# Date 2008-01-16 Time 05:11:24 PST -0800 (1200489084.34 s)
#phil __OFF__

Command line arguments: "../626.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18500
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 626

-------------------------------------------------------------------------------
  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: (70.25, 45.9914, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.40, per 1000 atoms: 1.20


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.96332
Completeness in resolution range: 0.929093
Completeness with d_max=infinity: 0.926369

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9633

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: (70.25, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.96332
Completeness in resolution range: 0.929093
Completeness with d_max=infinity: 0.926369

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2023 [2211/2236]  1988   223  10.1%
  bin  2:  4.2023 -  3.3474 [2136/2156]  1927   209   9.8%
  bin  3:  3.3474 -  2.9278 [2091/2110]  1882   209  10.0%
  bin  4:  2.9278 -  2.6617 [2084/2114]  1867   217  10.4%
  bin  5:  2.6617 -  2.4718 [2074/2093]  1868   206   9.9%
  bin  6:  2.4718 -  2.3266 [2057/2082]  1856   201   9.8%
  bin  7:  2.3266 -  2.2105 [2043/2071]  1834   209  10.2%
  bin  8:  2.2105 -  2.1145 [2039/2075]  1830   209  10.3%
  bin  9:  2.1145 -  2.0333 [2008/2081]  1821   187   9.3%
  bin 10:  2.0333 -  1.9633 [ 846/2066]   757    89  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_626/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 22
        2.19 -     2.87: 1200
        2.87 -     3.54: 4463
        3.54 -     4.22: 9207
        4.22 -     4.90: 13373
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.511 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.559 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.574 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 104 "  1.751 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.784 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28260 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_626/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_626/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.9914 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4655   r_free= 0.4693   ksol= 0.00   Bsol= 0.00   scale= 0.888    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.282938                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6876 0.99   1434  157 0.3767 0.3563      6.5964      6.5235|
|  2:  4.6876 -  3.7393 0.99   1387  157 0.4025 0.4278      6.8091       6.805|
|  3:  3.7393 -  3.2721 0.99   1356  150 0.4288 0.4085      6.6669      6.6527|
|  4:  3.2721 -  2.9754 0.99   1345  150 0.4648 0.4897      6.5291      6.5428|
|  5:  2.9754 -  2.7636 0.99   1345  149 0.5006 0.4814      6.3508      6.3884|
|  6:  2.7636 -  2.6015 0.99   1338  148 0.4930 0.5260      6.2645      6.1913|
|  7:  2.6015 -  2.4718 0.99   1327  153 0.4968 0.5076      6.2275      6.1746|
|  8:  2.4718 -  2.3646 0.98   1320  149 0.5220 0.5330      6.1738      6.1689|
|  9:  2.3646 -  2.2739 0.98   1303  138 0.5038 0.5286      6.1211      6.1817|
| 10:  2.2739 -  2.1957 1.00   1342  149 0.5190 0.5329      6.0717       6.113|
| 11:  2.1957 -  2.1272 0.98   1314  146 0.5136 0.4892      6.0266      6.0045|
| 12:  2.1272 -  2.0666 0.98   1288  141 0.5080 0.5002      5.9423       5.958|
| 13:  2.0666 -  2.0123 0.88   1180  132 0.5044 0.4825      5.8835      5.7818|
| 14:  2.0123 -  1.9633 0.26    351   40 0.5340 0.5513       5.887       5.893|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6876  1434   157  0.74  30.61   0.82     0.79      61347.71|
|  2:  4.6876 -  3.7393  1387   157  0.71  34.64   0.90     0.81     107023.97|
|  3:  3.7393 -  3.2721  1356   150  0.58  45.90   0.92     0.76     119690.25|
|  4:  3.2721 -  2.9754  1345   150  0.46  54.86   0.89     0.64     112880.39|
|  5:  2.9754 -  2.7636  1345   149  0.39  60.28   0.87     0.56      84390.41|
|  6:  2.7636 -  2.6015  1338   148  0.36  62.78   0.89     0.51      73380.13|
|  7:  2.6015 -  2.4718  1327   153  0.35  63.29   0.91     0.49      65883.81|
|  8:  2.4718 -  2.3646  1320   149  0.33  65.43   0.90     0.48      60522.47|
|  9:  2.3646 -  2.2739  1303   138  0.33  64.90   0.93     0.49      56082.82|
| 10:  2.2739 -  2.1957  1342   149  0.34  64.75   0.91     0.50      49297.15|
| 11:  2.1957 -  2.1272  1314   146  0.31  66.85   0.94     0.48      50015.62|
| 12:  2.1272 -  2.0666  1288   141  0.31  67.09   0.93     0.49      44140.42|
| 13:  2.0666 -  2.0123  1180   132  0.31  66.57   0.94     0.53      38096.81|
| 14:  2.0123 -  1.9633   351    40  0.46  55.20   0.95     0.65      25734.34|
|alpha:            min =        0.48 max =            0.81 mean =         0.58|
|beta:             min =    25734.34 max =       119690.25 mean =     70637.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.12|
|phase err.(test): min =        0.00 max =           89.90 mean =        57.68|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.118831             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.703   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.810934              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.875   (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 |  1.511 -  1.850:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.850 -  2.189:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.189 -  2.528:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.528 -  2.867:     1163 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.867 -  3.206:     1940 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.206 -  3.544:     2523 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.544 -  3.883:     4621 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.883 -  4.222:     4586 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.222 -  4.561:     6086 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.561 -  4.900:     7287 |
|-----------------------------------------------------------------------------|
|-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 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.511 |       0.472 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4655   r_free= 0.4693   ksol= 0.00   Bsol= 0.00   scale= 0.888    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.282938                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4535   r_free= 0.4621   ksol= 0.34   Bsol= 50.00   scale= 0.932   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,1.54,4.27,0.00,0.00,0.00); trace/3= 0.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.274898                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.497128             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.679   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.282058              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.549   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4535      final r-factor (work) = 0.3660          |
| start r-factor (free) = 0.4621      final r-factor (free) = 0.4041          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.0852 = 10.50 * 0.50 * 6.2689 + 1.00 * 0.1827                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.5146 = 10.50 * 0.50 * 6.1688 + 1.00 * 0.1374                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3660      final r-factor (work) = 0.3340          |
| start r-factor (free) = 0.4041      final r-factor (free) = 0.4192          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9148 = 1.28 * 1.00 * 6.1688 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8101 = 1.28 * 1.00 * 6.0768 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.26   19.03    None  None   None       |
|    all(noH): 2823   0      0.00    98.26   19.03    None  None   None       |
|    Sol.    : 438    0      0.00    98.26   37.79    None  None   None       |
|    Mac.    : 2385   0      0.00    77.07   15.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.826:  839   |   5:    49.128 -  58.954:   77        |
|      1:     9.826 -  19.651:  937   |   6:    58.954 -  68.780:   37        |
|      2:    19.651 -  29.477:  517   |   7:    68.780 -  78.605:   21        |
|      3:    29.477 -  39.303:  256   |   8:    78.605 -  88.431:    6        |
|      4:    39.303 -  49.128:  131   |   9:    88.431 -  98.256:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3340 r_free = 0.4192             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3337 r_free = 0.4206             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3337   r_free= 0.4206   ksol= 0.34   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,1.54,4.27,0.00,0.00,0.00); trace/3= 0.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.083415                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3328   r_free= 0.4187   ksol= 0.35   Bsol= 72.83   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-0.14,2.15,-0.00,0.00,0.00); trace/3= 0.09                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.085439                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.593237              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.042   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.482695              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.566  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3328      final r-factor (work) = 0.2795          |
| start r-factor (free) = 0.4187      final r-factor (free) = 0.3596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1342 = 5.59 * 0.50 * 6.0778 + 1.00 * 0.1369                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9256 = 5.59 * 0.50 * 6.0240 + 1.00 * 0.0789                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2795      final r-factor (work) = 0.2693          |
| start r-factor (free) = 0.3596      final r-factor (free) = 0.3474          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9270 = 0.48 * 1.00 * 6.0240 + 1.00 * 0.0192                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8794 = 0.48 * 1.00 * 5.9349 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.37   18.55    None  None   None       |
|    all(noH): 2823   0      0.00    98.37   18.55    None  None   None       |
|    Sol.    : 438    0      0.00    98.37   38.09    None  None   None       |
|    Mac.    : 2385   0      0.00    72.04   14.97    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:     0.000 -   9.837:  849   |   5:    49.183 -  59.020:   69        |
|      1:     9.837 -  19.673:  997   |   6:    59.020 -  68.856:   28        |
|      2:    19.673 -  29.510:  483   |   7:    68.856 -  78.693:   19        |
|      3:    29.510 -  39.347:  229   |   8:    78.693 -  88.530:    5        |
|      4:    39.347 -  49.183:  142   |   9:    88.530 -  98.366:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2693 r_free = 0.3474             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2692 r_free = 0.3475             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2692   r_free= 0.3475   ksol= 0.35   Bsol= 72.83   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-0.14,2.15,-0.00,0.00,0.00); trace/3= 0.09                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.920369                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2697   r_free= 0.3469   ksol= 0.34   Bsol= 67.86   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,-0.64,1.47,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.920878                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.366712              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.357   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.705506              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.950  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2697      final r-factor (work) = 0.2138          |
| start r-factor (free) = 0.3469      final r-factor (free) = 0.2751          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0382 = 4.37 * 0.50 * 5.9355 + 1.00 * 0.0789                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7952 = 4.37 * 0.50 * 5.8293 + 1.00 * 0.0677                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2138      final r-factor (work) = 0.1942          |
| start r-factor (free) = 0.2751      final r-factor (free) = 0.2585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1255 = 0.71 * 1.00 * 5.8293 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0117 = 0.71 * 1.00 * 5.6675 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.10  18.67    None  None   None       |
|    all(noH): 2823   0      0.00    102.10  18.67    None  None   None       |
|    Sol.    : 438    0      3.36    102.10  44.77    None  None   None       |
|    Mac.    : 2385   0      0.00    90.73   13.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.210: 1016   |   5:    51.049 -  61.259:  106        |
|      1:    10.210 -  20.420: 1017   |   6:    61.259 -  71.468:   56        |
|      2:    20.420 -  30.629:  313   |   7:    71.468 -  81.678:   26        |
|      3:    30.629 -  40.839:  162   |   8:    81.678 -  91.888:   10        |
|      4:    40.839 -  51.049:  116   |   9:    91.888 - 102.098:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1942 r_free = 0.2585             target_work(ml) = 5.637         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1940 r_free = 0.2583             target_work(ml) = 5.637         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1940   r_free= 0.2583   ksol= 0.34   Bsol= 67.86   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,-0.64,1.47,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.636640                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1937   r_free= 0.2579   ksol= 0.33   Bsol= 72.36   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.83,0.29,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.636662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.377801              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.039  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190534              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.866  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1937      final r-factor (work) = 0.1599          |
| start r-factor (free) = 0.2579      final r-factor (free) = 0.2157          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8108 = 2.38 * 0.50 * 5.6717 + 1.00 * 0.0677                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6587 = 2.38 * 0.50 * 5.5555 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1599      final r-factor (work) = 0.1535          |
| start r-factor (free) = 0.2157      final r-factor (free) = 0.2025          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0718 = 0.19 * 1.00 * 5.5555 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0468 = 0.19 * 1.00 * 5.4443 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    97.92   17.75    None  None   None       |
|    all(noH): 2823   0      1.23    97.92   17.75    None  None   None       |
|    Sol.    : 438    0      5.12    97.92   43.18    None  None   None       |
|    Mac.    : 2385   0      1.23    87.98   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.225 -  10.895: 1236   |   5:    49.575 -  59.245:   93        |
|      1:    10.895 -  20.565:  918   |   6:    59.245 -  68.915:   60        |
|      2:    20.565 -  30.235:  225   |   7:    68.915 -  78.585:   26        |
|      3:    30.235 -  39.905:  138   |   8:    78.585 -  88.255:   10        |
|      4:    39.905 -  49.575:  116   |   9:    88.255 -  97.925:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1535 r_free = 0.2025             target_work(ml) = 5.411         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1533 r_free = 0.2021             target_work(ml) = 5.410         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1533   r_free= 0.2021   ksol= 0.33   Bsol= 72.36   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.83,0.29,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.409666                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1534   r_free= 0.2017   ksol= 0.33   Bsol= 64.23   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.30,-0.04,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.408096                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.117947              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.892  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.484494              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.036  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1534      final r-factor (work) = 0.1305          |
| start r-factor (free) = 0.2017      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5409 = 3.12 * 0.50 * 5.4441 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3917 = 3.12 * 0.50 * 5.3404 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1305      final r-factor (work) = 0.1254          |
| start r-factor (free) = 0.1762      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.2777 = 2.48 * 1.00 * 5.3404 + 1.00 * 0.0094                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0480 = 2.48 * 1.00 * 5.2470 + 1.00 * 0.0117                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.59   17.98    None  None   None       |
|    all(noH): 2823   0      0.00    99.59   17.98    None  None   None       |
|    Sol.    : 438    0      6.22    99.59   45.50    None  None   None       |
|    Mac.    : 2385   0      0.00    88.40   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.959: 1076   |   5:    49.796 -  59.755:   94        |
|      1:     9.959 -  19.918: 1067   |   6:    59.755 -  69.714:   77        |
|      2:    19.918 -  29.878:  239   |   7:    69.714 -  79.673:   38        |
|      3:    29.878 -  39.837:  109   |   8:    79.673 -  89.633:   13        |
|      4:    39.837 -  49.796:  106   |   9:    89.633 -  99.592:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1254 r_free = 0.1749             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1253 r_free = 0.1749             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1749   ksol= 0.33   Bsol= 64.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.30,-0.04,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.240505                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6876 0.99   1434  157 0.0935 0.1300      5.3481      5.5847|
|  2:  4.6876 -  3.7393 0.99   1387  157 0.0864 0.1230      5.4642      5.7013|
|  3:  3.7393 -  3.2721 0.99   1356  150 0.1207 0.1638      5.5709      5.8687|
|  4:  3.2721 -  2.9754 0.99   1345  150 0.1456 0.1960      5.5784      5.7432|
|  5:  2.9754 -  2.7636 0.99   1345  149 0.1545 0.2017      5.4506       5.687|
|  6:  2.7636 -  2.6015 0.99   1338  148 0.1452 0.2210      5.3359      5.5806|
|  7:  2.6015 -  2.4718 0.99   1327  153 0.1450 0.1770      5.2866      5.4098|
|  8:  2.4718 -  2.3646 0.98   1320  149 0.1438 0.1911      5.2218      5.4593|
|  9:  2.3646 -  2.2739 0.98   1303  138 0.1375 0.2016      5.1418      5.3849|
| 10:  2.2739 -  2.1957 1.00   1342  149 0.1274 0.1746      5.0189      5.2293|
| 11:  2.1957 -  2.1272 0.98   1314  146 0.1262 0.2050      5.0132      5.4164|
| 12:  2.1272 -  2.0666 0.98   1288  141 0.1307 0.1923      4.9725      5.2234|
| 13:  2.0666 -  2.0123 0.88   1180  132 0.1121 0.1587       4.792      4.9656|
| 14:  2.0123 -  1.9633 0.26    351   40 0.0983 0.1756       4.629      4.9492|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6876  1434   157  0.94   8.91   0.97     0.94       6971.14|
|  2:  4.6876 -  3.7393  1387   157  0.95   8.29   1.02     1.01       9727.59|
|  3:  3.7393 -  3.2721  1356   150  0.92  13.12   1.04     1.04      12422.99|
|  4:  3.2721 -  2.9754  1345   150  0.89  16.74   1.02     1.00      13234.14|
|  5:  2.9754 -  2.7636  1345   149  0.88  18.11   1.00     0.98      10653.92|
|  6:  2.7636 -  2.6015  1338   148  0.87  19.00   0.98     0.94       8961.39|
|  7:  2.6015 -  2.4718  1327   153  0.88  18.54   1.00     0.97       8175.94|
|  8:  2.4718 -  2.3646  1320   149  0.88  18.48   1.00     0.96       7068.66|
|  9:  2.3646 -  2.2739  1303   138  0.89  17.87   1.00     0.94       6028.56|
| 10:  2.2739 -  2.1957  1342   149  0.89  17.25   1.00     0.97       4982.14|
| 11:  2.1957 -  2.1272  1314   146  0.89  17.71   0.99     0.93       4976.98|
| 12:  2.1272 -  2.0666  1288   141  0.89  17.88   1.01     1.01       4794.72|
| 13:  2.0666 -  2.0123  1180   132  0.89  17.38   0.99     0.97       3540.55|
| 14:  2.0123 -  1.9633   351    40  0.94  11.58   0.98     0.96       2245.11|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     2245.11 max =        13234.14 mean =      7762.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.92|
|phase err.(test): min =        0.00 max =           89.99 mean =        15.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1749   ksol= 0.33   Bsol= 64.24   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.31,-0.08,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.240476                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1749   ksol= 0.33   Bsol= 64.24   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.31,-0.08,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.240476                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6876 0.99   1434  157 0.0935 0.1300      5.3482       5.585|
|  2:  4.6876 -  3.7393 0.99   1387  157 0.0865 0.1230      5.4644      5.7014|
|  3:  3.7393 -  3.2721 0.99   1356  150 0.1207 0.1638      5.5712      5.8692|
|  4:  3.2721 -  2.9754 0.99   1345  150 0.1456 0.1960      5.5785      5.7433|
|  5:  2.9754 -  2.7636 0.99   1345  149 0.1544 0.2016      5.4504      5.6869|
|  6:  2.7636 -  2.6015 0.99   1338  148 0.1452 0.2210      5.3358       5.581|
|  7:  2.6015 -  2.4718 0.99   1327  153 0.1450 0.1772      5.2866      5.4101|
|  8:  2.4718 -  2.3646 0.98   1320  149 0.1438 0.1912      5.2219      5.4593|
|  9:  2.3646 -  2.2739 0.98   1303  138 0.1374 0.2016      5.1418      5.3853|
| 10:  2.2739 -  2.1957 1.00   1342  149 0.1274 0.1745      5.0189      5.2293|
| 11:  2.1957 -  2.1272 0.98   1314  146 0.1261 0.2047      5.0129       5.416|
| 12:  2.1272 -  2.0666 0.98   1288  141 0.1307 0.1924      4.9726       5.224|
| 13:  2.0666 -  2.0123 0.88   1180  132 0.1121 0.1585      4.7914      4.9642|
| 14:  2.0123 -  1.9633 0.26    351   40 0.0985 0.1755       4.628      4.9479|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6876  1434   157  0.94   8.91   0.97     0.94       6972.59|
|  2:  4.6876 -  3.7393  1387   157  0.95   8.29   1.02     1.01       9731.72|
|  3:  3.7393 -  3.2721  1356   150  0.92  13.12   1.04     1.04      12433.80|
|  4:  3.2721 -  2.9754  1345   150  0.89  16.74   1.02     1.00      13238.43|
|  5:  2.9754 -  2.7636  1345   149  0.88  18.10   1.00     0.98      10653.51|
|  6:  2.7636 -  2.6015  1338   148  0.87  18.99   0.98     0.94       8958.07|
|  7:  2.6015 -  2.4718  1327   153  0.88  18.53   1.00     0.97       8175.59|
|  8:  2.4718 -  2.3646  1320   149  0.88  18.49   1.00     0.96       7073.18|
|  9:  2.3646 -  2.2739  1303   138  0.89  17.87   1.00     0.95       6034.17|
| 10:  2.2739 -  2.1957  1342   149  0.89  17.25   1.00     0.97       4982.79|
| 11:  2.1957 -  2.1272  1314   146  0.89  17.69   0.99     0.93       4975.67|
| 12:  2.1272 -  2.0666  1288   141  0.89  17.88   1.01     1.01       4794.88|
| 13:  2.0666 -  2.0123  1180   132  0.89  17.37   0.99     0.97       3533.21|
| 14:  2.0123 -  1.9633   351    40  0.94  11.55   0.98     0.96       2235.46|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     2235.46 max =        13238.43 mean =      7764.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.92|
|phase err.(test): min =        0.00 max =           89.99 mean =        15.42|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.59   17.98    None  None   None       |
|    all(noH): 2823   0      0.00    99.59   17.98    None  None   None       |
|    Sol.    : 438    0      6.22    99.59   45.51    None  None   None       |
|    Mac.    : 2385   0      0.00    88.40   12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.962: 1076   |   5:    49.799 -  59.758:   94        |
|      1:     9.962 -  19.921: 1067   |   6:    59.758 -  69.717:   77        |
|      2:    19.921 -  29.881:  239   |   7:    69.717 -  79.676:   38        |
|      3:    29.881 -  39.840:  109   |   8:    79.676 -  89.636:   13        |
|      4:    39.840 -  49.799:  106   |   9:    89.636 -  99.595:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 344         
Filter by distance & map next to the model:
   mapped sites are within: 0.661 - 5.242
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 344
   mapped sites are within: 0.759 - 5.242

peak=    5.815 closest distance to " CG  PRO A  54 " =    1.433
peak=    5.810 closest distance to " O   HOH Z 245 " =    1.063
peak=    5.617 closest distance to " O   HOH Z 222 " =    1.251
peak=    5.484 closest distance to " NE2 GLN A  11 " =    1.193
peak=    5.440 closest distance to " O   HOH Z 142 " =    2.139
peak=    5.302 closest distance to " O   HOH Z   7 " =    1.720
peak=    5.215 closest distance to " O   HOH Z 417 " =    2.562
peak=    5.172 closest distance to " O   HOH Z  63 " =    1.788
peak=    5.150 closest distance to " O   HOH Z 287 " =    2.078
peak=    5.030 closest distance to " O   HOH Z 419 " =    2.296
peak=    4.982 closest distance to " O   HOH Z 427 " =    2.284
peak=    4.940 closest distance to " O   HOH Z 105 " =    1.162
peak=    4.929 closest distance to " O   HOH Z 103 " =    0.981
peak=    4.897 closest distance to " O   HOH Z  49 " =    1.587
peak=    4.895 closest distance to " O   HOH Z 423 " =    1.938
peak=    4.865 closest distance to " O   HOH Z  65 " =    1.262
peak=    4.771 closest distance to " O   HOH Z 126 " =    2.082
peak=    4.717 closest distance to " CB  SER A  63 " =    1.251
peak=    4.717 closest distance to " O   HOH Z 422 " =    1.027
peak=    4.612 closest distance to " O   HOH Z 369 " =    2.149
peak=    4.596 closest distance to " CB  GLN A 223 " =    1.575
peak=    4.576 closest distance to " O   HOH Z  69 " =    1.502
peak=    4.565 closest distance to " CZ3 TRP A 266 " =    1.149
peak=    4.546 closest distance to " O   HOH Z 385 " =    0.948
peak=    4.469 closest distance to " O   HOH Z   9 " =    2.089
peak=    4.467 closest distance to " O   HOH Z 380 " =    1.899
peak=    4.456 closest distance to " O   HOH Z  66 " =    1.046
peak=    4.453 closest distance to " O   HOH Z 127 " =    1.056
peak=    4.436 closest distance to " O   HOH Z 112 " =    1.131
peak=    4.426 closest distance to " O   HOH Z 278 " =    1.213
peak=    4.425 closest distance to " CB  ASN A 148 " =    1.472
peak=    4.423 closest distance to " CB  SER A 216 " =    1.067
peak=    4.355 closest distance to " O   HOH Z 403 " =    1.871
peak=    4.352 closest distance to " CB  PRO A  54 " =    1.105
peak=    4.351 closest distance to " CB  ARG A 275 " =    1.042
peak=    4.333 closest distance to " CA  VAL A 125 " =    1.209
peak=    4.321 closest distance to " NH2 ARG A  56 " =    2.094
peak=    4.289 closest distance to " O   HOH Z 425 " =    1.489
peak=    4.255 closest distance to " O   HOH Z 232 " =    2.197
peak=    4.248 closest distance to " CD  GLN A  77 " =    1.304
peak=    4.209 closest distance to " O   HOH Z  39 " =    1.076
peak=    4.202 closest distance to " OG ASER A 258 " =    3.081
peak=    4.187 closest distance to " NH1AARG A 145 " =    1.225
peak=    4.175 closest distance to " CB  GLU A 277 " =    3.587
peak=    4.171 closest distance to " CG  PRO A  90 " =    1.551
peak=    4.169 closest distance to " CG2 VAL A 257 " =    0.927
peak=    4.162 closest distance to " CA  ALA A  51 " =    1.043
peak=    4.153 closest distance to " CG  GLN A  58 " =    1.186
peak=    4.150 closest distance to " O   PRO A 198 " =    1.354
peak=    4.137 closest distance to " CG  PRO A 280 " =    1.072
peak=    4.108 closest distance to " O   HOH Z 375 " =    1.127
peak=    4.085 closest distance to " O   HOH Z  67 " =    1.171
peak=    4.075 closest distance to " CD  ARG A 159 " =    0.828
peak=    4.062 closest distance to " NH2AARG A 190 " =    1.978
peak=    4.058 closest distance to " O   HOH Z 298 " =    2.063
peak=    4.053 closest distance to " O   HOH Z  78 " =    1.646
peak=    4.050 closest distance to " O   HOH Z 139 " =    1.190
peak=    4.028 closest distance to " O   HOH Z 145 " =    1.430
peak=    4.020 closest distance to " O   HOH Z 414 " =    1.297
peak=    4.011 closest distance to " O   HOH Z 211 " =    1.229
peak=    4.010 closest distance to " O   HOH Z  77 " =    1.175
peak=    4.009 closest distance to " CB  PRO A  90 " =    1.101
peak=    3.979 closest distance to " O   HOH Z 394 " =    1.857
peak=    3.975 closest distance to " CG  TRP A 179 " =    2.228
peak=    3.970 closest distance to " CE  LYS A 119 " =    1.318
peak=    3.961 closest distance to " CA  ARG A 195 " =    1.340
peak=    3.930 closest distance to " O   HOH Z  40 " =    1.772
peak=    3.928 closest distance to " O   HOH Z 295 " =    1.181
peak=    3.903 closest distance to " CB  ASN A 142 " =    0.954
peak=    3.899 closest distance to " O   HOH Z  61 " =    1.700
peak=    3.877 closest distance to " O   HOH Z 130 " =    2.525
peak=    3.874 closest distance to " O   HOH Z  91 " =    2.380
peak=    3.872 closest distance to " CB  ARG A  79 " =    1.232
peak=    3.870 closest distance to " ND2BASN A 224 " =    0.913
peak=    3.870 closest distance to " O   HOH Z 365 " =    2.730
peak=    3.857 closest distance to " O   HOH Z   1 " =    1.754
peak=    3.847 closest distance to " N   TYR A  15 " =    1.191
peak=    3.843 closest distance to " O   HOH Z 327 " =    1.636
peak=    3.832 closest distance to " O   HOH Z 359 " =    1.477
peak=    3.831 closest distance to " CG  PRO A 198 " =    1.267
peak=    3.825 closest distance to " O   HOH Z 421 " =    2.171
peak=    3.820 closest distance to " CA  TYR A 116 " =    1.370
peak=    3.820 closest distance to " CA  TYR A  30 " =    1.058
peak=    3.802 closest distance to " O   HOH Z 218 " =    1.814
peak=    3.801 closest distance to " ND2 ASN A  60 " =    2.924
peak=    3.799 closest distance to " CE3 TRP A 150 " =    1.162
peak=    3.795 closest distance to " CG  LEU A 167 " =    1.288
peak=    3.776 closest distance to " CD2 TRP A 179 " =    1.276
peak=    3.765 closest distance to " CB  SER A 212 " =    1.343
peak=    3.764 closest distance to " CB  ARG A 190 " =    1.634
peak=    3.764 closest distance to " CG  LYS A  76 " =    1.787
peak=    3.761 closest distance to " NZ  LYS A 117 " =    2.889
peak=    3.759 closest distance to " O   HOH Z 201 " =    1.563
peak=    3.759 closest distance to " O   HOH Z 368 " =    3.663
peak=    3.753 closest distance to " O   HOH Z 180 " =    2.275
peak=    3.750 closest distance to " NE2 HIS A 207 " =    1.075
peak=    3.749 closest distance to " O   HOH Z  11 " =    1.041
peak=    3.744 closest distance to " N   CYS A 260 " =    0.867
peak=    3.744 closest distance to " O   HOH Z 437 " =    1.711
peak=    3.728 closest distance to " O   HOH Z 431 " =    1.129
peak=    3.723 closest distance to " O   HOH Z 126 " =    1.530
peak=    3.721 closest distance to " N   GLN A 278 " =    1.390
peak=    3.716 closest distance to " O   HOH Z 361 " =    1.293
peak=    3.711 closest distance to " O   HOH Z 392 " =    1.258
peak=    3.711 closest distance to " OE2 GLU A  53 " =    2.007
peak=    3.701 closest distance to " CB  ALA A 114 " =    0.840
peak=    3.701 closest distance to " CD  ARG A  66 " =    2.215
peak=    3.698 closest distance to " O   HOH Z  26 " =    1.403
peak=    3.698 closest distance to " O   HOH Z 293 " =    1.486
peak=    3.695 closest distance to " CB  ASN A  39 " =    0.938
peak=    3.694 closest distance to " O   HOH Z 251 " =    1.406
peak=    3.693 closest distance to " O   HOH Z  24 " =    1.999
peak=    3.689 closest distance to " O   HOH Z 214 " =    2.628
peak=    3.688 closest distance to " O   TYR A 116 " =    1.245
peak=    3.681 closest distance to " O   HOH Z 411 " =    3.674
peak=    3.671 closest distance to " O   HOH Z 100 " =    0.950
peak=    3.667 closest distance to " CB  GLN A 183 " =    1.204
peak=    3.665 closest distance to " CG AARG A 275 " =    1.286
peak=    3.664 closest distance to " CD  ARG A 259 " =    1.759
peak=    3.664 closest distance to " CA  ASN A 127 " =    1.188
peak=    3.664 closest distance to " CG  PRO A 213 " =    1.247
peak=    3.662 closest distance to " CG2 ILE A 120 " =    1.177
peak=    3.656 closest distance to " O   HOH Z 406 " =    1.604
peak=    3.650 closest distance to " O   HOH Z 222 " =    2.431
peak=    3.647 closest distance to " O   HOH Z 425 " =    2.024
peak=    3.646 closest distance to " O   HOH Z 368 " =    4.280
peak=    3.644 closest distance to " CE  LYS A  76 " =    0.893
peak=    3.642 closest distance to " CG  GLN A  89 " =    1.554
peak=    3.640 closest distance to " C   GLN A  73 " =    1.074
peak=    3.640 closest distance to " O   HOH Z   1 " =    1.732
peak=    3.637 closest distance to " O   HOH Z 130 " =    0.970
peak=    3.636 closest distance to " O   HOH Z  76 " =    1.227
peak=    3.636 closest distance to " O   HOH Z 207 " =    0.871
peak=    3.633 closest distance to " O   HOH Z  88 " =    3.784
peak=    3.630 closest distance to " CB  ASP A 124 " =    0.908
peak=    3.630 closest distance to " O   HOH Z 153 " =    3.766
peak=    3.627 closest distance to " CB  GLU A 128 " =    1.016
peak=    3.626 closest distance to " O   HOH Z 132 " =    1.030
peak=    3.622 closest distance to " CB  VAL A 265 " =    1.376
peak=    3.602 closest distance to " O   HOH Z 362 " =    2.137
peak=    3.593 closest distance to " CG2 ILE A  20 " =    1.594
peak=    3.588 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.578 closest distance to " O   HOH Z  42 " =    1.475
peak=    3.576 closest distance to " CG2 THR A 221 " =    1.118
peak=    3.574 closest distance to " NZ  LYS A 166 " =    0.975
peak=    3.561 closest distance to " O   HOH Z 258 " =    2.113
peak=    3.561 closest distance to " CG  PRO A 243 " =    1.047
peak=    3.561 closest distance to " O   HOH Z 216 " =    3.870
peak=    3.559 closest distance to " CB  ASP A 191 " =    1.316
peak=    3.553 closest distance to " CA  ALA A 160 " =    1.476
peak=    3.548 closest distance to " CG1 ILE A 120 " =    1.429
peak=    3.547 closest distance to " O   HOH Z  59 " =    1.828
peak=    3.543 closest distance to " O   HOH Z   3 " =    2.301
peak=    3.535 closest distance to " NH2AARG A 145 " =    1.169
peak=    3.524 closest distance to " O   HOH Z  40 " =    2.115
peak=    3.521 closest distance to " O   HOH Z 296 " =    1.049
peak=    3.520 closest distance to " CB  SER A 210 " =    0.870
peak=    3.510 closest distance to " CB  VAL A 202 " =    1.627
peak=    3.506 closest distance to " O   HOH Z 236 " =    1.522
peak=    3.494 closest distance to " O   HOH Z 393 " =    1.267
peak=    3.494 closest distance to " CB  GLN A  88 " =    1.389
peak=    3.480 closest distance to " CB  ALA A   1 " =    4.401
peak=    3.479 closest distance to " O   HOH Z 378 " =    1.064
peak=    3.477 closest distance to " O   HOH Z 273 " =    1.150
peak=    3.477 closest distance to " O   HOH Z 402 " =    1.498
peak=    3.474 closest distance to " CB  THR A  31 " =    1.609
peak=    3.472 closest distance to " O   HOH Z  43 " =    1.184
peak=    3.469 closest distance to " O   ALA A 165 " =    1.441
peak=    3.469 closest distance to " O   HOH Z 225 " =    1.672
peak=    3.465 closest distance to " CA  MET A 105 " =    0.977
peak=    3.463 closest distance to " O   HOH Z 357 " =    2.115
peak=    3.463 closest distance to " O   HOH Z  92 " =    1.256
peak=    3.462 closest distance to " N   VAL A 296 " =    1.881
peak=    3.460 closest distance to " O   HOH Z  97 " =    1.203
peak=    3.459 closest distance to " CB  ARG A 102 " =    0.834
peak=    3.453 closest distance to " CB  SER A  97 " =    0.772
peak=    3.453 closest distance to " NE1 TRP A 274 " =    0.938
peak=    3.452 closest distance to " CB  TRP A 179 " =    1.509
peak=    3.451 closest distance to " NH2 ARG A  56 " =    1.069
peak=    3.450 closest distance to " O   HOH Z 394 " =    3.766
peak=    3.447 closest distance to " CB  ALA A  43 " =    0.780
peak=    3.435 closest distance to " O   HOH Z 181 " =    2.271
peak=    3.428 closest distance to " O   HOH Z 193 " =    1.795
peak=    3.425 closest distance to " CB  ASP A 200 " =    0.954
peak=    3.423 closest distance to " CG  ARG A 159 " =    0.759
peak=    3.421 closest distance to " O   HOH Z   7 " =    3.328
peak=    3.419 closest distance to " NZ BLYS A 290 " =    0.946
peak=    3.419 closest distance to " ND2 ASN A 249 " =    0.843
peak=    3.417 closest distance to " CB  PHE A 130 " =    0.970
peak=    3.415 closest distance to " O   HOH Z 272 " =    1.815
peak=    3.412 closest distance to " N   ASN A 127 " =    1.360
peak=    3.411 closest distance to " O   HOH Z  90 " =    2.305
peak=    3.411 closest distance to " CD1 LEU A 167 " =    1.183
peak=    3.409 closest distance to " O   HOH Z 215 " =    1.702
peak=    3.408 closest distance to " O   HOH Z 119 " =    1.538
peak=    3.402 closest distance to " O   HOH Z  58 " =    1.750
peak=    3.400 closest distance to " CZ  PHE A  38 " =    1.269
peak=    3.398 closest distance to " O   HOH Z 391 " =    2.917
peak=    3.397 closest distance to " O   HOH Z 220 " =    1.461
peak=    3.393 closest distance to " CB  LYS A 117 " =    1.223
peak=    3.392 closest distance to " CB  SER A  62 " =    0.939
peak=    3.391 closest distance to " O   HOH Z  70 " =    1.034
peak=    3.391 closest distance to " O   HOH Z  61 " =    1.846
peak=    3.390 closest distance to " CA  SER A  87 " =    1.137
peak=    3.389 closest distance to " O   HOH Z  48 " =    1.681
peak=    3.384 closest distance to " O   GLN A 240 " =    1.759
peak=    3.383 closest distance to " O   HOH Z 119 " =    4.222
peak=    3.383 closest distance to " N   ASN A 224 " =    1.871
peak=    3.380 closest distance to " CB  SER A  99 " =    0.872
peak=    3.378 closest distance to " CA  PHE A 283 " =    1.283
peak=    3.376 closest distance to " CB  SER A 276 " =    1.118
peak=    3.375 closest distance to " O   HOH Z 234 " =    3.492
peak=    3.371 closest distance to " CG2 VAL A 197 " =    1.280
peak=    3.371 closest distance to " CA  ALA A   7 " =    0.899
peak=    3.368 closest distance to " OG BSER A 164 " =    2.432
peak=    3.365 closest distance to " O   HOH Z  46 " =    0.992
peak=    3.365 closest distance to " CB  TYR A  30 " =    1.562
peak=    3.359 closest distance to " CD  ARG A 195 " =    3.583
peak=    3.355 closest distance to " O   HOH Z 405 " =    1.600
peak=    3.352 closest distance to " CB  LEU A 300 " =    0.939
peak=    3.349 closest distance to " O   HOH Z 213 " =    2.253
peak=    3.347 closest distance to " OG BSER A  99 " =    2.398
peak=    3.345 closest distance to " CZ3 TRP A 274 " =    1.404
peak=    3.344 closest distance to " N   PHE A 130 " =    1.297
peak=    3.344 closest distance to " O   HOH Z 374 " =    1.285
peak=    3.342 closest distance to " CB  LEU A 237 " =    0.849
peak=    3.337 closest distance to " NZ  LYS A 119 " =    2.358
peak=    3.336 closest distance to " CA  GLY A 267 " =    1.129
peak=    3.333 closest distance to " O   HOH Z 104 " =    1.883
peak=    3.331 closest distance to " CA  SER A  95 " =    0.997
peak=    3.328 closest distance to " O   HOH Z 136 " =    1.084
peak=    3.325 closest distance to " O   HOH Z 116 " =    1.044
peak=    3.325 closest distance to " O   MET A 105 " =    1.773
peak=    3.325 closest distance to " N   GLU A   2 " =    1.393
peak=    3.324 closest distance to " O   HOH Z 122 " =    2.127
peak=    3.322 closest distance to " O   HOH Z  53 " =    2.342
peak=    3.316 closest distance to " CG2 ILE A 234 " =    0.887
peak=    3.315 closest distance to " O   HOH Z 345 " =    1.963
peak=    3.313 closest distance to " O   HOH Z  83 " =    1.259
peak=    3.311 closest distance to " O   HOH Z 235 " =    1.669
peak=    3.311 closest distance to " CB  TRP A 266 " =    1.108
peak=    3.311 closest distance to " SD BMET A  47 " =    1.127
peak=    3.308 closest distance to " O   HOH Z 156 " =    2.568
peak=    3.300 closest distance to " ND2 ASN A 187 " =    1.821
peak=    3.299 closest distance to " CA  ARG A 156 " =    1.079
peak=    3.297 closest distance to " O   HOH Z  68 " =    1.987
peak=    3.294 closest distance to " CB  ASP A 140 " =    1.071
peak=    3.292 closest distance to " CA  ILE A 263 " =    1.140
peak=    3.290 closest distance to " O   HOH Z 280 " =    1.521
peak=    3.290 closest distance to " O   HOH Z 410 " =    1.651
peak=    3.290 closest distance to " O   HOH Z 158 " =    0.971
peak=    3.289 closest distance to " O   HOH Z 143 " =    1.291
peak=    3.288 closest distance to " CB  LEU A 228 " =    1.153
peak=    3.286 closest distance to " O   HOH Z 265 " =    1.919
peak=    3.285 closest distance to " CG  LYS A 119 " =    1.101
peak=    3.283 closest distance to " CA  GLY A 136 " =    1.039
peak=    3.279 closest distance to " O   HOH Z 353 " =    1.769
peak=    3.278 closest distance to " O   HOH Z  88 " =    3.119
peak=    3.277 closest distance to " O   ASP A 200 " =    1.467
peak=    3.276 closest distance to " OE2 GLU A  53 " =    1.453
peak=    3.275 closest distance to " N   ALA A   1 " =    1.744
peak=    3.274 closest distance to " CD2 LEU A   5 " =    1.244
peak=    3.271 closest distance to " O   HOH Z 244 " =    1.578
peak=    3.270 closest distance to " CA  ASP A 162 " =    0.960
peak=    3.267 closest distance to " CB  TRP A 274 " =    1.097
peak=    3.264 closest distance to " CB  MET A  40 " =    0.786
peak=    3.259 closest distance to " O   HOH Z   2 " =    1.714
peak=    3.259 closest distance to " CB  LYS A 290 " =    0.991
peak=    3.257 closest distance to " O   HOH Z 328 " =    1.488
peak=    3.254 closest distance to " O   HOH Z 147 " =    1.164
peak=    3.253 closest distance to " O   HOH Z 371 " =    3.072
peak=    3.253 closest distance to " CD2 PHE A  59 " =    1.935
peak=    3.248 closest distance to " CB  GLU A 152 " =    1.233
peak=    3.245 closest distance to " ND1 HIS A  86 " =    1.756
peak=    3.239 closest distance to " CB  SER A   3 " =    1.474
peak=    3.239 closest distance to " CA  ARG A 159 " =    1.169
peak=    3.237 closest distance to " CB  GLU A 236 " =    1.382
peak=    3.237 closest distance to " N   THR A  42 " =    1.415
peak=    3.234 closest distance to " CA  ALA A 129 " =    1.309
peak=    3.228 closest distance to " O   HOH Z 124 " =    1.930
peak=    3.227 closest distance to " O   HOH Z  17 " =    1.834
peak=    3.224 closest distance to " CE  MET A  93 " =    1.384
peak=    3.221 closest distance to " CA  ILE A 106 " =    0.774
peak=    3.220 closest distance to " O   HOH Z 120 " =    3.687
peak=    3.215 closest distance to " CZ  PHE A 218 " =    1.184
peak=    3.211 closest distance to " O   HOH Z 203 " =    1.823
peak=    3.208 closest distance to " O   HOH Z  51 " =    1.778
peak=    3.206 closest distance to " OD1 ASN A  69 " =    2.756
peak=    3.199 closest distance to " CB  ARG A 138 " =    0.954
peak=    3.196 closest distance to " O   HOH Z 172 " =    2.234
peak=    3.195 closest distance to " O   HOH Z  80 " =    1.444
peak=    3.191 closest distance to " O   PHE A 192 " =    1.429
peak=    3.190 closest distance to " O   HOH Z 287 " =    2.149
peak=    3.190 closest distance to " O   HOH Z 188 " =    2.788
peak=    3.189 closest distance to " N   SER A  97 " =    0.766
peak=    3.189 closest distance to " CB  PRO A 163 " =    4.226
peak=    3.184 closest distance to " CB  TRP A 150 " =    0.959
peak=    3.180 closest distance to " CD1 ILE A  33 " =    1.785
peak=    3.175 closest distance to " O   HOH Z 132 " =    2.575
peak=    3.175 closest distance to " CB  HIS A 108 " =    0.825
peak=    3.175 closest distance to " O   HOH Z 248 " =    1.687
peak=    3.175 closest distance to " O   HOH Z 385 " =    3.757
peak=    3.172 closest distance to " CE3 TRP A  85 " =    1.048
peak=    3.168 closest distance to " O   HOH Z  90 " =    4.191
peak=    3.166 closest distance to " O   HOH Z 427 " =    1.192
peak=    3.166 closest distance to " CA  THR A 264 " =    0.840
peak=    3.163 closest distance to " CG2 THR A 178 " =    1.075
peak=    3.159 closest distance to " N   GLU A 152 " =    1.485
peak=    3.150 closest distance to " CB  ALA A 114 " =    1.433
peak=    3.149 closest distance to " O   HOH Z  90 " =    4.802
peak=    3.139 closest distance to " O   HOH Z 128 " =    3.041
peak=    3.137 closest distance to " CB  ALA A 184 " =    1.252
peak=    3.137 closest distance to " CA  ILE A 234 " =    1.136
peak=    3.134 closest distance to " O   CYS A 168 " =    1.509
peak=    3.128 closest distance to " CD  LYS A 119 " =    1.665
peak=    3.126 closest distance to " O   HOH Z 172 " =    4.904
peak=    3.124 closest distance to " CB  SER A 245 " =    3.306
peak=    3.121 closest distance to " O   HOH Z 207 " =    2.510
peak=    3.121 closest distance to " N   VAL A  72 " =    1.610
peak=    3.120 closest distance to " CA  GLY A  35 " =    0.944
peak=    3.117 closest distance to " CB  ASN A 215 " =    1.137
peak=    3.108 closest distance to " O   TRP A  70 " =    1.582
peak=    3.107 closest distance to " CG  PRO A 280 " =    2.250
peak=    3.105 closest distance to " CA  ASN A  74 " =    1.277
peak=    3.104 closest distance to " CA  ALA A 291 " =    0.917
peak=    3.103 closest distance to " C   PHE A 208 " =    1.291
peak=    3.101 closest distance to " O   ASN A  74 " =    1.463
peak=    3.097 closest distance to " NH2 ARG A  66 " =    5.242
peak=    3.082 closest distance to " O   HOH Z 189 " =    3.144
peak=    3.082 closest distance to " O   HOH Z 438 " =    2.452
peak=    3.075 closest distance to " O   HOH Z 303 " =    1.938
peak=    3.074 closest distance to " OD2 ASP A 286 " =    2.993
peak=    3.067 closest distance to " CA  ASN A 217 " =    1.256
peak=    3.062 closest distance to " O   HOH Z 422 " =    2.348
peak=    3.061 closest distance to " O   HOH Z 207 " =    1.217
peak=    3.054 closest distance to " CA  ALA A 180 " =    1.259
peak=    3.051 closest distance to " NE2 GLN A  58 " =    4.627
peak=    3.043 closest distance to " O   HOH Z 285 " =    1.949
peak=    3.042 closest distance to " CB  ALA A   1 " =    0.946
peak=    3.042 closest distance to " O   HOH Z 343 " =    2.800
peak=    3.019 closest distance to " CB  TYR A  30 " =    1.333

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.741 - 5.423
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 209
   mapped sites are within: 0.741 - 5.423

peak=   -4.608 closest distance to " CD  ARG A  14 " =    3.337
peak=   -4.470 closest distance to " O   ALA A  10 " =    1.575
peak=   -4.467 closest distance to " CZ2 TRP A  92 " =    2.838
peak=   -4.436 closest distance to " O   PRO A 198 " =    1.218
peak=   -4.333 closest distance to " CG  GLN A  55 " =    1.187
peak=   -4.276 closest distance to " CB  ALA A  43 " =    2.532
peak=   -4.249 closest distance to " CD1 LEU A 101 " =    2.280
peak=   -4.238 closest distance to " NE2 GLN A  55 " =    1.235
peak=   -4.225 closest distance to " O   HOH Z  28 " =    1.259
peak=   -4.150 closest distance to " O   HOH Z  60 " =    1.531
peak=   -4.132 closest distance to " CB  PRO A 243 " =    2.607
peak=   -4.111 closest distance to " O   HOH Z 131 " =    3.915
peak=   -4.102 closest distance to " O   HOH Z  69 " =    1.630
peak=   -4.065 closest distance to " O   HOH Z 377 " =    1.954
peak=   -4.050 closest distance to " CG1BVAL A  41 " =    2.857
peak=   -4.045 closest distance to " O   HOH Z 100 " =    1.019
peak=   -4.036 closest distance to " O   PRO A 163 " =    1.787
peak=   -4.027 closest distance to " O   SER A  22 " =    2.686
peak=   -3.954 closest distance to " OG BSER A 134 " =    1.522
peak=   -3.940 closest distance to " O   HOH Z  32 " =    1.893
peak=   -3.936 closest distance to " O   HOH Z 231 " =    0.915
peak=   -3.928 closest distance to " CB  ALA A 291 " =    2.141
peak=   -3.924 closest distance to " CD2 TYR A 293 " =    1.898
peak=   -3.910 closest distance to " OG  SER A 245 " =    1.559
peak=   -3.894 closest distance to " CD  ARG A 156 " =    2.050
peak=   -3.887 closest distance to " CA  GLY A  98 " =    1.843
peak=   -3.878 closest distance to " O   HOH Z 385 " =    1.334
peak=   -3.872 closest distance to " O   HOH Z 111 " =    1.640
peak=   -3.867 closest distance to " O   HOH Z 216 " =    1.451
peak=   -3.846 closest distance to " O   SER A 135 " =    1.518
peak=   -3.822 closest distance to " O   HOH Z 211 " =    0.741
peak=   -3.796 closest distance to " O   HOH Z 298 " =    2.419
peak=   -3.788 closest distance to " O   GLU A 152 " =    1.510
peak=   -3.773 closest distance to " CB  ALA A   9 " =    2.408
peak=   -3.766 closest distance to " O   HOH Z  24 " =    0.980
peak=   -3.744 closest distance to " CD1 TRP A 179 " =    1.234
peak=   -3.729 closest distance to " CA  GLY A 133 " =    1.958
peak=   -3.726 closest distance to " C   HIS A 108 " =    1.205
peak=   -3.710 closest distance to " CG  MET A 105 " =    1.033
peak=   -3.709 closest distance to " O   HOH Z 103 " =    0.786
peak=   -3.699 closest distance to " O   HOH Z 231 " =    2.125
peak=   -3.693 closest distance to " O   HOH Z 276 " =    1.187
peak=   -3.691 closest distance to " O   HOH Z 147 " =    2.077
peak=   -3.689 closest distance to " CD  GLU A 277 " =    1.109
peak=   -3.685 closest distance to " CA  HIS A 207 " =    1.115
peak=   -3.682 closest distance to " O   HOH Z 313 " =    1.575
peak=   -3.672 closest distance to " OE1 GLU A 277 " =    2.280
peak=   -3.635 closest distance to " CB  ASP A 200 " =    2.601
peak=   -3.632 closest distance to " NE2 GLN A 194 " =    1.947
peak=   -3.631 closest distance to " CG  GLN A  88 " =    0.906
peak=   -3.629 closest distance to " CG2 ILE A  20 " =    2.743
peak=   -3.628 closest distance to " O   HOH Z  39 " =    0.917
peak=   -3.626 closest distance to " CZ3 TRP A 179 " =    1.304
peak=   -3.622 closest distance to " O   HOH Z 275 " =    1.710
peak=   -3.613 closest distance to " CZ2 TRP A 274 " =    1.000
peak=   -3.610 closest distance to " CB  ASP A 171 " =    2.259
peak=   -3.610 closest distance to " O   LYS A  76 " =    1.916
peak=   -3.606 closest distance to " O   HOH Z  52 " =    1.675
peak=   -3.590 closest distance to " O   HOH Z 316 " =    1.834
peak=   -3.586 closest distance to " CB  ASP A  27 " =    2.484
peak=   -3.581 closest distance to " O   HOH Z  70 " =    0.877
peak=   -3.579 closest distance to " CA  GLY A 241 " =    2.275
peak=   -3.575 closest distance to " O   HOH Z 123 " =    2.588
peak=   -3.564 closest distance to " CG  ARG A 219 " =    2.670
peak=   -3.558 closest distance to " N   THR A 157 " =    1.563
peak=   -3.554 closest distance to " CB  ALA A 160 " =    2.088
peak=   -3.552 closest distance to " O   HOH Z 198 " =    1.335
peak=   -3.545 closest distance to " O   HOH Z 166 " =    1.735
peak=   -3.542 closest distance to " CD  PRO A 213 " =    2.106
peak=   -3.539 closest distance to " O   HOH Z 357 " =    2.280
peak=   -3.535 closest distance to " CG1 VAL A 250 " =    2.661
peak=   -3.530 closest distance to " O   ILE A  49 " =    1.688
peak=   -3.526 closest distance to " CG  ARG A 219 " =    2.445
peak=   -3.525 closest distance to " O   HOH Z  71 " =    1.120
peak=   -3.523 closest distance to " CD2 TYR A 116 " =    2.182
peak=   -3.523 closest distance to " O   HOH Z 411 " =    5.423
peak=   -3.520 closest distance to " CE BMET A  47 " =    1.289
peak=   -3.517 closest distance to " CZ  PHE A  59 " =    1.594
peak=   -3.515 closest distance to " OD1 ASP A 171 " =    1.632
peak=   -3.511 closest distance to " OG  SER A  97 " =    2.182
peak=   -3.507 closest distance to " CD2 PHE A  61 " =    2.038
peak=   -3.503 closest distance to " NH2 ARG A 219 " =    1.792
peak=   -3.494 closest distance to " CG2 THR A  52 " =    3.166
peak=   -3.492 closest distance to " O   HOH Z 359 " =    3.097
peak=   -3.489 closest distance to " O   HOH Z 412 " =    4.211
peak=   -3.482 closest distance to " O   HOH Z 389 " =    1.245
peak=   -3.481 closest distance to " O   HOH Z 185 " =    2.034
peak=   -3.480 closest distance to " CE2 TYR A  30 " =    2.492
peak=   -3.476 closest distance to " O   LEU A 300 " =    2.142
peak=   -3.469 closest distance to " CG  LEU A  83 " =    2.217
peak=   -3.460 closest distance to " CG  GLN A  58 " =    1.101
peak=   -3.460 closest distance to " O   HOH Z 105 " =    1.526
peak=   -3.454 closest distance to " O   HOH Z 414 " =    1.312
peak=   -3.450 closest distance to " O   HOH Z 348 " =    1.843
peak=   -3.448 closest distance to " NE2 GLN A 223 " =    1.719
peak=   -3.443 closest distance to " O   HOH Z 286 " =    1.540
peak=   -3.443 closest distance to " O   HOH Z 238 " =    1.052
peak=   -3.434 closest distance to " ND2 ASN A 249 " =    2.100
peak=   -3.432 closest distance to " O   HOH Z  60 " =    1.326
peak=   -3.430 closest distance to " O   HOH Z 217 " =    1.684
peak=   -3.428 closest distance to " O   HOH Z   5 " =    1.090
peak=   -3.427 closest distance to " CG1 VAL A 112 " =    2.656
peak=   -3.426 closest distance to " ND2 ASN A  45 " =    2.403
peak=   -3.420 closest distance to " C   ASP A 270 " =    1.331
peak=   -3.402 closest distance to " O   HOH Z  11 " =    1.629
peak=   -3.396 closest distance to " CA  ASN A 110 " =    0.999
peak=   -3.394 closest distance to " O   HOH Z 368 " =    1.452
peak=   -3.384 closest distance to " CG  TRP A 266 " =    1.647
peak=   -3.376 closest distance to " CE  MET A 105 " =    2.573
peak=   -3.369 closest distance to " O   HOH Z  77 " =    1.817
peak=   -3.366 closest distance to " O   HOH Z 351 " =    1.616
peak=   -3.364 closest distance to " O   HOH Z 181 " =    1.516
peak=   -3.364 closest distance to " O   VAL A  67 " =    2.854
peak=   -3.359 closest distance to " CA  GLY A 203 " =    2.374
peak=   -3.356 closest distance to " CG1 VAL A 125 " =    2.343
peak=   -3.352 closest distance to " O   HOH Z 193 " =    1.068
peak=   -3.350 closest distance to " CD1 LEU A 255 " =    2.945
peak=   -3.349 closest distance to " O   HOH Z  37 " =    1.535
peak=   -3.349 closest distance to " O   HOH Z 407 " =    3.002
peak=   -3.345 closest distance to " O   HOH Z  64 " =    1.012
peak=   -3.345 closest distance to " O   ARG A  56 " =    4.410
peak=   -3.342 closest distance to " CB  TYR A  68 " =    1.141
peak=   -3.325 closest distance to " O   HOH Z 128 " =    2.531
peak=   -3.316 closest distance to " O   HOH Z  69 " =    2.218
peak=   -3.315 closest distance to " O   HOH Z  67 " =    1.409
peak=   -3.314 closest distance to " NH2 ARG A  79 " =    2.344
peak=   -3.311 closest distance to " O   HOH Z 102 " =    1.588
peak=   -3.311 closest distance to " CB  ALA A 291 " =    2.025
peak=   -3.304 closest distance to " CG1 VAL A 265 " =    2.501
peak=   -3.301 closest distance to " CG  ASN A  39 " =    1.737
peak=   -3.301 closest distance to " O   HOH Z 278 " =    1.221
peak=   -3.293 closest distance to " C   SER A  28 " =    1.081
peak=   -3.292 closest distance to " CB  ASN A  39 " =    2.232
peak=   -3.283 closest distance to " O   HOH Z 428 " =    2.681
peak=   -3.275 closest distance to " CB  PRO A  54 " =    2.264
peak=   -3.275 closest distance to " O   HOH Z 364 " =    2.582
peak=   -3.274 closest distance to " CG1 VAL A 265 " =    2.681
peak=   -3.274 closest distance to " CG1 VAL A 126 " =    2.536
peak=   -3.272 closest distance to " O   HOH Z 143 " =    1.534
peak=   -3.272 closest distance to " CZ  PHE A 130 " =    1.033
peak=   -3.271 closest distance to " CB  ALA A 158 " =    1.712
peak=   -3.270 closest distance to " CE  LYS A  76 " =    2.895
peak=   -3.268 closest distance to " CB  SER A 210 " =    1.142
peak=   -3.263 closest distance to " OG  SER A  87 " =    1.483
peak=   -3.258 closest distance to " O   GLY A 196 " =    1.424
peak=   -3.257 closest distance to " CZ  TYR A 169 " =    1.974
peak=   -3.255 closest distance to " O   HOH Z 285 " =    1.698
peak=   -3.248 closest distance to " CD2 PHE A  61 " =    2.357
peak=   -3.242 closest distance to " N   GLN A  58 " =    1.343
peak=   -3.238 closest distance to " ND2 ASN A 285 " =    2.092
peak=   -3.237 closest distance to " O   HOH Z 426 " =    1.601
peak=   -3.237 closest distance to " CD1 TYR A 247 " =    2.811
peak=   -3.232 closest distance to " O   HOH Z 421 " =    2.915
peak=   -3.232 closest distance to " O   HOH Z 219 " =    4.426
peak=   -3.228 closest distance to " O   ARG A 145 " =    1.292
peak=   -3.226 closest distance to " SG BCYS A 201 " =    2.292
peak=   -3.213 closest distance to " CG1 VAL A 197 " =    2.392
peak=   -3.211 closest distance to " O   PRO A 198 " =    1.535
peak=   -3.211 closest distance to " OD2 ASP A  27 " =    1.497
peak=   -3.210 closest distance to " O   HOH Z 140 " =    1.036
peak=   -3.210 closest distance to " O   HOH Z 357 " =    1.819
peak=   -3.207 closest distance to " CG2 VAL A 232 " =    2.137
peak=   -3.205 closest distance to " O   HOH Z 201 " =    2.013
peak=   -3.200 closest distance to " N   ALA A  43 " =    2.583
peak=   -3.198 closest distance to " O   ASP A 171 " =    1.154
peak=   -3.195 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.194 closest distance to " CB  ALA A 227 " =    2.390
peak=   -3.192 closest distance to " O   HOH Z 263 " =    3.024
peak=   -3.192 closest distance to " CB  GLN A  11 " =    1.686
peak=   -3.191 closest distance to " O   HOH Z 435 " =    3.013
peak=   -3.190 closest distance to " O   TYR A 186 " =    1.598
peak=   -3.190 closest distance to " CB  ASP A 132 " =    2.466
peak=   -3.188 closest distance to " O   HOH Z 340 " =    2.046
peak=   -3.186 closest distance to " O   HOH Z 253 " =    3.753
peak=   -3.179 closest distance to " NZ  LYS A 166 " =    1.217
peak=   -3.177 closest distance to " O   HOH Z 438 " =    1.341
peak=   -3.176 closest distance to " N   LYS A 166 " =    1.875
peak=   -3.172 closest distance to " NE2 GLN A  77 " =    1.673
peak=   -3.169 closest distance to " O   HOH Z 105 " =    0.963
peak=   -3.168 closest distance to " O   HOH Z 389 " =    2.321
peak=   -3.166 closest distance to " C   LEU A 222 " =    0.805
peak=   -3.165 closest distance to " O   HOH Z  68 " =    1.413
peak=   -3.165 closest distance to " CE3 TRP A 274 " =    2.287
peak=   -3.164 closest distance to " O   HOH Z 100 " =    1.301
peak=   -3.158 closest distance to " CE3 TRP A 150 " =    2.430
peak=   -3.147 closest distance to " NH2AARG A 275 " =    5.262
peak=   -3.145 closest distance to " CB  ALA A 100 " =    2.128
peak=   -3.143 closest distance to " CB  ASP A 132 " =    2.521
peak=   -3.141 closest distance to " C   GLN A  58 " =    1.969
peak=   -3.134 closest distance to " O   HOH Z 175 " =    0.930
peak=   -3.131 closest distance to " O   HOH Z  49 " =    0.996
peak=   -3.131 closest distance to " O   HOH Z 372 " =    2.523
peak=   -3.130 closest distance to " CG  ARG A 269 " =    2.312
peak=   -3.126 closest distance to " O   HOH Z 163 " =    1.824
peak=   -3.123 closest distance to " CD2 HIS A 207 " =    1.931
peak=   -3.115 closest distance to " O   HOH Z 134 " =    3.789
peak=   -3.114 closest distance to " O   HOH Z 384 " =    3.329
peak=   -3.108 closest distance to " NH1AARG A 275 " =    2.259
peak=   -3.106 closest distance to " CZ  PHE A  38 " =    2.462
peak=   -3.102 closest distance to " O   LYS A 117 " =    1.763
peak=   -3.100 closest distance to " OG BSER A 210 " =    2.311
peak=   -3.096 closest distance to " O   HOH Z 165 " =    2.304
peak=   -3.094 closest distance to " OXT GLY A 302 " =    3.995
peak=   -3.086 closest distance to " CB  TRP A  85 " =    2.143
peak=   -3.086 closest distance to " C   GLU A   2 " =    1.719
peak=   -3.079 closest distance to " O   HOH Z  28 " =    2.124
peak=   -3.062 closest distance to " O   PHE A 218 " =    1.412
peak=   -3.054 closest distance to " O   HOH Z 359 " =    1.616
peak=   -3.038 closest distance to " NE  ARG A  36 " =    1.986

================= 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    :  0.4655 0.4693   6.282938e+00   6.270300e+00
   1_bss:  0.4535 0.4621   6.274898e+00   6.261564e+00
   1_xyz:  0.3660 0.4041   6.123563e+00   6.180060e+00
   1_adp:  0.3340 0.4192   6.083164e+00   6.195236e+00
   1_occ:  0.3337 0.4206   6.083415e+00   6.196148e+00
   2_bss:  0.3328 0.4187   6.085439e+00   6.197872e+00
   2_xyz:  0.2795 0.3596   5.944199e+00   6.098179e+00
   2_adp:  0.2693 0.3474   5.920314e+00   6.074698e+00
   2_occ:  0.2692 0.3475   5.920369e+00   6.075289e+00
   3_bss:  0.2697 0.3469   5.920878e+00   6.074627e+00
   3_xyz:  0.2138 0.2751   5.711912e+00   5.896196e+00
   3_adp:  0.1942 0.2585   5.637455e+00   5.838491e+00
   3_occ:  0.1940 0.2583   5.636640e+00   5.837466e+00
   4_bss:  0.1937 0.2579   5.636662e+00   5.837082e+00
   4_xyz:  0.1599 0.2157   5.458660e+00   5.681663e+00
   4_adp:  0.1535 0.2025   5.410647e+00   5.620318e+00
   4_occ:  0.1533 0.2021   5.409666e+00   5.619302e+00
   5_bss:  0.1534 0.2017   5.408096e+00   5.617531e+00
   5_xyz:  0.1305 0.1762   5.268295e+00   5.491585e+00
   5_adp:  0.1254 0.1749   5.240735e+00   5.478197e+00
   5_occ:  0.1253 0.1749   5.240505e+00   5.477849e+00
   5_bss:  0.1253 0.1749   5.240476e+00   5.477879e+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:  0.337  50.000  -3.350   1.536   4.271   0.000   0.000   0.000
   1_xyz:  0.337  50.000  -3.350   1.536   4.271   0.000   0.000   0.000
   1_adp:  0.337  50.000  -3.350   1.536   4.271   0.000   0.000   0.000
   1_occ:  0.337  50.000  -3.350   1.536   4.271   0.000   0.000   0.000
   2_bss:  0.351  72.828  -1.722  -0.143   2.148  -0.000   0.000   0.000
   2_xyz:  0.351  72.828  -1.722  -0.143   2.148  -0.000   0.000   0.000
   2_adp:  0.351  72.828  -1.722  -0.143   2.148  -0.000   0.000   0.000
   2_occ:  0.351  72.828  -1.722  -0.143   2.148  -0.000   0.000   0.000
   3_bss:  0.341  67.857  -1.562  -0.638   1.465  -0.000   0.000   0.000
   3_xyz:  0.341  67.857  -1.562  -0.638   1.465  -0.000   0.000   0.000
   3_adp:  0.341  67.857  -1.562  -0.638   1.465  -0.000   0.000   0.000
   3_occ:  0.341  67.857  -1.562  -0.638   1.465  -0.000   0.000   0.000
   4_bss:  0.333  72.362  -2.232  -1.834   0.291  -0.000   0.000   0.000
   4_xyz:  0.333  72.362  -2.232  -1.834   0.291  -0.000   0.000   0.000
   4_adp:  0.333  72.362  -2.232  -1.834   0.291  -0.000   0.000   0.000
   4_occ:  0.333  72.362  -2.232  -1.834   0.291  -0.000   0.000   0.000
   5_bss:  0.327  64.234  -2.401  -2.296  -0.043  -0.000  -0.000  -0.000
   5_xyz:  0.327  64.234  -2.401  -2.296  -0.043  -0.000  -0.000  -0.000
   5_adp:  0.327  64.234  -2.401  -2.296  -0.043  -0.000  -0.000  -0.000
   5_occ:  0.327  64.234  -2.401  -2.296  -0.043  -0.000  -0.000  -0.000
   5_bss:  0.327  64.237  -2.320  -2.308  -0.081  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.178 0.4296  0.5837    70644.680
   1_bss:  56.017 0.4435  0.6233    68193.044
   1_xyz:  45.834 0.5715  0.7844    48585.811
   1_adp:  47.087 0.5553  0.7726    50926.870
   1_occ:  47.247 0.5532  0.7691    51175.731
   2_bss:  46.974 0.5568  0.7576    51088.879
   2_xyz:  38.860 0.6542  0.8700    35598.946
   2_adp:  36.797 0.6794  0.8883    33119.182
   2_occ:  36.836 0.6789  0.8875    33166.920
   3_bss:  36.761 0.6797  0.8779    33031.670
   3_xyz:  28.120 0.7773  0.9717    20244.911
   3_adp:  25.784 0.8027  0.9778    17537.241
   3_occ:  25.752 0.8030  0.9778    17486.129
   4_bss:  25.699 0.8035  0.9444    17456.654
   4_xyz:  21.071 0.8502  0.9724    11975.565
   4_adp:  19.264 0.8687  0.9743    10609.246
   4_occ:  19.229 0.8690  0.9744    10575.472
   5_bss:  19.174 0.8694  0.9634    10502.217
   5_xyz:  16.299 0.8953  0.9792     8035.252
   5_adp:  15.875 0.8994  0.9741     7769.748
   5_occ:  15.869 0.8994  0.9740     7763.490
   5_bss:  15.867 0.8994  0.9746     7764.812
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.8268e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.8268e-01
   1_xyz:   1.608  0.011  0.107 16.116  0.007  4.105   1.3735e-01
   1_adp:   1.608  0.011  0.107 16.116  0.007  4.105   1.3735e-01
   1_occ:   1.608  0.011  0.107 16.116  0.007  4.105   1.3735e-01
   2_bss:   1.608  0.011  0.107 16.116  0.007  4.105   1.3735e-01
   2_xyz:   1.168  0.009  0.083 14.818  0.004  4.117   7.8852e-02
   2_adp:   1.168  0.009  0.083 14.818  0.004  4.117   7.8852e-02
   2_occ:   1.168  0.009  0.083 14.818  0.004  4.117   7.8852e-02
   3_bss:   1.168  0.009  0.083 14.818  0.004  4.117   7.8852e-02
   3_xyz:   1.119  0.007  0.079 14.885  0.004  4.109   6.7700e-02
   3_adp:   1.119  0.007  0.079 14.885  0.004  4.109   6.7700e-02
   3_occ:   1.119  0.007  0.079 14.885  0.004  4.109   6.7700e-02
   4_bss:   1.119  0.007  0.079 14.885  0.004  4.109   6.7700e-02
   4_xyz:   0.980  0.006  0.071 14.313  0.003  4.120   5.3781e-02
   4_adp:   0.980  0.006  0.071 14.313  0.003  4.120   5.3781e-02
   4_occ:   0.980  0.006  0.071 14.313  0.003  4.120   5.3781e-02
   5_bss:   0.980  0.006  0.071 14.313  0.003  4.120   5.3781e-02
   5_xyz:   1.057  0.008  0.076 14.653  0.004  4.110   6.6068e-02
   5_adp:   1.057  0.008  0.076 14.653  0.004  4.110   6.6068e-02
   5_occ:   1.057  0.008  0.076 14.653  0.004  4.110   6.6068e-02
   5_bss:   1.057  0.008  0.076 14.653  0.004  4.110   6.6068e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.511   2.4202e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.511   2.4202e-01
   1_xyz:   9.081  0.070  0.336 82.563  0.057  1.946   1.0483e-01
   1_adp:   9.081  0.070  0.336 82.563  0.057  1.946   1.0483e-01
   1_occ:   9.081  0.070  0.336 82.563  0.057  1.946   1.0483e-01
   2_bss:   9.081  0.070  0.336 82.563  0.057  1.946   1.0483e-01
   2_xyz:   8.597  0.100  0.313 82.452  0.030  2.293   1.4112e-01
   2_adp:   8.597  0.100  0.313 82.452  0.030  2.293   1.4112e-01
   2_occ:   8.597  0.100  0.313 82.452  0.030  2.293   1.4112e-01
   3_bss:   8.597  0.100  0.313 82.452  0.030  2.293   1.4112e-01
   3_xyz:   9.109  0.041  0.262 87.696  0.043  2.287   4.5387e-02
   3_adp:   9.109  0.041  0.262 87.696  0.043  2.287   4.5387e-02
   3_occ:   9.109  0.041  0.262 87.696  0.043  2.287   4.5387e-02
   4_bss:   9.109  0.041  0.262 87.696  0.043  2.287   4.5387e-02
   4_xyz:   6.352  0.056  0.191 82.044  0.025  2.374   4.6226e-02
   4_adp:   6.352  0.056  0.191 82.044  0.025  2.374   4.6226e-02
   4_occ:   6.352  0.056  0.191 82.044  0.025  2.374   4.6226e-02
   5_bss:   6.352  0.056  0.191 82.044  0.025  2.374   4.6226e-02
   5_xyz:   6.878  0.055  0.260 84.177  0.027  2.319   4.9178e-02
   5_adp:   6.878  0.055  0.260 84.177  0.027  2.319   4.9178e-02
   5_occ:   6.878  0.055  0.260 84.177  0.027  2.319   4.9178e-02
   5_bss:   6.878  0.055  0.260 84.177  0.027  2.319   4.9178e-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:  98.26   0.00  19.03  77.07   0.00  15.58  98.26   0.00  37.79
   1_occ:  98.26   0.00  19.03  77.07   0.00  15.58  98.26   0.00  37.79
   2_bss:  98.26   0.00  19.03  77.07   0.00  15.58  98.26   0.00  37.79
   2_xyz:  98.26   0.00  19.03  77.07   0.00  15.58  98.26   0.00  37.79
   2_adp:  98.37   0.00  18.55  72.04   0.00  14.97  98.37   0.00  38.09
   2_occ:  98.37   0.00  18.55  72.04   0.00  14.97  98.37   0.00  38.09
   3_bss:  98.37   0.00  18.55  72.04   0.00  14.97  98.37   0.00  38.09
   3_xyz:  98.37   0.00  18.55  72.04   0.00  14.97  98.37   0.00  38.09
   3_adp: 102.10   0.00  18.67  90.73   0.00  13.88 102.10   3.36  44.77
   3_occ: 102.10   0.00  18.67  90.73   0.00  13.88 102.10   3.36  44.77
   4_bss: 102.10   0.00  18.67  90.73   0.00  13.88 102.10   3.36  44.77
   4_xyz: 102.10   0.00  18.67  90.73   0.00  13.88 102.10   3.36  44.77
   4_adp:  97.92   1.23  17.75  87.98   1.23  13.08  97.92   5.12  43.18
   4_occ:  97.92   1.23  17.75  87.98   1.23  13.08  97.92   5.12  43.18
   5_bss:  97.92   1.23  17.75  87.98   1.23  13.08  97.92   5.12  43.18
   5_xyz:  97.92   1.23  17.75  87.98   1.23  13.08  97.92   5.12  43.18
   5_adp:  99.59   0.00  17.98  88.40   0.00  12.92  99.59   6.22  45.50
   5_occ:  99.59   0.00  17.98  88.40   0.00  12.92  99.59   6.22  45.50
   5_bss:  99.59   0.00  17.98  88.40   0.00  12.93  99.59   6.22  45.51
------------------------------------------------------------------------
 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:    1.959    0.011    0.358
   1_adp:    1.959    0.011    0.358
   1_occ:    1.959    0.011    0.358
   2_bss:    1.959    0.011    0.358
   2_xyz:    1.756    0.007    0.484
   2_adp:    1.756    0.007    0.484
   2_occ:    1.756    0.007    0.484
   3_bss:    1.756    0.007    0.484
   3_xyz:    1.592    0.048    0.662
   3_adp:    1.592    0.048    0.662
   3_occ:    1.592    0.048    0.662
   4_bss:    1.592    0.048    0.662
   4_xyz:    1.511    0.079    0.732
   4_adp:    1.511    0.079    0.732
   4_occ:    1.511    0.079    0.732
   5_bss:    1.511    0.079    0.732
   5_xyz:    1.658    0.048    0.783
   5_adp:    1.658    0.048    0.783
   5_occ:    1.658    0.048    0.783
   5_bss:    1.658    0.048    0.783
------------------------------------------------------------------------

CPU time actual refinement: 333.70


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_626/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_626/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_626/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_626/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_626/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.56 
  Macro-tasks:
    bulk solvent and scale       = 39.93  
    individual site refinement   = 137.59 
    weights calculation          = 28.92  
    collect and process          = 6.07   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 212.60 
  Micro-tasks:
    mask                            = 2.29   
    f_calc                          = 109.03 
    alpha_beta                      = 8.20   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 112.71 
    fmodel                         = 6.48   
    r_factors                      = 0.14   
    phase_errors                   = 11.19  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 251.42 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.759 micro seconds
Total CPU time: 5.78 minutes
from_scatterers_fft:    638 calls, 108.54 s
gradients_fft:          583 calls, 101.42 s

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

# Date 2008-01-16 Time 05:17:11 PST -0800 (1200489431.46 s)
Start R-work = 0.4655, R-free = 0.4693 (no bulk solvent and anisotropic scale)
Final R-work = 0.1471, R-free = 0.1920 (no bulk solvent and anisotropic scale)

Start R-work = 0.4535, R-free = 0.4621
Final R-work = 0.1253, R-free = 0.1749