# Date 2008-01-16 Time 04:06:06 PST -0800 (1200485166.39 s)
#phil __OFF__

Command line arguments: "../173.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7948
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 173

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.6953, 87.6859, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.831 1.96083
Completeness in resolution range: 0.939611
Completeness with d_max=infinity: 0.936735

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8310
                             d_min =   1.9608

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.831 1.96083
Completeness in resolution range: 0.939611
Completeness with d_max=infinity: 0.936735

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8314 -  4.1956 [2195/2222]  1974   221  10.1%
  bin  2:  4.1956 -  3.3427 [2100/2116]  1886   214  10.2%
  bin  3:  3.3427 -  2.9238 [2077/2096]  1876   201   9.7%
  bin  4:  2.9238 -  2.6582 [2054/2084]  1847   207  10.1%
  bin  5:  2.6582 -  2.4686 [2031/2050]  1826   205  10.1%
  bin  6:  2.4686 -  2.3236 [2032/2068]  1826   206  10.1%
  bin  7:  2.3236 -  2.2077 [2028/2062]  1835   193   9.5%
  bin  8:  2.2077 -  2.1118 [2016/2050]  1801   215  10.7%
  bin  9:  2.1118 -  2.0307 [2014/2041]  1819   195   9.7%
  bin 10:  2.0307 -  1.9608 [1042/2059]   940   102   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_173/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:
        1.42 -     2.11: 17
        2.11 -     2.81: 825
        2.81 -     3.51: 4503
        3.51 -     4.20: 9382
        4.20 -     4.90: 13823
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.416 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.486 3.120 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.508 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.591 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.680 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28545 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_173/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_173/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.69535 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3846   r_free= 0.3775   ksol= 0.00   Bsol= 0.00   scale= 0.949    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.163204                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6795 0.99   1421  158 0.2996 0.2998      6.4089      6.3867|
|  2:  4.6795 -  3.7338 0.99   1375  153 0.2986 0.3081      6.5432      6.5957|
|  3:  3.7338 -  3.2675 0.99   1339  149 0.3508 0.3338      6.4948      6.5114|
|  4:  3.2675 -  2.9714 0.99   1333  143 0.3675 0.3956      6.3648        6.45|
|  5:  2.9714 -  2.7599 0.99   1310  153 0.3911 0.3679      6.2153      6.2038|
|  6:  2.7599 -  2.5981 0.99   1330  145 0.4082 0.4462      6.1393      6.0832|
|  7:  2.5981 -  2.4686 0.99   1301  147 0.4148 0.3402      6.1218      5.9828|
|  8:  2.4686 -  2.3616 0.98   1313  142 0.4369 0.4070       6.098      6.1109|
|  9:  2.3616 -  2.2710 0.98   1314  146 0.4519 0.4467      6.0556      6.0727|
| 10:  2.2710 -  2.1929 0.98   1289  137 0.4482 0.3860      6.0327      5.9693|
| 11:  2.1929 -  2.1245 1.00   1308  158 0.4504 0.4499      5.9503      5.9532|
| 12:  2.1245 -  2.0640 0.97   1289  135 0.4551 0.4403      5.9071      5.9366|
| 13:  2.0640 -  2.0098 0.94   1241  136 0.4533 0.4888       5.831      5.7803|
| 14:  2.0098 -  1.9608 0.36    467   57 0.4497 0.4199      5.8401      5.7011|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8314 -  4.6795  1421   158  0.78  26.93   0.86     0.80      46308.77|
|  2:  4.6795 -  3.7338  1375   153  0.80  26.19   0.97     0.89      63988.42|
|  3:  3.7338 -  3.2675  1339   149  0.73  32.85   0.97     0.90      67444.89|
|  4:  3.2675 -  2.9714  1333   143  0.68  37.56   0.96     0.85      60947.78|
|  5:  2.9714 -  2.7599  1310   153  0.62  42.30   0.97     0.81      48688.40|
|  6:  2.7599 -  2.5981  1330   145  0.61  43.27   0.95     0.80      41805.86|
|  7:  2.5981 -  2.4686  1301   147  0.63  41.82   0.97     0.82      36826.93|
|  8:  2.4686 -  2.3616  1313   142  0.61  43.64   0.98     0.81      33906.85|
|  9:  2.3616 -  2.2710  1314   146  0.60  44.11   0.97     0.82      32435.09|
| 10:  2.2710 -  2.1929  1289   137  0.58  45.50   1.00     0.80      30573.27|
| 11:  2.1929 -  2.1245  1308   158  0.56  47.28   0.98     0.84      31210.24|
| 12:  2.1245 -  2.0640  1289   135  0.54  49.51   1.00     0.82      29689.73|
| 13:  2.0640 -  2.0098  1241   136  0.50  52.50   0.99     0.76      27754.38|
| 14:  2.0098 -  1.9608   467    57  0.48  53.45   1.04     0.62      23600.54|
|alpha:            min =        0.62 max =            0.90 mean =         0.82|
|beta:             min =    23600.54 max =        67444.89 mean =     42186.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.14|
|phase err.(test): min =        0.00 max =           89.23 mean =        41.07|
|-----------------------------------------------------------------------------|

============================== 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 = 4.494026              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.138   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.882293              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.908   (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 |  1.416 -  1.764:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.764 -  2.113:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.113 -  2.461:       29 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.461 -  2.810:      796 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.810 -  3.158:     2071 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.158 -  3.506:     2432 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.506 -  3.855:     4610 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.855 -  4.203:     4772 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.203 -  4.552:     6275 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.552 -  4.900:     7548 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.416 |       0.559 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.675)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3846   r_free= 0.3775   ksol= 0.00   Bsol= 0.00   scale= 0.949    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.163204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3742   r_free= 0.3668   ksol= 0.33   Bsol= 31.85   scale= 0.976   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.10,-2.17,2.03,-0.00,0.00,0.00); trace/3= -0.01                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.147071                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.886514              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.805   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.505365              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.555   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3742      final r-factor (work) = 0.2368          |
| start r-factor (free) = 0.3668      final r-factor (free) = 0.2684          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1376 = 3.89 * 0.50 * 6.1497 + 1.00 * 0.1871                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5775 = 3.89 * 0.50 * 5.9150 + 1.00 * 0.0832                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2368      final r-factor (work) = 0.2149          |
| start r-factor (free) = 0.2684      final r-factor (free) = 0.2772          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9954 = 0.51 * 1.00 * 5.9150 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8903 = 0.51 * 1.00 * 5.6979 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.675)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.80   17.47    None  None   None       |
|    all(noH): 2823   0      0.00    73.80   17.47    None  None   None       |
|    Sol.    : 438    0      5.06    72.79   39.20    None  None   None       |
|    Mac.    : 2385   0      0.00    73.80   13.48    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 -   7.380:  523   |   5:    36.902 -  44.282:  117        |
|      1:     7.380 -  14.761: 1140   |   6:    44.282 -  51.662:   86        |
|      2:    14.761 -  22.141:  507   |   7:    51.662 -  59.042:   59        |
|      3:    22.141 -  29.521:  208   |   8:    59.042 -  66.423:   42        |
|      4:    29.521 -  36.902:  129   |   9:    66.423 -  73.803:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2149 r_free = 0.2772             target_work(ml) = 5.711         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2147 r_free = 0.2774             target_work(ml) = 5.711         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2147   r_free= 0.2774   ksol= 0.33   Bsol= 31.85   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.10,-2.17,2.03,-0.00,0.00,0.00); trace/3= -0.01                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.710639                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2115   r_free= 0.2744   ksol= 0.33   Bsol= 48.99   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.46,-0.04,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.703671                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.311882              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.372   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.234900              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.752  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2115      final r-factor (work) = 0.1548          |
| start r-factor (free) = 0.2744      final r-factor (free) = 0.2043          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6784 = 2.31 * 0.50 * 5.7054 + 1.00 * 0.0832                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5093 = 2.31 * 0.50 * 5.5864 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1548      final r-factor (work) = 0.1466          |
| start r-factor (free) = 0.2043      final r-factor (free) = 0.1926          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3229 = 0.23 * 1.00 * 5.5864 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2753 = 0.23 * 1.00 * 5.3947 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.675)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.56   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    77.56   17.20    None  None   None       |
|    Sol.    : 438    0      4.94    71.61   39.25    None  None   None       |
|    Mac.    : 2385   0      0.00    77.56   13.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.756:  472   |   5:    38.778 -  46.533:  117        |
|      1:     7.756 -  15.511: 1362   |   6:    46.533 -  54.289:   94        |
|      2:    15.511 -  23.267:  429   |   7:    54.289 -  62.045:   56        |
|      3:    23.267 -  31.022:  156   |   8:    62.045 -  69.800:   21        |
|      4:    31.022 -  38.778:  113   |   9:    69.800 -  77.556:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1466 r_free = 0.1926             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1464 r_free = 0.1925             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1925   ksol= 0.33   Bsol= 48.99   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.46,-0.04,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.365162                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1923   ksol= 0.33   Bsol= 48.99   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-2.42,-0.54,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.363068                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.864549              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.592  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268245              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.696  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1464      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1923      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4762 = 3.86 * 0.50 * 5.3950 + 1.00 * 0.0517                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2607 = 3.86 * 0.50 * 5.2750 + 1.00 * 0.0679                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4230 = 0.27 * 1.00 * 5.2750 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3954 = 0.27 * 1.00 * 5.1720 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.675)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.37    80.17   17.07    None  None   None       |
|    all(noH): 2823   0      1.37    80.17   17.07    None  None   None       |
|    Sol.    : 438    0      5.20    73.77   39.36    None  None   None       |
|    Mac.    : 2385   0      1.37    80.17   12.97    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:     1.372 -   9.252:  822   |   5:    40.770 -  48.650:  109        |
|      1:     9.252 -  17.131: 1200   |   6:    48.650 -  56.529:   88        |
|      2:    17.131 -  25.011:  299   |   7:    56.529 -  64.409:   49        |
|      3:    25.011 -  32.890:  127   |   8:    64.409 -  72.288:   14        |
|      4:    32.890 -  40.770:  111   |   9:    72.288 -  80.168:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1579             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1580             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1580   ksol= 0.33   Bsol= 48.99   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-2.42,-0.54,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.160688                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1581   ksol= 0.33   Bsol= 48.99   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-2.42,-0.54,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161060                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.429305              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.556  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205667              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.808  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3507 = 2.43 * 0.50 * 5.1725 + 1.00 * 0.0679                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3131 = 2.43 * 0.50 * 5.1470 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0665 = 0.21 * 1.00 * 5.1470 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0639 = 0.21 * 1.00 * 5.1364 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.675)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.77    80.63   16.77    None  None   None       |
|    all(noH): 2823   0      1.77    80.63   16.77    None  None   None       |
|    Sol.    : 438    0      4.02    72.93   38.33    None  None   None       |
|    Mac.    : 2385   0      1.77    80.63   12.81    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:     1.772 -   9.658:  925   |   5:    41.200 -  49.085:   91        |
|      1:     9.658 -  17.543: 1143   |   6:    49.085 -  56.971:   82        |
|      2:    17.543 -  25.429:  274   |   7:    56.971 -  64.856:   37        |
|      3:    25.429 -  33.314:  125   |   8:    64.856 -  72.742:   12        |
|      4:    33.314 -  41.200:  130   |   9:    72.742 -  80.627:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1547             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1548             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1548   ksol= 0.33   Bsol= 48.99   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-2.42,-0.54,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135465                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1548   ksol= 0.32   Bsol= 48.99   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-2.42,-0.54,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135403                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.380823              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.172  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.923297              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.672  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1756 = 2.38 * 0.50 * 5.1362 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1685 = 2.38 * 0.50 * 5.1286 + 1.00 * 0.0633                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7427 = 0.92 * 1.00 * 5.1286 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7407 = 0.92 * 1.00 * 5.1251 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.675)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    85.22   16.85    None  None   None       |
|    all(noH): 2823   0      0.87    85.22   16.85    None  None   None       |
|    Sol.    : 438    0      5.59    76.26   39.29    None  None   None       |
|    Mac.    : 2385   0      0.87    85.22   12.73    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:     0.869 -   9.304:  886   |   5:    43.047 -  51.482:   91        |
|      1:     9.304 -  17.740: 1194   |   6:    51.482 -  59.918:   82        |
|      2:    17.740 -  26.175:  266   |   7:    59.918 -  68.353:   34        |
|      3:    26.175 -  34.611:  127   |   8:    68.353 -  76.789:   11        |
|      4:    34.611 -  43.047:  130   |   9:    76.789 -  85.224:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1079 r_free = 0.1557             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1079 r_free = 0.1556             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1556   ksol= 0.32   Bsol= 48.99   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-2.42,-0.54,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129507                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6795 0.99   1421  158 0.0986 0.1304      5.4012      5.5724|
|  2:  4.6795 -  3.7338 0.99   1375  153 0.0839 0.1104      5.4247      5.6216|
|  3:  3.7338 -  3.2675 0.99   1339  149 0.1043 0.1533      5.4498      5.8307|
|  4:  3.2675 -  2.9714 0.99   1333  143 0.1165 0.1507      5.4117      5.5642|
|  5:  2.9714 -  2.7599 0.99   1310  153 0.1219 0.1532      5.2701      5.4874|
|  6:  2.7599 -  2.5981 0.99   1330  145 0.1188 0.2009      5.1811      5.4753|
|  7:  2.5981 -  2.4686 0.99   1301  147 0.1209 0.1646      5.1438      5.3409|
|  8:  2.4686 -  2.3616 0.98   1313  142 0.1098 0.1565      5.0554      5.2646|
|  9:  2.3616 -  2.2710 0.98   1314  146 0.1128 0.1949      5.0024      5.3463|
| 10:  2.2710 -  2.1929 0.98   1289  137 0.1090 0.1608      4.9334      5.1544|
| 11:  2.1929 -  2.1245 1.00   1308  158 0.1102 0.1850      4.9083      5.2879|
| 12:  2.1245 -  2.0640 0.97   1289  135 0.1129 0.1593       4.875      5.1243|
| 13:  2.0640 -  2.0098 0.94   1241  136 0.1007 0.1759      4.7412      4.9849|
| 14:  2.0098 -  1.9608 0.36    467   57 0.0880 0.1715      4.5899      4.9536|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8314 -  4.6795  1421   158  0.94   9.40   0.98     0.95       7559.80|
|  2:  4.6795 -  3.7338  1375   153  0.95   7.95   1.02     1.01       9114.12|
|  3:  3.7338 -  3.2675  1339   149  0.93  11.30   1.03     1.02       9988.02|
|  4:  3.2675 -  2.9714  1333   143  0.92  13.08   1.01     1.00       9687.77|
|  5:  2.9714 -  2.7599  1310   153  0.91  15.26   1.00     0.97       7735.54|
|  6:  2.7599 -  2.5981  1330   145  0.90  16.38   0.98     0.96       6856.40|
|  7:  2.5981 -  2.4686  1301   147  0.91  15.38   0.99     0.95       6042.79|
|  8:  2.4686 -  2.3616  1313   142  0.91  15.07   1.00     0.96       5401.56|
|  9:  2.3616 -  2.2710  1314   146  0.91  15.65   1.00     0.96       4852.17|
| 10:  2.2710 -  2.1929  1289   137  0.90  15.77   1.00     0.96       4333.62|
| 11:  2.1929 -  2.1245  1308   158  0.90  16.23   0.99     0.96       4284.08|
| 12:  2.1245 -  2.0640  1289   135  0.90  16.11   1.00     1.00       4037.12|
| 13:  2.0640 -  2.0098  1241   136  0.91  15.75   0.99     0.97       3203.47|
| 14:  2.0098 -  1.9608   467    57  0.93  12.57   0.98     0.94       2248.80|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2248.80 max =         9988.02 mean =      6328.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.42 mean =        13.59|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1556   ksol= 0.32   Bsol= 48.96   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.18,-0.44,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129415                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1556   ksol= 0.32   Bsol= 48.96   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.18,-0.44,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129415                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6795 0.99   1421  158 0.0985 0.1306      5.4002      5.5728|
|  2:  4.6795 -  3.7338 0.99   1375  153 0.0839 0.1105       5.425      5.6214|
|  3:  3.7338 -  3.2675 0.99   1339  149 0.1043 0.1531      5.4497      5.8303|
|  4:  3.2675 -  2.9714 0.99   1333  143 0.1164 0.1506      5.4115      5.5644|
|  5:  2.9714 -  2.7599 0.99   1310  153 0.1218 0.1532        5.27      5.4871|
|  6:  2.7599 -  2.5981 0.99   1330  145 0.1189 0.2010      5.1813      5.4758|
|  7:  2.5981 -  2.4686 0.99   1301  147 0.1209 0.1643      5.1439      5.3403|
|  8:  2.4686 -  2.3616 0.98   1313  142 0.1097 0.1564      5.0554      5.2644|
|  9:  2.3616 -  2.2710 0.98   1314  146 0.1128 0.1951      5.0023       5.346|
| 10:  2.2710 -  2.1929 0.98   1289  137 0.1090 0.1604      4.9332      5.1531|
| 11:  2.1929 -  2.1245 1.00   1308  158 0.1102 0.1848      4.9079      5.2875|
| 12:  2.1245 -  2.0640 0.97   1289  135 0.1129 0.1595       4.875      5.1241|
| 13:  2.0640 -  2.0098 0.94   1241  136 0.1006 0.1761      4.7414      4.9858|
| 14:  2.0098 -  1.9608 0.36    467   57 0.0880 0.1717      4.5906      4.9547|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8314 -  4.6795  1421   158  0.94   9.39   0.98     0.95       7542.81|
|  2:  4.6795 -  3.7338  1375   153  0.95   7.94   1.02     1.01       9110.40|
|  3:  3.7338 -  3.2675  1339   149  0.93  11.30   1.03     1.03       9986.38|
|  4:  3.2675 -  2.9714  1333   143  0.92  13.07   1.01     1.00       9681.56|
|  5:  2.9714 -  2.7599  1310   153  0.91  15.27   1.00     0.98       7739.27|
|  6:  2.7599 -  2.5981  1330   145  0.90  16.39   0.98     0.96       6857.06|
|  7:  2.5981 -  2.4686  1301   147  0.91  15.38   0.99     0.96       6042.80|
|  8:  2.4686 -  2.3616  1313   142  0.91  15.07   1.00     0.97       5403.15|
|  9:  2.3616 -  2.2710  1314   146  0.91  15.64   1.00     0.96       4847.05|
| 10:  2.2710 -  2.1929  1289   137  0.90  15.76   1.00     0.97       4330.48|
| 11:  2.1929 -  2.1245  1308   158  0.90  16.21   1.00     0.97       4275.58|
| 12:  2.1245 -  2.0640  1289   135  0.90  16.10   1.01     1.00       4035.95|
| 13:  2.0640 -  2.0098  1241   136  0.91  15.76   1.00     0.98       3205.68|
| 14:  2.0098 -  1.9608   467    57  0.93  12.59   0.98     0.95       2253.48|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2253.48 max =         9986.38 mean =      6325.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.09 mean =        13.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.675)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    85.19   16.82    None  None   None       |
|    all(noH): 2823   0      0.84    85.19   16.82    None  None   None       |
|    Sol.    : 438    0      5.56    76.23   39.26    None  None   None       |
|    Mac.    : 2385   0      0.84    85.19   12.70    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:     0.839 -   9.275:  886   |   5:    43.017 -  51.453:   91        |
|      1:     9.275 -  17.710: 1194   |   6:    51.453 -  59.888:   82        |
|      2:    17.710 -  26.146:  266   |   7:    59.888 -  68.324:   34        |
|      3:    26.146 -  34.581:  127   |   8:    68.324 -  76.759:   11        |
|      4:    34.581 -  43.017:  130   |   9:    76.759 -  85.195:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 275         
Filter by distance & map next to the model:
   mapped sites are within: 0.499 - 5.494
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 275
   mapped sites are within: 0.700 - 5.494

peak=    5.571 closest distance to " NH2 ARG A  56 " =    2.155
peak=    5.468 closest distance to " CB  ARG A 275 " =    0.940
peak=    5.411 closest distance to " NE2 GLN A  11 " =    1.167
peak=    5.379 closest distance to " O   HOH Z 142 " =    1.697
peak=    5.195 closest distance to " O   HOH Z 232 " =    2.413
peak=    5.157 closest distance to " CG  PRO A  54 " =    1.254
peak=    4.994 closest distance to " O   HOH Z 126 " =    1.769
peak=    4.922 closest distance to " CB  GLN A 223 " =    1.444
peak=    4.865 closest distance to " O   HOH Z 369 " =    2.257
peak=    4.615 closest distance to " O   HOH Z 287 " =    2.038
peak=    4.571 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.564 closest distance to " CG  PRO A 213 " =    1.221
peak=    4.545 closest distance to " CB  ARG A  79 " =    1.415
peak=    4.531 closest distance to " CB  GLU A 152 " =    1.211
peak=    4.524 closest distance to " O   HOH Z 417 " =    1.275
peak=    4.507 closest distance to " O   HOH Z  78 " =    1.788
peak=    4.505 closest distance to " CB  PRO A  54 " =    0.948
peak=    4.382 closest distance to " O   HOH Z 427 " =    3.003
peak=    4.372 closest distance to " CG  TRP A 179 " =    2.148
peak=    4.331 closest distance to " ND2 ASN A 187 " =    1.532
peak=    4.321 closest distance to " O   HOH Z 250 " =    1.475
peak=    4.319 closest distance to " CB  ARG A 190 " =    1.697
peak=    4.301 closest distance to " O   HOH Z 298 " =    1.803
peak=    4.269 closest distance to " O   HOH Z 158 " =    3.078
peak=    4.267 closest distance to " CB  VAL A 265 " =    1.260
peak=    4.250 closest distance to " O   SER A  87 " =    2.165
peak=    4.247 closest distance to " CD2 TRP A 179 " =    1.328
peak=    4.244 closest distance to " C   PRO A 198 " =    1.457
peak=    4.239 closest distance to " CB  SER A  63 " =    1.147
peak=    4.235 closest distance to " CB  ASN A 148 " =    1.510
peak=    4.223 closest distance to " O   HOH Z 403 " =    1.800
peak=    4.218 closest distance to " O   HOH Z 189 " =    2.840
peak=    4.214 closest distance to " O   HOH Z  15 " =    2.239
peak=    4.189 closest distance to " O   HOH Z 402 " =    1.373
peak=    4.182 closest distance to " CA  TYR A  30 " =    0.897
peak=    4.131 closest distance to " O   HOH Z  97 " =    2.421
peak=    4.124 closest distance to " CZ  PHE A 218 " =    1.085
peak=    4.118 closest distance to " NH2AARG A 190 " =    2.015
peak=    4.116 closest distance to " O   HOH Z  40 " =    1.770
peak=    4.111 closest distance to " O   HOH Z 132 " =    2.782
peak=    4.081 closest distance to " O   HOH Z  61 " =    1.636
peak=    4.075 closest distance to " NZ  LYS A 117 " =    3.111
peak=    4.054 closest distance to " CG2 VAL A 257 " =    0.833
peak=    4.047 closest distance to " O   HOH Z 272 " =    1.830
peak=    4.001 closest distance to " CB  ASN A 110 " =    1.091
peak=    3.983 closest distance to " O   HOH Z 346 " =    1.677
peak=    3.966 closest distance to " O   HOH Z 406 " =    1.572
peak=    3.960 closest distance to " O   HOH Z 209 " =    2.247
peak=    3.913 closest distance to " CG  PRO A  90 " =    1.142
peak=    3.910 closest distance to " O   HOH Z 327 " =    1.521
peak=    3.906 closest distance to " CB  VAL A 202 " =    1.588
peak=    3.904 closest distance to " CG  PRO A 198 " =    1.256
peak=    3.899 closest distance to " CB  THR A  31 " =    1.543
peak=    3.896 closest distance to " O   HOH Z 291 " =    1.521
peak=    3.887 closest distance to " O   HOH Z 128 " =    1.986
peak=    3.886 closest distance to " N   TYR A 116 " =    1.548
peak=    3.883 closest distance to " CG2 ILE A 120 " =    1.149
peak=    3.880 closest distance to " CG  PRO A 243 " =    0.998
peak=    3.869 closest distance to " O   HOH Z  44 " =    1.835
peak=    3.867 closest distance to " CA  ASN A 215 " =    1.038
peak=    3.863 closest distance to " CB  GLU A  46 " =    1.035
peak=    3.860 closest distance to " O   HOH Z 423 " =    1.999
peak=    3.854 closest distance to " O   HOH Z 173 " =    1.930
peak=    3.847 closest distance to " O   HOH Z 389 " =    1.773
peak=    3.843 closest distance to " O   HOH Z 234 " =    3.630
peak=    3.835 closest distance to " OG ASER A 258 " =    2.977
peak=    3.833 closest distance to " O   HOH Z 180 " =    2.193
peak=    3.816 closest distance to " O   HOH Z 392 " =    2.927
peak=    3.788 closest distance to " CB  ASP A 140 " =    1.082
peak=    3.769 closest distance to " N   ASN A  39 " =    1.248
peak=    3.768 closest distance to " CB  TRP A 266 " =    1.086
peak=    3.765 closest distance to " CG  ARG A  66 " =    2.460
peak=    3.765 closest distance to " CA  ARG A  36 " =    0.993
peak=    3.762 closest distance to " O   HOH Z 371 " =    1.764
peak=    3.761 closest distance to " O   HOH Z  97 " =    1.980
peak=    3.743 closest distance to " O   HOH Z  59 " =    1.831
peak=    3.733 closest distance to " O   HOH Z 193 " =    1.840
peak=    3.733 closest distance to " O   HOH Z 141 " =    1.714
peak=    3.726 closest distance to " O   HOH Z 368 " =    3.661
peak=    3.721 closest distance to " O   HOH Z  92 " =    2.436
peak=    3.707 closest distance to " CE  LYS A  76 " =    0.900
peak=    3.685 closest distance to " O   HOH Z  88 " =    2.720
peak=    3.684 closest distance to " O   HOH Z 128 " =    2.200
peak=    3.682 closest distance to " O   HOH Z 265 " =    2.217
peak=    3.671 closest distance to " CB  GLU A 277 " =    3.540
peak=    3.666 closest distance to " O   HOH Z 419 " =    2.216
peak=    3.661 closest distance to " O   ASN A  74 " =    1.432
peak=    3.653 closest distance to " O   HOH Z 425 " =    1.942
peak=    3.652 closest distance to " OG BSER A 164 " =    2.249
peak=    3.643 closest distance to " O  BHOH Z 338 " =    2.323
peak=    3.641 closest distance to " OD1 ASN A  69 " =    2.589
peak=    3.635 closest distance to " O   HOH Z 353 " =    2.642
peak=    3.613 closest distance to " O   HOH Z 126 " =    1.551
peak=    3.613 closest distance to " NH2BARG A 145 " =    2.058
peak=    3.612 closest distance to " CB  GLN A  88 " =    1.196
peak=    3.611 closest distance to " CB  SER A 212 " =    1.091
peak=    3.605 closest distance to " O   HOH Z 365 " =    2.708
peak=    3.600 closest distance to " CD2 LEU A 297 " =    0.932
peak=    3.592 closest distance to " O   HOH Z 368 " =    2.114
peak=    3.585 closest distance to " O   HOH Z 203 " =    1.692
peak=    3.581 closest distance to " CB  SER A  26 " =    1.727
peak=    3.576 closest distance to " CG  MET A 185 " =    1.076
peak=    3.575 closest distance to " O   HOH Z   1 " =    1.870
peak=    3.573 closest distance to " O   HOH Z  88 " =    2.465
peak=    3.572 closest distance to " O   HOH Z  61 " =    1.457
peak=    3.568 closest distance to " O   HOH Z 337 " =    3.524
peak=    3.564 closest distance to " O   HOH Z 415 " =    3.685
peak=    3.546 closest distance to " O   HOH Z 172 " =    3.458
peak=    3.542 closest distance to " NH1AARG A 145 " =    1.226
peak=    3.538 closest distance to " O   HOH Z  10 " =    1.794
peak=    3.536 closest distance to " O   HOH Z 248 " =    1.500
peak=    3.529 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.528 closest distance to " CA  ALA A  84 " =    1.242
peak=    3.527 closest distance to " N   PHE A 130 " =    1.283
peak=    3.504 closest distance to " CA  TYR A  30 " =    1.038
peak=    3.502 closest distance to " CB  GLN A  89 " =    1.388
peak=    3.500 closest distance to " O   HOH Z 411 " =    3.903
peak=    3.497 closest distance to " O   HOH Z 214 " =    2.234
peak=    3.497 closest distance to " O   HOH Z 132 " =    2.317
peak=    3.490 closest distance to " CB  ASN A 142 " =    1.077
peak=    3.489 closest distance to " O   HOH Z 193 " =    1.968
peak=    3.487 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.484 closest distance to " CG AARG A 275 " =    1.114
peak=    3.481 closest distance to " O   HOH Z 245 " =    1.341
peak=    3.476 closest distance to " CA  ARG A 195 " =    1.211
peak=    3.473 closest distance to " ND2 ASN A 249 " =    0.859
peak=    3.470 closest distance to " CG  GLN A  11 " =    1.896
peak=    3.464 closest distance to " CB  LEU A  83 " =    0.781
peak=    3.459 closest distance to " CB  ALA A 114 " =    1.088
peak=    3.458 closest distance to " CB  LEU A 228 " =    1.084
peak=    3.451 closest distance to " OG BSER A  99 " =    2.332
peak=    3.450 closest distance to " O   HOH Z 185 " =    1.849
peak=    3.450 closest distance to " CG1BVAL A  72 " =    1.566
peak=    3.447 closest distance to " O   HOH Z  40 " =    1.399
peak=    3.446 closest distance to " O   HOH Z 329 " =    4.059
peak=    3.442 closest distance to " O   HOH Z 261 " =    1.909
peak=    3.440 closest distance to " CD  LYS A  76 " =    1.839
peak=    3.434 closest distance to " O   HOH Z 359 " =    1.546
peak=    3.429 closest distance to " CB  ILE A 120 " =    1.337
peak=    3.426 closest distance to " C   PHE A  59 " =    0.935
peak=    3.424 closest distance to " CA  ALA A 233 " =    1.113
peak=    3.421 closest distance to " O   HOH Z 285 " =    2.320
peak=    3.414 closest distance to " CD  LYS A 166 " =    1.238
peak=    3.413 closest distance to " O   HOH Z 357 " =    1.986
peak=    3.412 closest distance to " CA  ASN A 217 " =    1.185
peak=    3.403 closest distance to " O   HOH Z 233 " =    1.823
peak=    3.402 closest distance to " CZ3 TRP A 266 " =    1.061
peak=    3.401 closest distance to " CB  GLU A 128 " =    0.981
peak=    3.401 closest distance to " O   HOH Z 394 " =    3.883
peak=    3.400 closest distance to " O   HOH Z 421 " =    1.972
peak=    3.390 closest distance to " CB  PHE A 204 " =    0.706
peak=    3.387 closest distance to " CG  GLU A  37 " =    0.942
peak=    3.381 closest distance to " CB  TYR A 169 " =    0.760
peak=    3.380 closest distance to " CA  TYR A 116 " =    1.292
peak=    3.378 closest distance to " O   HOH Z 280 " =    3.003
peak=    3.377 closest distance to " O  BHOH Z  74 " =    1.312
peak=    3.375 closest distance to " CG  LEU A 167 " =    1.280
peak=    3.374 closest distance to " O   HOH Z 148 " =    3.438
peak=    3.373 closest distance to " O   HOH Z 407 " =    2.535
peak=    3.364 closest distance to " CB  SER A   3 " =    1.257
peak=    3.363 closest distance to " CB  ARG A 139 " =    1.073
peak=    3.363 closest distance to " CA  THR A 264 " =    0.906
peak=    3.362 closest distance to " OG  SER A  62 " =    2.748
peak=    3.360 closest distance to " N   ARG A 156 " =    1.283
peak=    3.359 closest distance to " O   HOH Z  66 " =    2.156
peak=    3.358 closest distance to " CD1 ILE A 199 " =    1.114
peak=    3.357 closest distance to " CA  MET A  40 " =    1.153
peak=    3.352 closest distance to " O   HOH Z  21 " =    1.835
peak=    3.351 closest distance to " O   HOH Z  62 " =    2.308
peak=    3.346 closest distance to " CB  PRO A  90 " =    1.081
peak=    3.342 closest distance to " CB  ASN A 215 " =    1.148
peak=    3.339 closest distance to " O   HOH Z 299 " =    4.286
peak=    3.339 closest distance to " NE2 HIS A 207 " =    1.257
peak=    3.335 closest distance to " O   HOH Z 213 " =    1.830
peak=    3.330 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.329 closest distance to " O   HOH Z 371 " =    2.908
peak=    3.326 closest distance to " O   THR A 220 " =    1.321
peak=    3.321 closest distance to " O   HOH Z 344 " =    3.171
peak=    3.320 closest distance to " CB  LYS A 117 " =    1.216
peak=    3.316 closest distance to " CB  LYS A 290 " =    0.996
peak=    3.314 closest distance to " O   ALA A   1 " =    1.710
peak=    3.314 closest distance to " CG  LYS A 119 " =    1.091
peak=    3.310 closest distance to " CD1 ILE A 106 " =    0.854
peak=    3.307 closest distance to " O   HOH Z 305 " =    3.533
peak=    3.306 closest distance to " O   HOH Z 433 " =    1.871
peak=    3.305 closest distance to " N   ASP A 162 " =    1.054
peak=    3.301 closest distance to " CA  MET A 105 " =    0.975
peak=    3.298 closest distance to " OE1 GLU A   2 " =    2.177
peak=    3.297 closest distance to " CA  ALA A  51 " =    0.879
peak=    3.291 closest distance to " O   HOH Z   1 " =    1.591
peak=    3.290 closest distance to " CA  THR A 221 " =    1.082
peak=    3.286 closest distance to " OD2 ASP A 286 " =    2.880
peak=    3.285 closest distance to " O   HOH Z 342 " =    0.949
peak=    3.284 closest distance to " O   HOH Z 422 " =    2.549
peak=    3.282 closest distance to " CG1 ILE A  33 " =    1.180
peak=    3.281 closest distance to " CA  ARG A 159 " =    1.264
peak=    3.278 closest distance to " O   HOH Z 345 " =    3.242
peak=    3.265 closest distance to " NZ  LYS A  48 " =    1.135
peak=    3.264 closest distance to " CB  ALA A  34 " =    1.042
peak=    3.257 closest distance to " CB  SER A  62 " =    1.354
peak=    3.255 closest distance to " O   HOH Z 380 " =    1.922
peak=    3.254 closest distance to " CG2 ILE A  20 " =    1.453
peak=    3.253 closest distance to " O   HOH Z  85 " =    2.432
peak=    3.249 closest distance to " CG  MET A 113 " =    1.076
peak=    3.246 closest distance to " OG  SER A  22 " =    2.595
peak=    3.245 closest distance to " CA  ALA A 158 " =    1.324
peak=    3.243 closest distance to " CA  ASP A 162 " =    1.064
peak=    3.242 closest distance to " O   HOH Z 325 " =    2.510
peak=    3.235 closest distance to " CA  ILE A 234 " =    1.019
peak=    3.232 closest distance to " O   HOH Z  85 " =    1.366
peak=    3.228 closest distance to " CA  SER A  87 " =    1.000
peak=    3.227 closest distance to " CG1 ILE A  49 " =    1.481
peak=    3.226 closest distance to " CE AMET A  47 " =    1.437
peak=    3.224 closest distance to " N   HIS A 108 " =    1.892
peak=    3.223 closest distance to " CB  TRP A 179 " =    1.351
peak=    3.222 closest distance to " O   HOH Z 130 " =    2.258
peak=    3.222 closest distance to " O   HOH Z 147 " =    1.797
peak=    3.219 closest distance to " O   HOH Z  90 " =    2.173
peak=    3.218 closest distance to " CG2 ILE A 239 " =    0.711
peak=    3.218 closest distance to " CA  ALA A 291 " =    0.783
peak=    3.216 closest distance to " CG1 VAL A 153 " =    0.962
peak=    3.216 closest distance to " O   HOH Z 234 " =    2.210
peak=    3.214 closest distance to " CB  TYR A 116 " =    0.762
peak=    3.212 closest distance to " CD  ARG A  66 " =    2.532
peak=    3.204 closest distance to " O   HOH Z 336 " =    1.680
peak=    3.204 closest distance to " O   HOH Z  44 " =    2.878
peak=    3.201 closest distance to " O   HOH Z 257 " =    2.176
peak=    3.194 closest distance to " CB  ALA A 248 " =    1.398
peak=    3.189 closest distance to " O   HOH Z 227 " =    2.052
peak=    3.188 closest distance to " OD2 ASP A 286 " =    3.193
peak=    3.188 closest distance to " O   HOH Z 273 " =    2.806
peak=    3.179 closest distance to " O   HOH Z 187 " =    2.178
peak=    3.176 closest distance to " CB  THR A  52 " =    0.700
peak=    3.175 closest distance to " CB  ALA A 114 " =    1.368
peak=    3.175 closest distance to " CB  LEU A 300 " =    0.924
peak=    3.173 closest distance to " CG2 THR A 221 " =    1.063
peak=    3.168 closest distance to " O   HOH Z 361 " =    3.128
peak=    3.166 closest distance to " O   HOH Z 245 " =    2.118
peak=    3.166 closest distance to " CA  SER A  32 " =    1.674
peak=    3.161 closest distance to " CZ2 TRP A 179 " =    1.783
peak=    3.154 closest distance to " O   HOH Z 267 " =    2.032
peak=    3.153 closest distance to " O   HOH Z 319 " =    2.455
peak=    3.149 closest distance to " OG1 THR A 264 " =    0.748
peak=    3.149 closest distance to " O   HOH Z 302 " =    1.881
peak=    3.146 closest distance to " O   HOH Z 251 " =    1.576
peak=    3.145 closest distance to " O   HOH Z 188 " =    2.264
peak=    3.143 closest distance to " CA  ASN A 127 " =    1.118
peak=    3.142 closest distance to " CG1 VAL A 126 " =    1.182
peak=    3.138 closest distance to " CB  HIS A 108 " =    0.838
peak=    3.138 closest distance to " CG2AVAL A 121 " =    2.375
peak=    3.137 closest distance to " O   HOH Z 188 " =    1.422
peak=    3.128 closest distance to " O   HOH Z  78 " =    2.103
peak=    3.126 closest distance to " O   HOH Z 116 " =    1.771
peak=    3.125 closest distance to " CG2 VAL A 197 " =    1.132
peak=    3.120 closest distance to " CA  LYS A 290 " =    1.430
peak=    3.117 closest distance to " O   HOH Z 430 " =    5.494
peak=    3.113 closest distance to " O   HOH Z 261 " =    1.930
peak=    3.110 closest distance to " CB  ALA A 291 " =    1.224
peak=    3.107 closest distance to " O   HOH Z  43 " =    1.790
peak=    3.101 closest distance to " CG  ARG A 269 " =    1.290
peak=    3.101 closest distance to " CB  ASP A 124 " =    0.720
peak=    3.100 closest distance to " NE  ARG A  79 " =    0.981
peak=    3.096 closest distance to " CD1 LEU A  96 " =    0.718
peak=    3.096 closest distance to " CD1AILE A 234 " =    0.873
peak=    3.085 closest distance to " CB  ALA A   1 " =    4.756
peak=    3.077 closest distance to " CA  GLU A  46 " =    1.033
peak=    3.076 closest distance to " O   HOH Z  47 " =    1.545
peak=    3.064 closest distance to " N   SER A 135 " =    1.260
peak=    3.032 closest distance to " O   HOH Z   1 " =    2.393

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.892 - 5.873
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 198
   mapped sites are within: 0.892 - 5.873

peak=   -4.575 closest distance to " CG  GLN A  58 " =    1.038
peak=   -4.535 closest distance to " CD  ARG A  14 " =    3.414
peak=   -4.480 closest distance to " C   HIS A 108 " =    1.114
peak=   -4.469 closest distance to " O   HOH Z 266 " =    5.316
peak=   -4.469 closest distance to " OG BSER A 134 " =    1.312
peak=   -4.408 closest distance to " CB  PRO A 280 " =    2.104
peak=   -4.330 closest distance to " CB  PRO A 243 " =    2.659
peak=   -4.289 closest distance to " CG  GLN A 223 " =    2.084
peak=   -4.275 closest distance to " CD  ARG A 156 " =    2.082
peak=   -4.261 closest distance to " O   HOH Z 198 " =    1.429
peak=   -4.255 closest distance to " CG1 VAL A 112 " =    2.766
peak=   -4.125 closest distance to " O   PRO A 198 " =    1.266
peak=   -4.124 closest distance to " O   HOH Z 372 " =    2.238
peak=   -4.106 closest distance to " O   VAL A  67 " =    2.665
peak=   -4.089 closest distance to " CD2 PHE A 192 " =    2.052
peak=   -4.084 closest distance to " O   HOH Z 231 " =    2.329
peak=   -4.023 closest distance to " CA  VAL A  67 " =    2.885
peak=   -3.928 closest distance to " CE  MET A 105 " =    2.410
peak=   -3.921 closest distance to " N   ALA A  43 " =    2.548
peak=   -3.888 closest distance to " CE2 TYR A  30 " =    2.764
peak=   -3.873 closest distance to " OXT GLY A 302 " =    2.857
peak=   -3.860 closest distance to " N   ALA A 248 " =    1.633
peak=   -3.857 closest distance to " OD2 ASP A 191 " =    1.371
peak=   -3.856 closest distance to " O   HOH Z 351 " =    1.426
peak=   -3.836 closest distance to " CD  ARG A 139 " =    1.600
peak=   -3.830 closest distance to " ND2 ASN A 249 " =    2.363
peak=   -3.821 closest distance to " O   HOH Z 407 " =    2.756
peak=   -3.788 closest distance to " CB  ASN A  39 " =    2.348
peak=   -3.778 closest distance to " CB  ALA A  43 " =    2.496
peak=   -3.770 closest distance to " CZ  TYR A 169 " =    1.785
peak=   -3.764 closest distance to " OD2 ASP A 171 " =    2.336
peak=   -3.761 closest distance to " CZ3 TRP A 179 " =    1.198
peak=   -3.759 closest distance to " O   HOH Z 290 " =    1.218
peak=   -3.742 closest distance to " CB  ALA A 248 " =    2.286
peak=   -3.721 closest distance to " CG  PHE A 283 " =    2.663
peak=   -3.712 closest distance to " OD1 ASP A 171 " =    1.647
peak=   -3.706 closest distance to " ND2 ASN A  45 " =    1.794
peak=   -3.705 closest distance to " O   HOH Z 313 " =    1.884
peak=   -3.695 closest distance to " O   HOH Z  38 " =    1.733
peak=   -3.694 closest distance to " O   PHE A 218 " =    1.594
peak=   -3.689 closest distance to " CD1 LEU A 255 " =    2.761
peak=   -3.682 closest distance to " CA  ASP A 298 " =    1.104
peak=   -3.680 closest distance to " CB  ALA A 161 " =    2.467
peak=   -3.673 closest distance to " ND2 ASN A 187 " =    1.464
peak=   -3.659 closest distance to " OG  SER A  97 " =    2.204
peak=   -3.637 closest distance to " O   SER A 210 " =    1.974
peak=   -3.634 closest distance to " O   HOH Z 196 " =    2.134
peak=   -3.631 closest distance to " CG2 ILE A 263 " =    2.184
peak=   -3.631 closest distance to " CD2 TYR A 293 " =    1.895
peak=   -3.627 closest distance to " O   HOH Z 102 " =    1.642
peak=   -3.619 closest distance to " O   VAL A 174 " =    2.263
peak=   -3.616 closest distance to " OD1 ASN A 148 " =    1.486
peak=   -3.602 closest distance to " CE BMET A  47 " =    1.339
peak=   -3.597 closest distance to " CB  ALA A 291 " =    2.225
peak=   -3.588 closest distance to " CD2 TYR A 247 " =    2.492
peak=   -3.584 closest distance to " O   HOH Z  63 " =    1.587
peak=   -3.579 closest distance to " O   HOH Z 185 " =    2.329
peak=   -3.565 closest distance to " O   HOH Z 348 " =    2.189
peak=   -3.563 closest distance to " O   HOH Z 395 " =    5.119
peak=   -3.543 closest distance to " O   HOH Z 389 " =    1.879
peak=   -3.536 closest distance to " O   HOH Z 353 " =    2.220
peak=   -3.535 closest distance to " O   ALA A 161 " =    1.675
peak=   -3.533 closest distance to " ND2 ASN A  45 " =    1.142
peak=   -3.530 closest distance to " O   HOH Z 362 " =    5.873
peak=   -3.530 closest distance to " CD1 PHE A  59 " =    2.045
peak=   -3.527 closest distance to " CG  ARG A 269 " =    2.240
peak=   -3.521 closest distance to " O   HOH Z 283 " =    2.413
peak=   -3.520 closest distance to " O   SER A  95 " =    1.499
peak=   -3.517 closest distance to " CD1 LEU A 101 " =    2.326
peak=   -3.516 closest distance to " O   HOH Z 211 " =    1.511
peak=   -3.511 closest distance to " OE2 GLU A 152 " =    1.265
peak=   -3.505 closest distance to " NE  ARG A 156 " =    1.923
peak=   -3.504 closest distance to " N   GLN A  58 " =    1.642
peak=   -3.502 closest distance to " O   PRO A 163 " =    2.011
peak=   -3.480 closest distance to " CB  ALA A 291 " =    2.231
peak=   -3.474 closest distance to " ND2 ASN A  60 " =    4.134
peak=   -3.473 closest distance to " O   HOH Z 429 " =    2.007
peak=   -3.469 closest distance to " CE2 PHE A  61 " =    2.641
peak=   -3.465 closest distance to " CB  ASP A 132 " =    2.282
peak=   -3.461 closest distance to " N   MET A 188 " =    1.954
peak=   -3.449 closest distance to " O   HOH Z 114 " =    3.041
peak=   -3.444 closest distance to " O   ALA A  10 " =    1.692
peak=   -3.438 closest distance to " CG2 THR A  18 " =    2.867
peak=   -3.432 closest distance to " CD2 PHE A 225 " =    1.166
peak=   -3.429 closest distance to " O   HOH Z 174 " =    2.454
peak=   -3.429 closest distance to " O   PRO A 198 " =    1.272
peak=   -3.424 closest distance to " O   VAL A 189 " =    2.708
peak=   -3.423 closest distance to " OE1 GLN A 183 " =    1.522
peak=   -3.421 closest distance to " NH2AARG A 275 " =    5.172
peak=   -3.419 closest distance to " O   HOH Z  13 " =    1.774
peak=   -3.413 closest distance to " CA  GLY A 203 " =    2.372
peak=   -3.413 closest distance to " O   HOH Z   6 " =    2.177
peak=   -3.407 closest distance to " O   HOH Z  11 " =    1.753
peak=   -3.403 closest distance to " CD2 PHE A  61 " =    2.322
peak=   -3.401 closest distance to " O   HOH Z 421 " =    3.194
peak=   -3.397 closest distance to " O   HOH Z 385 " =    2.013
peak=   -3.394 closest distance to " CD2 LEU A 237 " =    2.766
peak=   -3.389 closest distance to " O   ALA A 292 " =    2.050
peak=   -3.387 closest distance to " CG2 THR A 178 " =    2.296
peak=   -3.380 closest distance to " CG1 VAL A  78 " =    3.012
peak=   -3.379 closest distance to " CB  TRP A  85 " =    2.495
peak=   -3.371 closest distance to " OD1 ASP A 191 " =    1.720
peak=   -3.364 closest distance to " O   HOH Z 351 " =    1.398
peak=   -3.361 closest distance to " O   HOH Z 165 " =    2.081
peak=   -3.356 closest distance to " O   HOH Z  15 " =    1.521
peak=   -3.352 closest distance to " O   TRP A  70 " =    1.437
peak=   -3.350 closest distance to " O   HOH Z 243 " =    1.932
peak=   -3.348 closest distance to " CB  ASP A 286 " =    1.757
peak=   -3.347 closest distance to " CA  GLY A 241 " =    3.253
peak=   -3.344 closest distance to " CG  GLU A 277 " =    1.348
peak=   -3.339 closest distance to " O   ALA A  34 " =    2.165
peak=   -3.334 closest distance to " NE2 GLN A 278 " =    1.739
peak=   -3.329 closest distance to " N   THR A  52 " =    1.755
peak=   -3.328 closest distance to " O   HOH Z 394 " =    1.421
peak=   -3.326 closest distance to " O   SER A 135 " =    1.461
peak=   -3.326 closest distance to " CE2 PHE A 218 " =    2.447
peak=   -3.326 closest distance to " CZ  PHE A  59 " =    1.527
peak=   -3.325 closest distance to " O   HOH Z 281 " =    2.779
peak=   -3.305 closest distance to " O   VAL A 189 " =    1.728
peak=   -3.299 closest distance to " O   HOH Z 359 " =    3.151
peak=   -3.297 closest distance to " CA  GLY A 241 " =    2.372
peak=   -3.295 closest distance to " O   HOH Z 298 " =    2.446
peak=   -3.294 closest distance to " O   HOH Z 123 " =    2.297
peak=   -3.291 closest distance to " O   GLN A  89 " =    1.514
peak=   -3.287 closest distance to " NE2 GLN A 194 " =    1.842
peak=   -3.287 closest distance to " CZ2 TRP A 274 " =    0.979
peak=   -3.286 closest distance to " O   HOH Z 317 " =    1.489
peak=   -3.285 closest distance to " CB  PRO A 163 " =    2.404
peak=   -3.282 closest distance to " CB  GLN A  11 " =    1.862
peak=   -3.282 closest distance to " O   HOH Z   6 " =    1.440
peak=   -3.281 closest distance to " O   HOH Z  71 " =    2.328
peak=   -3.280 closest distance to " O   HOH Z 298 " =    1.310
peak=   -3.278 closest distance to " CG1 VAL A 250 " =    2.599
peak=   -3.277 closest distance to " CA  GLY A 133 " =    2.029
peak=   -3.267 closest distance to " OD2 ASP A  50 " =    1.556
peak=   -3.266 closest distance to " N   GLY A  23 " =    2.480
peak=   -3.261 closest distance to " O   HOH Z 253 " =    3.794
peak=   -3.257 closest distance to " CE3 TRP A 274 " =    2.325
peak=   -3.252 closest distance to " CB  ASP A 132 " =    2.406
peak=   -3.250 closest distance to " O   ALA A 180 " =    1.052
peak=   -3.248 closest distance to " CG  ARG A  66 " =    2.402
peak=   -3.242 closest distance to " O   HOH Z 191 " =    5.816
peak=   -3.241 closest distance to " NH2BARG A 275 " =    1.980
peak=   -3.240 closest distance to " OH  TYR A 172 " =    1.802
peak=   -3.235 closest distance to " O   HOH Z  43 " =    1.648
peak=   -3.232 closest distance to " CB  TYR A  15 " =    2.229
peak=   -3.231 closest distance to " O   HOH Z 357 " =    2.093
peak=   -3.220 closest distance to " N   PHE A  59 " =    1.829
peak=   -3.216 closest distance to " O   ASN A 252 " =    1.359
peak=   -3.216 closest distance to " CG2 ILE A  49 " =    2.745
peak=   -3.214 closest distance to " NE2 GLN A  88 " =    1.171
peak=   -3.207 closest distance to " O   GLN A 240 " =    2.024
peak=   -3.206 closest distance to " O   LYS A  76 " =    1.847
peak=   -3.204 closest distance to " O   HOH Z 134 " =    3.188
peak=   -3.199 closest distance to " OD1 ASN A 301 " =    1.884
peak=   -3.190 closest distance to " CG1 VAL A 197 " =    2.113
peak=   -3.190 closest distance to " C   GLY A 262 " =    1.909
peak=   -3.189 closest distance to " O   HOH Z 166 " =    2.037
peak=   -3.188 closest distance to " O   HOH Z  60 " =    1.838
peak=   -3.184 closest distance to " O   HOH Z 369 " =    2.226
peak=   -3.183 closest distance to " CD  GLN A 223 " =    0.892
peak=   -3.183 closest distance to " O   VAL A 125 " =    2.183
peak=   -3.179 closest distance to " ND2 ASN A 285 " =    2.174
peak=   -3.178 closest distance to " OXT GLY A 302 " =    3.483
peak=   -3.178 closest distance to " O   HOH Z 216 " =    1.485
peak=   -3.175 closest distance to " O   ARG A 145 " =    1.574
peak=   -3.163 closest distance to " CG1 VAL A 265 " =    2.584
peak=   -3.161 closest distance to " O   TRP A  92 " =    1.835
peak=   -3.158 closest distance to " O   LEU A 167 " =    1.490
peak=   -3.158 closest distance to " O   LYS A 181 " =    2.870
peak=   -3.155 closest distance to " O   HOH Z 252 " =    4.260
peak=   -3.148 closest distance to " O   SER A 276 " =    1.678
peak=   -3.146 closest distance to " CA  GLY A  57 " =    2.155
peak=   -3.139 closest distance to " O   HOH Z 132 " =    1.524
peak=   -3.131 closest distance to " C   ALA A 158 " =    1.418
peak=   -3.129 closest distance to " ND2 ASN A  60 " =    1.337
peak=   -3.128 closest distance to " CG1 VAL A 268 " =    2.440
peak=   -3.124 closest distance to " O   SER A   3 " =    0.990
peak=   -3.122 closest distance to " O   HOH Z 166 " =    1.524
peak=   -3.121 closest distance to " O   HOH Z   3 " =    2.011
peak=   -3.120 closest distance to " OG BSER A 134 " =    1.755
peak=   -3.117 closest distance to " CB  SER A 210 " =    1.207
peak=   -3.115 closest distance to " CG1 VAL A 125 " =    1.894
peak=   -3.114 closest distance to " OE1 GLN A 194 " =    1.708
peak=   -3.111 closest distance to " O   HOH Z 174 " =    4.108
peak=   -3.111 closest distance to " O   GLY A  80 " =    2.504
peak=   -3.106 closest distance to " NE2 GLN A  88 " =    1.866
peak=   -3.098 closest distance to " O   ALA A 227 " =    1.637
peak=   -3.097 closest distance to " O   HOH Z  10 " =    1.426
peak=   -3.091 closest distance to " CD1 ILE A 199 " =    2.364
peak=   -3.087 closest distance to " CE3 TRP A 150 " =    2.249
peak=   -3.086 closest distance to " O   ALA A   1 " =    1.786
peak=   -3.081 closest distance to " CG1AVAL A  41 " =    2.604
peak=   -3.079 closest distance to " CB  PHE A  16 " =    2.518
peak=   -3.052 closest distance to " O   ALA A  51 " =    1.169
peak=   -3.051 closest distance to " N   ASP A 286 " =    2.191
peak=   -3.043 closest distance to " O   HOH Z 110 " =    1.423
peak=   -3.015 closest distance to " N   GLY A 196 " =    1.688

================= 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    :  0.3846 0.3775   6.163204e+00   6.149452e+00
   1_bss:  0.3742 0.3668   6.147071e+00   6.130231e+00
   1_xyz:  0.2368 0.2684   5.760441e+00   5.855278e+00
   1_adp:  0.2149 0.2772   5.710689e+00   5.887803e+00
   1_occ:  0.2147 0.2774   5.710639e+00   5.888313e+00
   2_bss:  0.2115 0.2744   5.703671e+00   5.884498e+00
   2_xyz:  0.1548 0.2043   5.419737e+00   5.625613e+00
   2_adp:  0.1466 0.1926   5.365654e+00   5.566656e+00
   2_occ:  0.1464 0.1925   5.365162e+00   5.566754e+00
   3_bss:  0.1464 0.1923   5.363068e+00   5.564325e+00
   3_xyz:  0.1192 0.1621   5.188913e+00   5.414006e+00
   3_adp:  0.1150 0.1579   5.161087e+00   5.391649e+00
   3_occ:  0.1149 0.1580   5.160688e+00   5.391464e+00
   4_bss:  0.1151 0.1581   5.161060e+00   5.390157e+00
   4_xyz:  0.1111 0.1554   5.138406e+00   5.377154e+00
   4_adp:  0.1105 0.1547   5.135469e+00   5.374234e+00
   4_occ:  0.1104 0.1548   5.135465e+00   5.374479e+00
   5_bss:  0.1104 0.1548   5.135403e+00   5.374421e+00
   5_xyz:  0.1087 0.1549   5.129751e+00   5.376936e+00
   5_adp:  0.1079 0.1557   5.129744e+00   5.383299e+00
   5_occ:  0.1079 0.1556   5.129507e+00   5.383082e+00
   5_bss:  0.1078 0.1556   5.129415e+00   5.382967e+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:  0.326  31.847   0.097  -2.170   2.034  -0.000   0.000   0.000
   1_xyz:  0.326  31.847   0.097  -2.170   2.034  -0.000   0.000   0.000
   1_adp:  0.326  31.847   0.097  -2.170   2.034  -0.000   0.000   0.000
   1_occ:  0.326  31.847   0.097  -2.170   2.034  -0.000   0.000   0.000
   2_bss:  0.330  48.989  -2.295  -2.461  -0.042  -0.000  -0.000  -0.000
   2_xyz:  0.330  48.989  -2.295  -2.461  -0.042  -0.000  -0.000  -0.000
   2_adp:  0.330  48.989  -2.295  -2.461  -0.042  -0.000  -0.000  -0.000
   2_occ:  0.330  48.989  -2.295  -2.461  -0.042  -0.000  -0.000  -0.000
   3_bss:  0.327  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   3_xyz:  0.327  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   3_adp:  0.327  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   3_occ:  0.327  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   4_bss:  0.327  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   4_xyz:  0.327  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   4_adp:  0.327  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   4_occ:  0.327  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   5_bss:  0.325  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   5_xyz:  0.325  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   5_adp:  0.325  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   5_occ:  0.325  48.989  -2.975  -2.419  -0.543  -0.000  -0.000  -0.000
   5_bss:  0.320  48.960  -2.833  -2.175  -0.443  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.137 0.6314  0.8186    42183.725
   1_bss:  39.751 0.6463  0.8440    38848.726
   1_xyz:  26.251 0.7993  0.9916    18306.450
   1_adp:  27.401 0.7864  0.9816    19645.216
   1_occ:  27.450 0.7858  0.9810    19703.061
   2_bss:  27.146 0.7888  0.9299    19313.571
   2_xyz:  19.371 0.8676  0.9853    10474.028
   2_adp:  17.806 0.8829  0.9911     9413.041
   2_occ:  17.808 0.8828  0.9908     9403.018
   3_bss:  17.734 0.8834  0.9767     9315.642
   3_xyz:  14.773 0.9080  0.9877     6766.791
   3_adp:  14.312 0.9121  0.9833     6487.663
   3_occ:  14.310 0.9121  0.9832     6481.219
   4_bss:  14.286 0.9123  0.9831     6463.899
   4_xyz:  13.869 0.9160  0.9849     6260.480
   4_adp:  13.803 0.9167  0.9804     6234.442
   4_occ:  13.808 0.9166  0.9802     6232.603
   5_bss:  13.807 0.9166  0.9802     6230.955
   5_xyz:  13.851 0.9163  0.9801     6297.716
   5_adp:  13.960 0.9155  0.9736     6332.726
   5_occ:  13.954 0.9155  0.9735     6327.374
   5_bss:  13.952 0.9155  0.9781     6324.517
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8713e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8713e-01
   1_xyz:   1.237  0.009  0.078 15.210  0.005  4.109   8.3230e-02
   1_adp:   1.237  0.009  0.078 15.210  0.005  4.109   8.3230e-02
   1_occ:   1.237  0.009  0.078 15.210  0.005  4.109   8.3230e-02
   2_bss:   1.237  0.009  0.078 15.210  0.005  4.109   8.3230e-02
   2_xyz:   0.937  0.006  0.066 14.506  0.004  4.118   5.1708e-02
   2_adp:   0.937  0.006  0.066 14.506  0.004  4.118   5.1708e-02
   2_occ:   0.937  0.006  0.066 14.506  0.004  4.118   5.1708e-02
   3_bss:   0.937  0.006  0.066 14.506  0.004  4.118   5.1708e-02
   3_xyz:   1.087  0.008  0.078 15.000  0.004  4.110   6.7924e-02
   3_adp:   1.087  0.008  0.078 15.000  0.004  4.110   6.7924e-02
   3_occ:   1.087  0.008  0.078 15.000  0.004  4.110   6.7924e-02
   4_bss:   1.087  0.008  0.078 15.000  0.004  4.110   6.7924e-02
   4_xyz:   1.018  0.007  0.077 14.740  0.004  4.112   6.1360e-02
   4_adp:   1.018  0.007  0.077 14.740  0.004  4.112   6.1360e-02
   4_occ:   1.018  0.007  0.077 14.740  0.004  4.112   6.1360e-02
   5_bss:   1.018  0.007  0.077 14.740  0.004  4.112   6.1360e-02
   5_xyz:   1.039  0.008  0.079 14.745  0.004  4.113   6.3290e-02
   5_adp:   1.039  0.008  0.079 14.745  0.004  4.113   6.3290e-02
   5_occ:   1.039  0.008  0.079 14.745  0.004  4.113   6.3290e-02
   5_bss:   1.039  0.008  0.079 14.745  0.004  4.113   6.3290e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.416   2.4066e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.416   2.4066e-01
   1_xyz:   8.899  0.044  0.302 85.503  0.044  2.123   8.3588e-02
   1_adp:   8.899  0.044  0.302 85.503  0.044  2.123   8.3588e-02
   1_occ:   8.899  0.044  0.302 85.503  0.044  2.123   8.3588e-02
   2_bss:   8.899  0.044  0.302 85.503  0.044  2.123   8.3588e-02
   2_xyz:   6.571  0.052  0.222 81.222  0.038  2.382   4.9642e-02
   2_adp:   6.571  0.052  0.222 81.222  0.038  2.382   4.9642e-02
   2_occ:   6.571  0.052  0.222 81.222  0.038  2.382   4.9642e-02
   3_bss:   6.571  0.052  0.222 81.222  0.038  2.382   4.9642e-02
   3_xyz:   7.038  0.055  0.270 85.417  0.031  2.124   5.8965e-02
   3_adp:   7.038  0.055  0.270 85.417  0.031  2.124   5.8965e-02
   3_occ:   7.038  0.055  0.270 85.417  0.031  2.124   5.8965e-02
   4_bss:   7.038  0.055  0.270 85.417  0.031  2.124   5.8965e-02
   4_xyz:   6.788  0.049  0.255 83.150  0.041  2.319   4.9844e-02
   4_adp:   6.788  0.049  0.255 83.150  0.041  2.319   4.9844e-02
   4_occ:   6.788  0.049  0.255 83.150  0.041  2.319   4.9844e-02
   5_bss:   6.788  0.049  0.255 83.150  0.041  2.319   4.9844e-02
   5_xyz:   6.804  0.051  0.269 83.835  0.039  2.326   4.8599e-02
   5_adp:   6.804  0.051  0.269 83.835  0.039  2.326   4.8599e-02
   5_occ:   6.804  0.051  0.269 83.835  0.039  2.326   4.8599e-02
   5_bss:   6.804  0.051  0.269 83.835  0.039  2.326   4.8599e-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:  73.80   0.00  17.47  73.80   0.00  13.48  72.79   5.06  39.20
   1_occ:  73.80   0.00  17.47  73.80   0.00  13.48  72.79   5.06  39.20
   2_bss:  73.80   0.00  17.47  73.80   0.00  13.48  72.79   5.06  39.20
   2_xyz:  73.80   0.00  17.47  73.80   0.00  13.48  72.79   5.06  39.20
   2_adp:  77.56   0.00  17.20  77.56   0.00  13.16  71.61   4.94  39.25
   2_occ:  77.56   0.00  17.20  77.56   0.00  13.16  71.61   4.94  39.25
   3_bss:  77.56   0.00  17.20  77.56   0.00  13.16  71.61   4.94  39.25
   3_xyz:  77.56   0.00  17.20  77.56   0.00  13.16  71.61   4.94  39.25
   3_adp:  80.17   1.37  17.07  80.17   1.37  12.97  73.77   5.20  39.36
   3_occ:  80.17   1.37  17.07  80.17   1.37  12.97  73.77   5.20  39.36
   4_bss:  80.17   1.37  17.07  80.17   1.37  12.97  73.77   5.20  39.36
   4_xyz:  80.17   1.37  17.07  80.17   1.37  12.97  73.77   5.20  39.36
   4_adp:  80.63   1.77  16.77  80.63   1.77  12.81  72.93   4.02  38.33
   4_occ:  80.63   1.77  16.77  80.63   1.77  12.81  72.93   4.02  38.33
   5_bss:  80.63   1.77  16.77  80.63   1.77  12.81  72.93   4.02  38.33
   5_xyz:  80.63   1.77  16.77  80.63   1.77  12.81  72.93   4.02  38.33
   5_adp:  85.22   0.87  16.85  85.22   0.87  12.73  76.26   5.59  39.29
   5_occ:  85.22   0.87  16.85  85.22   0.87  12.73  76.26   5.59  39.29
   5_bss:  85.19   0.84  16.82  85.19   0.84  12.70  76.23   5.56  39.26
------------------------------------------------------------------------
 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:    1.748    0.020    0.323
   1_adp:    1.748    0.020    0.323
   1_occ:    1.748    0.020    0.323
   2_bss:    1.748    0.020    0.323
   2_xyz:    1.532    0.038    0.410
   2_adp:    1.532    0.038    0.410
   2_occ:    1.532    0.038    0.410
   3_bss:    1.532    0.038    0.410
   3_xyz:    1.441    0.022    0.481
   3_adp:    1.441    0.022    0.481
   3_occ:    1.441    0.022    0.481
   4_bss:    1.441    0.022    0.481
   4_xyz:    1.382    0.056    0.498
   4_adp:    1.382    0.056    0.498
   4_occ:    1.382    0.056    0.498
   5_bss:    1.382    0.056    0.498
   5_xyz:    1.479    0.040    0.509
   5_adp:    1.479    0.040    0.509
   5_occ:    1.479    0.040    0.509
   5_bss:    1.479    0.040    0.509
------------------------------------------------------------------------

CPU time actual refinement: 321.99


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_173/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_173/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_173/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_173/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_173/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.84 
  Macro-tasks:
    bulk solvent and scale       = 35.88  
    individual site refinement   = 132.10 
    weights calculation          = 29.17  
    collect and process          = 6.52   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 203.80 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 102.83 
    alpha_beta                      = 7.94   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 111.52 
    fmodel                         = 6.43   
    r_factors                      = 0.19   
    phase_errors                   = 10.74  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 242.84 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.584 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    643 calls, 102.41 s
gradients_fft:          588 calls,  98.00 s

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

# Date 2008-01-16 Time 04:11:41 PST -0800 (1200485501.19 s)
Start R-work = 0.3846, R-free = 0.3775 (no bulk solvent and anisotropic scale)
Final R-work = 0.1330, R-free = 0.1753 (no bulk solvent and anisotropic scale)

Start R-work = 0.3742, R-free = 0.3668
Final R-work = 0.1078, R-free = 0.1556