " CB  GLU A 175 " =    1.399
peak=    3.236 closest distance to " CA  GLU A  46 " =    0.810
peak=    3.236 closest distance to " O   HOH Z 102 " =    1.332
peak=    3.235 closest distance to " O   HOH Z 281 " =    4.109
peak=    3.233 closest distance to " CB  ASN A 170 " =    1.169
peak=    3.231 closest distance to " O   HOH Z  33 " =    1.929
peak=    3.229 closest distance to " O   HOH Z 409 " =    3.056
peak=    3.228 closest distance to " CD  LYS A 166 " =    1.454
peak=    3.224 closest distance to " O   HOH Z 124 " =    3.568
peak=    3.223 closest distance to " O   HOH Z 377 " =    1.487
peak=    3.223 closest distance to " CG1 ILE A  49 " =    1.601
peak=    3.222 closest distance to " O   HOH Z 423 " =    3.244
peak=    3.220 closest distance to " N   HIS A 108 " =    1.862
peak=    3.214 closest distance to " O   HOH Z 250 " =    1.445
peak=    3.211 closest distance to " CA  ASP A 149 " =    1.502
peak=    3.209 closest distance to " CB  ASP A 124 " =    0.877
peak=    3.204 closest distance to " O   HOH Z 358 " =    1.534
peak=    3.201 closest distance to " CB  VAL A 126 " =    0.706
peak=    3.196 closest distance to " O   HOH Z 134 " =    1.996
peak=    3.192 closest distance to " CB  ASN A 127 " =    0.791
peak=    3.188 closest distance to " CE2 TYR A 186 " =    0.959
peak=    3.187 closest distance to " O   SER A  87 " =    2.356
peak=    3.185 closest distance to " O   HOH Z 303 " =    2.326
peak=    3.184 closest distance to " O   HOH Z 419 " =    2.634
peak=    3.184 closest distance to " CA  ARG A  36 " =    0.935
peak=    3.184 closest distance to " O   HOH Z 261 " =    1.676
peak=    3.182 closest distance to " CB  ALA A  71 " =    1.260
peak=    3.178 closest distance to " O   HOH Z 410 " =    1.336
peak=    3.176 closest distance to " CD  ARG A  24 " =    1.616
peak=    3.175 closest distance to " OH  TYR A 169 " =    0.937
peak=    3.175 closest distance to " N   ASN A 252 " =    1.180
peak=    3.175 closest distance to " NH2AARG A 190 " =    1.452
peak=    3.174 closest distance to " O   HOH Z 435 " =    1.950
peak=    3.174 closest distance to " CZ3 TRP A  85 " =    0.923
peak=    3.172 closest distance to " O   HOH Z 371 " =    3.309
peak=    3.171 closest distance to " O   HOH Z 142 " =    1.672
peak=    3.171 closest distance to " O   HOH Z 200 " =    1.205
peak=    3.170 closest distance to " CE  MET A 188 " =    1.509
peak=    3.169 closest distance to " CD  LYS A  76 " =    1.964
peak=    3.169 closest distance to " NH2AARG A 145 " =    2.144
peak=    3.168 closest distance to " O   HOH Z 146 " =    1.388
peak=    3.167 closest distance to " CB  ARG A 259 " =    1.828
peak=    3.166 closest distance to " CD2 HIS A  86 " =    1.292
peak=    3.165 closest distance to " CA  GLY A 241 " =    0.756
peak=    3.162 closest distance to " OD2 ASP A 286 " =    3.039
peak=    3.161 closest distance to " CE3 TRP A  85 " =    1.264
peak=    3.160 closest distance to " O   HOH Z  43 " =    1.572
peak=    3.156 closest distance to " CB  ALA A 137 " =    1.306
peak=    3.150 closest distance to " CB  PRO A  90 " =    1.278
peak=    3.137 closest distance to " CG  GLN A  11 " =    1.443
peak=    3.136 closest distance to " O   HOH Z 287 " =    1.655
peak=    3.135 closest distance to " O   SER A 164 " =    1.525
peak=    3.133 closest distance to " O   HOH Z  66 " =    2.027
peak=    3.127 closest distance to " CB  ASN A 148 " =    1.743
peak=    3.123 closest distance to " CB  ILE A 120 " =    1.324
peak=    3.122 closest distance to " O   HOH Z 171 " =    3.951
peak=    3.120 closest distance to " O   HOH Z 260 " =    1.327
peak=    3.119 closest distance to " CA  ALA A 295 " =    0.997
peak=    3.118 closest distance to " CB  TYR A 247 " =    1.051
peak=    3.116 closest distance to " CB  ILE A 234 " =    0.970
peak=    3.115 closest distance to " CB  LEU A  83 " =    0.808
peak=    3.115 closest distance to " CB  SER A  97 " =    2.042
peak=    3.111 closest distance to " O   HOH Z 313 " =    2.166
peak=    3.110 closest distance to " N   THR A  52 " =    1.093
peak=    3.108 closest distance to " CB  VAL A 265 " =    1.305
peak=    3.106 closest distance to " CB  SER A  28 " =    1.024
peak=    3.102 closest distance to " CA  ILE A  33 " =    1.549
peak=    3.102 closest distance to " N   TYR A 116 " =    1.867
peak=    3.094 closest distance to " O   HOH Z 154 " =    2.628
peak=    3.092 closest distance to " CA  THR A 221 " =    0.974
peak=    3.084 closest distance to " CB  GLN A 240 " =    1.606
peak=    3.083 closest distance to " O   HOH Z  14 " =    1.346
peak=    3.074 closest distance to " CA  ASP A 132 " =    1.310
peak=    3.067 closest distance to " O   HOH Z 411 " =    1.536
peak=    3.066 closest distance to " O   HOH Z 237 " =    1.890
peak=    3.064 closest distance to " ND2 ASN A  69 " =    1.612
peak=    3.062 closest distance to " NH1 ARG A  14 " =    1.265
peak=    3.057 closest distance to " CA  ALA A 158 " =    1.083
peak=    3.046 closest distance to " O   HOH Z 279 " =    2.415
peak=    3.045 closest distance to " CG AARG A 275 " =    1.156
peak=    3.045 closest distance to " ND1 HIS A  81 " =    1.326
peak=    3.042 closest distance to " N   ARG A 156 " =    1.491
peak=    3.035 closest distance to " CA  THR A 221 " =    1.301
peak=    3.019 closest distance to " O   HOH Z 428 " =    1.639

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 5.886
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 223
   mapped sites are within: 0.701 - 5.886

peak=   -4.980 closest distance to " N   ARG A 275 " =    0.858
peak=   -4.534 closest distance to " C   ASN A 285 " =    2.603
peak=   -4.391 closest distance to " O   HOH Z 166 " =    1.701
peak=   -4.258 closest distance to " N   ALA A  43 " =    2.651
peak=   -4.229 closest distance to " CD  GLN A  88 " =    0.885
peak=   -4.204 closest distance to " CA  GLU A 277 " =    1.141
peak=   -4.147 closest distance to " O   HOH Z 411 " =    4.679
peak=   -4.144 closest distance to " NH2 ARG A  66 " =    0.993
peak=   -4.123 closest distance to " O   HOH Z  37 " =    1.379
peak=   -4.114 closest distance to " O   HOH Z 120 " =    0.903
peak=   -4.081 closest distance to " O   HOH Z 290 " =    0.951
peak=   -4.065 closest distance to " OG  SER A  97 " =    2.267
peak=   -4.027 closest distance to " O   HOH Z  13 " =    1.639
peak=   -4.026 closest distance to " CD1 PHE A  59 " =    1.823
peak=   -4.021 closest distance to " CB  LEU A 167 " =    2.172
peak=   -4.014 closest distance to " O   HOH Z 184 " =    1.087
peak=   -3.994 closest distance to " O   HOH Z 128 " =    4.372
peak=   -3.935 closest distance to " O   HOH Z  11 " =    1.049
peak=   -3.911 closest distance to " CG  ASP A 231 " =    0.794
peak=   -3.896 closest distance to " NH2 ARG A  66 " =    0.928
peak=   -3.895 closest distance to " OD2 ASP A 171 " =    2.308
peak=   -3.869 closest distance to " O   HOH Z 151 " =    1.429
peak=   -3.858 closest distance to " OG1 THR A  82 " =    1.849
peak=   -3.850 closest distance to " O   HOH Z 400 " =    1.107
peak=   -3.844 closest distance to " CD2 LEU A 237 " =    2.412
peak=   -3.842 closest distance to " O   HOH Z  38 " =    0.828
peak=   -3.824 closest distance to " CG2 ILE A  49 " =    2.601
peak=   -3.794 closest distance to " CB  SER A 276 " =    0.864
peak=   -3.773 closest distance to " O   HOH Z  91 " =    2.122
peak=   -3.750 closest distance to " CA  VAL A 197 " =    0.997
peak=   -3.742 closest distance to " CA  VAL A  67 " =    2.801
peak=   -3.728 closest distance to " C   SER A 206 " =    1.454
peak=   -3.714 closest distance to " O   TYR A  15 " =    1.428
peak=   -3.708 closest distance to " OH  TYR A 169 " =    0.966
peak=   -3.697 closest distance to " O   HOH Z  52 " =    1.822
peak=   -3.696 closest distance to " C   SER A 271 " =    1.210
peak=   -3.695 closest distance to " CD  GLN A 223 " =    0.886
peak=   -3.689 closest distance to " O   HOH Z  19 " =    2.108
peak=   -3.674 closest distance to " O   HOH Z 221 " =    1.452
peak=   -3.672 closest distance to " CE  MET A  93 " =    1.344
peak=   -3.664 closest distance to " CD  ARG A  14 " =    3.305
peak=   -3.662 closest distance to " O   HOH Z 325 " =    1.650
peak=   -3.662 closest distance to " CB  SER A 146 " =    2.117
peak=   -3.656 closest distance to " O   HOH Z 418 " =    1.563
peak=   -3.653 closest distance to " O   HOH Z 210 " =    0.961
peak=   -3.650 closest distance to " CA  GLY A  23 " =    2.314
peak=   -3.643 closest distance to " O   HOH Z 414 " =    1.836
peak=   -3.642 closest distance to " OD2 ASP A 171 " =    1.852
peak=   -3.641 closest distance to " CA  ASN A 127 " =    1.064
peak=   -3.638 closest distance to " O   HOH Z 221 " =    1.279
peak=   -3.638 closest distance to " C   THR A 279 " =    1.216
peak=   -3.636 closest distance to " CD2 TRP A 274 " =    2.292
peak=   -3.634 closest distance to " O   HOH Z 348 " =    2.220
peak=   -3.633 closest distance to " O   HOH Z  71 " =    1.431
peak=   -3.630 closest distance to " O   HOH Z 423 " =    1.161
peak=   -3.625 closest distance to " O   HOH Z 350 " =    0.924
peak=   -3.616 closest distance to " O   HOH Z 407 " =    1.782
peak=   -3.610 closest distance to " CA  GLY A 203 " =    2.301
peak=   -3.605 closest distance to " O   HOH Z 118 " =    5.746
peak=   -3.603 closest distance to " O   PRO A 198 " =    1.359
peak=   -3.600 closest distance to " O   GLY A 196 " =    1.159
peak=   -3.593 closest distance to " O   HOH Z 109 " =    3.334
peak=   -3.592 closest distance to " CG2BVAL A  41 " =    2.679
peak=   -3.583 closest distance to " O   ALA A   1 " =    2.059
peak=   -3.569 closest distance to " O   HOH Z 388 " =    1.937
peak=   -3.562 closest distance to " O   HOH Z 414 " =    1.429
peak=   -3.558 closest distance to " CD1 LEU A  25 " =    2.524
peak=   -3.545 closest distance to " N   GLN A  58 " =    1.532
peak=   -3.537 closest distance to " O   HOH Z  60 " =    2.354
peak=   -3.530 closest distance to " C   HIS A 108 " =    1.097
peak=   -3.528 closest distance to " O   HOH Z 351 " =    1.683
peak=   -3.524 closest distance to " OE1 GLN A  88 " =    0.956
peak=   -3.520 closest distance to " CA  SER A 164 " =    2.103
peak=   -3.509 closest distance to " O   ALA A   7 " =    1.701
peak=   -3.509 closest distance to " O   HOH Z 185 " =    2.455
peak=   -3.503 closest distance to " CD  GLN A  77 " =    1.115
peak=   -3.493 closest distance to " CG  GLN A  58 " =    1.118
peak=   -3.492 closest distance to " O   PHE A 218 " =    1.377
peak=   -3.491 closest distance to " O   HOH Z   7 " =    0.988
peak=   -3.486 closest distance to " O   HOH Z  10 " =    1.613
peak=   -3.470 closest distance to " CG2 THR A 221 " =    2.241
peak=   -3.463 closest distance to " O   HOH Z 148 " =    3.154
peak=   -3.454 closest distance to " CA  TYR A  68 " =    2.818
peak=   -3.454 closest distance to " OD1 ASN A 148 " =    1.628
peak=   -3.443 closest distance to " O   HOH Z 251 " =    1.653
peak=   -3.443 closest distance to " O   VAL A 174 " =    2.031
peak=   -3.442 closest distance to " O   HOH Z  17 " =    1.209
peak=   -3.437 closest distance to " OXT GLY A 302 " =    2.963
peak=   -3.431 closest distance to " O   GLY A 118 " =    2.361
peak=   -3.431 closest distance to " OG  SER A  32 " =    1.193
peak=   -3.426 closest distance to " CB  CYS A 254 " =    2.185
peak=   -3.406 closest distance to " O   HOH Z 308 " =    1.527
peak=   -3.404 closest distance to " CB  ALA A 161 " =    2.708
peak=   -3.400 closest distance to " CD2 PHE A  59 " =    2.278
peak=   -3.400 closest distance to " O   HOH Z 377 " =    0.905
peak=   -3.394 closest distance to " O   ALA A 256 " =    1.646
peak=   -3.394 closest distance to " O   HOH Z 231 " =    2.036
peak=   -3.391 closest distance to " OD2 ASP A 298 " =    1.027
peak=   -3.390 closest distance to " O   HOH Z 103 " =    2.213
peak=   -3.390 closest distance to " CD1 LEU A 167 " =    2.177
peak=   -3.381 closest distance to " CG  MET A 105 " =    0.894
peak=   -3.381 closest distance to " CB  ALA A  10 " =    1.847
peak=   -3.380 closest distance to " CG  ASP A  50 " =    2.499
peak=   -3.379 closest distance to " CB  ASN A 170 " =    2.130
peak=   -3.374 closest distance to " CD  PRO A 198 " =    1.083
peak=   -3.370 closest distance to " CB  ALA A  43 " =    2.634
peak=   -3.368 closest distance to " CD2 PHE A  61 " =    1.876
peak=   -3.366 closest distance to " O   HOH Z  86 " =    2.653
peak=   -3.365 closest distance to " O   HOH Z 423 " =    1.925
peak=   -3.363 closest distance to " CD2 LEU A 300 " =    2.717
peak=   -3.361 closest distance to " CA  GLY A 241 " =    2.274
peak=   -3.359 closest distance to " CH2 TRP A 177 " =    2.011
peak=   -3.358 closest distance to " CD  LYS A 119 " =    0.956
peak=   -3.349 closest distance to " CG  ARG A 269 " =    2.413
peak=   -3.345 closest distance to " O   HOH Z 222 " =    1.226
peak=   -3.344 closest distance to " N   SER A 134 " =    1.161
peak=   -3.340 closest distance to " O   HOH Z 313 " =    1.326
peak=   -3.339 closest distance to " O   HOH Z  83 " =    1.543
peak=   -3.338 closest distance to " CA  SER A 276 " =    1.359
peak=   -3.334 closest distance to " O   HOH Z 124 " =    1.519
peak=   -3.333 closest distance to " O   HOH Z 213 " =    1.596
peak=   -3.332 closest distance to " O   HOH Z  93 " =    1.749
peak=   -3.330 closest distance to " O   HOH Z 399 " =    2.318
peak=   -3.329 closest distance to " NZ  LYS A 119 " =    1.491
peak=   -3.327 closest distance to " ND2BASN A 224 " =    2.173
peak=   -3.321 closest distance to " N   ALA A 226 " =    2.108
peak=   -3.314 closest distance to " N   THR A 157 " =    1.839
peak=   -3.306 closest distance to " O   HOH Z 243 " =    2.360
peak=   -3.306 closest distance to " OE2 GLU A   2 " =    1.483
peak=   -3.302 closest distance to " CE2 PHE A  38 " =    1.898
peak=   -3.302 closest distance to " CG  LYS A 166 " =    1.911
peak=   -3.301 closest distance to " O   GLY A 136 " =    2.581
peak=   -3.301 closest distance to " O   HOH Z   7 " =    1.539
peak=   -3.297 closest distance to " CD1 PHE A  16 " =    2.533
peak=   -3.295 closest distance to " O   HOH Z 198 " =    1.646
peak=   -3.291 closest distance to " OD1 ASP A 191 " =    1.823
peak=   -3.291 closest distance to " O   HOH Z 231 " =    1.536
peak=   -3.290 closest distance to " CD  ARG A 219 " =    2.604
peak=   -3.289 closest distance to " OD2 ASP A 171 " =    2.781
peak=   -3.283 closest distance to " O   HOH Z 234 " =    4.288
peak=   -3.282 closest distance to " O   HOH Z  94 " =    1.864
peak=   -3.280 closest distance to " O   HOH Z  30 " =    0.986
peak=   -3.278 closest distance to " CD  GLN A 194 " =    2.112
peak=   -3.277 closest distance to " ND2 ASN A  45 " =    1.740
peak=   -3.275 closest distance to " O   HOH Z 422 " =    1.084
peak=   -3.272 closest distance to " CB  TYR A  15 " =    2.369
peak=   -3.270 closest distance to " CB  PRO A 243 " =    2.735
peak=   -3.270 closest distance to " SG  CYS A 254 " =    3.328
peak=   -3.270 closest distance to " OG ASER A 134 " =    1.230
peak=   -3.258 closest distance to " O   HOH Z  33 " =    0.701
peak=   -3.253 closest distance to " CA  VAL A 232 " =    2.425
peak=   -3.249 closest distance to " C   ASN A 187 " =    1.959
peak=   -3.248 closest distance to " CA  TYR A  68 " =    2.689
peak=   -3.244 closest distance to " CD1 TYR A 247 " =    2.414
peak=   -3.243 closest distance to " O   HOH Z 157 " =    3.671
peak=   -3.240 closest distance to " O   HOH Z 377 " =    2.125
peak=   -3.233 closest distance to " O   HOH Z 200 " =    1.290
peak=   -3.232 closest distance to " CD  GLU A 236 " =    1.035
peak=   -3.231 closest distance to " O   HOH Z 207 " =    2.043
peak=   -3.229 closest distance to " N   LEU A 261 " =    1.165
peak=   -3.222 closest distance to " O   HOH Z 150 " =    1.658
peak=   -3.219 closest distance to " CE2 TYR A  30 " =    2.663
peak=   -3.218 closest distance to " OG  SER A  62 " =    4.927
peak=   -3.216 closest distance to " CG  PRO A 243 " =    1.492
peak=   -3.211 closest distance to " O   TRP A  92 " =    1.887
peak=   -3.209 closest distance to " CD1 LEU A 228 " =    2.531
peak=   -3.209 closest distance to " CD2 LEU A 167 " =    1.791
peak=   -3.206 closest distance to " O   HOH Z 396 " =    1.442
peak=   -3.205 closest distance to " CG  TRP A 266 " =    1.862
peak=   -3.194 closest distance to " O   HOH Z 136 " =    1.702
peak=   -3.189 closest distance to " O   HOH Z 127 " =    1.537
peak=   -3.175 closest distance to " O   HOH Z 186 " =    3.753
peak=   -3.174 closest distance to " CD  LYS A 289 " =    2.345
peak=   -3.169 closest distance to " CA  ALA A   8 " =    1.683
peak=   -3.168 closest distance to " O   HOH Z 119 " =    4.443
peak=   -3.160 closest distance to " O   HOH Z 252 " =    1.135
peak=   -3.159 closest distance to " ND2 ASN A  60 " =    1.812
peak=   -3.155 closest distance to " ND2 ASN A  60 " =    1.365
peak=   -3.153 closest distance to " O   HOH Z  39 " =    1.704
peak=   -3.149 closest distance to " CD  ARG A 195 " =    5.003
peak=   -3.148 closest distance to " CD1 TRP A 179 " =    1.026
peak=   -3.148 closest distance to " CD2 HIS A 115 " =    1.057
peak=   -3.147 closest distance to " O   VAL A 125 " =    2.151
peak=   -3.143 closest distance to " O   HOH Z 140 " =    1.116
peak=   -3.142 closest distance to " O   THR A  18 " =    1.588
peak=   -3.138 closest distance to " OG ASER A  12 " =    1.684
peak=   -3.138 closest distance to " CG  GLN A 223 " =    1.287
peak=   -3.137 closest distance to " NH2 ARG A 269 " =    2.441
peak=   -3.132 closest distance to " CA  SER A 216 " =    0.971
peak=   -3.131 closest distance to " O   HOH Z 384 " =    2.272
peak=   -3.128 closest distance to " O   HOH Z 174 " =    1.865
peak=   -3.128 closest distance to " O   HOH Z 182 " =    0.875
peak=   -3.125 closest distance to " CG2BVAL A  41 " =    1.354
peak=   -3.122 closest distance to " O   ASP A 171 " =    1.023
peak=   -3.121 closest distance to " O   HOH Z 166 " =    2.419
peak=   -3.118 closest distance to " O   HOH Z 280 " =    1.875
peak=   -3.117 closest distance to " O   HOH Z 380 " =    4.241
peak=   -3.108 closest distance to " O   HOH Z 402 " =    1.142
peak=   -3.104 closest distance to " O   HOH Z 423 " =    2.044
peak=   -3.103 closest distance to " O   HOH Z 215 " =    3.439
peak=   -3.103 closest distance to " O   HOH Z  76 " =    2.109
peak=   -3.099 closest distance to " O   ARG A 275 " =    1.769
peak=   -3.097 closest distance to " O   HOH Z 401 " =    1.326
peak=   -3.096 closest distance to " CD  GLN A  11 " =    0.970
peak=   -3.095 closest distance to " O   HOH Z   6 " =    1.619
peak=   -3.094 closest distance to " OG  SER A  87 " =    1.614
peak=   -3.092 closest distance to " CE3 TRP A 150 " =    1.945
peak=   -3.090 closest distance to " CA  HIS A  86 " =    2.176
peak=   -3.086 closest distance to " O   HOH Z 191 " =    5.886
peak=   -3.084 closest distance to " O   HOH Z 436 " =    1.294
peak=   -3.082 closest distance to " O   HOH Z 134 " =    2.061
peak=   -3.077 closest distance to " CG  LYS A 193 " =    2.653
peak=   -3.040 closest distance to " O   HOH Z 105 " =    1.916
peak=   -3.031 closest distance to " CG  GLU A   2 " =    1.597
peak=   -3.025 closest distance to " O   HOH Z 393 " =    1.071
peak=   -3.019 closest distance to " O   ALA A  34 " =    1.995
peak=   -3.015 closest distance to " O   HOH Z 259 " =    2.303
peak=   -3.011 closest distance to " O   HOH Z 436 " =    1.630

================= 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    :  0.4775 0.4598   6.287941e+00   6.267547e+00
   1_bss:  0.4709 0.4510   6.284271e+00   6.258447e+00
   1_xyz:  0.3820 0.4177   6.158652e+00   6.207698e+00
   1_adp:  0.3531 0.4218   6.120362e+00   6.210083e+00
   1_occ:  0.3530 0.4224   6.120000e+00   6.210687e+00
   2_bss:  0.3529 0.4194   6.121059e+00   6.208863e+00
   2_xyz:  0.2802 0.3347   5.925267e+00   6.058299e+00
   2_adp:  0.2525 0.3261   5.870332e+00   6.043287e+00
   2_occ:  0.2522 0.3253   5.869357e+00   6.042181e+00
   3_bss:  0.2523 0.3242   5.867210e+00   6.040407e+00
   3_xyz:  0.2090 0.2668   5.689464e+00   5.874773e+00
   3_adp:  0.1944 0.2526   5.631679e+00   5.826520e+00
   3_occ:  0.1943 0.2524   5.631473e+00   5.826117e+00
   4_bss:  0.1945 0.2523   5.631507e+00   5.826314e+00
   4_xyz:  0.1578 0.2085   5.440828e+00   5.661061e+00
   4_adp:  0.1468 0.1942   5.377327e+00   5.588233e+00
   4_occ:  0.1467 0.1941   5.376960e+00   5.587687e+00
   5_bss:  0.1472 0.1948   5.379516e+00   5.588210e+00
   5_xyz:  0.1357 0.1830   5.309227e+00   5.525737e+00
   5_adp:  0.1334 0.1799   5.296766e+00   5.512018e+00
   5_occ:  0.1333 0.1799   5.296722e+00   5.512170e+00
   5_bss:  0.1333 0.1799   5.296438e+00   5.511605e+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:  0.273  16.583  -0.283   3.719  -0.559   0.000  -0.000  -0.000
   1_xyz:  0.273  16.583  -0.283   3.719  -0.559   0.000  -0.000  -0.000
   1_adp:  0.273  16.583  -0.283   3.719  -0.559   0.000  -0.000  -0.000
   1_occ:  0.273  16.583  -0.283   3.719  -0.559   0.000  -0.000  -0.000
   2_bss:  0.315  58.238  -0.701   2.208  -0.398   0.000  -0.000  -0.000
   2_xyz:  0.315  58.238  -0.701   2.208  -0.398   0.000  -0.000  -0.000
   2_adp:  0.315  58.238  -0.701   2.208  -0.398   0.000  -0.000  -0.000
   2_occ:  0.315  58.238  -0.701   2.208  -0.398   0.000  -0.000  -0.000
   3_bss:  0.323  68.598  -0.633   1.019  -0.564   0.000  -0.000  -0.000
   3_xyz:  0.323  68.598  -0.633   1.019  -0.564   0.000  -0.000  -0.000
   3_adp:  0.323  68.598  -0.633   1.019  -0.564   0.000  -0.000  -0.000
   3_occ:  0.323  68.598  -0.633   1.019  -0.564   0.000  -0.000  -0.000
   4_bss:  0.333  76.749  -1.190   0.134  -1.011   0.000  -0.000  -0.000
   4_xyz:  0.333  76.749  -1.190   0.134  -1.011   0.000  -0.000  -0.000
   4_adp:  0.333  76.749  -1.190   0.134  -1.011   0.000  -0.000  -0.000
   4_occ:  0.333  76.749  -1.190   0.134  -1.011   0.000  -0.000  -0.000
   5_bss:  0.327  71.341  -1.486  -0.560  -1.133  -0.000  -0.000  -0.000
   5_xyz:  0.327  71.341  -1.486  -0.560  -1.133  -0.000  -0.000  -0.000
   5_adp:  0.327  71.341  -1.486  -0.560  -1.133  -0.000  -0.000  -0.000
   5_occ:  0.327  71.341  -1.486  -0.560  -1.133  -0.000  -0.000  -0.000
   5_bss:  0.323  64.562  -1.661  -0.900  -1.240  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.266 0.4554  0.6159    68929.107
   1_bss:  54.610 0.4622  0.6453    65960.955
   1_xyz:  48.229 0.5419  0.7433    52756.883
   1_adp:  48.832 0.5337  0.7310    53076.520
   1_occ:  48.917 0.5326  0.7287    53211.240
   2_bss:  48.700 0.5353  0.7213    52821.074
   2_xyz:  36.578 0.6820  0.8897    31652.124
   2_adp:  35.242 0.6979  0.8908    30244.230
   2_occ:  35.173 0.6987  0.8908    30150.129
   3_bss:  34.987 0.7006  0.8806    29795.131
   3_xyz:  27.410 0.7853  0.9567    19054.063
   3_adp:  25.426 0.8071  0.9603    17105.953
   3_occ:  25.409 0.8073  0.9603    17091.150
   4_bss:  25.360 0.8078  0.9402    17039.391
   4_xyz:  20.744 0.8531  0.9702    11352.749
   4_adp:  18.697 0.8737  0.9736     9857.721
   4_occ:  18.690 0.8738  0.9737     9857.904
   5_bss:  18.721 0.8736  0.9615     9903.129
   5_xyz:  17.221 0.8873  0.9689     8611.003
   5_adp:  16.857 0.8910  0.9647     8439.437
   5_occ:  16.858 0.8910  0.9646     8443.566
   5_bss:  16.846 0.8911  0.9568     8427.447
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8622e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8622e-01
   1_xyz:   1.616  0.012  0.099 15.901  0.006  4.108   1.3863e-01
   1_adp:   1.616  0.012  0.099 15.901  0.006  4.108   1.3863e-01
   1_occ:   1.616  0.012  0.099 15.901  0.006  4.108   1.3863e-01
   2_bss:   1.616  0.012  0.099 15.901  0.006  4.108   1.3863e-01
   2_xyz:   1.634  0.012  0.106 15.874  0.007  4.121   1.4134e-01
   2_adp:   1.634  0.012  0.106 15.874  0.007  4.121   1.4134e-01
   2_occ:   1.634  0.012  0.106 15.874  0.007  4.121   1.4134e-01
   3_bss:   1.634  0.012  0.106 15.874  0.007  4.121   1.4134e-01
   3_xyz:   1.070  0.008  0.069 14.678  0.004  4.125   6.8603e-02
   3_adp:   1.070  0.008  0.069 14.678  0.004  4.125   6.8603e-02
   3_occ:   1.070  0.008  0.069 14.678  0.004  4.125   6.8603e-02
   4_bss:   1.070  0.008  0.069 14.678  0.004  4.125   6.8603e-02
   4_xyz:   1.155  0.009  0.080 14.663  0.004  4.115   7.5991e-02
   4_adp:   1.155  0.009  0.080 14.663  0.004  4.115   7.5991e-02
   4_occ:   1.155  0.009  0.080 14.663  0.004  4.115   7.5991e-02
   5_bss:   1.155  0.009  0.080 14.663  0.004  4.115   7.5991e-02
   5_xyz:   1.029  0.008  0.073 14.396  0.004  4.122   6.1447e-02
   5_adp:   1.029  0.008  0.073 14.396  0.004  4.122   6.1447e-02
   5_occ:   1.029  0.008  0.073 14.396  0.004  4.122   6.1447e-02
   5_bss:   1.029  0.008  0.073 14.396  0.004  4.122   6.1447e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.329   2.4449e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.329   2.4449e-01
   1_xyz:  10.590  0.065  0.368 86.616  0.021  2.044   1.1011e-01
   1_adp:  10.590  0.065  0.368 86.616  0.021  2.044   1.1011e-01
   1_occ:  10.590  0.065  0.368 86.616  0.021  2.044   1.1011e-01
   2_bss:  10.590  0.065  0.368 86.616  0.021  2.044   1.1011e-01
   2_xyz:   9.337  0.058  0.350 83.133  0.057  2.074   1.0553e-01
   2_adp:   9.337  0.058  0.350 83.133  0.057  2.074   1.0553e-01
   2_occ:   9.337  0.058  0.350 83.133  0.057  2.074   1.0553e-01
   3_bss:   9.337  0.058  0.350 83.133  0.057  2.074   1.0553e-01
   3_xyz:   7.500  0.041  0.212 84.895  0.026  2.262   1.1340e-01
   3_adp:   7.500  0.041  0.212 84.895  0.026  2.262   1.1340e-01
   3_occ:   7.500  0.041  0.212 84.895  0.026  2.262   1.1340e-01
   4_bss:   7.500  0.041  0.212 84.895  0.026  2.262   1.1340e-01
   4_xyz:   7.559  0.061  0.245 89.622  0.034  2.226   5.4775e-02
   4_adp:   7.559  0.061  0.245 89.622  0.034  2.226   5.4775e-02
   4_occ:   7.559  0.061  0.245 89.622  0.034  2.226   5.4775e-02
   5_bss:   7.559  0.061  0.245 89.622  0.034  2.226   5.4775e-02
   5_xyz:   7.873  0.046  0.217 83.357  0.037  2.347   4.1213e-02
   5_adp:   7.873  0.046  0.217 83.357  0.037  2.347   4.1213e-02
   5_occ:   7.873  0.046  0.217 83.357  0.037  2.347   4.1213e-02
   5_bss:   7.873  0.046  0.217 83.357  0.037  2.347   4.1213e-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: 110.86   0.00  17.82 110.86   0.00  14.42  69.90   0.00  36.36
   1_occ: 110.86   0.00  17.82 110.86   0.00  14.42  69.90   0.00  36.36
   2_bss: 110.86   0.00  17.82 110.86   0.00  14.42  69.90   0.00  36.36
   2_xyz: 110.86   0.00  17.82 110.86   0.00  14.42  69.90   0.00  36.36
   2_adp:  92.09   0.00  19.02  86.99   0.00  14.81  92.09   1.88  41.96
   2_occ:  92.09   0.00  19.02  86.99   0.00  14.81  92.09   1.88  41.96
   3_bss:  92.09   0.00  19.02  86.99   0.00  14.81  92.09   1.88  41.96
   3_xyz:  92.09   0.00  19.02  86.99   0.00  14.81  92.09   1.88  41.96
   3_adp: 108.65   0.00  19.27 108.65   0.00  14.20 101.18   3.41  46.89
   3_occ: 108.65   0.00  19.27 108.65   0.00  14.20 101.18   3.41  46.89
   4_bss: 108.65   0.00  19.27 108.65   0.00  14.20 101.18   3.41  46.89
   4_xyz: 108.65   0.00  19.27 108.65   0.00  14.20 101.18   3.41  46.89
   4_adp: 109.25   0.85  18.06 109.25   0.85  13.08 105.82   4.73  45.15
   4_occ: 109.25   0.85  18.06 109.25   0.85  13.08 105.82   4.73  45.15
   5_bss: 109.25   0.85  18.06 109.25   0.85  13.08 105.82   4.73  45.15
   5_xyz: 109.25   0.85  18.06 109.25   0.85  13.08 105.82   4.73  45.15
   5_adp: 109.76   1.04  17.43 109.76   1.04  12.68 107.10   4.82  43.29
   5_occ: 109.76   1.04  17.43 109.76   1.04  12.68 107.10   4.82  43.29
   5_bss: 109.73   1.00  17.40 109.73   1.00  12.65 107.06   4.78  43.26
------------------------------------------------------------------------
 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:    2.187    0.019    0.345
   1_adp:    2.187    0.019    0.345
   1_occ:    2.187    0.019    0.345
   2_bss:    2.187    0.019    0.345
   2_xyz:    1.813    0.054    0.667
   2_adp:    1.813    0.054    0.667
   2_occ:    1.813    0.054    0.667
   3_bss:    1.813    0.054    0.667
   3_xyz:    1.744    0.061    0.751
   3_adp:    1.744    0.061    0.751
   3_occ:    1.744    0.061    0.751
   4_bss:    1.744    0.061    0.751
   4_xyz:    1.723    0.033    0.847
   4_adp:    1.723    0.033    0.847
   4_occ:    1.723    0.033    0.847
   5_bss:    1.723    0.033    0.847
   5_xyz:    1.760    0.031    0.879
   5_adp:    1.760    0.031    0.879
   5_occ:    1.760    0.031    0.879
   5_bss:    1.760    0.031    0.879
------------------------------------------------------------------------

CPU time actual refinement: 364.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1201/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_1201/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1201/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1201/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1201/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 364.37 
  Macro-tasks:
    bulk solvent and scale       = 50.65  
    individual site refinement   = 149.07 
    weights calculation          = 30.73  
    collect and process          = 6.40   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 236.96 
  Micro-tasks:
    mask                            = 2.52   
    f_calc                          = 116.16 
    alpha_beta                      = 8.23   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 124.06 
    fmodel                         = 8.10   
    r_factors                      = 0.28   
    phase_errors                   = 10.44  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 271.14 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.166 micro seconds
Total CPU time: 6.30 minutes
from_scatterers_fft:    630 calls, 115.83 s
gradients_fft:          575 calls, 111.20 s

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

# Date 2008-01-16 Time 06:41:24 PST -0800 (1200494484.57 s)
Start R-work = 0.4775, R-free = 0.4598 (no bulk solvent and anisotropic scale)
Final R-work = 0.1514, R-free = 0.1969 (no bulk solvent and anisotropic scale)

Start R-work = 0.4709, R-free = 0.4510
Final R-work = 0.1333, R-free = 0.1799