# Date 2008-01-16 Time 05:41:30 PST -0800 (1200490890.32 s)
#phil __OFF__

Command line arguments: "../837.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29198
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 837

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 48.1033, 84.6622, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9947 1.96157
Completeness in resolution range: 0.922356
Completeness with d_max=infinity: 0.919628

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9947
                             d_min =   1.9616

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9947 1.96157
Completeness in resolution range: 0.922356
Completeness with d_max=infinity: 0.919628

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9952 -  4.1981 [2234/2263]  2011   223  10.0%
  bin  2:  4.1981 -  3.3443 [2133/2156]  1921   212   9.9%
  bin  3:  3.3443 -  2.9251 [2097/2122]  1888   209  10.0%
  bin  4:  2.9251 -  2.6593 [2100/2126]  1892   208   9.9%
  bin  5:  2.6593 -  2.4696 [2101/2135]  1891   210  10.0%
  bin  6:  2.4696 -  2.3245 [2052/2080]  1848   204   9.9%
  bin  7:  2.3245 -  2.2085 [2048/2084]  1843   205  10.0%
  bin  8:  2.2085 -  2.1126 [2061/2103]  1852   209  10.1%
  bin  9:  2.1126 -  2.0315 [1984/2071]  1788   196   9.9%
  bin 10:  2.0315 -  1.9616 [ 779/2098]   696    83  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_837/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:
        1.38 -     2.09: 15
        2.09 -     2.79: 675
        2.79 -     3.49: 4458
        3.49 -     4.20: 9311
        4.20 -     4.90: 13774
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.385 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.420 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.457 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.612 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.661 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28228 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_837/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_837/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 48.10325 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4639   r_free= 0.4513   ksol= 0.00   Bsol= 0.00   scale= 0.889    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.279257                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6827 0.99   1451  163 0.3745 0.3942      6.5711      6.5853|
|  2:  4.6827 -  3.7357 0.99   1382  149 0.4071 0.4140      6.8351      6.7949|
|  3:  3.7357 -  3.2691 0.99   1375  152 0.4394 0.3967      6.6616       6.676|
|  4:  3.2691 -  2.9727 0.98   1345  155 0.4509 0.4410      6.5086       6.468|
|  5:  2.9727 -  2.7610 0.99   1353  150 0.4808 0.4536      6.3579      6.3212|
|  6:  2.7610 -  2.5991 0.99   1349  148 0.5051 0.4428      6.2712      6.1433|
|  7:  2.5991 -  2.4696 0.98   1348  145 0.4887 0.4376      6.2386      6.1902|
|  8:  2.4696 -  2.3625 0.98   1305  145 0.5096 0.5374      6.1335       6.203|
|  9:  2.3625 -  2.2719 0.99   1336  148 0.5323 0.4961      6.1438      6.1054|
| 10:  2.2719 -  2.1937 0.99   1315  151 0.4947 0.5179      6.0787      6.0986|
| 11:  2.1937 -  2.1253 0.97   1321  144 0.5142 0.5281       6.013      6.0034|
| 12:  2.1253 -  2.0647 0.98   1303  145 0.4945 0.5189      5.9254      5.9841|
| 13:  2.0647 -  2.0105 0.85   1124  131 0.5144 0.4308      5.8604      5.8161|
| 14:  2.0105 -  1.9616 0.24    323   33 0.5621 0.5046      5.8212      5.7205|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9952 -  4.6827  1451   163  0.67  36.41   0.82     0.71      79925.52|
|  2:  4.6827 -  3.7357  1382   149  0.70  35.61   0.90     0.78     104179.16|
|  3:  3.7357 -  3.2691  1375   152  0.60  43.49   0.91     0.78     108335.23|
|  4:  3.2691 -  2.9727  1345   155  0.54  48.65   0.91     0.73      93087.36|
|  5:  2.9727 -  2.7610  1353   150  0.48  53.36   0.87     0.68      73977.26|
|  6:  2.7610 -  2.5991  1349   148  0.46  54.96   0.89     0.65      61687.05|
|  7:  2.5991 -  2.4696  1348   145  0.45  55.84   0.92     0.61      56759.25|
|  8:  2.4696 -  2.3625  1305   145  0.39  61.03   0.88     0.57      56261.33|
|  9:  2.3625 -  2.2719  1336   148  0.37  61.96   0.91     0.55      52311.85|
| 10:  2.2719 -  2.1937  1315   151  0.36  62.98   0.96     0.54      50202.93|
| 11:  2.1937 -  2.1253  1321   144  0.35  63.85   0.92     0.52      45361.80|
| 12:  2.1253 -  2.0647  1303   145  0.32  66.16   0.95     0.51      42960.99|
| 13:  2.0647 -  2.0105  1124   131  0.34  64.58   0.94     0.53      35164.43|
| 14:  2.0105 -  1.9616   323    33  0.38  61.27   0.88     0.59      28289.42|
|alpha:            min =        0.51 max =            0.78 mean =         0.63|
|beta:             min =    28289.42 max =       108335.23 mean =     66240.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.28|
|phase err.(test): min =        0.00 max =           89.74 mean =        54.39|
|-----------------------------------------------------------------------------|

============================== 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 = 16.039106             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.530   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.546804              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.116   (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 |  1.385 -  1.736:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.736 -  2.088:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.088 -  2.439:       31 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.439 -  2.791:      644 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.791 -  3.142:     2127 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.142 -  3.494:     2331 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.494 -  3.845:     4534 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.845 -  4.197:     4777 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.197 -  4.548:     6240 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.548 -  4.900:     7534 |
|-----------------------------------------------------------------------------|
|-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 |        0.191 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.385 |       0.585 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.968)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4639   r_free= 0.4513   ksol= 0.00   Bsol= 0.00   scale= 0.889    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.279257                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4539   r_free= 0.4388   ksol= 0.29   Bsol= 20.00   scale= 0.929   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,4.50,0.81,0.00,0.00,0.00); trace/3= 0.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.271244                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.687482             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.183   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.188987              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.970   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4539      final r-factor (work) = 0.3511          |
| start r-factor (free) = 0.4388      final r-factor (free) = 0.3922          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0995 = 13.69 * 0.50 * 6.2698 + 1.00 * 0.1906                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.2063 = 13.69 * 0.50 * 6.1433 + 1.00 * 0.1634                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3511      final r-factor (work) = 0.3240          |
| start r-factor (free) = 0.3922      final r-factor (free) = 0.3957          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3108 = 1.19 * 1.00 * 6.1433 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2540 = 1.19 * 1.00 * 6.0571 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.968)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.60  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    122.60  17.62    None  None   None       |
|    Sol.    : 438    0      0.00    68.97   36.54    None  None   None       |
|    Mac.    : 2385   0      0.00    122.60  14.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.260: 1184   |   5:    61.302 -  73.562:    7        |
|      1:    12.260 -  24.521:  969   |   6:    73.562 -  85.822:    1        |
|      2:    24.521 -  36.781:  382   |   7:    85.822 -  98.083:    0        |
|      3:    36.781 -  49.041:  193   |   8:    98.083 - 110.343:    0        |
|      4:    49.041 -  61.302:   86   |   9:   110.343 - 122.604:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3240 r_free = 0.3957             target_work(ml) = 6.061         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3238 r_free = 0.3955             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3238   r_free= 0.3955   ksol= 0.29   Bsol= 20.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,4.50,0.81,0.00,0.00,0.00); trace/3= 0.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.059526                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3225   r_free= 0.3914   ksol= 0.32   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,2.57,-0.11,0.00,-0.00,-0.00); trace/3= 0.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.059228                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.540233             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.920  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.851005              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.026   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3225      final r-factor (work) = 0.2489          |
| start r-factor (free) = 0.3914      final r-factor (free) = 0.3013          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.1188 = 11.54 * 0.50 * 6.0580 + 1.00 * 0.1634                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.5294 = 11.54 * 0.50 * 5.9655 + 1.00 * 0.1080                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2489      final r-factor (work) = 0.2237          |
| start r-factor (free) = 0.3013      final r-factor (free) = 0.2960          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0685 = 1.85 * 1.00 * 5.9655 + 1.00 * 0.0264                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7191 = 1.85 * 1.00 * 5.7803 + 1.00 * 0.0198                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.968)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.62  19.11    None  None   None       |
|    all(noH): 2823   0      0.00    105.62  19.11    None  None   None       |
|    Sol.    : 438    0      2.37    105.62  44.34    None  None   None       |
|    Mac.    : 2385   0      0.00    104.47  14.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.562: 1131   |   5:    52.808 -  63.370:   86        |
|      1:    10.562 -  21.123:  887   |   6:    63.370 -  73.931:   57        |
|      2:    21.123 -  31.685:  313   |   7:    73.931 -  84.493:   34        |
|      3:    31.685 -  42.247:  166   |   8:    84.493 -  95.055:   19        |
|      4:    42.247 -  52.808:  121   |   9:    95.055 - 105.616:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2237 r_free = 0.2960             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2235 r_free = 0.2962             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2235   r_free= 0.2962   ksol= 0.32   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,2.57,-0.11,0.00,-0.00,-0.00); trace/3= 0.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.774887                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2232   r_free= 0.2953   ksol= 0.32   Bsol= 58.86   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,1.27,-0.40,0.00,-0.00,-0.00); trace/3= -0.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.771733                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.465868              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.825  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.191948              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.019  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2232      final r-factor (work) = 0.1790          |
| start r-factor (free) = 0.2953      final r-factor (free) = 0.2377          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9040 = 5.47 * 0.50 * 5.7799 + 1.00 * 0.1080                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6240 = 5.47 * 0.50 * 5.6904 + 1.00 * 0.0726                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1790      final r-factor (work) = 0.1683          |
| start r-factor (free) = 0.2377      final r-factor (free) = 0.2124          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1119 = 0.19 * 1.00 * 5.6904 + 1.00 * 0.0197                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0726 = 0.19 * 1.00 * 5.5370 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.968)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.61   17.54    None  None   None       |
|    all(noH): 2823   0      0.00    99.61   17.54    None  None   None       |
|    Sol.    : 438    0      5.50    96.84   41.64    None  None   None       |
|    Mac.    : 2385   0      0.00    99.61   13.11    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 -   9.961: 1180   |   5:    49.803 -  59.764:   84        |
|      1:     9.961 -  19.921:  939   |   6:    59.764 -  69.724:   47        |
|      2:    19.921 -  29.882:  256   |   7:    69.724 -  79.685:   20        |
|      3:    29.882 -  39.843:  140   |   8:    79.685 -  89.646:   16        |
|      4:    39.843 -  49.803:  132   |   9:    89.646 -  99.606:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1683 r_free = 0.2124             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1680 r_free = 0.2124             target_work(ml) = 5.483         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1680   r_free= 0.2124   ksol= 0.32   Bsol= 58.86   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,1.27,-0.40,0.00,-0.00,-0.00); trace/3= -0.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.483445                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1679   r_free= 0.2113   ksol= 0.32   Bsol= 59.84   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-0.07,-1.12,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.484723                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.059902              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.503  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.675741              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.105  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1679      final r-factor (work) = 0.1443          |
| start r-factor (free) = 0.2113      final r-factor (free) = 0.1875          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7787 = 2.06 * 0.50 * 5.5401 + 1.00 * 0.0726                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6380 = 2.06 * 0.50 * 5.4174 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1443      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.1875      final r-factor (free) = 0.1857          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0880 = 1.68 * 1.00 * 5.4174 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9405 = 1.68 * 1.00 * 5.3273 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.968)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.97  17.97    None  None   None       |
|    all(noH): 2823   0      0.00    110.97  17.97    None  None   None       |
|    Sol.    : 438    0      1.21    108.47  46.09    None  None   None       |
|    Mac.    : 2385   0      0.00    110.97  12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.097: 1377   |   5:    55.487 -  66.584:   82        |
|      1:    11.097 -  22.195:  864   |   6:    66.584 -  77.682:   54        |
|      2:    22.195 -  33.292:  178   |   7:    77.682 -  88.779:   26        |
|      3:    33.292 -  44.390:  111   |   8:    88.779 -  99.877:   13        |
|      4:    44.390 -  55.487:  109   |   9:    99.877 - 110.974:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1358 r_free = 0.1857             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1358 r_free = 0.1856             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1856   ksol= 0.32   Bsol= 59.84   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-0.07,-1.12,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.320409                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1360   r_free= 0.1857   ksol= 0.33   Bsol= 64.24   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-0.49,-1.18,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.321686                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.513265              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.247  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.329375              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.977  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1360      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1857      final r-factor (free) = 0.1755          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7536 = 2.51 * 0.50 * 5.3279 + 1.00 * 0.0583                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6989 = 2.51 * 0.50 * 5.2811 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.1755      final r-factor (free) = 0.1728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7527 = 0.33 * 1.00 * 5.2811 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7491 = 0.33 * 1.00 * 5.2430 + 1.00 * 0.0222                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.968)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.71  17.80    None  None   None       |
|    all(noH): 2823   0      0.00    110.71  17.80    None  None   None       |
|    Sol.    : 438    0      3.51    108.11  45.56    None  None   None       |
|    Mac.    : 2385   0      0.00    110.71  12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.071: 1406   |   5:    55.353 -  66.424:   81        |
|      1:    11.071 -  22.141:  853   |   6:    66.424 -  77.494:   54        |
|      2:    22.141 -  33.212:  167   |   7:    77.494 -  88.565:   26        |
|      3:    33.212 -  44.283:  108   |   8:    88.565 -  99.636:   12        |
|      4:    44.283 -  55.353:  108   |   9:    99.636 - 110.706:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1234 r_free = 0.1728             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1233 r_free = 0.1727             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1727   ksol= 0.33   Bsol= 64.24   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-0.49,-1.18,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234278                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6827 0.99   1451  163 0.0966 0.1315      5.3837      5.5603|
|  2:  4.6827 -  3.7357 0.99   1382  149 0.0883 0.1131      5.4576      5.6761|
|  3:  3.7357 -  3.2691 0.99   1375  152 0.1154 0.1742      5.5424      5.9328|
|  4:  3.2691 -  2.9727 0.98   1345  155 0.1391 0.1739      5.5483      5.7075|
|  5:  2.9727 -  2.7610 0.99   1353  150 0.1512 0.1929      5.4314      5.5699|
|  6:  2.7610 -  2.5991 0.99   1349  148 0.1423 0.2135      5.3202       5.543|
|  7:  2.5991 -  2.4696 0.98   1348  145 0.1369 0.1901      5.2509      5.4645|
|  8:  2.4696 -  2.3625 0.98   1305  145 0.1388 0.1900      5.1731      5.3888|
|  9:  2.3625 -  2.2719 0.99   1336  148 0.1289 0.1845      5.0995      5.3192|
| 10:  2.2719 -  2.1937 0.99   1315  151 0.1253 0.1928      5.0524      5.3432|
| 11:  2.1937 -  2.1253 0.97   1321  144 0.1224 0.1936      4.9873      5.2656|
| 12:  2.1253 -  2.0647 0.98   1303  145 0.1268 0.1938      4.9386      5.2006|
| 13:  2.0647 -  2.0105 0.85   1124  131 0.1280 0.1793      4.8643      5.0568|
| 14:  2.0105 -  1.9616 0.24    323   33 0.1271 0.2123      4.7697      5.0947|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9952 -  4.6827  1451   163  0.94   9.58   0.97     0.94       7582.28|
|  2:  4.6827 -  3.7357  1382   149  0.95   8.72   1.01     1.00       9814.95|
|  3:  3.7357 -  3.2691  1375   152  0.92  12.74   1.03     1.02      11947.73|
|  4:  3.2691 -  2.9727  1345   155  0.90  15.99   1.02     0.99      12595.76|
|  5:  2.9727 -  2.7610  1353   150  0.88  18.74   1.00     0.99      10585.12|
|  6:  2.7610 -  2.5991  1349   148  0.88  18.17   0.99     0.96       8747.04|
|  7:  2.5991 -  2.4696  1348   145  0.89  17.63   0.99     0.96       7558.14|
|  8:  2.4696 -  2.3625  1305   145  0.88  18.26   1.00     0.96       6731.87|
|  9:  2.3625 -  2.2719  1336   148  0.89  17.59   0.99     0.96       5789.26|
| 10:  2.2719 -  2.1937  1315   151  0.89  17.31   0.99     0.95       5333.06|
| 11:  2.1937 -  2.1253  1321   144  0.89  17.68   0.99     0.95       4938.57|
| 12:  2.1253 -  2.0647  1303   145  0.89  17.37   0.98     0.96       4474.03|
| 13:  2.0647 -  2.0105  1124   131  0.88  18.35   0.99     0.98       3934.88|
| 14:  2.0105 -  1.9616   323    33  0.88  18.13   0.97     0.93       3232.16|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3232.16 max =        12595.76 mean =      7691.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.75 mean =        15.95|
|phase err.(test): min =        0.00 max =           89.72 mean =        15.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1726   ksol= 0.32   Bsol= 61.03   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-0.61,-1.09,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234207                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1726   ksol= 0.32   Bsol= 61.03   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-0.61,-1.09,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234207                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6827 0.99   1451  163 0.0966 0.1316      5.3839      5.5596|
|  2:  4.6827 -  3.7357 0.99   1382  149 0.0881 0.1128      5.4565      5.6736|
|  3:  3.7357 -  3.2691 0.99   1375  152 0.1154 0.1739      5.5417       5.933|
|  4:  3.2691 -  2.9727 0.98   1345  155 0.1392 0.1739      5.5485      5.7079|
|  5:  2.9727 -  2.7610 0.99   1353  150 0.1512 0.1926      5.4315      5.5692|
|  6:  2.7610 -  2.5991 0.99   1349  148 0.1424 0.2134      5.3202       5.543|
|  7:  2.5991 -  2.4696 0.98   1348  145 0.1370 0.1900      5.2509       5.464|
|  8:  2.4696 -  2.3625 0.98   1305  145 0.1387 0.1900      5.1733      5.3899|
|  9:  2.3625 -  2.2719 0.99   1336  148 0.1287 0.1847      5.0994      5.3199|
| 10:  2.2719 -  2.1937 0.99   1315  151 0.1253 0.1929      5.0529      5.3431|
| 11:  2.1937 -  2.1253 0.97   1321  144 0.1223 0.1934      4.9868      5.2648|
| 12:  2.1253 -  2.0647 0.98   1303  145 0.1269 0.1941      4.9389      5.2017|
| 13:  2.0647 -  2.0105 0.85   1124  131 0.1280 0.1790      4.8643      5.0549|
| 14:  2.0105 -  1.9616 0.24    323   33 0.1272 0.2125      4.7698      5.0952|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9952 -  4.6827  1451   163  0.94   9.59   0.97     0.94       7585.36|
|  2:  4.6827 -  3.7357  1382   149  0.95   8.71   1.01     1.00       9789.98|
|  3:  3.7357 -  3.2691  1375   152  0.92  12.71   1.03     1.02      11914.63|
|  4:  3.2691 -  2.9727  1345   155  0.90  15.99   1.02     0.99      12596.49|
|  5:  2.9727 -  2.7610  1353   150  0.88  18.72   1.00     0.99      10573.38|
|  6:  2.7610 -  2.5991  1349   148  0.88  18.16   0.99     0.96       8736.98|
|  7:  2.5991 -  2.4696  1348   145  0.89  17.62   0.99     0.96       7552.84|
|  8:  2.4696 -  2.3625  1305   145  0.88  18.27   1.00     0.96       6736.27|
|  9:  2.3625 -  2.2719  1336   148  0.89  17.60   0.99     0.96       5800.78|
| 10:  2.2719 -  2.1937  1315   151  0.89  17.32   0.99     0.95       5337.68|
| 11:  2.1937 -  2.1253  1321   144  0.89  17.68   0.99     0.96       4938.78|
| 12:  2.1253 -  2.0647  1303   145  0.89  17.37   0.98     0.96       4474.71|
| 13:  2.0647 -  2.0105  1124   131  0.88  18.35   0.99     0.99       3932.25|
| 14:  2.0105 -  1.9616   323    33  0.88  18.13   0.97     0.94       3226.47|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3226.47 max =        12596.49 mean =      7686.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.73 mean =        15.94|
|phase err.(test): min =        0.00 max =           89.63 mean =        15.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.968)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.71  17.80    None  None   None       |
|    all(noH): 2823   0      0.00    110.71  17.80    None  None   None       |
|    Sol.    : 438    0      3.51    108.11  45.56    None  None   None       |
|    Mac.    : 2385   0      0.00    110.71  12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.074: 1406   |   5:    55.356 -  66.427:   81        |
|      1:    11.074 -  22.144:  853   |   6:    66.427 -  77.497:   54        |
|      2:    22.144 -  33.215:  167   |   7:    77.497 -  88.568:   26        |
|      3:    33.215 -  44.285:  108   |   8:    88.568 -  99.638:   12        |
|      4:    44.285 -  55.356:  108   |   9:    99.638 - 110.709:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.563 - 5.548
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 338
   mapped sites are within: 0.726 - 5.548

peak=    6.941 closest distance to " O   HOH Z 120 " =    1.014
peak=    5.959 closest distance to " O   HOH Z 210 " =    1.442
peak=    5.872 closest distance to " NH2 ARG A  56 " =    2.371
peak=    5.716 closest distance to " CB  SER A  63 " =    1.266
peak=    5.272 closest distance to " O   HOH Z 350 " =    0.801
peak=    5.112 closest distance to " CG  PRO A  54 " =    1.207
peak=    5.020 closest distance to " O   HOH Z 134 " =    2.078
peak=    4.962 closest distance to " O   HOH Z 132 " =    1.585
peak=    4.951 closest distance to " O   PRO A 198 " =    1.593
peak=    4.930 closest distance to " O   HOH Z 422 " =    0.886
peak=    4.895 closest distance to " O   HOH Z 433 " =    1.957
peak=    4.813 closest distance to " O   HOH Z  15 " =    2.135
peak=    4.792 closest distance to " O   HOH Z 142 " =    1.685
peak=    4.785 closest distance to " O   HOH Z 126 " =    1.849
peak=    4.748 closest distance to " CA  TYR A  30 " =    0.974
peak=    4.704 closest distance to " CB  GLN A 223 " =    1.401
peak=    4.668 closest distance to " O   HOH Z 124 " =    1.444
peak=    4.662 closest distance to " O   HOH Z  80 " =    2.118
peak=    4.657 closest distance to " O   HOH Z 352 " =    1.309
peak=    4.640 closest distance to " O   HOH Z 389 " =    2.057
peak=    4.609 closest distance to " CG  PRO A 213 " =    1.345
peak=    4.606 closest distance to " O   HOH Z   7 " =    0.965
peak=    4.557 closest distance to " O   HOH Z 133 " =    1.860
peak=    4.552 closest distance to " O   HOH Z 247 " =    1.438
peak=    4.543 closest distance to " CG  PRO A 198 " =    1.295
peak=    4.524 closest distance to " O   HOH Z 196 " =    2.111
peak=    4.495 closest distance to " O   HOH Z  44 " =    2.403
peak=    4.482 closest distance to " O   HOH Z  47 " =    1.742
peak=    4.437 closest distance to " CG  PRO A 280 " =    0.798
peak=    4.416 closest distance to " CG  PRO A  90 " =    1.224
peak=    4.390 closest distance to " CB  ARG A 275 " =    0.910
peak=    4.337 closest distance to " O   HOH Z  61 " =    1.568
peak=    4.335 closest distance to " O   HOH Z 163 " =    1.730
peak=    4.335 closest distance to " O   HOH Z 250 " =    2.355
peak=    4.333 closest distance to " CB  PRO A  54 " =    0.800
peak=    4.303 closest distance to " CG  GLN A  77 " =    0.726
peak=    4.296 closest distance to " CB  GLN A 183 " =    1.282
peak=    4.263 closest distance to " O   HOH Z 357 " =    2.078
peak=    4.251 closest distance to " O   HOH Z 234 " =    3.769
peak=    4.218 closest distance to " O   HOH Z 271 " =    1.325
peak=    4.218 closest distance to " CB  LEU A 228 " =    1.166
peak=    4.214 closest distance to " O   HOH Z  20 " =    1.828
peak=    4.213 closest distance to " O   HOH Z  43 " =    1.869
peak=    4.206 closest distance to " O   HOH Z 369 " =    2.173
peak=    4.205 closest distance to " CB  SER A 141 " =    1.039
peak=    4.203 closest distance to " CB  TRP A 179 " =    1.330
peak=    4.169 closest distance to " O   HOH Z  97 " =    1.917
peak=    4.158 closest distance to " NE2 GLN A  11 " =    1.099
peak=    4.154 closest distance to " CB  GLU A 128 " =    1.126
peak=    4.127 closest distance to " CB  ARG A 190 " =    1.722
peak=    4.118 closest distance to " CG2BVAL A  41 " =    0.990
peak=    4.107 closest distance to " CG  ARG A  66 " =    2.681
peak=    4.097 closest distance to " O   HOH Z  39 " =    2.075
peak=    4.093 closest distance to " O   HOH Z 203 " =    1.797
peak=    4.090 closest distance to " O   HOH Z 394 " =    1.584
peak=    4.064 closest distance to " O   HOH Z  47 " =    1.505
peak=    4.059 closest distance to " CB  VAL A 202 " =    1.537
peak=    4.052 closest distance to " O   HOH Z 431 " =    1.198
peak=    4.050 closest distance to " O   HOH Z 118 " =    1.847
peak=    4.002 closest distance to " O   HOH Z 428 " =    1.159
peak=    3.999 closest distance to " CB  ASN A 148 " =    1.296
peak=    3.991 closest distance to " O   HOH Z 412 " =    3.086
peak=    3.988 closest distance to " O   HOH Z  67 " =    1.910
peak=    3.988 closest distance to " CG2 THR A 221 " =    1.147
peak=    3.986 closest distance to " O   HOH Z 298 " =    1.941
peak=    3.970 closest distance to " O   HOH Z 154 " =    1.483
peak=    3.966 closest distance to " CB  SER A   3 " =    1.324
peak=    3.964 closest distance to " O   HOH Z 214 " =    1.150
peak=    3.960 closest distance to " O   HOH Z 271 " =    2.108
peak=    3.954 closest distance to " O   HOH Z  39 " =    1.834
peak=    3.950 closest distance to " O   HOH Z 371 " =    3.238
peak=    3.941 closest distance to " CE  LYS A 119 " =    1.106
peak=    3.940 closest distance to " O   HOH Z 406 " =    1.414
peak=    3.940 closest distance to " OE1 GLN A  11 " =    1.936
peak=    3.931 closest distance to " O   HOH Z  78 " =    2.180
peak=    3.920 closest distance to " O   HOH Z 132 " =    2.395
peak=    3.916 closest distance to " O   HOH Z 272 " =    1.163
peak=    3.883 closest distance to " O   SER A  87 " =    2.260
peak=    3.880 closest distance to " CB  ARG A  79 " =    1.370
peak=    3.877 closest distance to " O   HOH Z 363 " =    1.025
peak=    3.877 closest distance to " CB  SER A  62 " =    0.863
peak=    3.862 closest distance to " OG  SER A  62 " =    3.085
peak=    3.858 closest distance to " O   HOH Z 437 " =    1.984
peak=    3.840 closest distance to " O   HOH Z 189 " =    2.117
peak=    3.834 closest distance to " O   HOH Z 402 " =    1.643
peak=    3.831 closest distance to " O   HOH Z 221 " =    1.080
peak=    3.797 closest distance to " CG1 ILE A  33 " =    1.244
peak=    3.757 closest distance to " O   HOH Z  44 " =    1.850
peak=    3.757 closest distance to " C   SER A  32 " =    1.142
peak=    3.755 closest distance to " O   HOH Z 361 " =    3.404
peak=    3.755 closest distance to " O   HOH Z 236 " =    0.916
peak=    3.750 closest distance to " CA  ASN A 176 " =    1.479
peak=    3.748 closest distance to " CA  ALA A  21 " =    1.343
peak=    3.747 closest distance to " CB  GLN A  58 " =    0.911
peak=    3.746 closest distance to " NZ  LYS A 117 " =    3.215
peak=    3.745 closest distance to " O   HOH Z  88 " =    3.733
peak=    3.738 closest distance to " O   HOH Z 336 " =    1.601
peak=    3.734 closest distance to " O   HOH Z 193 " =    1.815
peak=    3.734 closest distance to " O   HOH Z 279 " =    2.259
peak=    3.732 closest distance to " O   GLY A  23 " =    2.441
peak=    3.724 closest distance to " O   HOH Z 174 " =    2.181
peak=    3.721 closest distance to " CB  TYR A 169 " =    0.867
peak=    3.718 closest distance to " CA  GLY A 196 " =    1.108
peak=    3.717 closest distance to " CD2 LEU A 297 " =    1.016
peak=    3.709 closest distance to " O   HOH Z 102 " =    1.226
peak=    3.706 closest distance to " CG2 VAL A 197 " =    1.240
peak=    3.703 closest distance to " O   HOH Z 130 " =    1.215
peak=    3.693 closest distance to " O   ALA A 165 " =    1.296
peak=    3.669 closest distance to " O   HOH Z 154 " =    2.338
peak=    3.668 closest distance to " O   HOH Z 326 " =    1.469
peak=    3.667 closest distance to " O   HOH Z 377 " =    1.253
peak=    3.665 closest distance to " O   HOH Z 408 " =    1.820
peak=    3.663 closest distance to " O   HOH Z 109 " =    2.132
peak=    3.654 closest distance to " N   ASN A  39 " =    1.324
peak=    3.648 closest distance to " O   HOH Z 142 " =    1.886
peak=    3.646 closest distance to " CB  GLU A 152 " =    1.080
peak=    3.644 closest distance to " CG1 ILE A 120 " =    1.104
peak=    3.640 closest distance to " CB  PRO A  54 " =    1.326
peak=    3.639 closest distance to " CB  ALA A 100 " =    1.474
peak=    3.635 closest distance to " O   HOH Z 132 " =    1.688
peak=    3.628 closest distance to " O   HOH Z 301 " =    1.491
peak=    3.624 closest distance to " CD  LYS A 166 " =    1.425
peak=    3.623 closest distance to " O   HOH Z 344 " =    3.113
peak=    3.620 closest distance to " CH2 TRP A 274 " =    1.935
peak=    3.619 closest distance to " O   HOH Z 316 " =    2.994
peak=    3.615 closest distance to " CD  ARG A 269 " =    0.959
peak=    3.610 closest distance to " O   HOH Z  30 " =    1.815
peak=    3.608 closest distance to " CA  GLU A 152 " =    0.955
peak=    3.600 closest distance to " CA  ASP A 191 " =    0.840
peak=    3.599 closest distance to " O   HOH Z  22 " =    2.531
peak=    3.598 closest distance to " O   HOH Z 150 " =    1.743
peak=    3.598 closest distance to " SD AMET A  47 " =    1.477
peak=    3.598 closest distance to " CD  ARG A 195 " =    1.119
peak=    3.593 closest distance to " O   HOH Z 128 " =    2.211
peak=    3.583 closest distance to " CA  VAL A 125 " =    1.181
peak=    3.577 closest distance to " CG2 VAL A  78 " =    0.970
peak=    3.573 closest distance to " O   HOH Z 245 " =    1.328
peak=    3.572 closest distance to " O   HOH Z 418 " =    1.582
peak=    3.561 closest distance to " CB  PHE A 283 " =    0.964
peak=    3.551 closest distance to " CA  ARG A 195 " =    1.109
peak=    3.551 closest distance to " CD1 LEU A 300 " =    1.235
peak=    3.542 closest distance to " O   GLY A 211 " =    1.317
peak=    3.536 closest distance to " O   HOH Z 345 " =    1.689
peak=    3.536 closest distance to " NE2 HIS A 115 " =    0.972
peak=    3.534 closest distance to " O   HOH Z 345 " =    2.726
peak=    3.533 closest distance to " OG1 THR A 294 " =    2.444
peak=    3.532 closest distance to " O   HOH Z 374 " =    2.551
peak=    3.529 closest distance to " CB  ASN A 285 " =    0.870
peak=    3.526 closest distance to " CA  ARG A  36 " =    1.101
peak=    3.526 closest distance to " NH2AARG A 145 " =    2.187
peak=    3.526 closest distance to " O   HOH Z 195 " =    1.357
peak=    3.522 closest distance to " O   HOH Z 358 " =    1.330
peak=    3.522 closest distance to " O   HOH Z 358 " =    2.032
peak=    3.518 closest distance to " O   HOH Z 284 " =    2.889
peak=    3.515 closest distance to " CA  ALA A 158 " =    1.093
peak=    3.511 closest distance to " CA  LEU A  83 " =    1.444
peak=    3.506 closest distance to " CB  GLU A 277 " =    3.722
peak=    3.505 closest distance to " O   HOH Z 141 " =    1.658
peak=    3.504 closest distance to " CB  PHE A  16 " =    1.375
peak=    3.503 closest distance to " O   THR A 251 " =    1.277
peak=    3.502 closest distance to " CD2 LEU A 255 " =    1.209
peak=    3.490 closest distance to " O   HOH Z  63 " =    2.199
peak=    3.482 closest distance to " CB  MET A 105 " =    1.129
peak=    3.482 closest distance to " OH  TYR A  30 " =    1.451
peak=    3.481 closest distance to " OD1 ASN A  69 " =    2.372
peak=    3.480 closest distance to " CD  LYS A 119 " =    1.244
peak=    3.476 closest distance to " O   HOH Z  11 " =    1.304
peak=    3.476 closest distance to " O   HOH Z 128 " =    2.123
peak=    3.474 closest distance to " C   ILE A 106 " =    1.830
peak=    3.461 closest distance to " O   HOH Z  66 " =    2.208
peak=    3.460 closest distance to " CZ3 TRP A  85 " =    0.988
peak=    3.458 closest distance to " CG  ARG A  66 " =    0.963
peak=    3.454 closest distance to " O   ASP A 124 " =    1.681
peak=    3.447 closest distance to " O   HOH Z 250 " =    1.456
peak=    3.447 closest distance to " CA  THR A 221 " =    1.537
peak=    3.443 closest distance to " O   HOH Z 339 " =    1.328
peak=    3.440 closest distance to " NH1 ARG A 269 " =    0.772
peak=    3.439 closest distance to " O   HOH Z 438 " =    2.550
peak=    3.438 closest distance to " CD1 TRP A 266 " =    1.227
peak=    3.437 closest distance to " CA  ALA A 295 " =    1.083
peak=    3.436 closest distance to " CB  TRP A 266 " =    0.955
peak=    3.435 closest distance to " CB  TRP A 179 " =    1.957
peak=    3.434 closest distance to " CD BLYS A 290 " =    1.009
peak=    3.432 closest distance to " O   HOH Z 404 " =    1.467
peak=    3.432 closest distance to " OG BSER A 164 " =    2.427
peak=    3.429 closest distance to " CB  TYR A 116 " =    1.321
peak=    3.428 closest distance to " CA  LYS A 166 " =    1.341
peak=    3.423 closest distance to " O   HOH Z 207 " =    2.506
peak=    3.423 closest distance to " CG2 THR A 220 " =    0.777
peak=    3.422 closest distance to " O   HOH Z 423 " =    1.895
peak=    3.418 closest distance to " O   HOH Z 289 " =    1.639
peak=    3.416 closest distance to " CB  ALA A  71 " =    1.289
peak=    3.414 closest distance to " CB  ASP A 140 " =    0.762
peak=    3.414 closest distance to " O   GLY A  91 " =    1.237
peak=    3.411 closest distance to " CA  ALA A 160 " =    0.936
peak=    3.411 closest distance to " CA  ALA A  51 " =    0.955
peak=    3.408 closest distance to " O   HOH Z 380 " =    1.884
peak=    3.406 closest distance to " OG  SER A 245 " =    1.501
peak=    3.401 closest distance to " O   HOH Z 162 " =    2.000
peak=    3.400 closest distance to " O   ASN A  74 " =    1.729
peak=    3.396 closest distance to " O   HOH Z 402 " =    2.903
peak=    3.384 closest distance to " O   HOH Z 108 " =    1.147
peak=    3.380 closest distance to " CB  MET A  47 " =    1.043
peak=    3.373 closest distance to " NZ  LYS A 119 " =    1.665
peak=    3.371 closest distance to " CA  ASP A 124 " =    0.774
peak=    3.370 closest distance to " CB  PRO A 198 " =    0.920
peak=    3.368 closest distance to " O   HOH Z  38 " =    3.584
peak=    3.366 closest distance to " CB  GLN A 194 " =    0.906
peak=    3.365 closest distance to " O   HOH Z 403 " =    1.819
peak=    3.361 closest distance to " CA  VAL A  41 " =    0.860
peak=    3.360 closest distance to " CD2 TRP A 179 " =    1.318
peak=    3.354 closest distance to " CG1 VAL A 153 " =    1.156
peak=    3.353 closest distance to " CG  PRO A 243 " =    1.252
peak=    3.352 closest distance to " O   HOH Z 263 " =    2.112
peak=    3.346 closest distance to " NH2BARG A 145 " =    2.008
peak=    3.345 closest distance to " O   HOH Z 409 " =    3.187
peak=    3.343 closest distance to " O   HOH Z 261 " =    1.764
peak=    3.338 closest distance to " ND1 HIS A  81 " =    1.465
peak=    3.333 closest distance to " C   GLY A  80 " =    1.181
peak=    3.333 closest distance to " O   HOH Z 128 " =    1.640
peak=    3.330 closest distance to " O   HOH Z 227 " =    1.883
peak=    3.329 closest distance to " OG BSER A 210 " =    0.950
peak=    3.326 closest distance to " NZ  LYS A 117 " =    0.758
peak=    3.325 closest distance to " CA  GLU A  46 " =    0.789
peak=    3.324 closest distance to " O   HOH Z 142 " =    1.377
peak=    3.320 closest distance to " CB  GLN A  73 " =    0.947
peak=    3.318 closest distance to " OD1 ASP A 238 " =    0.887
peak=    3.318 closest distance to " O   HOH Z 426 " =    1.464
peak=    3.318 closest distance to " CD  ARG A 159 " =    0.856
peak=    3.317 closest distance to " O   HOH Z 214 " =    1.823
peak=    3.317 closest distance to " O   HOH Z 287 " =    1.784
peak=    3.316 closest distance to " O   HOH Z 155 " =    2.991
peak=    3.311 closest distance to " CG  GLN A  11 " =    1.301
peak=    3.309 closest distance to " CA  ASN A 127 " =    1.145
peak=    3.308 closest distance to " OD2 ASP A 286 " =    2.825
peak=    3.303 closest distance to " CA  ARG A  66 " =    1.111
peak=    3.301 closest distance to " CD  PRO A  54 " =    1.132
peak=    3.300 closest distance to " O   HOH Z  59 " =    1.872
peak=    3.300 closest distance to " CB  ARG A 139 " =    0.856
peak=    3.297 closest distance to " OG  SER A  97 " =    3.419
peak=    3.291 closest distance to " O   HOH Z 272 " =    1.875
peak=    3.290 closest distance to " O   HOH Z 139 " =    4.254
peak=    3.290 closest distance to " O   HOH Z 112 " =    1.572
peak=    3.289 closest distance to " O   SER A  26 " =    1.689
peak=    3.279 closest distance to " NH2 ARG A 156 " =    1.250
peak=    3.277 closest distance to " O   HOH Z 166 " =    1.602
peak=    3.277 closest distance to " CA  PRO A  90 " =    0.937
peak=    3.275 closest distance to " O   HOH Z 261 " =    1.713
peak=    3.274 closest distance to " CA  VAL A 197 " =    1.022
peak=    3.274 closest distance to " O   HOH Z 427 " =    3.340
peak=    3.271 closest distance to " O   HOH Z 425 " =    1.403
peak=    3.270 closest distance to " O   HOH Z 425 " =    2.233
peak=    3.269 closest distance to " O   HOH Z 417 " =    3.105
peak=    3.267 closest distance to " O   HOH Z 123 " =    2.118
peak=    3.259 closest distance to " O   HOH Z 136 " =    1.242
peak=    3.257 closest distance to " CG1 ILE A  49 " =    1.555
peak=    3.257 closest distance to " CG2 ILE A  20 " =    1.357
peak=    3.250 closest distance to " CB  GLN A  88 " =    1.158
peak=    3.249 closest distance to " O   HOH Z 208 " =    1.674
peak=    3.241 closest distance to " O   HOH Z 155 " =    1.346
peak=    3.241 closest distance to " O   HOH Z 255 " =    1.770
peak=    3.240 closest distance to " O   HOH Z 426 " =    3.294
peak=    3.233 closest distance to " O   HOH Z 189 " =    2.916
peak=    3.232 closest distance to " CB  THR A 157 " =    1.226
peak=    3.230 closest distance to " O   HOH Z  50 " =    3.390
peak=    3.229 closest distance to " O   HOH Z 280 " =    2.349
peak=    3.224 closest distance to " O   HOH Z 260 " =    1.361
peak=    3.224 closest distance to " CA  GLN A 223 " =    0.840
peak=    3.223 closest distance to " O   HOH Z  88 " =    1.653
peak=    3.223 closest distance to " O   HOH Z  48 " =    1.997
peak=    3.210 closest distance to " ND2 ASN A 187 " =    1.534
peak=    3.206 closest distance to " O   HOH Z 353 " =    2.666
peak=    3.205 closest distance to " O   HOH Z 334 " =    1.663
peak=    3.203 closest distance to " O   HOH Z  48 " =    2.958
peak=    3.202 closest distance to " CE3 TRP A 274 " =    3.527
peak=    3.201 closest distance to " O   HOH Z 147 " =    1.710
peak=    3.200 closest distance to " O   HOH Z  49 " =    1.838
peak=    3.197 closest distance to " O   HOH Z 367 " =    3.082
peak=    3.191 closest distance to " O   HOH Z 373 " =    1.569
peak=    3.190 closest distance to " O   HOH Z 124 " =    3.153
peak=    3.189 closest distance to " O   HOH Z  49 " =    1.048
peak=    3.186 closest distance to " CB  PRO A  90 " =    1.065
peak=    3.185 closest distance to " O   HOH Z 234 " =    4.164
peak=    3.185 closest distance to " O   HOH Z 386 " =    2.278
peak=    3.183 closest distance to " O   HOH Z 291 " =    1.523
peak=    3.183 closest distance to " O   HOH Z 238 " =    5.548
peak=    3.176 closest distance to " O   HOH Z 365 " =    2.796
peak=    3.175 closest distance to " NH2BARG A 102 " =    0.984
peak=    3.174 closest distance to " CD1 TRP A 274 " =    1.001
peak=    3.171 closest distance to " N   TYR A 116 " =    1.846
peak=    3.169 closest distance to " CD1 LEU A  96 " =    0.771
peak=    3.167 closest distance to " CB  VAL A 265 " =    1.356
peak=    3.167 closest distance to " CA  ALA A 100 " =    1.212
peak=    3.162 closest distance to " O   HOH Z 265 " =    2.277
peak=    3.162 closest distance to " O   HOH Z 435 " =    1.706
peak=    3.162 closest distance to " O   HOH Z 327 " =    3.245
peak=    3.156 closest distance to " CB  ALA A 256 " =    1.004
peak=    3.156 closest distance to " CA  GLY A 211 " =    1.128
peak=    3.153 closest distance to " CD1 LEU A 222 " =    0.779
peak=    3.151 closest distance to " O   HOH Z  39 " =    3.028
peak=    3.150 closest distance to " CA  THR A 221 " =    0.944
peak=    3.149 closest distance to " O   HOH Z 156 " =    2.555
peak=    3.139 closest distance to " CA  LEU A 282 " =    1.095
peak=    3.138 closest distance to " CB  ILE A 199 " =    1.027
peak=    3.137 closest distance to " CD AARG A 275 " =    1.303
peak=    3.137 closest distance to " CA  ASP A 162 " =    1.271
peak=    3.127 closest distance to " CG2 THR A  42 " =    0.906
peak=    3.127 closest distance to " O   HOH Z 162 " =    2.242
peak=    3.126 closest distance to " OD1 ASN A  60 " =    1.537
peak=    3.124 closest distance to " O   HOH Z 146 " =    1.056
peak=    3.123 closest distance to " O   HOH Z 368 " =    2.613
peak=    3.121 closest distance to " O  BHOH Z 338 " =    2.203
peak=    3.121 closest distance to " CA  TRP A 150 " =    0.909
peak=    3.118 closest distance to " O   HOH Z 403 " =    1.383
peak=    3.109 closest distance to " N   TYR A 247 " =    1.159
peak=    3.108 closest distance to " OD2 ASP A 298 " =    4.108
peak=    3.106 closest distance to " O   HOH Z 419 " =    1.601
peak=    3.103 closest distance to " O   HOH Z 432 " =    1.995
peak=    3.100 closest distance to " CB  ASN A 148 " =    1.990
peak=    3.097 closest distance to " CB  THR A  31 " =    1.852
peak=    3.088 closest distance to " O   HOH Z 287 " =    1.966
peak=    3.086 closest distance to " OE1 GLN A  73 " =    1.248
peak=    3.083 closest distance to " CG  LEU A 167 " =    1.093
peak=    3.082 closest distance to " O   HOH Z 427 " =    0.940
peak=    3.075 closest distance to " O   HOH Z   1 " =    3.147
peak=    3.071 closest distance to " NH1 ARG A  14 " =    1.274
peak=    3.069 closest distance to " O   HOH Z 192 " =    1.448
peak=    3.062 closest distance to " CA  THR A 246 " =    1.089
peak=    3.061 closest distance to " CG2 ILE A 151 " =    0.899
peak=    3.040 closest distance to " O   HOH Z 126 " =    2.039
peak=    3.031 closest distance to " O   HOH Z   6 " =    2.004
peak=    3.010 closest distance to " CB  ALA A 248 " =    1.457

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 229         
Filter by distance & map next to the model:
   mapped sites are within: 0.834 - 5.342
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 229 from: 229
   mapped sites are within: 0.834 - 5.342

peak=   -4.471 closest distance to " OG  SER A  97 " =    2.226
peak=   -4.350 closest distance to " O   HOH Z 155 " =    1.472
peak=   -4.186 closest distance to " O   HOH Z 266 " =    4.547
peak=   -4.156 closest distance to " CA  SER A 164 " =    2.166
peak=   -4.152 closest distance to " NH2 ARG A  66 " =    1.089
peak=   -4.117 closest distance to " O   HOH Z 196 " =    1.647
peak=   -4.075 closest distance to " CA  GLY A 203 " =    2.269
peak=   -4.041 closest distance to " CG2BVAL A  41 " =    2.477
peak=   -4.036 closest distance to " O   PRO A 198 " =    1.333
peak=   -4.023 closest distance to " CB  LEU A 167 " =    2.113
peak=   -4.001 closest distance to " CA  VAL A 197 " =    0.963
peak=   -3.950 closest distance to " N   ALA A  43 " =    2.679
peak=   -3.941 closest distance to " CD1 PHE A  59 " =    1.910
peak=   -3.908 closest distance to " CB  SER A 146 " =    2.174
peak=   -3.905 closest distance to " OXT GLY A 302 " =    2.743
peak=   -3.896 closest distance to " OG ASER A 134 " =    1.192
peak=   -3.866 closest distance to " O   HOH Z 290 " =    0.928
peak=   -3.864 closest distance to " CA  SER A 276 " =    1.429
peak=   -3.853 closest distance to " O   HOH Z 221 " =    1.349
peak=   -3.840 closest distance to " O   ALA A   1 " =    2.094
peak=   -3.823 closest distance to " ND2 ASN A 187 " =    1.611
peak=   -3.816 closest distance to " CA  VAL A  67 " =    2.948
peak=   -3.815 closest distance to " C   HIS A 108 " =    1.070
peak=   -3.793 closest distance to " CD2 LEU A 300 " =    2.796
peak=   -3.789 closest distance to " NE2 GLN A 223 " =    1.121
peak=   -3.767 closest distance to " CG  PRO A 243 " =    1.599
peak=   -3.749 closest distance to " C   ASN A 285 " =    2.446
peak=   -3.744 closest distance to " SG  CYS A 254 " =    3.336
peak=   -3.717 closest distance to " OG BSER A 210 " =    2.248
peak=   -3.712 closest distance to " O   HOH Z  86 " =    2.580
peak=   -3.710 closest distance to " O   HOH Z  52 " =    1.918
peak=   -3.704 closest distance to " O   HOH Z 165 " =    2.070
peak=   -3.699 closest distance to " CD2 LEU A 237 " =    2.509
peak=   -3.689 closest distance to " OD2 ASP A 171 " =    1.775
peak=   -3.683 closest distance to " O   PHE A 218 " =    1.386
peak=   -3.682 closest distance to " O   HOH Z 350 " =    1.347
peak=   -3.664 closest distance to " O   HOH Z 388 " =    2.005
peak=   -3.658 closest distance to " O   HOH Z 151 " =    1.410
peak=   -3.654 closest distance to " CB  PHE A 208 " =    2.291
peak=   -3.637 closest distance to " CG2 THR A 221 " =    2.285
peak=   -3.636 closest distance to " CD1 TYR A 247 " =    2.361
peak=   -3.621 closest distance to " NE  ARG A 156 " =    1.833
peak=   -3.620 closest distance to " O   HOH Z 234 " =    4.162
peak=   -3.611 closest distance to " OH  TYR A 169 " =    0.877
peak=   -3.604 closest distance to " O   HOH Z 423 " =    2.330
peak=   -3.602 closest distance to " O   HOH Z 185 " =    2.140
peak=   -3.588 closest distance to " C   ILE A 239 " =    2.304
peak=   -3.579 closest distance to " OD2 ASP A 171 " =    2.297
peak=   -3.576 closest distance to " O   ALA A  10 " =    1.798
peak=   -3.561 closest distance to " CB  ALA A 131 " =    2.246
peak=   -3.555 closest distance to " O   HOH Z 136 " =    1.565
peak=   -3.555 closest distance to " O   HOH Z 407 " =    1.665
peak=   -3.553 closest distance to " N   GLN A  58 " =    1.576
peak=   -3.550 closest distance to " O   HOH Z 103 " =    1.816
peak=   -3.547 closest distance to " O   HOH Z 380 " =    4.394
peak=   -3.542 closest distance to " O   HOH Z  93 " =    1.470
peak=   -3.537 closest distance to " CA  TYR A  68 " =    2.691
peak=   -3.530 closest distance to " CD1 LEU A 101 " =    2.576
peak=   -3.527 closest distance to " O   HOH Z 275 " =    1.511
peak=   -3.522 closest distance to " O   HOH Z  71 " =    1.577
peak=   -3.519 closest distance to " O   HOH Z 377 " =    1.035
peak=   -3.509 closest distance to " O   HOH Z 198 " =    1.482
peak=   -3.506 closest distance to " O   HOH Z 313 " =    1.275
peak=   -3.504 closest distance to " OE2 GLU A 152 " =    2.216
peak=   -3.493 closest distance to " CD  GLN A  77 " =    1.219
peak=   -3.490 closest distance to " CE2 TYR A  30 " =    2.720
peak=   -3.489 closest distance to " O   HOH Z  19 " =    2.309
peak=   -3.488 closest distance to " ND2 ASN A  60 " =    1.488
peak=   -3.488 closest distance to " CE  MET A 105 " =    2.175
peak=   -3.487 closest distance to " O   HOH Z 396 " =    1.769
peak=   -3.486 closest distance to " C   THR A 279 " =    1.147
peak=   -3.485 closest distance to " CZ  ARG A  66 " =    1.229
peak=   -3.476 closest distance to " ND2 ASN A  45 " =    1.144
peak=   -3.475 closest distance to " O   HOH Z 210 " =    2.679
peak=   -3.474 closest distance to " NH2 ARG A  79 " =    1.843
peak=   -3.473 closest distance to " O   HOH Z 292 " =    4.405
peak=   -3.471 closest distance to " OD1 ASP A 191 " =    1.766
peak=   -3.466 closest distance to " O   HOH Z  78 " =    1.967
peak=   -3.465 closest distance to " O   HOH Z 120 " =    1.119
peak=   -3.465 closest distance to " O   TRP A  92 " =    1.861
peak=   -3.455 closest distance to " O   HOH Z 259 " =    1.142
peak=   -3.454 closest distance to " CG  ASP A 231 " =    0.859
peak=   -3.449 closest distance to " O   TYR A  15 " =    1.555
peak=   -3.449 closest distance to " O   GLY A 196 " =    1.013
peak=   -3.448 closest distance to " CD2 PHE A  59 " =    2.293
peak=   -3.446 closest distance to " NH1 ARG A 195 " =    1.066
peak=   -3.446 closest distance to " CD2 LEU A 237 " =    2.590
peak=   -3.444 closest distance to " CA  ASP A 298 " =    1.079
peak=   -3.431 closest distance to " ND2 ASN A  39 " =    1.362
peak=   -3.431 closest distance to " CB  CYS A 254 " =    2.370
peak=   -3.430 closest distance to " O   HOH Z 418 " =    1.389
peak=   -3.428 closest distance to " O   HOH Z 109 " =    3.565
peak=   -3.422 closest distance to " O   HOH Z 407 " =    0.834
peak=   -3.419 closest distance to " OD1 ASN A 148 " =    1.610
peak=   -3.419 closest distance to " CD1 TRP A 179 " =    1.127
peak=   -3.417 closest distance to " CB  TRP A  85 " =    2.474
peak=   -3.416 closest distance to " O   HOH Z  10 " =    1.531
peak=   -3.412 closest distance to " O   HOH Z  91 " =    2.114
peak=   -3.410 closest distance to " CG2 ILE A  49 " =    2.572
peak=   -3.405 closest distance to " N   THR A 235 " =    1.246
peak=   -3.404 closest distance to " CD  GLU A 236 " =    1.030
peak=   -3.399 closest distance to " CE2 TRP A  85 " =    1.054
peak=   -3.399 closest distance to " O   HOH Z  25 " =    2.221
peak=   -3.396 closest distance to " CD1 LEU A 228 " =    2.402
peak=   -3.392 closest distance to " O   HOH Z 150 " =    1.502
peak=   -3.382 closest distance to " O   HOH Z 222 " =    1.120
peak=   -3.379 closest distance to " CG2AVAL A  41 " =    2.841
peak=   -3.376 closest distance to " O   ALA A 256 " =    1.411
peak=   -3.375 closest distance to " O   HOH Z 210 " =    1.075
peak=   -3.370 closest distance to " ND2 ASN A  60 " =    1.570
peak=   -3.368 closest distance to " O   HOH Z 118 " =    5.342
peak=   -3.368 closest distance to " O   HOH Z 176 " =    1.603
peak=   -3.363 closest distance to " CD  GLN A 223 " =    1.593
peak=   -3.362 closest distance to " OG  SER A 273 " =    2.170
peak=   -3.360 closest distance to " CD2 LEU A 167 " =    1.673
peak=   -3.356 closest distance to " O   HOH Z   7 " =    1.599
peak=   -3.353 closest distance to " O   HOH Z  38 " =    1.357
peak=   -3.351 closest distance to " CG  LEU A  83 " =    2.195
peak=   -3.347 closest distance to " CB  ALA A 244 " =    2.610
peak=   -3.342 closest distance to " CE  MET A  93 " =    1.209
peak=   -3.340 closest distance to " CB  ALA A 291 " =    2.287
peak=   -3.337 closest distance to " O   VAL A 174 " =    1.980
peak=   -3.335 closest distance to " O   HOH Z  37 " =    1.599
peak=   -3.334 closest distance to " O   HOH Z 171 " =    2.347
peak=   -3.329 closest distance to " O   HOH Z   6 " =    1.587
peak=   -3.328 closest distance to " O   HOH Z  15 " =    1.672
peak=   -3.315 closest distance to " C   ASN A 187 " =    2.002
peak=   -3.312 closest distance to " N   ALA A 226 " =    2.063
peak=   -3.309 closest distance to " O   HOH Z  39 " =    1.568
peak=   -3.304 closest distance to " CE2 TRP A 274 " =    1.358
peak=   -3.295 closest distance to " NE2 GLN A 194 " =    1.835
peak=   -3.290 closest distance to " O   HOH Z 120 " =    1.243
peak=   -3.288 closest distance to " CD1 LEU A 101 " =    2.666
peak=   -3.283 closest distance to " N   SER A 134 " =    1.268
peak=   -3.283 closest distance to " O   HOH Z 422 " =    1.837
peak=   -3.281 closest distance to " O   HOH Z 313 " =    1.752
peak=   -3.278 closest distance to " CD  ARG A 139 " =    1.547
peak=   -3.278 closest distance to " C   SER A 206 " =    1.436
peak=   -3.277 closest distance to " CD1 PHE A 130 " =    2.339
peak=   -3.275 closest distance to " OG BSER A 134 " =    1.249
peak=   -3.275 closest distance to " OE1 GLN A 223 " =    2.423
peak=   -3.273 closest distance to " C   GLY A  91 " =    1.447
peak=   -3.271 closest distance to " OD2 ASP A 171 " =    2.997
peak=   -3.270 closest distance to " O   GLY A 196 " =    2.436
peak=   -3.268 closest distance to " CB  ASP A 124 " =    2.327
peak=   -3.268 closest distance to " O   HOH Z  90 " =    1.951
peak=   -3.267 closest distance to " O   HOH Z 118 " =    3.437
peak=   -3.266 closest distance to " CG2 VAL A 189 " =    2.162
peak=   -3.261 closest distance to " CG2 THR A   4 " =    1.771
peak=   -3.260 closest distance to " OG  SER A  32 " =    1.190
peak=   -3.255 closest distance to " O   ALA A   1 " =    2.295
peak=   -3.254 closest distance to " C   ALA A   8 " =    1.559
peak=   -3.248 closest distance to " CG  GLU A  53 " =    1.386
peak=   -3.248 closest distance to " CB  HIS A  86 " =    2.576
peak=   -3.248 closest distance to " CE  MET A 105 " =    1.965
peak=   -3.247 closest distance to " CG  PHE A 225 " =    1.378
peak=   -3.245 closest distance to " O   HOH Z  64 " =    1.437
peak=   -3.245 closest distance to " CG  GLN A  58 " =    1.243
peak=   -3.239 closest distance to " NH1 ARG A  66 " =    4.136
peak=   -3.238 closest distance to " O   HOH Z  40 " =    2.781
peak=   -3.234 closest distance to " NH2BARG A 275 " =    1.623
peak=   -3.234 closest distance to " O   HOH Z 166 " =    2.290
peak=   -3.232 closest distance to " CD1 LEU A  25 " =    2.483
peak=   -3.231 closest distance to " CD  PRO A 213 " =    2.284
peak=   -3.227 closest distance to " O   HOH Z 424 " =    2.981
peak=   -3.225 closest distance to " O   HOH Z 197 " =    2.039
peak=   -3.224 closest distance to " CA  GLY A 133 " =    2.115
peak=   -3.219 closest distance to " OE1 GLN A  88 " =    1.123
peak=   -3.218 closest distance to " O   HOH Z 434 " =    4.084
peak=   -3.214 closest distance to " O   HOH Z 148 " =    3.414
peak=   -3.213 closest distance to " O   HOH Z 318 " =    1.476
peak=   -3.212 closest distance to " O   ALA A 160 " =    1.365
peak=   -3.212 closest distance to " OG ASER A  12 " =    1.545
peak=   -3.207 closest distance to " O   HOH Z 151 " =    1.837
peak=   -3.207 closest distance to " OE1 GLN A  77 " =    2.459
peak=   -3.206 closest distance to " CH2 TRP A 179 " =    1.180
peak=   -3.206 closest distance to " O   HOH Z 368 " =    2.161
peak=   -3.206 closest distance to " CB  ALA A   9 " =    2.583
peak=   -3.204 closest distance to " O   HOH Z 422 " =    1.398
peak=   -3.201 closest distance to " O   HOH Z  97 " =    1.466
peak=   -3.199 closest distance to " O   HOH Z 384 " =    1.896
peak=   -3.186 closest distance to " O   HOH Z 137 " =    1.354
peak=   -3.184 closest distance to " O   SER A 146 " =    0.873
peak=   -3.180 closest distance to " O   HOH Z 231 " =    1.815
peak=   -3.179 closest distance to " O   HOH Z  17 " =    1.037
peak=   -3.175 closest distance to " CG  TRP A 266 " =    1.935
peak=   -3.173 closest distance to " O   ASP A 191 " =    1.243
peak=   -3.173 closest distance to " CB  ASN A 170 " =    1.997
peak=   -3.164 closest distance to " N   ASP A 272 " =    1.244
peak=   -3.162 closest distance to " O   ALA A  34 " =    2.542
peak=   -3.161 closest distance to " OE1 GLN A  77 " =    1.722
peak=   -3.158 closest distance to " OG  SER A  87 " =    1.674
peak=   -3.157 closest distance to " O   HOH Z 414 " =    1.495
peak=   -3.155 closest distance to " CB  ALA A 161 " =    2.638
peak=   -3.155 closest distance to " CD  ARG A 195 " =    5.126
peak=   -3.154 closest distance to " O   HOH Z 150 " =    2.177
peak=   -3.150 closest distance to " CH2 TRP A 177 " =    1.926
peak=   -3.145 closest distance to " O   HOH Z 385 " =    3.787
peak=   -3.144 closest distance to " NH2BARG A 145 " =    2.271
peak=   -3.144 closest distance to " O   HOH Z 265 " =    2.170
peak=   -3.143 closest distance to " O   HOH Z   7 " =    1.266
peak=   -3.141 closest distance to " O   HOH Z 426 " =    1.908
peak=   -3.133 closest distance to " O   HOH Z  43 " =    4.934
peak=   -3.132 closest distance to " NH1 ARG A 195 " =    2.834
peak=   -3.132 closest distance to " NE1 TRP A 177 " =    1.986
peak=   -3.130 closest distance to " O   VAL A 125 " =    2.061
peak=   -3.128 closest distance to " O   HOH Z 284 " =    2.168
peak=   -3.125 closest distance to " O   HOH Z  11 " =    1.607
peak=   -3.114 closest distance to " O   HOH Z 427 " =    1.657
peak=   -3.114 closest distance to " ND2 ASN A 173 " =    1.614
peak=   -3.112 closest distance to " O   HOH Z 113 " =    2.094
peak=   -3.112 closest distance to " O   HOH Z 292 " =    3.039
peak=   -3.108 closest distance to " O   ASP A 171 " =    1.064
peak=   -3.107 closest distance to " NH2 ARG A 159 " =    2.387
peak=   -3.103 closest distance to " ND2 ASN A  45 " =    1.690
peak=   -3.103 closest distance to " O   HOH Z 213 " =    1.404
peak=   -3.098 closest distance to " NE2 GLN A  58 " =    0.955
peak=   -3.084 closest distance to " CG2 VAL A 296 " =    1.985
peak=   -3.081 closest distance to " O   HOH Z 134 " =    2.016
peak=   -3.077 closest distance to " O   HOH Z 111 " =    1.343
peak=   -3.076 closest distance to " CB  ARG A 219 " =    2.543
peak=   -3.076 closest distance to " CG  LEU A 281 " =    1.780
peak=   -3.071 closest distance to " OG1 THR A  82 " =    1.504
peak=   -3.069 closest distance to " O   HOH Z 405 " =    2.260
peak=   -3.067 closest distance to " O   ALA A  34 " =    1.973
peak=   -3.054 closest distance to " O   HOH Z 259 " =    2.174
peak=   -3.053 closest distance to " CD  PRO A 198 " =    1.077
peak=   -3.025 closest distance to " O   HOH Z 120 " =    1.334
peak=   -3.024 closest distance to " O   HOH Z 354 " =    1.731

================= 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    :  0.4639 0.4513   6.279257e+00   6.260796e+00
   1_bss:  0.4539 0.4388   6.271244e+00   6.247831e+00
   1_xyz:  0.3511 0.3922   6.100818e+00   6.165949e+00
   1_adp:  0.3240 0.3957   6.060588e+00   6.172116e+00
   1_occ:  0.3238 0.3955   6.059526e+00   6.171766e+00
   2_bss:  0.3225 0.3914   6.059228e+00   6.170165e+00
   2_xyz:  0.2489 0.3013   5.829439e+00   5.976147e+00
   2_adp:  0.2237 0.2960   5.775252e+00   5.963416e+00
   2_occ:  0.2235 0.2962   5.774887e+00   5.963296e+00
   3_bss:  0.2232 0.2953   5.771733e+00   5.961357e+00
   3_xyz:  0.1790 0.2377   5.557714e+00   5.771040e+00
   3_adp:  0.1683 0.2124   5.484148e+00   5.671570e+00
   3_occ:  0.1680 0.2124   5.483445e+00   5.670498e+00
   4_bss:  0.1679 0.2113   5.484723e+00   5.669453e+00
   4_xyz:  0.1443 0.1875   5.357132e+00   5.554503e+00
   4_adp:  0.1358 0.1857   5.320772e+00   5.538222e+00
   4_occ:  0.1358 0.1856   5.320409e+00   5.537825e+00
   5_bss:  0.1360 0.1857   5.321686e+00   5.538785e+00
   5_xyz:  0.1247 0.1755   5.246652e+00   5.479931e+00
   5_adp:  0.1234 0.1728   5.234431e+00   5.464180e+00
   5_occ:  0.1233 0.1727   5.234278e+00   5.464561e+00
   5_bss:  0.1232 0.1726   5.234207e+00   5.464296e+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:  0.293  20.001  -2.939   4.500   0.808   0.000   0.000   0.000
   1_xyz:  0.293  20.001  -2.939   4.500   0.808   0.000   0.000   0.000
   1_adp:  0.293  20.001  -2.939   4.500   0.808   0.000   0.000   0.000
   1_occ:  0.293  20.001  -2.939   4.500   0.808   0.000   0.000   0.000
   2_bss:  0.322  50.000  -1.473   2.572  -0.114   0.000  -0.000  -0.000
   2_xyz:  0.322  50.000  -1.473   2.572  -0.114   0.000  -0.000  -0.000
   2_adp:  0.322  50.000  -1.473   2.572  -0.114   0.000  -0.000  -0.000
   2_occ:  0.322  50.000  -1.473   2.572  -0.114   0.000  -0.000  -0.000
   3_bss:  0.319  58.865  -1.205   1.269  -0.401   0.000  -0.000  -0.000
   3_xyz:  0.319  58.865  -1.205   1.269  -0.401   0.000  -0.000  -0.000
   3_adp:  0.319  58.865  -1.205   1.269  -0.401   0.000  -0.000  -0.000
   3_occ:  0.319  58.865  -1.205   1.269  -0.401   0.000  -0.000  -0.000
   4_bss:  0.322  59.843  -1.841  -0.071  -1.124  -0.000  -0.000  -0.000
   4_xyz:  0.322  59.843  -1.841  -0.071  -1.124  -0.000  -0.000  -0.000
   4_adp:  0.322  59.843  -1.841  -0.071  -1.124  -0.000  -0.000  -0.000
   4_occ:  0.322  59.843  -1.841  -0.071  -1.124  -0.000  -0.000  -0.000
   5_bss:  0.325  64.237  -1.877  -0.490  -1.181  -0.000  -0.000  -0.000
   5_xyz:  0.325  64.237  -1.877  -0.490  -1.181  -0.000  -0.000  -0.000
   5_adp:  0.325  64.237  -1.877  -0.490  -1.181  -0.000  -0.000  -0.000
   5_occ:  0.325  64.237  -1.877  -0.490  -1.181  -0.000  -0.000  -0.000
   5_bss:  0.323  61.032  -1.764  -0.609  -1.092  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.296 0.4676  0.6314    66236.361
   1_bss:  53.095 0.4814  0.6656    62474.912
   1_xyz:  44.371 0.5895  0.7985    45320.014
   1_adp:  45.029 0.5807  0.7830    45951.071
   1_occ:  44.976 0.5814  0.7828    45862.204
   2_bss:  44.553 0.5866  0.7821    45331.167
   2_xyz:  32.386 0.7301  0.9315    25130.545
   2_adp:  31.508 0.7405  0.9199    24408.808
   2_occ:  31.500 0.7405  0.9196    24382.458
   3_bss:  31.295 0.7426  0.9083    24064.674
   3_xyz:  24.120 0.8190  0.9725    14714.536
   3_adp:  20.747 0.8543  0.9917    11854.863
   3_occ:  20.732 0.8545  0.9920    11851.265
   4_bss:  20.664 0.8551  0.9624    11801.798
   4_xyz:  17.836 0.8820  0.9750     9132.221
   4_adp:  17.427 0.8859  0.9692     8887.727
   4_occ:  17.420 0.8860  0.9693     8885.166
   5_bss:  17.429 0.8859  0.9637     8908.562
   5_xyz:  16.237 0.8961  0.9708     7868.162
   5_adp:  15.891 0.8993  0.9697     7685.838
   5_occ:  15.894 0.8993  0.9695     7691.226
   5_bss:  15.890 0.8993  0.9708     7686.269
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9060e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9060e-01
   1_xyz:   1.763  0.015  0.103 16.468  0.007  4.109   1.6340e-01
   1_adp:   1.763  0.015  0.103 16.468  0.007  4.109   1.6340e-01
   1_occ:   1.763  0.015  0.103 16.468  0.007  4.109   1.6340e-01
   2_bss:   1.763  0.015  0.103 16.468  0.007  4.109   1.6340e-01
   2_xyz:   1.463  0.011  0.096 15.245  0.006  4.117   1.0800e-01
   2_adp:   1.463  0.011  0.096 15.245  0.006  4.117   1.0800e-01
   2_occ:   1.463  0.011  0.096 15.245  0.006  4.117   1.0800e-01
   3_bss:   1.463  0.011  0.096 15.245  0.006  4.117   1.0800e-01
   3_xyz:   1.117  0.008  0.072 14.781  0.005  4.112   7.2618e-02
   3_adp:   1.117  0.008  0.072 14.781  0.005  4.112   7.2618e-02
   3_occ:   1.117  0.008  0.072 14.781  0.005  4.112   7.2618e-02
   4_bss:   1.117  0.008  0.072 14.781  0.005  4.112   7.2618e-02
   4_xyz:   1.002  0.007  0.070 14.369  0.004  4.121   5.8312e-02
   4_adp:   1.002  0.007  0.070 14.369  0.004  4.121   5.8312e-02
   4_occ:   1.002  0.007  0.070 14.369  0.004  4.121   5.8312e-02
   5_bss:   1.002  0.007  0.070 14.369  0.004  4.121   5.8312e-02
   5_xyz:   1.043  0.007  0.073 14.550  0.004  4.112   6.2464e-02
   5_adp:   1.043  0.007  0.073 14.550  0.004  4.112   6.2464e-02
   5_occ:   1.043  0.007  0.073 14.550  0.004  4.112   6.2464e-02
   5_bss:   1.043  0.007  0.073 14.550  0.004  4.112   6.2464e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.385   2.4320e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.385   2.4320e-01
   1_xyz:  11.065  0.144  0.377 88.801  0.026  1.999   1.2863e-01
   1_adp:  11.065  0.144  0.377 88.801  0.026  1.999   1.2863e-01
   1_occ:  11.065  0.144  0.377 88.801  0.026  1.999   1.2863e-01
   2_bss:  11.065  0.144  0.377 88.801  0.026  1.999   1.2863e-01
   2_xyz:   8.906  0.052  0.332 82.756  0.049  2.117   1.0086e-01
   2_adp:   8.906  0.052  0.332 82.756  0.049  2.117   1.0086e-01
   2_occ:   8.906  0.052  0.332 82.756  0.049  2.117   1.0086e-01
   3_bss:   8.906  0.052  0.332 82.756  0.049  2.117   1.0086e-01
   3_xyz:   7.206  0.061  0.199 86.570  0.045  2.277   7.3871e-02
   3_adp:   7.206  0.061  0.199 86.570  0.045  2.277   7.3871e-02
   3_occ:   7.206  0.061  0.199 86.570  0.045  2.277   7.3871e-02
   4_bss:   7.206  0.061  0.199 86.570  0.045  2.277   7.3871e-02
   4_xyz:   6.996  0.049  0.219 82.727  0.034  2.346   4.1977e-02
   4_adp:   6.996  0.049  0.219 82.727  0.034  2.346   4.1977e-02
   4_occ:   6.996  0.049  0.219 82.727  0.034  2.346   4.1977e-02
   5_bss:   6.996  0.049  0.219 82.727  0.034  2.346   4.1977e-02
   5_xyz:   7.437  0.047  0.234 81.646  0.033  2.338   4.6958e-02
   5_adp:   7.437  0.047  0.234 81.646  0.033  2.338   4.6958e-02
   5_occ:   7.437  0.047  0.234 81.646  0.033  2.338   4.6958e-02
   5_bss:   7.437  0.047  0.234 81.646  0.033  2.338   4.6958e-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: 122.60   0.00  17.62 122.60   0.00  14.15  68.97   0.00  36.54
   1_occ: 122.60   0.00  17.62 122.60   0.00  14.15  68.97   0.00  36.54
   2_bss: 122.60   0.00  17.62 122.60   0.00  14.15  68.97   0.00  36.54
   2_xyz: 122.60   0.00  17.62 122.60   0.00  14.15  68.97   0.00  36.54
   2_adp: 105.62   0.00  19.11 104.47   0.00  14.48 105.62   2.37  44.34
   2_occ: 105.62   0.00  19.11 104.47   0.00  14.48 105.62   2.37  44.34
   3_bss: 105.62   0.00  19.11 104.47   0.00  14.48 105.62   2.37  44.34
   3_xyz: 105.62   0.00  19.11 104.47   0.00  14.48 105.62   2.37  44.34
   3_adp:  99.61   0.00  17.54  99.61   0.00  13.11  96.84   5.50  41.64
   3_occ:  99.61   0.00  17.54  99.61   0.00  13.11  96.84   5.50  41.64
   4_bss:  99.61   0.00  17.54  99.61   0.00  13.11  96.84   5.50  41.64
   4_xyz:  99.61   0.00  17.54  99.61   0.00  13.11  96.84   5.50  41.64
   4_adp: 110.97   0.00  17.97 110.97   0.00  12.81 108.47   1.21  46.09
   4_occ: 110.97   0.00  17.97 110.97   0.00  12.81 108.47   1.21  46.09
   5_bss: 110.97   0.00  17.97 110.97   0.00  12.81 108.47   1.21  46.09
   5_xyz: 110.97   0.00  17.97 110.97   0.00  12.81 108.47   1.21  46.09
   5_adp: 110.71   0.00  17.80 110.71   0.00  12.70 108.11   3.51  45.56
   5_occ: 110.71   0.00  17.80 110.71   0.00  12.70 108.11   3.51  45.56
   5_bss: 110.71   0.00  17.80 110.71   0.00  12.70 108.11   3.51  45.56
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.417    0.015    0.432
   1_adp:    2.417    0.015    0.432
   1_occ:    2.417    0.015    0.432
   2_bss:    2.417    0.015    0.432
   2_xyz:    1.884    0.023    0.657
   2_adp:    1.884    0.023    0.657
   2_occ:    1.884    0.023    0.657
   3_bss:    1.884    0.023    0.657
   3_xyz:    1.654    0.097    0.770
   3_adp:    1.654    0.097    0.770
   3_occ:    1.654    0.097    0.770
   4_bss:    1.654    0.097    0.770
   4_xyz:    1.508    0.081    0.828
   4_adp:    1.508    0.081    0.828
   4_occ:    1.508    0.081    0.828
   5_bss:    1.508    0.081    0.828
   5_xyz:    1.572    0.079    0.862
   5_adp:    1.572    0.079    0.862
   5_occ:    1.572    0.079    0.862
   5_bss:    1.572    0.079    0.862
------------------------------------------------------------------------

CPU time actual refinement: 343.44


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_837/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_837/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_837/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_837/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_837/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.29 
  Macro-tasks:
    bulk solvent and scale       = 43.25  
    individual site refinement   = 142.66 
    weights calculation          = 28.68  
    collect and process          = 6.37   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 221.06 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 109.17 
    alpha_beta                      = 8.36   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 118.80 
    fmodel                         = 7.17   
    r_factors                      = 0.30   
    phase_errors                   = 10.47  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 258.13 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.828 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    656 calls, 108.86 s
gradients_fft:          601 calls, 105.22 s

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

# Date 2008-01-16 Time 05:47:26 PST -0800 (1200491246.04 s)
Start R-work = 0.4639, R-free = 0.4513 (no bulk solvent and anisotropic scale)
Final R-work = 0.1419, R-free = 0.1899 (no bulk solvent and anisotropic scale)

Start R-work = 0.4539, R-free = 0.4388
Final R-work = 0.1232, R-free = 0.1726