# Date 2008-01-16 Time 04:28:00 PST -0800 (1200486480.22 s)
#phil __OFF__

Command line arguments: "../330.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3365
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 330

-------------------------------------------------------------------------------
  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: (69.1963, 47.6339, 84.2302, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95147
Completeness in resolution range: 0.940739
Completeness with d_max=infinity: 0.937901

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8572
                             d_min =   1.9515

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: (69.1963, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95147
Completeness in resolution range: 0.940739
Completeness with d_max=infinity: 0.937901

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8576 -  4.1761 [2186/2215]  1966   220  10.1%
  bin  2:  4.1761 -  3.3270 [2098/2121]  1887   211  10.1%
  bin  3:  3.3270 -  2.9100 [2067/2092]  1861   206  10.0%
  bin  4:  2.9100 -  2.6456 [2050/2067]  1851   199   9.7%
  bin  5:  2.6456 -  2.4568 [2046/2089]  1835   211  10.3%
  bin  6:  2.4568 -  2.3126 [2019/2047]  1828   191   9.5%
  bin  7:  2.3126 -  2.1971 [2019/2055]  1813   206  10.2%
  bin  8:  2.1971 -  2.1018 [1998/2040]  1799   199  10.0%
  bin  9:  2.1018 -  2.0211 [2006/2064]  1810   196   9.8%
  bin 10:  2.0211 -  1.9515 [1100/2033]   980   120  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_330/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.31 -     2.03: 25
        2.03 -     2.74: 325
        2.74 -     3.46: 4665
        3.46 -     4.18: 9502
        4.18 -     4.90: 14198
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.308 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.443 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.526 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.559 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.618 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28710 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_330/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_330/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 69.19625 47.63395 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4641   r_free= 0.4590   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.269670                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6580 0.99   1419  158 0.3682 0.3811      6.5449      6.5644|
|  2:  4.6580 -  3.7163 0.99   1368  150 0.3965 0.3827      6.7814      6.7612|
|  3:  3.7163 -  3.2521 0.99   1335  152 0.4247 0.4195      6.6405      6.7304|
|  4:  3.2521 -  2.9573 0.99   1332  143 0.4424 0.4332      6.4881      6.4751|
|  5:  2.9573 -  2.7468 0.99   1326  148 0.4776 0.4431      6.3526      6.3062|
|  6:  2.7468 -  2.5857 0.99   1312  149 0.4907 0.4773      6.2572      6.1719|
|  7:  2.5857 -  2.4568 0.98   1308  147 0.5021 0.4367      6.2385      6.1829|
|  8:  2.4568 -  2.3503 0.98   1306  142 0.5178 0.5468      6.1728      6.1873|
|  9:  2.3503 -  2.2602 0.99   1305  140 0.5316 0.5344      6.1324      6.1554|
| 10:  2.2602 -  2.1824 0.98   1291  146 0.5084 0.5511      6.1015      6.1465|
| 11:  2.1824 -  2.1144 0.97   1284  143 0.5409 0.5343      6.0379      6.0008|
| 12:  2.1144 -  2.0541 0.98   1285  148 0.5240 0.5509      5.9586      6.0012|
| 13:  2.0541 -  2.0002 0.92   1216  132 0.5299 0.5409        5.88      5.8735|
| 14:  2.0002 -  1.9515 0.41    543   61 0.5432 0.5000      5.8359      5.7258|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6580  1419   158  0.68  36.11   0.84     0.71      75140.68|
|  2:  4.6580 -  3.7163  1368   150  0.70  34.94   0.92     0.80     102827.37|
|  3:  3.7163 -  3.2521  1335   152  0.62  42.43   0.93     0.81     106483.66|
|  4:  3.2521 -  2.9573  1332   143  0.55  47.95   0.94     0.77      91826.77|
|  5:  2.9573 -  2.7468  1326   148  0.50  52.21   0.89     0.71      72702.41|
|  6:  2.7468 -  2.5857  1312   149  0.46  55.13   0.92     0.65      62217.13|
|  7:  2.5857 -  2.4568  1308   147  0.43  57.78   0.91     0.59      59885.51|
|  8:  2.4568 -  2.3503  1306   142  0.36  63.04   0.91     0.53      59364.88|
|  9:  2.3503 -  2.2602  1305   140  0.29  68.31   0.93     0.45      58908.85|
| 10:  2.2602 -  2.1824  1291   146  0.25  71.65   0.96     0.37      56166.57|
| 11:  2.1824 -  2.1144  1284   143  0.17  77.18   0.93     0.27      54119.69|
| 12:  2.1144 -  2.0541  1285   148  0.16  78.47   0.95     0.26      50637.81|
| 13:  2.0541 -  2.0002  1216   132  0.17  77.75   0.94     0.27      42848.35|
| 14:  2.0002 -  1.9515   543    61  0.24  71.92   0.92     0.36      33093.46|
|alpha:            min =        0.26 max =            0.81 mean =         0.55|
|beta:             min =    33093.46 max =       106483.66 mean =     68047.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.66|
|phase err.(test): min =        0.00 max =           89.87 mean =        58.70|
|-----------------------------------------------------------------------------|

============================== 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 = 22.337732             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.130   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.018071              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.038   (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 |  1.308 -  1.667:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.667 -  2.026:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.026 -  2.385:       34 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.385 -  2.745:      291 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.745 -  3.104:     2338 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.104 -  3.463:     2327 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.463 -  3.822:     4343 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.822 -  4.181:     5159 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.181 -  4.541:     6388 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.541 -  4.900:     7810 |
|-----------------------------------------------------------------------------|
|-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 |        0.210 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.308 |       0.906 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.540)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4641   r_free= 0.4590   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.269670                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4560   r_free= 0.4512   ksol= 0.32   Bsol= 20.00   scale= 0.943   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,1.61,2.05,0.00,0.00,0.00); trace/3= 0.54                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.263396                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.573869             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.932   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.322648              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.773   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4560      final r-factor (work) = 0.2955          |
| start r-factor (free) = 0.4512      final r-factor (free) = 0.3255          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 58.3745 = 18.57 * 0.50 * 6.2631 + 1.00 * 0.2098                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.9292 = 18.57 * 0.50 * 6.1110 + 1.00 * 0.1771                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2955      final r-factor (work) = 0.2671          |
| start r-factor (free) = 0.3255      final r-factor (free) = 0.3373          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0891 = 1.32 * 1.00 * 6.1110 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7946 = 1.32 * 1.00 * 5.8787 + 1.00 * 0.0191                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.540)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.66   19.14    None  None   None       |
|    all(noH): 2823   0      0.00    91.66   19.14    None  None   None       |
|    Sol.    : 438    0      2.18    91.66   41.89    None  None   None       |
|    Mac.    : 2385   0      0.00    82.86   14.96    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 -   9.166:  834   |   5:    45.831 -  54.997:  109        |
|      1:     9.166 -  18.332:  950   |   6:    54.997 -  64.163:   76        |
|      2:    18.332 -  27.499:  413   |   7:    64.163 -  73.330:   41        |
|      3:    27.499 -  36.665:  237   |   8:    73.330 -  82.496:   15        |
|      4:    36.665 -  45.831:  140   |   9:    82.496 -  91.662:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2671 r_free = 0.3373             target_work(ml) = 5.891         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2667 r_free = 0.3374             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2667   r_free= 0.3374   ksol= 0.32   Bsol= 20.00   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,1.61,2.05,0.00,0.00,0.00); trace/3= 0.54                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.889747                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2632   r_free= 0.3339   ksol= 0.33   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-0.14,-0.15,-0.00,-0.00,-0.00); trace/3= -0.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.884566                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.530256              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.143   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.459795              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.322  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2632      final r-factor (work) = 0.2024          |
| start r-factor (free) = 0.3339      final r-factor (free) = 0.2624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4946 = 4.53 * 0.50 * 5.8794 + 1.00 * 0.1771                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1728 = 4.53 * 0.50 * 5.7864 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2024      final r-factor (work) = 0.1885          |
| start r-factor (free) = 0.2624      final r-factor (free) = 0.2445          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6785 = 0.46 * 1.00 * 5.7864 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5996 = 0.46 * 1.00 * 5.6302 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.540)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.40   18.22    None  None   None       |
|    all(noH): 2823   0      0.00    96.40   18.22    None  None   None       |
|    Sol.    : 438    0      5.05    96.40   41.80    None  None   None       |
|    Mac.    : 2385   0      0.00    88.49   13.89    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 -   9.640:  950   |   5:    48.199 -  57.839:   97        |
|      1:     9.640 -  19.280: 1065   |   6:    57.839 -  67.479:   65        |
|      2:    19.280 -  28.919:  315   |   7:    67.479 -  77.118:   25        |
|      3:    28.919 -  38.559:  149   |   8:    77.118 -  86.758:   12        |
|      4:    38.559 -  48.199:  142   |   9:    86.758 -  96.398:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1885 r_free = 0.2445             target_work(ml) = 5.594         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1883 r_free = 0.2446             target_work(ml) = 5.594         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1883   r_free= 0.2446   ksol= 0.33   Bsol= 50.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-0.14,-0.15,-0.00,-0.00,-0.00); trace/3= -0.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.593603                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1886   r_free= 0.2438   ksol= 0.32   Bsol= 41.88   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-0.71,-1.00,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.592370                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.580006              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.784  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.437100              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.835  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1886      final r-factor (work) = 0.1484          |
| start r-factor (free) = 0.2438      final r-factor (free) = 0.1980          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3300 = 2.58 * 0.50 * 5.6311 + 1.00 * 0.0659                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1420 = 2.58 * 0.50 * 5.4920 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1484      final r-factor (work) = 0.1394          |
| start r-factor (free) = 0.1980      final r-factor (free) = 0.1873          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4114 = 0.44 * 1.00 * 5.4920 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3519 = 0.44 * 1.00 * 5.3581 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.540)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.28   17.86    None  None   None       |
|    all(noH): 2823   0      0.00    93.28   17.86    None  None   None       |
|    Sol.    : 438    0      6.79    92.54   42.65    None  None   None       |
|    Mac.    : 2385   0      0.00    93.28   13.31    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 -   9.328:  911   |   5:    46.639 -  55.967:  118        |
|      1:     9.328 -  18.656: 1165   |   6:    55.967 -  65.295:   65        |
|      2:    18.656 -  27.984:  270   |   7:    65.295 -  74.623:   33        |
|      3:    27.984 -  37.311:  116   |   8:    74.623 -  83.951:   14        |
|      4:    37.311 -  46.639:  123   |   9:    83.951 -  93.278:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1394 r_free = 0.1873             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1393 r_free = 0.1872             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1872   ksol= 0.32   Bsol= 41.88   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-0.71,-1.00,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.328647                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1869   ksol= 0.32   Bsol= 44.58   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-1.35,-1.65,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.330686                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.652446              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.579  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.472272              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.034  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1397      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1869      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1690 = 2.65 * 0.50 * 5.3624 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0566 = 2.65 * 0.50 * 5.2740 + 1.00 * 0.0621                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5006 = 0.47 * 1.00 * 5.2740 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4682 = 0.47 * 1.00 * 5.2060 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.540)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.24    96.02   17.55    None  None   None       |
|    all(noH): 2823   0      1.24    96.02   17.55    None  None   None       |
|    Sol.    : 438    0      6.11    90.72   42.31    None  None   None       |
|    Mac.    : 2385   0      1.24    96.02   13.00    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:     1.243 -  10.721: 1213   |   5:    48.634 -  58.112:  103        |
|      1:    10.721 -  20.199:  971   |   6:    58.112 -  67.590:   61        |
|      2:    20.199 -  29.678:  213   |   7:    67.590 -  77.069:   28        |
|      3:    29.678 -  39.156:  104   |   8:    77.069 -  86.547:    9        |
|      4:    39.156 -  48.634:  115   |   9:    86.547 -  96.025:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1671             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1671             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1671   ksol= 0.32   Bsol= 44.58   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-1.35,-1.65,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195256                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1671   ksol= 0.32   Bsol= 44.58   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-1.42,-1.67,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195251                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.333652              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.992  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.285918              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.530  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1365 = 2.33 * 0.50 * 5.2059 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1027 = 2.33 * 0.50 * 5.1779 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1635      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4899 = 0.29 * 1.00 * 5.1779 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4843 = 0.29 * 1.00 * 5.1610 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.540)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.59    95.69   17.06    None  None   None       |
|    all(noH): 2823   0      1.59    95.69   17.06    None  None   None       |
|    Sol.    : 438    0      5.30    88.97   40.60    None  None   None       |
|    Mac.    : 2385   0      1.59    95.69   12.74    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:     1.586 -  10.996: 1304   |   5:    48.637 -  58.047:   87        |
|      1:    10.996 -  20.406:  910   |   6:    58.047 -  67.457:   55        |
|      2:    20.406 -  29.816:  198   |   7:    67.457 -  76.867:   22        |
|      3:    29.816 -  39.227:  119   |   8:    76.867 -  86.278:    8        |
|      4:    39.227 -  48.637:  114   |   9:    86.278 -  95.688:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1623             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1623             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1623   ksol= 0.32   Bsol= 44.58   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-1.42,-1.67,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157690                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6580 0.99   1419  158 0.0987 0.1307      5.3783      5.5503|
|  2:  4.6580 -  3.7163 0.99   1368  150 0.0831 0.1075      5.4189       5.615|
|  3:  3.7163 -  3.2521 0.99   1335  152 0.1042 0.1594      5.4542      5.8483|
|  4:  3.2521 -  2.9573 0.99   1332  143 0.1266 0.1610      5.4723      5.6553|
|  5:  2.9573 -  2.7468 0.99   1326  148 0.1301 0.1750      5.3232      5.4934|
|  6:  2.7468 -  2.5857 0.99   1312  149 0.1271 0.2019      5.2415      5.4805|
|  7:  2.5857 -  2.4568 0.98   1308  147 0.1239 0.1689      5.1579      5.3885|
|  8:  2.4568 -  2.3503 0.98   1306  142 0.1180 0.1673      5.0893      5.2783|
|  9:  2.3503 -  2.2602 0.99   1305  140 0.1211 0.1898      5.0462      5.3455|
| 10:  2.2602 -  2.1824 0.98   1291  146 0.1145 0.1869      4.9937      5.2598|
| 11:  2.1824 -  2.1144 0.97   1284  143 0.1132 0.1801      4.9258      5.2209|
| 12:  2.1144 -  2.0541 0.98   1285  148 0.1133 0.1691      4.8631      5.0986|
| 13:  2.0541 -  2.0002 0.92   1216  132 0.1114 0.1980       4.781      5.1062|
| 14:  2.0002 -  1.9515 0.41    543   61 0.1130 0.1638      4.7268      4.9111|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6580  1419   158  0.94   9.12   0.98     0.96       7232.93|
|  2:  4.6580 -  3.7163  1368   150  0.95   7.77   1.02     1.01       8804.17|
|  3:  3.7163 -  3.2521  1335   152  0.93  11.30   1.03     1.03      10093.91|
|  4:  3.2521 -  2.9573  1332   143  0.91  14.43   1.01     1.00      10790.20|
|  5:  2.9573 -  2.7468  1326   148  0.90  16.16   1.00     0.97       8420.55|
|  6:  2.7468 -  2.5857  1312   149  0.90  16.33   0.99     0.96       7445.86|
|  7:  2.5857 -  2.4568  1308   147  0.90  15.88   0.99     0.96       6183.63|
|  8:  2.4568 -  2.3503  1306   142  0.90  15.81   1.00     0.98       5715.09|
|  9:  2.3503 -  2.2602  1305   140  0.90  16.30   1.00     0.97       5173.67|
| 10:  2.2602 -  2.1824  1291   146  0.90  15.79   1.00     0.96       4765.31|
| 11:  2.1824 -  2.1144  1284   143  0.90  16.36   1.00     0.96       4325.04|
| 12:  2.1144 -  2.0541  1285   148  0.91  15.17   1.00     0.99       3800.71|
| 13:  2.0541 -  2.0002  1216   132  0.90  16.34   1.00     0.99       3351.47|
| 14:  2.0002 -  1.9515   543    61  0.90  16.25   0.99     0.95       2900.37|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2900.37 max =        10790.20 mean =      6558.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.35|
|phase err.(test): min =        0.00 max =           88.67 mean =        13.95|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1620   ksol= 0.32   Bsol= 44.87   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-1.32,-1.54,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158421                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1620   ksol= 0.32   Bsol= 44.87   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-1.32,-1.54,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158421                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6580 0.99   1419  158 0.0985 0.1288      5.3743      5.5354|
|  2:  4.6580 -  3.7163 0.99   1368  150 0.0849 0.1083      5.4309      5.6393|
|  3:  3.7163 -  3.2521 0.99   1335  152 0.1039 0.1584      5.4611      5.8425|
|  4:  3.2521 -  2.9573 0.99   1332  143 0.1274 0.1606      5.4732      5.6509|
|  5:  2.9573 -  2.7468 0.99   1326  148 0.1303 0.1744      5.3235      5.4913|
|  6:  2.7468 -  2.5857 0.99   1312  149 0.1270 0.2028      5.2404      5.4813|
|  7:  2.5857 -  2.4568 0.98   1308  147 0.1238 0.1694      5.1569      5.3921|
|  8:  2.4568 -  2.3503 0.98   1306  142 0.1176 0.1673      5.0885      5.2777|
|  9:  2.3503 -  2.2602 0.99   1305  140 0.1210 0.1888      5.0443      5.3424|
| 10:  2.2602 -  2.1824 0.98   1291  146 0.1144 0.1871      4.9926      5.2589|
| 11:  2.1824 -  2.1144 0.97   1284  143 0.1133 0.1796       4.925      5.2191|
| 12:  2.1144 -  2.0541 0.98   1285  148 0.1131 0.1699      4.8624      5.1015|
| 13:  2.0541 -  2.0002 0.92   1216  132 0.1113 0.1981      4.7812      5.1067|
| 14:  2.0002 -  1.9515 0.41    543   61 0.1132 0.1629      4.7275      4.9084|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6580  1419   158  0.94   8.91   0.98     0.96       7052.17|
|  2:  4.6580 -  3.7163  1368   150  0.95   7.93   1.02     1.01       8929.97|
|  3:  3.7163 -  3.2521  1335   152  0.93  11.47   1.04     1.03      10384.05|
|  4:  3.2521 -  2.9573  1332   143  0.91  14.43   1.02     1.00      10765.64|
|  5:  2.9573 -  2.7468  1326   148  0.90  16.11   1.00     0.98       8386.58|
|  6:  2.7468 -  2.5857  1312   149  0.90  16.34   0.99     0.96       7430.69|
|  7:  2.5857 -  2.4568  1308   147  0.90  15.89   0.99     0.96       6176.51|
|  8:  2.4568 -  2.3503  1306   142  0.90  15.81   1.01     0.98       5720.01|
|  9:  2.3503 -  2.2602  1305   140  0.90  16.31   1.01     0.98       5166.11|
| 10:  2.2602 -  2.1824  1291   146  0.90  15.76   1.00     0.96       4751.37|
| 11:  2.1824 -  2.1144  1284   143  0.90  16.35   1.01     0.97       4316.84|
| 12:  2.1144 -  2.0541  1285   148  0.91  15.16   1.01     1.00       3798.59|
| 13:  2.0541 -  2.0002  1216   132  0.90  16.33   1.00     1.00       3351.69|
| 14:  2.0002 -  1.9515   543    61  0.90  16.27   0.99     0.95       2901.00|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2901.00 max =        10765.64 mean =      6568.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.35|
|phase err.(test): min =        0.00 max =           89.72 mean =        13.95|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.540)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    95.63   17.00    None  None   None       |
|    all(noH): 2823   0      1.53    95.63   17.00    None  None   None       |
|    Sol.    : 438    0      5.25    88.91   40.55    None  None   None       |
|    Mac.    : 2385   0      1.53    95.63   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.529 -  10.940: 1304   |   5:    48.580 -  57.990:   87        |
|      1:    10.940 -  20.350:  910   |   6:    57.990 -  67.401:   55        |
|      2:    20.350 -  29.760:  198   |   7:    67.401 -  76.811:   22        |
|      3:    29.760 -  39.170:  119   |   8:    76.811 -  86.221:    8        |
|      4:    39.170 -  48.580:  114   |   9:    86.221 -  95.631:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.414 - 5.964
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 313
   mapped sites are within: 0.724 - 5.964

peak=    7.442 closest distance to " O   HOH Z 138 " =    1.049
peak=    5.836 closest distance to " NH2 ARG A  56 " =    2.256
peak=    5.504 closest distance to " O   HOH Z 124 " =    1.575
peak=    5.282 closest distance to " O   HOH Z 132 " =    1.565
peak=    5.273 closest distance to " O   HOH Z 278 " =    1.238
peak=    5.253 closest distance to " O   HOH Z 199 " =    1.061
peak=    5.228 closest distance to " CB  SER A  63 " =    1.142
peak=    5.171 closest distance to " O   HOH Z 272 " =    1.908
peak=    5.152 closest distance to " CG  PRO A 213 " =    1.215
peak=    5.099 closest distance to " O   HOH Z 142 " =    1.648
peak=    5.066 closest distance to " CG  PRO A  54 " =    1.208
peak=    5.021 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.979 closest distance to " O   HOH Z 403 " =    1.850
peak=    4.945 closest distance to " O   HOH Z 234 " =    3.676
peak=    4.938 closest distance to " CB  GLN A 223 " =    1.425
peak=    4.855 closest distance to " O   HOH Z 108 " =    1.593
peak=    4.795 closest distance to " O   HOH Z 126 " =    1.889
peak=    4.628 closest distance to " O   HOH Z 193 " =    1.772
peak=    4.627 closest distance to " O   HOH Z  15 " =    2.067
peak=    4.594 closest distance to " O   HOH Z  97 " =    1.870
peak=    4.592 closest distance to " O   SER A  87 " =    2.136
peak=    4.550 closest distance to " CG  PRO A 198 " =    1.244
peak=    4.509 closest distance to " O   HOH Z 209 " =    2.370
peak=    4.504 closest distance to " CA  TYR A  30 " =    1.018
peak=    4.502 closest distance to " O   HOH Z 316 " =    2.917
peak=    4.489 closest distance to " O   HOH Z  80 " =    1.697
peak=    4.477 closest distance to " NH2BARG A 145 " =    2.088
peak=    4.435 closest distance to " O   HOH Z 326 " =    1.654
peak=    4.411 closest distance to " CB  SER A   3 " =    1.279
peak=    4.406 closest distance to " CG1 ILE A  33 " =    1.293
peak=    4.403 closest distance to " O   HOH Z 334 " =    1.513
peak=    4.399 closest distance to " O   HOH Z 368 " =    1.995
peak=    4.390 closest distance to " O   HOH Z 154 " =    1.509
peak=    4.373 closest distance to " C   PRO A 198 " =    1.550
peak=    4.354 closest distance to " O   HOH Z 134 " =    1.721
peak=    4.312 closest distance to " O   HOH Z  59 " =    2.181
peak=    4.284 closest distance to " O   HOH Z 406 " =    1.518
peak=    4.283 closest distance to " O   HOH Z 227 " =    1.620
peak=    4.270 closest distance to " CB  GLN A 183 " =    1.291
peak=    4.259 closest distance to " O   HOH Z  40 " =    1.659
peak=    4.258 closest distance to " O   HOH Z 189 " =    1.718
peak=    4.256 closest distance to " CB  GLU A 152 " =    1.127
peak=    4.255 closest distance to " O   HOH Z 389 " =    1.894
peak=    4.249 closest distance to " NZ  LYS A 117 " =    3.086
peak=    4.245 closest distance to " O   HOH Z 402 " =    1.403
peak=    4.231 closest distance to " O   HOH Z 102 " =    1.323
peak=    4.201 closest distance to " O   HOH Z 426 " =    1.421
peak=    4.140 closest distance to " O   HOH Z 247 " =    1.319
peak=    4.139 closest distance to " CG  ARG A  66 " =    2.675
peak=    4.115 closest distance to " O   HOH Z 427 " =    2.606
peak=    4.110 closest distance to " CB  GLU A 277 " =    3.529
peak=    4.084 closest distance to " O   HOH Z 232 " =    2.356
peak=    4.078 closest distance to " O   HOH Z 260 " =    1.303
peak=    4.052 closest distance to " O   HOH Z 236 " =    1.952
peak=    4.047 closest distance to " O   GLY A  23 " =    2.297
peak=    4.045 closest distance to " O   HOH Z 128 " =    2.008
peak=    4.036 closest distance to " O   HOH Z 163 " =    2.069
peak=    4.035 closest distance to " O   HOH Z 411 " =    3.553
peak=    4.031 closest distance to " O   HOH Z  49 " =    2.209
peak=    4.020 closest distance to " O   HOH Z 132 " =    1.970
peak=    4.020 closest distance to " CB  ARG A 190 " =    1.706
peak=    4.018 closest distance to " CA  ALA A  21 " =    1.233
peak=    4.017 closest distance to " O   HOH Z  11 " =    1.302
peak=    4.015 closest distance to " O   HOH Z 183 " =    1.527
peak=    4.014 closest distance to " OD2 ASP A 286 " =    2.700
peak=    4.001 closest distance to " CD  ARG A 269 " =    1.028
peak=    3.998 closest distance to " N   ASN A  39 " =    1.227
peak=    3.993 closest distance to " CB  GLU A 128 " =    1.192
peak=    3.979 closest distance to " CB  SER A 141 " =    1.063
peak=    3.974 closest distance to " NE2 GLN A  11 " =    1.053
peak=    3.968 closest distance to " O   HOH Z   6 " =    2.142
peak=    3.964 closest distance to " O   HOH Z  63 " =    1.952
peak=    3.963 closest distance to " O   HOH Z 416 " =    2.819
peak=    3.948 closest distance to " O   HOH Z 298 " =    1.841
peak=    3.946 closest distance to " O   HOH Z 303 " =    1.948
peak=    3.943 closest distance to " O   HOH Z  78 " =    1.668
peak=    3.929 closest distance to " CB  ARG A  79 " =    1.341
peak=    3.927 closest distance to " CB  ARG A 139 " =    1.062
peak=    3.924 closest distance to " O   HOH Z 313 " =    1.785
peak=    3.903 closest distance to " O   HOH Z 357 " =    1.937
peak=    3.897 closest distance to " O   HOH Z 423 " =    1.945
peak=    3.895 closest distance to " NH2AARG A 145 " =    2.201
peak=    3.889 closest distance to " O   HOH Z  54 " =    1.672
peak=    3.879 closest distance to " CB  ASN A 148 " =    1.610
peak=    3.865 closest distance to " NH2 ARG A 156 " =    1.125
peak=    3.865 closest distance to " O   HOH Z 369 " =    2.229
peak=    3.859 closest distance to " O   HOH Z  97 " =    2.460
peak=    3.842 closest distance to " ND2 ASN A 187 " =    1.634
peak=    3.839 closest distance to " O   HOH Z  67 " =    1.837
peak=    3.829 closest distance to " O   HOH Z  43 " =    1.546
peak=    3.828 closest distance to " CG1BVAL A  72 " =    1.566
peak=    3.824 closest distance to " O   HOH Z 408 " =    1.594
peak=    3.821 closest distance to " O   HOH Z 203 " =    1.857
peak=    3.820 closest distance to " O   HOH Z 156 " =    3.138
peak=    3.806 closest distance to " O   HOH Z 214 " =    0.887
peak=    3.798 closest distance to " O   HOH Z 345 " =    1.734
peak=    3.778 closest distance to " O   HOH Z 144 " =    2.132
peak=    3.768 closest distance to " CG AARG A 275 " =    0.931
peak=    3.767 closest distance to " O   HOH Z 261 " =    1.639
peak=    3.766 closest distance to " CB  PRO A  54 " =    0.812
peak=    3.765 closest distance to " CG  ARG A  66 " =    1.037
peak=    3.761 closest distance to " O   HOH Z 279 " =    2.063
peak=    3.759 closest distance to " O   HOH Z 194 " =    1.870
peak=    3.752 closest distance to " O   HOH Z 421 " =    1.620
peak=    3.744 closest distance to " O   HOH Z 118 " =    1.130
peak=    3.744 closest distance to " CB  TYR A 169 " =    0.783
peak=    3.743 closest distance to " O   HOH Z  88 " =    3.128
peak=    3.736 closest distance to " O   HOH Z 214 " =    2.134
peak=    3.736 closest distance to " NZ  LYS A 119 " =    1.738
peak=    3.735 closest distance to " CB  VAL A 202 " =    1.580
peak=    3.734 closest distance to " O   HOH Z  44 " =    2.000
peak=    3.729 closest distance to " OE1 GLN A  11 " =    1.796
peak=    3.728 closest distance to " O   HOH Z 147 " =    1.765
peak=    3.726 closest distance to " O   HOH Z  47 " =    1.535
peak=    3.720 closest distance to " CA  THR A 221 " =    0.950
peak=    3.720 closest distance to " O   HOH Z  54 " =    2.323
peak=    3.717 closest distance to " CD  PRO A  54 " =    1.169
peak=    3.716 closest distance to " CB  TRP A 179 " =    1.238
peak=    3.713 closest distance to " O   HOH Z  71 " =    1.481
peak=    3.711 closest distance to " O   HOH Z 344 " =    2.860
peak=    3.699 closest distance to " O   HOH Z 346 " =    1.519
peak=    3.690 closest distance to " O   HOH Z 280 " =    2.434
peak=    3.661 closest distance to " CA  ASP A 140 " =    1.147
peak=    3.661 closest distance to " O   HOH Z  66 " =    2.246
peak=    3.657 closest distance to " CD2 TRP A 179 " =    1.380
peak=    3.656 closest distance to " CG  GLN A  58 " =    2.385
peak=    3.656 closest distance to " O   HOH Z  19 " =    1.635
peak=    3.638 closest distance to " O   HOH Z 365 " =    2.766
peak=    3.638 closest distance to " CA  ALA A  51 " =    0.932
peak=    3.636 closest distance to " CE  LYS A 119 " =    1.097
peak=    3.635 closest distance to " O   HOH Z 276 " =    1.307
peak=    3.629 closest distance to " O   HOH Z 284 " =    2.855
peak=    3.622 closest distance to " CG2BVAL A  41 " =    0.848
peak=    3.620 closest distance to " CD  LYS A 166 " =    1.311
peak=    3.618 closest distance to " CD2 LEU A 297 " =    0.963
peak=    3.611 closest distance to " O   HOH Z  20 " =    2.240
peak=    3.606 closest distance to " O   HOH Z 173 " =    2.097
peak=    3.605 closest distance to " CD  ARG A 139 " =    1.435
peak=    3.601 closest distance to " CA  ARG A  36 " =    1.030
peak=    3.601 closest distance to " O   HOH Z  21 " =    1.811
peak=    3.570 closest distance to " CB  LEU A 228 " =    1.162
peak=    3.568 closest distance to " CB  SER A 216 " =    0.809
peak=    3.563 closest distance to " CG AARG A 275 " =    1.014
peak=    3.560 closest distance to " O   HOH Z 250 " =    1.451
peak=    3.551 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.547 closest distance to " OD1 ASN A  69 " =    2.507
peak=    3.542 closest distance to " CG  PRO A 243 " =    1.251
peak=    3.541 closest distance to " O   HOH Z 336 " =    1.673
peak=    3.540 closest distance to " O   HOH Z 166 " =    1.223
peak=    3.536 closest distance to " O   HOH Z 419 " =    1.553
peak=    3.536 closest distance to " O   HOH Z 327 " =    1.854
peak=    3.532 closest distance to " CD BLYS A 290 " =    1.077
peak=    3.528 closest distance to " CA  ASN A 176 " =    1.144
peak=    3.526 closest distance to " NH2AARG A 190 " =    1.207
peak=    3.524 closest distance to " O   HOH Z 128 " =    2.123
peak=    3.524 closest distance to " O   HOH Z  61 " =    1.443
peak=    3.518 closest distance to " N   HIS A 108 " =    1.869
peak=    3.517 closest distance to " OG BSER A 210 " =    1.258
peak=    3.516 closest distance to " OD2 ASP A 298 " =    4.004
peak=    3.508 closest distance to " O   HOH Z  59 " =    1.678
peak=    3.498 closest distance to " O   HOH Z 163 " =    1.444
peak=    3.491 closest distance to " OG BSER A 164 " =    2.504
peak=    3.486 closest distance to " CB  MET A  47 " =    0.979
peak=    3.477 closest distance to " O   HOH Z 155 " =    2.779
peak=    3.477 closest distance to " CA  ASP A 191 " =    0.996
peak=    3.475 closest distance to " O   HOH Z 156 " =    2.763
peak=    3.472 closest distance to " O   HOH Z 245 " =    1.348
peak=    3.471 closest distance to " O   HOH Z 374 " =    2.556
peak=    3.461 closest distance to " CD2 PHE A 225 " =    1.144
peak=    3.458 closest distance to " CA  LYS A 117 " =    1.315
peak=    3.457 closest distance to " O   HOH Z 438 " =    2.389
peak=    3.455 closest distance to " O   HOH Z 345 " =    2.665
peak=    3.449 closest distance to " O   HOH Z 434 " =    1.589
peak=    3.448 closest distance to " OG  SER A  62 " =    2.948
peak=    3.447 closest distance to " CG2 ILE A  20 " =    1.428
peak=    3.445 closest distance to " NZ  LYS A 117 " =    0.989
peak=    3.444 closest distance to " CD  LYS A 119 " =    1.644
peak=    3.443 closest distance to " O   ALA A 165 " =    1.279
peak=    3.441 closest distance to " CG2 THR A 221 " =    1.120
peak=    3.441 closest distance to " CB  SER A  62 " =    0.770
peak=    3.436 closest distance to " O   HOH Z 281 " =    4.253
peak=    3.435 closest distance to " O   HOH Z  30 " =    1.857
peak=    3.435 closest distance to " CD  ARG A 195 " =    0.874
peak=    3.430 closest distance to " CD  GLN A 194 " =    1.555
peak=    3.429 closest distance to " O   HOH Z 273 " =    2.724
peak=    3.421 closest distance to " O   HOH Z 207 " =    1.693
peak=    3.417 closest distance to " O   SER A  26 " =    1.716
peak=    3.415 closest distance to " NZ  LYS A  76 " =    1.322
peak=    3.415 closest distance to " OE1 GLN A  58 " =    5.964
peak=    3.406 closest distance to " O   HOH Z 358 " =    2.160
peak=    3.404 closest distance to " O   HOH Z  10 " =    1.760
peak=    3.400 closest distance to " CB  PRO A 198 " =    1.164
peak=    3.397 closest distance to " O   HOH Z 114 " =    1.200
peak=    3.387 closest distance to " O   HOH Z 394 " =    1.533
peak=    3.382 closest distance to " NH1BARG A 145 " =    1.088
peak=    3.375 closest distance to " O   HOH Z 197 " =    2.443
peak=    3.373 closest distance to " CB  ALA A 291 " =    1.254
peak=    3.372 closest distance to " O   HOH Z 414 " =    1.571
peak=    3.370 closest distance to " CA  VAL A  41 " =    0.869
peak=    3.369 closest distance to " O   HOH Z 118 " =    0.907
peak=    3.368 closest distance to " O   HOH Z 375 " =    2.192
peak=    3.364 closest distance to " CA  ALA A 160 " =    0.839
peak=    3.358 closest distance to " OD1 ASP A 253 " =    1.964
peak=    3.354 closest distance to " CD2 HIS A  81 " =    1.236
peak=    3.352 closest distance to " O   HOH Z 250 " =    1.807
peak=    3.352 closest distance to " O   HOH Z 427 " =    3.058
peak=    3.351 closest distance to " O   HOH Z 133 " =    1.145
peak=    3.346 closest distance to " CB  VAL A 265 " =    1.217
peak=    3.340 closest distance to " CB  ARG A 259 " =    1.931
peak=    3.340 closest distance to " O   HOH Z 166 " =    3.446
peak=    3.338 closest distance to " O   HOH Z 132 " =    2.694
peak=    3.337 closest distance to " O   HOH Z 267 " =    2.012
peak=    3.334 closest distance to " O   HOH Z 260 " =    1.003
peak=    3.331 closest distance to " CB  ALA A 100 " =    1.229
peak=    3.330 closest distance to " CA  GLY A  80 " =    0.927
peak=    3.330 closest distance to " O   GLY A  91 " =    1.473
peak=    3.327 closest distance to " O   HOH Z 291 " =    1.512
peak=    3.324 closest distance to " CA  ARG A 195 " =    1.289
peak=    3.319 closest distance to " O   HOH Z  61 " =    1.498
peak=    3.316 closest distance to " CB  SER A  26 " =    1.680
peak=    3.313 closest distance to " O   HOH Z 361 " =    2.354
peak=    3.312 closest distance to " O   HOH Z  51 " =    1.502
peak=    3.308 closest distance to " CA  ARG A  66 " =    1.209
peak=    3.308 closest distance to " NH1AARG A 145 " =    1.161
peak=    3.302 closest distance to " O   HOH Z 282 " =    1.994
peak=    3.299 closest distance to " O   HOH Z 255 " =    1.620
peak=    3.298 closest distance to " O   HOH Z 380 " =    1.874
peak=    3.297 closest distance to " CB  SER A 273 " =    0.812
peak=    3.295 closest distance to " O   HOH Z 193 " =    2.325
peak=    3.293 closest distance to " O   HOH Z 435 " =    1.794
peak=    3.288 closest distance to " CB  ALA A 248 " =    1.318
peak=    3.287 closest distance to " OG1 THR A 294 " =    3.968
peak=    3.282 closest distance to " OD1 ASP A 238 " =    0.867
peak=    3.282 closest distance to " CG1 ILE A 120 " =    0.986
peak=    3.282 closest distance to " CD2 LEU A 255 " =    1.127
peak=    3.278 closest distance to " CA  ASN A 217 " =    1.376
peak=    3.270 closest distance to " CB  ALA A   9 " =    1.453
peak=    3.269 closest distance to " CA  MET A  40 " =    1.021
peak=    3.269 closest distance to " CD1 LEU A 228 " =    1.681
peak=    3.266 closest distance to " CG2AVAL A 121 " =    2.146
peak=    3.262 closest distance to " O   HOH Z 108 " =    1.920
peak=    3.261 closest distance to " O   HOH Z 299 " =    4.326
peak=    3.260 closest distance to " O   HOH Z 227 " =    1.736
peak=    3.258 closest distance to " O   HOH Z 353 " =    2.810
peak=    3.255 closest distance to " CB  TYR A  30 " =    1.431
peak=    3.253 closest distance to " CE  MET A 188 " =    2.179
peak=    3.252 closest distance to " O   HOH Z 155 " =    1.506
peak=    3.249 closest distance to " O   HOH Z  35 " =    2.377
peak=    3.243 closest distance to " CG  MET A  93 " =    1.011
peak=    3.241 closest distance to " CG1 VAL A 153 " =    1.146
peak=    3.240 closest distance to " CZ AARG A 102 " =    1.734
peak=    3.240 closest distance to " CB  ARG A 102 " =    0.724
peak=    3.238 closest distance to " CD  ARG A 159 " =    0.770
peak=    3.238 closest distance to " CB  GLN A  88 " =    1.121
peak=    3.237 closest distance to " CG  GLN A  77 " =    1.955
peak=    3.234 closest distance to " O   ALA A   1 " =    1.616
peak=    3.234 closest distance to " O   HOH Z 145 " =    2.327
peak=    3.233 closest distance to " O   GLY A  57 " =    0.964
peak=    3.225 closest distance to " CD2 LEU A  83 " =    1.533
peak=    3.220 closest distance to " O   HOH Z 362 " =    3.605
peak=    3.215 closest distance to " O   HOH Z 197 " =    1.991
peak=    3.213 closest distance to " CG  MET A 185 " =    1.077
peak=    3.212 closest distance to " O   HOH Z 299 " =    2.238
peak=    3.207 closest distance to " CG2 VAL A 197 " =    1.087
peak=    3.206 closest distance to " O   HOH Z 126 " =    1.588
peak=    3.203 closest distance to " O   HOH Z 337 " =    3.557
peak=    3.197 closest distance to " CB  THR A  52 " =    1.131
peak=    3.195 closest distance to " O   HOH Z 261 " =    1.989
peak=    3.195 closest distance to " O   TRP A 274 " =    1.758
peak=    3.193 closest distance to " O   HOH Z 266 " =    1.598
peak=    3.190 closest distance to " CG2 ILE A 120 " =    1.296
peak=    3.186 closest distance to " O   HOH Z 124 " =    2.791
peak=    3.182 closest distance to " O   HOH Z 189 " =    1.379
peak=    3.181 closest distance to " O   HOH Z  50 " =    1.298
peak=    3.181 closest distance to " CD1 LEU A  96 " =    0.755
peak=    3.179 closest distance to " O   SER A 164 " =    1.262
peak=    3.178 closest distance to " O   HOH Z  85 " =    1.899
peak=    3.175 closest distance to " O   HOH Z 303 " =    1.575
peak=    3.175 closest distance to " CB  GLN A 103 " =    0.901
peak=    3.174 closest distance to " NE AARG A 275 " =    1.206
peak=    3.170 closest distance to " CH2 TRP A 274 " =    2.014
peak=    3.170 closest distance to " CB  PRO A 163 " =    3.907
peak=    3.169 closest distance to " O   HOH Z 327 " =    2.796
peak=    3.169 closest distance to " CB  GLN A 194 " =    0.851
peak=    3.166 closest distance to " CD1 LEU A 300 " =    1.251
peak=    3.157 closest distance to " CB  ASN A 127 " =    0.776
peak=    3.155 closest distance to " CA  ALA A 291 " =    0.916
peak=    3.153 closest distance to " O   HOH Z 195 " =    1.983
peak=    3.152 closest distance to " OH  TYR A  30 " =    1.143
peak=    3.147 closest distance to " O   HOH Z 359 " =    1.494
peak=    3.143 closest distance to " CA  ALA A 233 " =    1.295
peak=    3.141 closest distance to " O   HOH Z 116 " =    1.067
peak=    3.141 closest distance to " O   HOH Z  85 " =    1.846
peak=    3.141 closest distance to " CA  ASP A 162 " =    1.098
peak=    3.127 closest distance to " O   HOH Z 125 " =    2.353
peak=    3.122 closest distance to " O   HOH Z 112 " =    1.550
peak=    3.115 closest distance to " O   HOH Z  20 " =    1.309
peak=    3.114 closest distance to " OG BSER A 258 " =    3.306
peak=    3.109 closest distance to " CA  LEU A 282 " =    1.223
peak=    3.108 closest distance to " CG  GLN A  89 " =    1.500
peak=    3.103 closest distance to " CZ  PHE A  38 " =    1.469
peak=    3.100 closest distance to " CB  GLN A 278 " =    0.766
peak=    3.089 closest distance to " O   HOH Z 148 " =    3.091
peak=    3.081 closest distance to " O   HOH Z 106 " =    1.636
peak=    3.077 closest distance to " CE AMET A  47 " =    1.398
peak=    3.069 closest distance to " CA  ALA A  84 " =    1.247
peak=    3.066 closest distance to " O   HOH Z 336 " =    1.596
peak=    3.033 closest distance to " CG  GLN A  11 " =    1.046
peak=    3.025 closest distance to " CB  GLN A  58 " =    0.751

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.559 - 5.981
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 215
   mapped sites are within: 0.789 - 5.981

peak=   -4.645 closest distance to " O   HOH Z 266 " =    4.025
peak=   -4.630 closest distance to " CA  SER A 164 " =    1.988
peak=   -4.494 closest distance to " C   HIS A 108 " =    1.125
peak=   -4.332 closest distance to " O   HOH Z  13 " =    1.475
peak=   -4.306 closest distance to " CG  LYS A 193 " =    2.395
peak=   -4.278 closest distance to " OXT GLY A 302 " =    2.916
peak=   -4.222 closest distance to " CD  ARG A 156 " =    2.018
peak=   -4.184 closest distance to " O   HOH Z 138 " =    0.861
peak=   -4.158 closest distance to " O   HOH Z 234 " =    4.110
peak=   -4.120 closest distance to " O   HOH Z 377 " =    1.785
peak=   -4.045 closest distance to " O   VAL A  67 " =    2.796
peak=   -4.044 closest distance to " O   HOH Z  11 " =    1.648
peak=   -4.041 closest distance to " CD1 LEU A 101 " =    2.484
peak=   -4.033 closest distance to " N   ALA A 248 " =    1.767
peak=   -4.018 closest distance to " SG  CYS A 254 " =    3.281
peak=   -4.016 closest distance to " ND2 ASN A 187 " =    1.442
peak=   -3.976 closest distance to " O   TRP A  92 " =    1.864
peak=   -3.971 closest distance to " CD  GLN A  58 " =    0.968
peak=   -3.921 closest distance to " O   HOH Z 292 " =    4.446
peak=   -3.892 closest distance to " O   HOH Z 423 " =    2.295
peak=   -3.861 closest distance to " NH2 ARG A  79 " =    1.920
peak=   -3.849 closest distance to " OG ASER A 134 " =    1.314
peak=   -3.825 closest distance to " O   PRO A 198 " =    1.277
peak=   -3.825 closest distance to " O   HOH Z 407 " =    3.158
peak=   -3.794 closest distance to " OG  SER A  97 " =    2.053
peak=   -3.790 closest distance to " C   ALA A 158 " =    1.172
peak=   -3.788 closest distance to " OD1 ASN A  39 " =    2.215
peak=   -3.779 closest distance to " N   SER A 276 " =    1.337
peak=   -3.769 closest distance to " C   THR A 279 " =    1.200
peak=   -3.767 closest distance to " O   HOH Z  52 " =    1.660
peak=   -3.754 closest distance to " N   GLN A  58 " =    1.699
peak=   -3.750 closest distance to " ND2 ASN A  45 " =    0.945
peak=   -3.746 closest distance to " CZ  TYR A 169 " =    1.929
peak=   -3.743 closest distance to " O   HOH Z 290 " =    0.951
peak=   -3.740 closest distance to " OG BSER A 134 " =    1.417
peak=   -3.731 closest distance to " C   GLY A  80 " =    2.415
peak=   -3.718 closest distance to " CH2 TRP A 179 " =    1.329
peak=   -3.710 closest distance to " O   HOH Z  11 " =    1.858
peak=   -3.694 closest distance to " O   HOH Z  97 " =    1.418
peak=   -3.685 closest distance to " CD  ARG A 139 " =    1.614
peak=   -3.678 closest distance to " CD2 LEU A 300 " =    2.801
peak=   -3.672 closest distance to " CB  ALA A 291 " =    2.337
peak=   -3.664 closest distance to " O   HOH Z 118 " =    2.907
peak=   -3.651 closest distance to " O   HOH Z 138 " =    1.249
peak=   -3.649 closest distance to " O   HOH Z  92 " =    1.487
peak=   -3.649 closest distance to " CA  GLY A 133 " =    1.743
peak=   -3.646 closest distance to " O   HOH Z 165 " =    2.088
peak=   -3.642 closest distance to " CE  MET A 105 " =    1.846
peak=   -3.638 closest distance to " O   HOH Z 418 " =    1.309
peak=   -3.633 closest distance to " O   HOH Z 388 " =    2.046
peak=   -3.631 closest distance to " CD1 PHE A 130 " =    2.198
peak=   -3.630 closest distance to " OG  SER A  62 " =    1.347
peak=   -3.627 closest distance to " O   HOH Z 435 " =    2.512
peak=   -3.621 closest distance to " O   VAL A 174 " =    1.920
peak=   -3.616 closest distance to " O   ALA A 256 " =    1.392
peak=   -3.604 closest distance to " O   HOH Z 126 " =    1.932
peak=   -3.604 closest distance to " CD1 LEU A 228 " =    2.205
peak=   -3.603 closest distance to " CD  GLN A  58 " =    1.376
peak=   -3.590 closest distance to " O   HOH Z 265 " =    1.979
peak=   -3.585 closest distance to " O   VAL A  67 " =    2.659
peak=   -3.583 closest distance to " CB  ALA A 161 " =    2.549
peak=   -3.582 closest distance to " O   ALA A   1 " =    1.970
peak=   -3.577 closest distance to " CG1 VAL A  78 " =    2.681
peak=   -3.576 closest distance to " O   GLY A 196 " =    0.965
peak=   -3.570 closest distance to " CD2 LEU A 237 " =    2.691
peak=   -3.564 closest distance to " O   HOH Z  71 " =    1.369
peak=   -3.557 closest distance to " CE2 TYR A  30 " =    2.811
peak=   -3.553 closest distance to " O   ALA A 161 " =    1.545
peak=   -3.553 closest distance to " O   PHE A 218 " =    1.470
peak=   -3.539 closest distance to " CD  ARG A 195 " =    5.122
peak=   -3.532 closest distance to " CG  ASP A 132 " =    2.271
peak=   -3.529 closest distance to " O   HOH Z 166 " =    1.897
peak=   -3.515 closest distance to " N   GLN A 122 " =    1.607
peak=   -3.511 closest distance to " CD1 TYR A 247 " =    2.324
peak=   -3.509 closest distance to " O   ASN A 187 " =    1.424
peak=   -3.509 closest distance to " CG  GLU A  53 " =    1.433
peak=   -3.495 closest distance to " N   SER A  12 " =    1.398
peak=   -3.491 closest distance to " CD1 PHE A  59 " =    1.911
peak=   -3.476 closest distance to " CB  CYS A 254 " =    2.740
peak=   -3.475 closest distance to " O   SER A 146 " =    0.919
peak=   -3.473 closest distance to " OD1 ASP A 200 " =    1.196
peak=   -3.472 closest distance to " O   HOH Z  17 " =    1.316
peak=   -3.466 closest distance to " CB  PHE A 192 " =    1.922
peak=   -3.464 closest distance to " OE2 GLU A   2 " =    1.707
peak=   -3.463 closest distance to " ND2 ASN A  69 " =    1.549
peak=   -3.449 closest distance to " C   ASN A 285 " =    2.172
peak=   -3.448 closest distance to " ND2 ASN A  45 " =    1.033
peak=   -3.448 closest distance to " O   HOH Z 362 " =    5.981
peak=   -3.445 closest distance to " O   SER A 135 " =    1.583
peak=   -3.444 closest distance to " N   ALA A 248 " =    2.243
peak=   -3.440 closest distance to " OG  SER A   3 " =    1.770
peak=   -3.432 closest distance to " O   ALA A 160 " =    1.417
peak=   -3.429 closest distance to " CA  ASN A 148 " =    1.652
peak=   -3.428 closest distance to " CB  PRO A 163 " =    2.809
peak=   -3.423 closest distance to " CB  PHE A 208 " =    2.224
peak=   -3.421 closest distance to " CB  ASN A  39 " =    2.268
peak=   -3.418 closest distance to " O   HOH Z  63 " =    1.150
peak=   -3.416 closest distance to " CD1 LEU A  83 " =    2.274
peak=   -3.412 closest distance to " O   HOH Z 311 " =    3.408
peak=   -3.409 closest distance to " CA  TRP A 274 " =    1.598
peak=   -3.401 closest distance to " OG BSER A 134 " =    1.732
peak=   -3.397 closest distance to " OD2 ASP A  50 " =    1.361
peak=   -3.393 closest distance to " N   SER A 206 " =    1.813
peak=   -3.389 closest distance to " NH2 ARG A  66 " =    4.736
peak=   -3.383 closest distance to " CB  ALA A 244 " =    2.035
peak=   -3.382 closest distance to " O   PRO A 198 " =    1.305
peak=   -3.378 closest distance to " OD1 ASP A 191 " =    1.689
peak=   -3.370 closest distance to " CB  ALA A 248 " =    1.938
peak=   -3.367 closest distance to " O   HOH Z 150 " =    1.531
peak=   -3.363 closest distance to " O   SER A  26 " =    1.237
peak=   -3.362 closest distance to " CB  ASP A 124 " =    2.133
peak=   -3.357 closest distance to " O   HOH Z  93 " =    1.404
peak=   -3.346 closest distance to " C   SER A 206 " =    1.691
peak=   -3.345 closest distance to " O  BHOH Z 338 " =    1.545
peak=   -3.343 closest distance to " O   LEU A 167 " =    1.620
peak=   -3.342 closest distance to " CG  LEU A  83 " =    1.899
peak=   -3.341 closest distance to " CG  ARG A 219 " =    2.303
peak=   -3.337 closest distance to " CA  GLN A  58 " =    1.469
peak=   -3.337 closest distance to " CD  GLN A  58 " =    1.340
peak=   -3.334 closest distance to " C   LEU A 143 " =    1.293
peak=   -3.331 closest distance to " CB  ASP A 162 " =    2.554
peak=   -3.328 closest distance to " CG1AVAL A  41 " =    2.608
peak=   -3.323 closest distance to " CG  ARG A 259 " =    2.712
peak=   -3.319 closest distance to " O   MET A  40 " =    2.612
peak=   -3.314 closest distance to " O   HOH Z 116 " =    1.089
peak=   -3.314 closest distance to " CD2 PHE A  59 " =    2.400
peak=   -3.312 closest distance to " O   HOH Z 377 " =    1.366
peak=   -3.311 closest distance to " O   HOH Z 100 " =    0.923
peak=   -3.311 closest distance to " O   PHE A  59 " =    2.415
peak=   -3.308 closest distance to " O   HOH Z 196 " =    1.874
peak=   -3.304 closest distance to " O   HOH Z 283 " =    1.662
peak=   -3.303 closest distance to " CA  GLY A  98 " =    2.117
peak=   -3.301 closest distance to " N   THR A 220 " =    2.314
peak=   -3.298 closest distance to " O   HOH Z 198 " =    2.104
peak=   -3.295 closest distance to " O   HOH Z 185 " =    2.204
peak=   -3.291 closest distance to " O   HOH Z 360 " =    2.625
peak=   -3.286 closest distance to " CA  GLY A 203 " =    2.234
peak=   -3.285 closest distance to " O   HOH Z  38 " =    1.534
peak=   -3.280 closest distance to " O   SER A 273 " =    1.379
peak=   -3.277 closest distance to " O   HOH Z  10 " =    1.436
peak=   -3.275 closest distance to " NH1 ARG A  66 " =    5.171
peak=   -3.267 closest distance to " CG  PHE A 283 " =    2.548
peak=   -3.262 closest distance to " O   HOH Z 193 " =    1.947
peak=   -3.259 closest distance to " OD2 ASP A 171 " =    2.304
peak=   -3.259 closest distance to " O   SER A 210 " =    1.854
peak=   -3.258 closest distance to " O   HOH Z 396 " =    1.599
peak=   -3.258 closest distance to " O   HOH Z 136 " =    1.648
peak=   -3.256 closest distance to " O   HOH Z 313 " =    1.046
peak=   -3.254 closest distance to " CB  SER A 258 " =    2.068
peak=   -3.252 closest distance to " ND2 ASN A  39 " =    1.209
peak=   -3.252 closest distance to " CE3 TRP A 150 " =    1.988
peak=   -3.247 closest distance to " O   LEU A 222 " =    1.300
peak=   -3.243 closest distance to " SD  MET A 188 " =    2.251
peak=   -3.240 closest distance to " O   ASN A  45 " =    1.851
peak=   -3.237 closest distance to " CA  GLY A 241 " =    2.282
peak=   -3.235 closest distance to " O   ASP A 191 " =    1.409
peak=   -3.234 closest distance to " O   HOH Z 417 " =    2.618
peak=   -3.234 closest distance to " O   HOH Z  41 " =    2.189
peak=   -3.232 closest distance to " CG2 VAL A 189 " =    2.185
peak=   -3.229 closest distance to " O   LEU A 228 " =    2.358
peak=   -3.229 closest distance to " CG  ASP A  50 " =    2.324
peak=   -3.224 closest distance to " O   HOH Z 281 " =    2.767
peak=   -3.221 closest distance to " CG  LYS A 119 " =    2.865
peak=   -3.218 closest distance to " O   HOH Z  15 " =    1.600
peak=   -3.211 closest distance to " OG1 THR A 178 " =    1.280
peak=   -3.207 closest distance to " O   HOH Z  78 " =    1.820
peak=   -3.202 closest distance to " O   HOH Z 427 " =    1.339
peak=   -3.201 closest distance to " O   ALA A  34 " =    2.408
peak=   -3.198 closest distance to " O   VAL A 197 " =    1.122
peak=   -3.197 closest distance to " O   HOH Z 166 " =    1.534
peak=   -3.197 closest distance to " O   HOH Z 132 " =    1.262
peak=   -3.195 closest distance to " CG  ASP A 231 " =    0.789
peak=   -3.190 closest distance to " O   TYR A 186 " =    1.392
peak=   -3.185 closest distance to " OG  SER A  63 " =    1.394
peak=   -3.184 closest distance to " CG  GLU A 277 " =    1.183
peak=   -3.183 closest distance to " O   HOH Z 151 " =    1.518
peak=   -3.181 closest distance to " O   HOH Z  19 " =    2.017
peak=   -3.180 closest distance to " NZ  LYS A 117 " =    1.632
peak=   -3.179 closest distance to " O   HOH Z  43 " =    1.641
peak=   -3.172 closest distance to " CB  MET A  93 " =    2.027
peak=   -3.171 closest distance to " CD  PRO A 163 " =    2.211
peak=   -3.169 closest distance to " OD1 ASP A 171 " =    1.707
peak=   -3.168 closest distance to " CA  ASP A 298 " =    1.112
peak=   -3.168 closest distance to " CD  GLN A  88 " =    0.951
peak=   -3.167 closest distance to " CB  LEU A 167 " =    2.078
peak=   -3.166 closest distance to " CD2 TYR A 293 " =    2.019
peak=   -3.166 closest distance to " CD1 LEU A  25 " =    2.452
peak=   -3.164 closest distance to " ND2 ASN A 252 " =    1.666
peak=   -3.163 closest distance to " O   ALA A  51 " =    1.483
peak=   -3.162 closest distance to " O   HOH Z 251 " =    1.443
peak=   -3.160 closest distance to " NE2 GLN A 194 " =    1.713
peak=   -3.159 closest distance to " CG  ARG A 269 " =    2.192
peak=   -3.158 closest distance to " O   HOH Z 405 " =    2.374
peak=   -3.149 closest distance to " O   HOH Z 385 " =    3.409
peak=   -3.147 closest distance to " OH  TYR A 214 " =    1.403
peak=   -3.140 closest distance to " O   HOH Z 431 " =    2.242
peak=   -3.138 closest distance to " O   HOH Z 384 " =    2.303
peak=   -3.137 closest distance to " CG  ASN A 110 " =    1.147
peak=   -3.132 closest distance to " O   HOH Z 414 " =    1.474
peak=   -3.125 closest distance to " N   ALA A 226 " =    1.951
peak=   -3.119 closest distance to " CB  ALA A  10 " =    2.211
peak=   -3.119 closest distance to " OXT GLY A 302 " =    2.903
peak=   -3.114 closest distance to " O   HOH Z 222 " =    1.325
peak=   -3.112 closest distance to " O   HOH Z 140 " =    0.835
peak=   -3.106 closest distance to " CE1 HIS A  81 " =    1.380
peak=   -3.100 closest distance to " O   HOH Z 351 " =    1.535
peak=   -3.085 closest distance to " O   HOH Z 361 " =    3.422
peak=   -3.077 closest distance to " O   THR A  52 " =    1.794
peak=   -3.073 closest distance to " O   HOH Z 111 " =    3.319
peak=   -3.062 closest distance to " CD2 LEU A 237 " =    2.172
peak=   -3.046 closest distance to " O   ASP A 298 " =    1.747
peak=   -3.034 closest distance to " O   HOH Z 310 " =    3.575
peak=   -3.026 closest distance to " N   VAL A 189 " =    1.693

================= 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    :  0.4641 0.4590   6.269670e+00   6.263786e+00
   1_bss:  0.4560 0.4512   6.263396e+00   6.249241e+00
   1_xyz:  0.2955 0.3255   5.944670e+00   6.023163e+00
   1_adp:  0.2671 0.3373   5.890689e+00   6.047726e+00
   1_occ:  0.2667 0.3374   5.889747e+00   6.046883e+00
   2_bss:  0.2632 0.3339   5.884566e+00   6.043578e+00
   2_xyz:  0.2024 0.2624   5.658155e+00   5.860709e+00
   2_adp:  0.1885 0.2445   5.593777e+00   5.793060e+00
   2_occ:  0.1883 0.2446   5.593603e+00   5.792817e+00
   3_bss:  0.1886 0.2438   5.592370e+00   5.790153e+00
   3_xyz:  0.1484 0.1980   5.384767e+00   5.603333e+00
   3_adp:  0.1394 0.1873   5.328887e+00   5.544639e+00
   3_occ:  0.1393 0.1872   5.328647e+00   5.544474e+00
   4_bss:  0.1397 0.1869   5.330686e+00   5.545744e+00
   4_xyz:  0.1222 0.1696   5.217910e+00   5.445913e+00
   4_adp:  0.1188 0.1671   5.195275e+00   5.426431e+00
   4_occ:  0.1187 0.1671   5.195256e+00   5.426775e+00
   5_bss:  0.1187 0.1671   5.195251e+00   5.426796e+00
   5_xyz:  0.1131 0.1635   5.163762e+00   5.405667e+00
   5_adp:  0.1125 0.1623   5.157832e+00   5.399908e+00
   5_occ:  0.1124 0.1623   5.157690e+00   5.400280e+00
   5_bss:  0.1126 0.1620   5.158421e+00   5.400065e+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:  0.318  20.001  -2.034   1.615   2.046   0.000   0.000   0.000
   1_xyz:  0.318  20.001  -2.034   1.615   2.046   0.000   0.000   0.000
   1_adp:  0.318  20.001  -2.034   1.615   2.046   0.000   0.000   0.000
   1_occ:  0.318  20.001  -2.034   1.615   2.046   0.000   0.000   0.000
   2_bss:  0.328  50.001  -2.490  -0.139  -0.148  -0.000  -0.000  -0.000
   2_xyz:  0.328  50.001  -2.490  -0.139  -0.148  -0.000  -0.000  -0.000
   2_adp:  0.328  50.001  -2.490  -0.139  -0.148  -0.000  -0.000  -0.000
   2_occ:  0.328  50.001  -2.490  -0.139  -0.148  -0.000  -0.000  -0.000
   3_bss:  0.318  41.877  -2.546  -0.713  -1.003  -0.000  -0.000  -0.000
   3_xyz:  0.318  41.877  -2.546  -0.713  -1.003  -0.000  -0.000  -0.000
   3_adp:  0.318  41.877  -2.546  -0.713  -1.003  -0.000  -0.000  -0.000
   3_occ:  0.318  41.877  -2.546  -0.713  -1.003  -0.000  -0.000  -0.000
   4_bss:  0.321  44.578  -2.843  -1.351  -1.654  -0.000  -0.000  -0.000
   4_xyz:  0.321  44.578  -2.843  -1.351  -1.654  -0.000  -0.000  -0.000
   4_adp:  0.321  44.578  -2.843  -1.351  -1.654  -0.000  -0.000  -0.000
   4_occ:  0.321  44.578  -2.843  -1.351  -1.654  -0.000  -0.000  -0.000
   5_bss:  0.323  44.578  -2.721  -1.418  -1.674  -0.000  -0.000  -0.000
   5_xyz:  0.323  44.578  -2.721  -1.418  -1.674  -0.000  -0.000  -0.000
   5_adp:  0.323  44.578  -2.721  -1.418  -1.674  -0.000  -0.000  -0.000
   5_occ:  0.323  44.578  -2.721  -1.418  -1.674  -0.000  -0.000  -0.000
   5_bss:  0.321  44.866  -2.539  -1.324  -1.538  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.665 0.4094  0.5516    68043.611
   1_bss:  57.218 0.4263  0.5864    64014.496
   1_xyz:  33.887 0.7143  0.9433    28109.253
   1_adp:  35.762 0.6912  0.9211    30120.114
   1_occ:  35.720 0.6917  0.9210    30052.670
   2_bss:  35.377 0.6953  0.8813    29472.858
   2_xyz:  26.796 0.7906  0.9676    17873.202
   2_adp:  23.842 0.8231  0.9817    15171.252
   2_occ:  23.848 0.8231  0.9815    15175.301
   3_bss:  23.731 0.8242  0.9651    15021.432
   3_xyz:  18.969 0.8708  0.9960     9979.288
   3_adp:  17.528 0.8848  0.9977     8939.249
   3_occ:  17.521 0.8849  0.9977     8937.790
   4_bss:  17.511 0.8850  0.9787     8965.374
   4_xyz:  15.515 0.9021  0.9862     7234.719
   4_adp:  14.992 0.9068  0.9828     6974.160
   4_occ:  14.994 0.9068  0.9827     6978.272
   5_bss:  14.991 0.9069  0.9834     6980.124
   5_xyz:  14.467 0.9113  0.9841     6628.372
   5_adp:  14.310 0.9127  0.9786     6555.277
   5_occ:  14.311 0.9127  0.9785     6558.310
   5_bss:  14.314 0.9127  0.9813     6567.532
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   2.0977e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   2.0977e-01
   1_xyz:   1.799  0.016  0.107 16.814  0.008  4.113   1.7708e-01
   1_adp:   1.799  0.016  0.107 16.814  0.008  4.113   1.7708e-01
   1_occ:   1.799  0.016  0.107 16.814  0.008  4.113   1.7708e-01
   2_bss:   1.799  0.016  0.107 16.814  0.008  4.113   1.7708e-01
   2_xyz:   1.088  0.007  0.070 15.071  0.004  4.109   6.5898e-02
   2_adp:   1.088  0.007  0.070 15.071  0.004  4.109   6.5898e-02
   2_occ:   1.088  0.007  0.070 15.071  0.004  4.109   6.5898e-02
   3_bss:   1.088  0.007  0.070 15.071  0.004  4.109   6.5898e-02
   3_xyz:   0.994  0.006  0.065 14.690  0.004  4.114   5.7296e-02
   3_adp:   0.994  0.006  0.065 14.690  0.004  4.114   5.7296e-02
   3_occ:   0.994  0.006  0.065 14.690  0.004  4.114   5.7296e-02
   4_bss:   0.994  0.006  0.065 14.690  0.004  4.114   5.7296e-02
   4_xyz:   1.053  0.007  0.072 14.974  0.004  4.108   6.2092e-02
   4_adp:   1.053  0.007  0.072 14.974  0.004  4.108   6.2092e-02
   4_occ:   1.053  0.007  0.072 14.974  0.004  4.108   6.2092e-02
   5_bss:   1.053  0.007  0.072 14.974  0.004  4.108   6.2092e-02
   5_xyz:   1.033  0.007  0.072 14.924  0.004  4.109   6.0953e-02
   5_adp:   1.033  0.007  0.072 14.924  0.004  4.109   6.0953e-02
   5_occ:   1.033  0.007  0.072 14.924  0.004  4.109   6.0953e-02
   5_bss:   1.033  0.007  0.072 14.924  0.004  4.109   6.0953e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.308   2.4122e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.308   2.4122e-01
   1_xyz:   9.870  0.119  0.351 88.532  0.051  2.106   2.0703e-01
   1_adp:   9.870  0.119  0.351 88.532  0.051  2.106   2.0703e-01
   1_occ:   9.870  0.119  0.351 88.532  0.051  2.106   2.0703e-01
   2_bss:   9.870  0.119  0.351 88.532  0.051  2.106   2.0703e-01
   2_xyz:   7.970  0.036  0.230 87.740  0.047  2.260   5.8218e-02
   2_adp:   7.970  0.036  0.230 87.740  0.047  2.260   5.8218e-02
   2_occ:   7.970  0.036  0.230 87.740  0.047  2.260   5.8218e-02
   3_bss:   7.970  0.036  0.230 87.740  0.047  2.260   5.8218e-02
   3_xyz:   7.455  0.042  0.235 87.594  0.027  2.343   3.8056e-02
   3_adp:   7.455  0.042  0.235 87.594  0.027  2.343   3.8056e-02
   3_occ:   7.455  0.042  0.235 87.594  0.027  2.343   3.8056e-02
   4_bss:   7.455  0.042  0.235 87.594  0.027  2.343   3.8056e-02
   4_xyz:   6.945  0.040  0.221 87.425  0.031  2.335   4.3044e-02
   4_adp:   6.945  0.040  0.221 87.425  0.031  2.335   4.3044e-02
   4_occ:   6.945  0.040  0.221 87.425  0.031  2.335   4.3044e-02
   5_bss:   6.945  0.040  0.221 87.425  0.031  2.335   4.3044e-02
   5_xyz:   7.138  0.035  0.232 85.520  0.023  2.323   4.2530e-02
   5_adp:   7.138  0.035  0.232 85.520  0.023  2.323   4.2530e-02
   5_occ:   7.138  0.035  0.232 85.520  0.023  2.323   4.2530e-02
   5_bss:   7.138  0.035  0.232 85.520  0.023  2.323   4.2530e-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:  91.66   0.00  19.14  82.86   0.00  14.96  91.66   2.18  41.89
   1_occ:  91.66   0.00  19.14  82.86   0.00  14.96  91.66   2.18  41.89
   2_bss:  91.66   0.00  19.14  82.86   0.00  14.96  91.66   2.18  41.89
   2_xyz:  91.66   0.00  19.14  82.86   0.00  14.96  91.66   2.18  41.89
   2_adp:  96.40   0.00  18.22  88.49   0.00  13.89  96.40   5.05  41.80
   2_occ:  96.40   0.00  18.22  88.49   0.00  13.89  96.40   5.05  41.80
   3_bss:  96.40   0.00  18.22  88.49   0.00  13.89  96.40   5.05  41.80
   3_xyz:  96.40   0.00  18.22  88.49   0.00  13.89  96.40   5.05  41.80
   3_adp:  93.28   0.00  17.86  93.28   0.00  13.31  92.54   6.79  42.65
   3_occ:  93.28   0.00  17.86  93.28   0.00  13.31  92.54   6.79  42.65
   4_bss:  93.28   0.00  17.86  93.28   0.00  13.31  92.54   6.79  42.65
   4_xyz:  93.28   0.00  17.86  93.28   0.00  13.31  92.54   6.79  42.65
   4_adp:  96.02   1.24  17.55  96.02   1.24  13.00  90.72   6.11  42.31
   4_occ:  96.02   1.24  17.55  96.02   1.24  13.00  90.72   6.11  42.31
   5_bss:  96.02   1.24  17.55  96.02   1.24  13.00  90.72   6.11  42.31
   5_xyz:  96.02   1.24  17.55  96.02   1.24  13.00  90.72   6.11  42.31
   5_adp:  95.69   1.59  17.06  95.69   1.59  12.74  88.97   5.30  40.60
   5_occ:  95.69   1.59  17.06  95.69   1.59  12.74  88.97   5.30  40.60
   5_bss:  95.63   1.53  17.00  95.63   1.53  12.68  88.91   5.25  40.55
------------------------------------------------------------------------
 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:    1.752    0.042    0.499
   1_adp:    1.752    0.042    0.499
   1_occ:    1.752    0.042    0.499
   2_bss:    1.752    0.042    0.499
   2_xyz:    1.468    0.059    0.584
   2_adp:    1.468    0.059    0.584
   2_occ:    1.468    0.059    0.584
   3_bss:    1.468    0.059    0.584
   3_xyz:    1.574    0.073    0.682
   3_adp:    1.574    0.073    0.682
   3_occ:    1.574    0.073    0.682
   4_bss:    1.574    0.073    0.682
   4_xyz:    1.628    0.078    0.726
   4_adp:    1.628    0.078    0.726
   4_occ:    1.628    0.078    0.726
   5_bss:    1.628    0.078    0.726
   5_xyz:    1.640    0.115    0.748
   5_adp:    1.640    0.115    0.748
   5_occ:    1.640    0.115    0.748
   5_bss:    1.640    0.115    0.748
------------------------------------------------------------------------

CPU time actual refinement: 335.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_330/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_330/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_330/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_330/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_330/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.96 
  Macro-tasks:
    bulk solvent and scale       = 41.90  
    individual site refinement   = 137.66 
    weights calculation          = 28.94  
    collect and process          = 6.51   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 215.11 
  Micro-tasks:
    mask                            = 2.46   
    f_calc                          = 106.42 
    alpha_beta                      = 8.17   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 114.98 
    fmodel                         = 7.04   
    r_factors                      = 0.23   
    phase_errors                   = 10.80  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 251.50 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.736 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    642 calls, 106.00 s
gradients_fft:          587 calls, 101.67 s

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

# Date 2008-01-16 Time 04:33:47 PST -0800 (1200486827.69 s)
Start R-work = 0.4641, R-free = 0.4590 (no bulk solvent and anisotropic scale)
Final R-work = 0.1359, R-free = 0.1816 (no bulk solvent and anisotropic scale)

Start R-work = 0.4560, R-free = 0.4512
Final R-work = 0.1126, R-free = 0.1620