# Date 2008-01-16 Time 05:37:22 PST -0800 (1200490642.21 s)
#phil __OFF__

Command line arguments: "../814.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10561
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 814

-------------------------------------------------------------------------------
  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, 47.6339, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95151
Completeness in resolution range: 0.921228
Completeness with d_max=infinity: 0.918507

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9515

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95151
Completeness in resolution range: 0.921228
Completeness with d_max=infinity: 0.918507

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1767 [2235/2264]  2012   223  10.0%
  bin  2:  4.1767 -  3.3272 [2130/2153]  1917   213  10.0%
  bin  3:  3.3272 -  2.9101 [2111/2136]  1898   213  10.1%
  bin  4:  2.9101 -  2.6457 [2092/2109]  1889   203   9.7%
  bin  5:  2.6457 -  2.4569 [2090/2133]  1878   212  10.1%
  bin  6:  2.4569 -  2.3126 [2065/2093]  1864   201   9.7%
  bin  7:  2.3126 -  2.1972 [2054/2090]  1844   210  10.2%
  bin  8:  2.1972 -  2.1018 [2058/2100]  1853   205  10.0%
  bin  9:  2.1018 -  2.0211 [2011/2073]  1808   203  10.1%
  bin 10:  2.0211 -  1.9515 [ 743/2113]   667    76  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_814/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.46 -     2.14: 21
        2.14 -     2.83: 1005
        2.83 -     3.52: 4418
        3.52 -     4.21: 9339
        4.21 -     4.90: 13652
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.455 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.594 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.602 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.679 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.754 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28430 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_814/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_814/model_refine_001.geo

CPU time processing inputs: 9.06


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


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


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


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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4387   r_free= 0.4335   ksol= 0.00   Bsol= 0.00   scale= 0.913    |
|                                                                             |
| 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: 6.248997                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6589 0.99   1450  164 0.3434 0.3487      6.5046      6.4962|
|  2:  4.6589 -  3.7166 0.99   1386  148 0.3648 0.3644      6.7364      6.7504|
|  3:  3.7166 -  3.2523 0.99   1372  154 0.3953 0.3858       6.597      6.6348|
|  4:  3.2523 -  2.9575 0.99   1351  151 0.4240 0.4078      6.4615      6.4508|
|  5:  2.9575 -  2.7469 0.99   1342  149 0.4492 0.4278      6.3123      6.2867|
|  6:  2.7469 -  2.5858 0.99   1352  152 0.4698 0.4433      6.2395      6.1451|
|  7:  2.5858 -  2.4569 0.98   1341  146 0.4641 0.4418      6.2184      6.1611|
|  8:  2.4569 -  2.3504 0.98   1322  144 0.4986 0.5102       6.132      6.1958|
|  9:  2.3504 -  2.2602 0.99   1323  148 0.5057 0.4909       6.124      6.1091|
| 10:  2.2602 -  2.1825 0.98   1337  149 0.4984 0.5264      6.0669      6.1133|
| 11:  2.1825 -  2.1144 0.97   1299  143 0.5046 0.5599      6.0138      6.0098|
| 12:  2.1144 -  2.0541 0.98   1323  148 0.5091 0.5430      5.9317       5.986|
| 13:  2.0541 -  2.0002 0.84   1128  131 0.5088 0.4426      5.8735      5.8238|
| 14:  2.0002 -  1.9515 0.22    304   32 0.5841 0.5091      5.8231      5.7723|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6589  1450   164  0.73  31.67   0.84     0.75      61313.50|
|  2:  4.6589 -  3.7166  1386   148  0.74  31.71   0.93     0.83      86110.83|
|  3:  3.7166 -  3.2523  1372   154  0.66  39.04   0.93     0.83      91974.89|
|  4:  3.2523 -  2.9575  1351   151  0.58  45.57   0.94     0.79      82864.47|
|  5:  2.9575 -  2.7469  1342   149  0.53  49.69   0.90     0.73      65794.05|
|  6:  2.7469 -  2.5858  1352   152  0.49  52.46   0.92     0.69      57649.03|
|  7:  2.5858 -  2.4569  1341   146  0.48  53.58   0.95     0.64      53743.41|
|  8:  2.4569 -  2.3504  1322   144  0.40  59.76   0.89     0.60      54675.41|
|  9:  2.3504 -  2.2602  1323   148  0.38  61.53   0.94     0.55      51150.37|
| 10:  2.2602 -  2.1825  1337   149  0.33  65.63   0.97     0.49      51577.25|
| 11:  2.1825 -  2.1144  1299   143  0.28  69.27   0.94     0.42      49006.89|
| 12:  2.1144 -  2.0541  1323   148  0.22  73.59   0.94     0.37      47807.47|
| 13:  2.0541 -  2.0002  1128   131  0.25  71.71   0.94     0.39      39812.81|
| 14:  2.0002 -  1.9515   304    32  0.31  67.16   0.87     0.49      31925.28|
|alpha:            min =        0.37 max =            0.83 mean =         0.63|
|beta:             min =    31925.28 max =        91974.89 mean =     60983.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.96|
|phase err.(test): min =        0.00 max =           89.95 mean =        54.03|
|-----------------------------------------------------------------------------|

============================== 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 = 7.994156              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.857   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.347133              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.309   (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 |  1.455 -  1.800:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.800 -  2.144:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.144 -  2.489:       28 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.489 -  2.833:      977 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.833 -  3.178:     2000 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.178 -  3.522:     2418 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.522 -  3.867:     4629 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.867 -  4.211:     4710 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.211 -  4.556:     6179 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.556 -  4.900:     7473 |
|-----------------------------------------------------------------------------|
|-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 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.455 |       0.562 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4387   r_free= 0.4335   ksol= 0.00   Bsol= 0.00   scale= 0.913    |
|                                                                             |
| 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: 6.248997                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4280   r_free= 0.4216   ksol= 0.33   Bsol= 50.00   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,2.13,2.34,0.00,0.00,0.00); trace/3= 0.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.241048                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.324183              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.796   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.002247              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.049   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4280      final r-factor (work) = 0.3333          |
| start r-factor (free) = 0.4216      final r-factor (free) = 0.3617          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9155 = 6.32 * 0.50 * 6.2388 + 1.00 * 0.1880                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4212 = 6.32 * 0.50 * 6.1091 + 1.00 * 0.1037                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3333      final r-factor (work) = 0.3046          |
| start r-factor (free) = 0.3617      final r-factor (free) = 0.3734          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1291 = 1.00 * 1.00 * 6.1091 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0321 = 1.00 * 1.00 * 5.9983 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.96   18.82    None  None   None       |
|    all(noH): 2823   0      0.00    92.96   18.82    None  None   None       |
|    Sol.    : 438    0      0.59    90.80   39.57    None  None   None       |
|    Mac.    : 2385   0      0.00    92.96   15.02    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 -   9.296:  832   |   5:    46.479 -  55.775:   89        |
|      1:     9.296 -  18.592:  945   |   6:    55.775 -  65.071:   56        |
|      2:    18.592 -  27.888:  455   |   7:    65.071 -  74.367:   32        |
|      3:    27.888 -  37.183:  252   |   8:    74.367 -  83.663:   14        |
|      4:    37.183 -  46.479:  143   |   9:    83.663 -  92.958:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3046 r_free = 0.3734             target_work(ml) = 6.007         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3045 r_free = 0.3740             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3045   r_free= 0.3740   ksol= 0.33   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,2.13,2.34,0.00,0.00,0.00); trace/3= 0.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.006339                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3033   r_free= 0.3725   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,0.65,0.49,0.00,0.00,0.00); trace/3= -0.30                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.005950                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.354300             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.009   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.598503              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.047  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3033      final r-factor (work) = 0.2131          |
| start r-factor (free) = 0.3725      final r-factor (free) = 0.2670          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.1553 = 10.35 * 0.50 * 5.9978 + 1.00 * 0.1037                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.5499 = 10.35 * 0.50 * 5.8837 + 1.00 * 0.0893                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2131      final r-factor (work) = 0.1847          |
| start r-factor (free) = 0.2670      final r-factor (free) = 0.2406          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5414 = 0.60 * 1.00 * 5.8837 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3827 = 0.60 * 1.00 * 5.6331 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.55   18.38    None  None   None       |
|    all(noH): 2823   0      0.00    91.55   18.38    None  None   None       |
|    Sol.    : 438    0      5.91    87.30   42.66    None  None   None       |
|    Mac.    : 2385   0      0.00    91.55   13.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.156:  845   |   5:    45.777 -  54.933:  104        |
|      1:     9.156 -  18.311: 1113   |   6:    54.933 -  64.088:   59        |
|      2:    18.311 -  27.467:  327   |   7:    64.088 -  73.244:   47        |
|      3:    27.467 -  36.622:  156   |   8:    73.244 -  82.399:   17        |
|      4:    36.622 -  45.777:  150   |   9:    82.399 -  91.555:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1847 r_free = 0.2406             target_work(ml) = 5.573         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1844 r_free = 0.2406             target_work(ml) = 5.573         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1844   r_free= 0.2406   ksol= 0.32   Bsol= 50.00   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,0.65,0.49,0.00,0.00,0.00); trace/3= -0.30                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.573166                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1831   r_free= 0.2397   ksol= 0.31   Bsol= 49.99   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-1.08,-1.33,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.568442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.803221              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.398   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.719966              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.755  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1831      final r-factor (work) = 0.1414          |
| start r-factor (free) = 0.2397      final r-factor (free) = 0.1895          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6294 = 4.80 * 0.50 * 5.6379 + 1.00 * 0.0893                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2063 = 4.80 * 0.50 * 5.4710 + 1.00 * 0.0671                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1414      final r-factor (work) = 0.1333          |
| start r-factor (free) = 0.1895      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9502 = 0.72 * 1.00 * 5.4710 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8486 = 0.72 * 1.00 * 5.3138 + 1.00 * 0.0229                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.93   18.23    None  None   None       |
|    all(noH): 2823   0      0.00    90.93   18.23    None  None   None       |
|    Sol.    : 438    0      5.88    87.31   42.81    None  None   None       |
|    Mac.    : 2385   0      0.00    90.93   13.72    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 -   9.093:  796   |   5:    45.466 -  54.560:  104        |
|      1:     9.093 -  18.187: 1196   |   6:    54.560 -  63.653:   64        |
|      2:    18.187 -  27.280:  308   |   7:    63.653 -  72.746:   47        |
|      3:    27.280 -  36.373:  145   |   8:    72.746 -  81.839:   18        |
|      4:    36.373 -  45.466:  139   |   9:    81.839 -  90.933:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1333 r_free = 0.1821             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1331 r_free = 0.1822             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1822   ksol= 0.31   Bsol= 49.99   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-1.08,-1.33,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.292368                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1822   ksol= 0.32   Bsol= 49.04   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.63,-1.84,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.294625                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.947319              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.105  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.595548              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 86.731   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1334      final r-factor (work) = 0.1276          |
| start r-factor (free) = 0.1822      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2431 = 1.95 * 0.50 * 5.3160 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1923 = 1.95 * 0.50 * 5.2782 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1276      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1750      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1616 = 0.60 * 1.00 * 5.2782 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1292 = 0.60 * 1.00 * 5.2377 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.77    92.46   17.87    None  None   None       |
|    all(noH): 2823   0      1.77    92.46   17.87    None  None   None       |
|    Sol.    : 438    0      5.37    87.05   42.66    None  None   None       |
|    Mac.    : 2385   0      1.77    92.46   13.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.773 -  10.842: 1160   |   5:    47.116 -  56.185:  100        |
|      1:    10.842 -  19.910:  985   |   6:    56.185 -  65.253:   66        |
|      2:    19.910 -  28.979:  225   |   7:    65.253 -  74.322:   33        |
|      3:    28.979 -  38.047:  121   |   8:    74.322 -  83.390:   18        |
|      4:    38.047 -  47.116:  109   |   9:    83.390 -  92.459:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1217 r_free = 0.1680             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1216 r_free = 0.1679             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1679   ksol= 0.32   Bsol= 49.04   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.63,-1.84,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.217153                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1679   ksol= 0.32   Bsol= 49.04   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.88,-2.08,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216950                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.718974              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.495  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.170115              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.500  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1679      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7926 = 3.72 * 0.50 * 5.2377 + 1.00 * 0.0531                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7103 = 3.72 * 0.50 * 5.1812 + 1.00 * 0.0760                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8912 = 0.17 * 1.00 * 5.1812 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8854 = 0.17 * 1.00 * 5.1588 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.64    89.31   17.17    None  None   None       |
|    all(noH): 2823   0      2.64    89.31   17.17    None  None   None       |
|    Sol.    : 438    0      5.45    82.94   39.81    None  None   None       |
|    Mac.    : 2385   0      2.64    89.31   13.01    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:     2.644 -  11.311: 1287   |   5:    45.976 -  54.642:   90        |
|      1:    11.311 -  19.977:  906   |   6:    54.642 -  63.308:   52        |
|      2:    19.977 -  28.643:  207   |   7:    63.308 -  71.974:   32        |
|      3:    28.643 -  37.309:  117   |   8:    71.974 -  80.640:   11        |
|      4:    37.309 -  45.976:  114   |   9:    80.640 -  89.307:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1597             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1596             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1596   ksol= 0.32   Bsol= 49.04   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.88,-2.08,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152160                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6589 0.99   1450  164 0.0941 0.1290      5.3449      5.5527|
|  2:  4.6589 -  3.7166 0.99   1386  148 0.0813 0.1050      5.3996      5.6185|
|  3:  3.7166 -  3.2523 0.99   1372  154 0.1047 0.1676       5.456      5.8887|
|  4:  3.2523 -  2.9575 0.99   1351  151 0.1278 0.1517      5.4682      5.5867|
|  5:  2.9575 -  2.7469 0.99   1342  149 0.1332 0.1875      5.3289      5.5207|
|  6:  2.7469 -  2.5858 0.99   1352  152 0.1265 0.1882      5.2207      5.4496|
|  7:  2.5858 -  2.4569 0.98   1341  146 0.1216 0.1758      5.1661       5.401|
|  8:  2.4569 -  2.3504 0.98   1322  144 0.1226 0.1709      5.0867      5.2946|
|  9:  2.3504 -  2.2602 0.99   1323  148 0.1156 0.1862      5.0296      5.3056|
| 10:  2.2602 -  2.1825 0.98   1337  149 0.1125 0.1741      4.9601      5.2531|
| 11:  2.1825 -  2.1144 0.97   1299  143 0.1113 0.1832      4.9053      5.2128|
| 12:  2.1144 -  2.0541 0.98   1323  148 0.1114 0.1685      4.8419       5.064|
| 13:  2.0541 -  2.0002 0.84   1128  131 0.1158 0.1736       4.775      5.0091|
| 14:  2.0002 -  1.9515 0.22    304   32 0.1159 0.1528      4.6497      4.8854|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6589  1450   164  0.94   8.88   0.98     0.96       6906.70|
|  2:  4.6589 -  3.7166  1386   148  0.95   7.87   1.01     1.00       8727.30|
|  3:  3.7166 -  3.2523  1372   154  0.93  11.44   1.02     1.02      10235.24|
|  4:  3.2523 -  2.9575  1351   151  0.91  14.75   1.01     0.98      10711.29|
|  5:  2.9575 -  2.7469  1342   149  0.89  16.71   0.99     0.96       8511.69|
|  6:  2.7469 -  2.5858  1352   152  0.90  16.47   0.99     0.96       7246.42|
|  7:  2.5858 -  2.4569  1341   146  0.90  15.69   0.99     0.96       6352.24|
|  8:  2.4569 -  2.3504  1322   144  0.89  16.95   1.00     0.97       5838.91|
|  9:  2.3504 -  2.2602  1323   148  0.90  16.55   1.00     0.97       5212.77|
| 10:  2.2602 -  2.1825  1337   149  0.91  15.41   1.00     0.96       4426.76|
| 11:  2.1825 -  2.1144  1299   143  0.90  15.76   0.99     0.96       4113.00|
| 12:  2.1144 -  2.0541  1323   148  0.91  15.46   1.00     0.99       3731.63|
| 13:  2.0541 -  2.0002  1128   131  0.90  16.06   1.00     0.99       3183.17|
| 14:  2.0002 -  1.9515   304    32  0.90  15.94   0.98     0.96       2462.78|
|alpha:            min =        0.96 max =            1.02 mean =         0.97|
|beta:             min =     2462.78 max =        10711.29 mean =      6552.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.73 mean =        14.40|
|phase err.(test): min =        0.00 max =           89.52 mean =        13.86|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1596   ksol= 0.32   Bsol= 48.94   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.79,-1.99,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1596   ksol= 0.32   Bsol= 48.94   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.79,-1.99,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152160                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6589 0.99   1450  164 0.0941 0.1290      5.3449      5.5527|
|  2:  4.6589 -  3.7166 0.99   1386  148 0.0813 0.1050      5.3996      5.6185|
|  3:  3.7166 -  3.2523 0.99   1372  154 0.1047 0.1676       5.456      5.8887|
|  4:  3.2523 -  2.9575 0.99   1351  151 0.1278 0.1517      5.4682      5.5867|
|  5:  2.9575 -  2.7469 0.99   1342  149 0.1332 0.1875      5.3289      5.5207|
|  6:  2.7469 -  2.5858 0.99   1352  152 0.1265 0.1882      5.2207      5.4496|
|  7:  2.5858 -  2.4569 0.98   1341  146 0.1216 0.1758      5.1661       5.401|
|  8:  2.4569 -  2.3504 0.98   1322  144 0.1226 0.1709      5.0867      5.2946|
|  9:  2.3504 -  2.2602 0.99   1323  148 0.1156 0.1862      5.0296      5.3056|
| 10:  2.2602 -  2.1825 0.98   1337  149 0.1125 0.1741      4.9601      5.2531|
| 11:  2.1825 -  2.1144 0.97   1299  143 0.1113 0.1832      4.9053      5.2128|
| 12:  2.1144 -  2.0541 0.98   1323  148 0.1114 0.1685      4.8419       5.064|
| 13:  2.0541 -  2.0002 0.84   1128  131 0.1158 0.1736       4.775      5.0091|
| 14:  2.0002 -  1.9515 0.22    304   32 0.1159 0.1528      4.6497      4.8854|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6589  1450   164  0.94   8.88   0.98     0.96       6906.70|
|  2:  4.6589 -  3.7166  1386   148  0.95   7.87   1.01     1.00       8727.30|
|  3:  3.7166 -  3.2523  1372   154  0.93  11.44   1.02     1.02      10235.24|
|  4:  3.2523 -  2.9575  1351   151  0.91  14.75   1.01     0.98      10711.29|
|  5:  2.9575 -  2.7469  1342   149  0.89  16.71   0.99     0.96       8511.69|
|  6:  2.7469 -  2.5858  1352   152  0.90  16.47   0.99     0.96       7246.42|
|  7:  2.5858 -  2.4569  1341   146  0.90  15.69   0.99     0.96       6352.24|
|  8:  2.4569 -  2.3504  1322   144  0.89  16.95   1.00     0.97       5838.91|
|  9:  2.3504 -  2.2602  1323   148  0.90  16.55   1.00     0.97       5212.77|
| 10:  2.2602 -  2.1825  1337   149  0.91  15.41   1.00     0.96       4426.76|
| 11:  2.1825 -  2.1144  1299   143  0.90  15.76   0.99     0.96       4113.00|
| 12:  2.1144 -  2.0541  1323   148  0.91  15.46   1.00     0.99       3731.63|
| 13:  2.0541 -  2.0002  1128   131  0.90  16.06   1.00     0.99       3183.17|
| 14:  2.0002 -  1.9515   304    32  0.90  15.94   0.98     0.96       2462.78|
|alpha:            min =        0.96 max =            1.02 mean =         0.97|
|beta:             min =     2462.78 max =        10711.29 mean =      6552.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.73 mean =        14.40|
|phase err.(test): min =        0.00 max =           89.52 mean =        13.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.55    89.21   17.08    None  None   None       |
|    all(noH): 2823   0      2.55    89.21   17.08    None  None   None       |
|    Sol.    : 438    0      5.36    82.85   39.72    None  None   None       |
|    Mac.    : 2385   0      2.55    89.21   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.548 -  11.214: 1287   |   5:    45.879 -  54.545:   90        |
|      1:    11.214 -  19.881:  906   |   6:    54.545 -  63.212:   52        |
|      2:    19.881 -  28.547:  207   |   7:    63.212 -  71.878:   32        |
|      3:    28.547 -  37.213:  117   |   8:    71.878 -  80.544:   11        |
|      4:    37.213 -  45.879:  114   |   9:    80.544 -  89.210:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.513 - 5.895
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 319
   mapped sites are within: 0.708 - 5.895

peak=    5.882 closest distance to " NH2 ARG A  56 " =    2.256
peak=    5.643 closest distance to " CB  SER A  63 " =    1.179
peak=    5.288 closest distance to " CB  GLN A 223 " =    1.463
peak=    5.116 closest distance to " CG  PRO A  54 " =    1.176
peak=    5.067 closest distance to " O   HOH Z  11 " =    1.372
peak=    4.922 closest distance to " O   HOH Z  15 " =    2.056
peak=    4.894 closest distance to " CB  GLN A 183 " =    1.257
peak=    4.850 closest distance to " O   HOH Z 132 " =    1.293
peak=    4.728 closest distance to " O   HOH Z 193 " =    1.869
peak=    4.669 closest distance to " CB  SER A   3 " =    1.422
peak=    4.618 closest distance to " O   HOH Z 214 " =    1.082
peak=    4.600 closest distance to " O   HOH Z 124 " =    1.427
peak=    4.592 closest distance to " O   HOH Z 234 " =    3.792
peak=    4.579 closest distance to " O   SER A  87 " =    2.140
peak=    4.536 closest distance to " O   HOH Z  80 " =    1.720
peak=    4.497 closest distance to " O   HOH Z 134 " =    1.654
peak=    4.469 closest distance to " CB  GLU A 277 " =    3.550
peak=    4.458 closest distance to " OD2 ASP A 286 " =    2.827
peak=    4.420 closest distance to " OD1 ASN A  69 " =    2.516
peak=    4.390 closest distance to " O   HOH Z 368 " =    2.091
peak=    4.382 closest distance to " O   HOH Z 154 " =    1.484
peak=    4.382 closest distance to " O   HOH Z 236 " =    1.898
peak=    4.379 closest distance to " O   HOH Z 313 " =    1.924
peak=    4.371 closest distance to " CB  GLU A 152 " =    1.162
peak=    4.363 closest distance to " O   HOH Z 126 " =    1.663
peak=    4.363 closest distance to " CB  ARG A 275 " =    0.895
peak=    4.327 closest distance to " CB  VAL A 202 " =    1.549
peak=    4.308 closest distance to " O   HOH Z 232 " =    2.294
peak=    4.300 closest distance to " CB  ASN A 148 " =    1.898
peak=    4.288 closest distance to " O   HOH Z 298 " =    1.937
peak=    4.282 closest distance to " O   HOH Z  97 " =    1.859
peak=    4.279 closest distance to " O   HOH Z 142 " =    1.554
peak=    4.275 closest distance to " O   HOH Z 371 " =    3.463
peak=    4.253 closest distance to " CB  TYR A 169 " =    0.908
peak=    4.245 closest distance to " O   HOH Z 326 " =    1.578
peak=    4.237 closest distance to " O   HOH Z 403 " =    1.777
peak=    4.225 closest distance to " O   HOH Z  40 " =    1.667
peak=    4.225 closest distance to " O   PRO A 198 " =    1.518
peak=    4.225 closest distance to " CG  PRO A 213 " =    1.164
peak=    4.220 closest distance to " O   HOH Z  54 " =    1.713
peak=    4.209 closest distance to " CA  TYR A  30 " =    0.986
peak=    4.157 closest distance to " CB  PRO A  54 " =    0.708
peak=    4.157 closest distance to " O   HOH Z  20 " =    1.716
peak=    4.157 closest distance to " O   HOH Z  49 " =    2.329
peak=    4.154 closest distance to " O   HOH Z 389 " =    1.858
peak=    4.144 closest distance to " CB  GLU A 128 " =    1.121
peak=    4.144 closest distance to " CA  ALA A  21 " =    1.214
peak=    4.143 closest distance to " O   HOH Z 193 " =    2.211
peak=    4.141 closest distance to " O   HOH Z 133 " =    1.576
peak=    4.133 closest distance to " ND2 ASN A 187 " =    1.627
peak=    4.129 closest distance to " CB  LEU A 228 " =    1.170
peak=    4.129 closest distance to " O   HOH Z 180 " =    2.222
peak=    4.127 closest distance to " CB  ARG A  79 " =    1.376
peak=    4.119 closest distance to " O   HOH Z  43 " =    1.511
peak=    4.117 closest distance to " O   HOH Z  93 " =    2.569
peak=    4.107 closest distance to " O   HOH Z 108 " =    1.404
peak=    4.099 closest distance to " CG1 ILE A  33 " =    1.185
peak=    4.094 closest distance to " O   HOH Z 260 " =    1.302
peak=    4.073 closest distance to " O   HOH Z 344 " =    2.847
peak=    4.069 closest distance to " O   HOH Z  78 " =    1.943
peak=    4.066 closest distance to " O   HOH Z 108 " =    2.028
peak=    4.062 closest distance to " O   HOH Z 279 " =    2.173
peak=    4.050 closest distance to " O   HOH Z 154 " =    2.347
peak=    4.046 closest distance to " O   HOH Z  67 " =    1.925
peak=    4.035 closest distance to " O   HOH Z 316 " =    2.967
peak=    4.021 closest distance to " NE2 GLN A  11 " =    1.065
peak=    4.014 closest distance to " O   HOH Z 426 " =    1.519
peak=    3.999 closest distance to " O   HOH Z 374 " =    2.624
peak=    3.988 closest distance to " NH2AARG A 190 " =    1.315
peak=    3.978 closest distance to " NH2 ARG A 156 " =    1.223
peak=    3.959 closest distance to " O   HOH Z 272 " =    1.888
peak=    3.953 closest distance to " O   HOH Z 247 " =    1.322
peak=    3.935 closest distance to " O   HOH Z 203 " =    1.774
peak=    3.931 closest distance to " O   HOH Z 411 " =    3.494
peak=    3.925 closest distance to " O   HOH Z  63 " =    1.950
peak=    3.924 closest distance to " NZ  LYS A 117 " =    3.182
peak=    3.924 closest distance to " O   HOH Z 207 " =    1.910
peak=    3.920 closest distance to " O   HOH Z   6 " =    2.120
peak=    3.913 closest distance to " CG1BVAL A  72 " =    1.635
peak=    3.901 closest distance to " O   HOH Z 261 " =    2.237
peak=    3.890 closest distance to " OG BSER A 164 " =    2.515
peak=    3.883 closest distance to " CG2 THR A 221 " =    1.050
peak=    3.882 closest distance to " CA  THR A 221 " =    0.969
peak=    3.879 closest distance to " O   HOH Z 369 " =    1.984
peak=    3.878 closest distance to " CG  PRO A 198 " =    1.416
peak=    3.868 closest distance to " O   HOH Z 128 " =    2.136
peak=    3.860 closest distance to " O   HOH Z 284 " =    2.923
peak=    3.855 closest distance to " O   HOH Z 126 " =    1.706
peak=    3.847 closest distance to " CG  ARG A  66 " =    2.654
peak=    3.846 closest distance to " NH1AARG A 145 " =    1.071
peak=    3.835 closest distance to " O   HOH Z 358 " =    2.124
peak=    3.818 closest distance to " NH2BARG A 145 " =    1.969
peak=    3.807 closest distance to " O   HOH Z 227 " =    1.732
peak=    3.784 closest distance to " O   HOH Z 102 " =    1.245
peak=    3.778 closest distance to " O   HOH Z  30 " =    1.432
peak=    3.778 closest distance to " CB  ARG A 139 " =    1.037
peak=    3.758 closest distance to " CB  ARG A 190 " =    1.648
peak=    3.756 closest distance to " O   HOH Z  88 " =    3.313
peak=    3.756 closest distance to " O   HOH Z 132 " =    2.459
peak=    3.755 closest distance to " O   HOH Z 406 " =    1.651
peak=    3.750 closest distance to " OE1 GLN A  11 " =    1.894
peak=    3.749 closest distance to " CG  PRO A  90 " =    1.110
peak=    3.746 closest distance to " O   HOH Z  21 " =    1.826
peak=    3.741 closest distance to " O   HOH Z 427 " =    2.739
peak=    3.721 closest distance to " O   HOH Z 147 " =    1.770
peak=    3.721 closest distance to " CB  SER A 141 " =    0.979
peak=    3.719 closest distance to " CD  LYS A 166 " =    1.404
peak=    3.713 closest distance to " CG AARG A 275 " =    0.931
peak=    3.709 closest distance to " CB  TRP A 179 " =    1.366
peak=    3.708 closest distance to " CB  PRO A  54 " =    1.235
peak=    3.707 closest distance to " N   ASN A  39 " =    1.271
peak=    3.702 closest distance to " O   HOH Z 118 " =    1.431
peak=    3.678 closest distance to " O   HOH Z 227 " =    1.706
peak=    3.674 closest distance to " O   HOH Z 345 " =    1.816
peak=    3.672 closest distance to " CG  GLN A  58 " =    2.483
peak=    3.665 closest distance to " O   HOH Z 278 " =    0.969
peak=    3.665 closest distance to " CB  ASN A 187 " =    1.153
peak=    3.657 closest distance to " O   HOH Z  35 " =    2.519
peak=    3.657 closest distance to " O   HOH Z  54 " =    2.304
peak=    3.653 closest distance to " CG  PRO A 243 " =    1.174
peak=    3.651 closest distance to " O   MET A 105 " =    1.779
peak=    3.651 closest distance to " O   HOH Z 197 " =    2.304
peak=    3.650 closest distance to " CA  ASP A 191 " =    0.840
peak=    3.629 closest distance to " CD2 LEU A 255 " =    1.174
peak=    3.628 closest distance to " O   HOH Z 189 " =    1.978
peak=    3.617 closest distance to " CB  ALA A 100 " =    1.241
peak=    3.610 closest distance to " O   HOH Z 423 " =    2.035
peak=    3.607 closest distance to " O   HOH Z 215 " =    1.522
peak=    3.602 closest distance to " CG2BVAL A  41 " =    0.897
peak=    3.600 closest distance to " O   ALA A 165 " =    1.299
peak=    3.600 closest distance to " O   HOH Z 163 " =    1.546
peak=    3.595 closest distance to " O   HOH Z  10 " =    1.798
peak=    3.592 closest distance to " O   HOH Z 419 " =    1.583
peak=    3.590 closest distance to " CD2 LEU A 297 " =    0.900
peak=    3.590 closest distance to " O   HOH Z 215 " =    1.567
peak=    3.589 closest distance to " CA  ASN A 176 " =    1.625
peak=    3.588 closest distance to " O   HOH Z 416 " =    2.721
peak=    3.585 closest distance to " O   HOH Z 135 " =    1.725
peak=    3.581 closest distance to " CA  ARG A  36 " =    1.137
peak=    3.580 closest distance to " O   HOH Z 295 " =    1.442
peak=    3.574 closest distance to " O   HOH Z 334 " =    1.412
peak=    3.572 closest distance to " CB  ASN A 285 " =    0.902
peak=    3.569 closest distance to " O   HOH Z  61 " =    1.559
peak=    3.560 closest distance to " NZ  LYS A 117 " =    1.090
peak=    3.552 closest distance to " O   HOH Z 394 " =    1.671
peak=    3.547 closest distance to " CB  ARG A 259 " =    1.910
peak=    3.545 closest distance to " O   ALA A 158 " =    1.213
peak=    3.540 closest distance to " CD  PRO A  54 " =    1.149
peak=    3.535 closest distance to " O   HOH Z 425 " =    1.395
peak=    3.533 closest distance to " O   HOH Z  48 " =    1.442
peak=    3.523 closest distance to " CB  ASN A 148 " =    0.984
peak=    3.518 closest distance to " OG  SER A  62 " =    3.087
peak=    3.510 closest distance to " O   HOH Z 207 " =    1.964
peak=    3.500 closest distance to " O   HOH Z 173 " =    2.075
peak=    3.492 closest distance to " O   HOH Z 292 " =    1.674
peak=    3.491 closest distance to " O   HOH Z 303 " =    2.073
peak=    3.486 closest distance to " O   HOH Z 116 " =    1.790
peak=    3.484 closest distance to " O   HOH Z 368 " =    2.464
peak=    3.470 closest distance to " O   HOH Z 327 " =    1.855
peak=    3.469 closest distance to " O   HOH Z 214 " =    2.099
peak=    3.467 closest distance to " O   HOH Z 388 " =    1.822
peak=    3.464 closest distance to " CG2AVAL A 121 " =    2.193
peak=    3.462 closest distance to " CB  ASN A  39 " =    0.804
peak=    3.459 closest distance to " O   HOH Z 166 " =    1.483
peak=    3.457 closest distance to " O   HOH Z 263 " =    2.276
peak=    3.455 closest distance to " O   HOH Z 276 " =    1.409
peak=    3.455 closest distance to " O   TRP A 274 " =    1.757
peak=    3.452 closest distance to " CZ2 TRP A 179 " =    1.745
peak=    3.449 closest distance to " CG  GLN A  89 " =    1.370
peak=    3.442 closest distance to " O   HOH Z  44 " =    1.921
peak=    3.441 closest distance to " O   HOH Z 427 " =    3.109
peak=    3.441 closest distance to " O   HOH Z 255 " =    1.665
peak=    3.437 closest distance to " O   HOH Z 106 " =    1.453
peak=    3.436 closest distance to " OD1 ASP A 238 " =    0.841
peak=    3.436 closest distance to " O   HOH Z 132 " =    1.911
peak=    3.430 closest distance to " O   HOH Z 281 " =    4.081
peak=    3.426 closest distance to " CD1 LEU A 300 " =    1.227
peak=    3.426 closest distance to " O   HOH Z 346 " =    1.582
peak=    3.423 closest distance to " O   HOH Z 266 " =    1.707
peak=    3.419 closest distance to " CB  PRO A 198 " =    0.977
peak=    3.416 closest distance to " O   HOH Z 341 " =    1.699
peak=    3.413 closest distance to " O   SER A  26 " =    1.709
peak=    3.411 closest distance to " CD  ARG A 269 " =    0.902
peak=    3.411 closest distance to " O   HOH Z 128 " =    2.162
peak=    3.402 closest distance to " CG2 ILE A 120 " =    1.162
peak=    3.399 closest distance to " O   HOH Z  61 " =    1.526
peak=    3.399 closest distance to " OG BSER A 258 " =    3.495
peak=    3.394 closest distance to " CB  SER A  62 " =    1.231
peak=    3.394 closest distance to " O   HOH Z 438 " =    2.379
peak=    3.389 closest distance to " CA  ASN A 215 " =    1.185
peak=    3.382 closest distance to " N   ASN A 127 " =    1.253
peak=    3.381 closest distance to " CD2 TRP A 179 " =    1.329
peak=    3.377 closest distance to " O   HOH Z 209 " =    2.354
peak=    3.374 closest distance to " CA  ASP A 140 " =    1.150
peak=    3.372 closest distance to " CA  ALA A  51 " =    0.811
peak=    3.370 closest distance to " O   HOH Z 336 " =    1.695
peak=    3.370 closest distance to " O   HOH Z 411 " =    1.695
peak=    3.367 closest distance to " O   HOH Z 248 " =    1.555
peak=    3.367 closest distance to " CD  LYS A 119 " =    1.555
peak=    3.366 closest distance to " CB  GLN A  88 " =    1.231
peak=    3.363 closest distance to " CA  MET A  40 " =    1.059
peak=    3.361 closest distance to " O   HOH Z 357 " =    1.975
peak=    3.361 closest distance to " O   HOH Z 285 " =    1.950
peak=    3.348 closest distance to " O   HOH Z 380 " =    1.903
peak=    3.346 closest distance to " O   HOH Z 332 " =    1.440
peak=    3.345 closest distance to " O   HOH Z 245 " =    1.370
peak=    3.328 closest distance to " ND1 HIS A  81 " =    1.602
peak=    3.324 closest distance to " CB  TRP A 150 " =    1.603
peak=    3.316 closest distance to " O   HOH Z 163 " =    1.844
peak=    3.314 closest distance to " O   HOH Z 355 " =    1.705
peak=    3.311 closest distance to " O   HOH Z 250 " =    1.661
peak=    3.310 closest distance to " CB  ALA A   1 " =    1.188
peak=    3.305 closest distance to " CA  LYS A 117 " =    1.266
peak=    3.304 closest distance to " NE AARG A 275 " =    1.370
peak=    3.302 closest distance to " CA  ASP A 124 " =    0.740
peak=    3.300 closest distance to " CA  ARG A 195 " =    1.259
peak=    3.299 closest distance to " CD BLYS A 290 " =    1.203
peak=    3.297 closest distance to " NZ  LYS A 119 " =    1.812
peak=    3.295 closest distance to " O   HOH Z 234 " =    1.811
peak=    3.295 closest distance to " CG2 THR A 220 " =    0.970
peak=    3.292 closest distance to " CB  ALA A   9 " =    1.508
peak=    3.291 closest distance to " CG  MET A 185 " =    1.238
peak=    3.291 closest distance to " CG2 VAL A 112 " =    1.613
peak=    3.289 closest distance to " O   HOH Z  63 " =    2.184
peak=    3.282 closest distance to " O   ALA A   1 " =    1.450
peak=    3.280 closest distance to " O   HOH Z 329 " =    3.448
peak=    3.277 closest distance to " O   HOH Z  44 " =    3.221
peak=    3.277 closest distance to " OD1 ASN A  60 " =    1.181
peak=    3.273 closest distance to " O   HOH Z 157 " =    1.637
peak=    3.270 closest distance to " CG2 VAL A 197 " =    1.181
peak=    3.266 closest distance to " O   HOH Z 327 " =    2.614
peak=    3.246 closest distance to " CA  GLN A 223 " =    0.839
peak=    3.245 closest distance to " OE1 GLN A  58 " =    5.895
peak=    3.242 closest distance to " CA  GLY A 267 " =    1.035
peak=    3.238 closest distance to " N   PHE A 130 " =    1.402
peak=    3.233 closest distance to " CA  ILE A  33 " =    1.655
peak=    3.231 closest distance to " CG  GLU A 277 " =    2.143
peak=    3.231 closest distance to " CB  THR A  31 " =    1.773
peak=    3.226 closest distance to " O   HOH Z 337 " =    3.731
peak=    3.226 closest distance to " O   HOH Z 189 " =    1.435
peak=    3.222 closest distance to " CB  TYR A  30 " =    1.374
peak=    3.221 closest distance to " CG1 VAL A 153 " =    1.049
peak=    3.220 closest distance to " CG  MET A  93 " =    1.031
peak=    3.218 closest distance to " O   HOH Z 250 " =    1.439
peak=    3.213 closest distance to " OG  SER A  22 " =    2.871
peak=    3.210 closest distance to " CD  ARG A 195 " =    0.916
peak=    3.206 closest distance to " CB  GLN A 278 " =    0.827
peak=    3.205 closest distance to " C   PRO A 163 " =    1.695
peak=    3.201 closest distance to " CB  VAL A 265 " =    1.244
peak=    3.201 closest distance to " O   HOH Z 291 " =    1.513
peak=    3.200 closest distance to " CA  VAL A 126 " =    0.972
peak=    3.200 closest distance to " OD2 ASP A 298 " =    4.067
peak=    3.196 closest distance to " O   HOH Z 194 " =    1.939
peak=    3.196 closest distance to " CH2 TRP A 274 " =    2.232
peak=    3.193 closest distance to " O   HOH Z 273 " =    2.693
peak=    3.193 closest distance to " O   HOH Z 166 " =    3.220
peak=    3.192 closest distance to " O   HOH Z 106 " =    2.224
peak=    3.186 closest distance to " O   HOH Z 261 " =    2.081
peak=    3.186 closest distance to " NZ  LYS A  76 " =    1.213
peak=    3.185 closest distance to " O   HOH Z 192 " =    1.975
peak=    3.184 closest distance to " O   HOH Z 150 " =    1.597
peak=    3.177 closest distance to " NE2 GLN A  58 " =    4.400
peak=    3.173 closest distance to " O   HOH Z 402 " =    1.464
peak=    3.172 closest distance to " CB  ALA A 244 " =    0.920
peak=    3.169 closest distance to " CD1 ILE A 106 " =    0.937
peak=    3.164 closest distance to " CB  ALA A 291 " =    1.241
peak=    3.162 closest distance to " O   GLY A 211 " =    1.276
peak=    3.162 closest distance to " NH1BARG A 145 " =    1.093
peak=    3.155 closest distance to " NH2 ARG A  79 " =    1.278
peak=    3.152 closest distance to " CG  GLN A  55 " =    2.245
peak=    3.150 closest distance to " O   HOH Z 134 " =    3.755
peak=    3.149 closest distance to " O   HOH Z 162 " =    1.519
peak=    3.148 closest distance to " CA  GLU A 152 " =    0.871
peak=    3.147 closest distance to " O   HOH Z 425 " =    2.178
peak=    3.145 closest distance to " CZ3 TRP A  85 " =    1.052
peak=    3.145 closest distance to " CB  SER A  62 " =    0.758
peak=    3.144 closest distance to " CA  ASN A  74 " =    1.135
peak=    3.142 closest distance to " CB  ALA A 256 " =    1.175
peak=    3.140 closest distance to " CA  SER A  87 " =    0.903
peak=    3.139 closest distance to " CA  LEU A 282 " =    1.236
peak=    3.137 closest distance to " NZ  LYS A 166 " =    2.933
peak=    3.136 closest distance to " O   HOH Z 156 " =    2.913
peak=    3.134 closest distance to " O   HOH Z 339 " =    2.121
peak=    3.124 closest distance to " O   HOH Z 353 " =    2.774
peak=    3.119 closest distance to " O   HOH Z 387 " =    2.472
peak=    3.116 closest distance to " CB  TRP A 266 " =    0.908
peak=    3.115 closest distance to " O   HOH Z 362 " =    3.461
peak=    3.114 closest distance to " O   HOH Z  71 " =    1.114
peak=    3.111 closest distance to " O   GLN A  58 " =    1.611
peak=    3.109 closest distance to " O   THR A  31 " =    1.539
peak=    3.107 closest distance to " O   HOH Z  19 " =    1.632
peak=    3.105 closest distance to " CB  MET A  40 " =    0.943
peak=    3.104 closest distance to " CG1 VAL A 202 " =    2.108
peak=    3.103 closest distance to " CD2 HIS A  81 " =    1.213
peak=    3.103 closest distance to " CB  THR A 157 " =    1.021
peak=    3.096 closest distance to " CA  ASP A 162 " =    1.139
peak=    3.096 closest distance to " CG  LEU A 167 " =    1.188
peak=    3.094 closest distance to " CA  ALA A 248 " =    1.162
peak=    3.089 closest distance to " O   HOH Z  63 " =    2.090
peak=    3.084 closest distance to " CA  ALA A 158 " =    1.094
peak=    3.079 closest distance to " OD2 ASP A 286 " =    3.243
peak=    3.077 closest distance to " CG BARG A 102 " =    1.818
peak=    3.076 closest distance to " O   HOH Z  50 " =    3.464
peak=    3.072 closest distance to " O   HOH Z 299 " =    2.243
peak=    3.060 closest distance to " O   HOH Z 280 " =    2.427
peak=    3.059 closest distance to " CA  LEU A 101 " =    1.498
peak=    3.056 closest distance to " O   HOH Z 427 " =    3.340
peak=    3.052 closest distance to " O   HOH Z 155 " =    2.857
peak=    3.051 closest distance to " N   SER A 135 " =    1.329
peak=    3.040 closest distance to " O   HOH Z 109 " =    2.749
peak=    3.037 closest distance to " O   HOH Z   4 " =    1.866
peak=    3.036 closest distance to " O   HOH Z  73 " =    1.850
peak=    3.028 closest distance to " O   HOH Z 280 " =    2.805
peak=    3.015 closest distance to " O  BHOH Z 338 " =    2.314

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.574 - 5.311
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 211
   mapped sites are within: 0.774 - 5.311

peak=   -4.448 closest distance to " O   VAL A  67 " =    2.721
peak=   -4.442 closest distance to " O   HOH Z 266 " =    4.075
peak=   -4.417 closest distance to " CD  ARG A 156 " =    1.948
peak=   -4.298 closest distance to " OXT GLY A 302 " =    2.899
peak=   -4.281 closest distance to " O   HOH Z 290 " =    0.961
peak=   -4.240 closest distance to " NE2 GLN A  58 " =    0.945
peak=   -4.151 closest distance to " O   HOH Z  17 " =    1.219
peak=   -4.094 closest distance to " O   HOH Z  52 " =    1.589
peak=   -4.056 closest distance to " O   HOH Z  13 " =    1.436
peak=   -4.039 closest distance to " N   GLN A  58 " =    1.718
peak=   -4.029 closest distance to " O   HOH Z  10 " =    1.537
peak=   -3.995 closest distance to " O   HOH Z  11 " =    1.597
peak=   -3.963 closest distance to " CB  ALA A 161 " =    2.592
peak=   -3.955 closest distance to " CD2 LEU A 300 " =    2.902
peak=   -3.948 closest distance to " CD1 LEU A 101 " =    2.546
peak=   -3.930 closest distance to " OG ASER A 134 " =    1.346
peak=   -3.910 closest distance to " O   HOH Z 234 " =    4.271
peak=   -3.897 closest distance to " CB  ALA A 291 " =    2.376
peak=   -3.887 closest distance to " NH2 ARG A  66 " =    1.629
peak=   -3.886 closest distance to " C   HIS A 108 " =    1.102
peak=   -3.881 closest distance to " O   HOH Z  43 " =    1.695
peak=   -3.881 closest distance to " CG2 THR A   4 " =    1.921
peak=   -3.869 closest distance to " O   VAL A  67 " =    2.831
peak=   -3.852 closest distance to " CD  ARG A 139 " =    1.657
peak=   -3.848 closest distance to " OG  SER A  97 " =    2.189
peak=   -3.825 closest distance to " O   HOH Z  97 " =    1.632
peak=   -3.823 closest distance to " O   HOH Z  15 " =    1.553
peak=   -3.820 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -3.811 closest distance to " CH2 TRP A 179 " =    1.190
peak=   -3.798 closest distance to " O   HOH Z 166 " =    1.919
peak=   -3.781 closest distance to " O   HOH Z 407 " =    3.436
peak=   -3.780 closest distance to " O   HOH Z 353 " =    2.308
peak=   -3.775 closest distance to " O   PRO A 163 " =    2.078
peak=   -3.758 closest distance to " O   HOH Z 377 " =    1.873
peak=   -3.756 closest distance to " O   HOH Z 292 " =    4.480
peak=   -3.747 closest distance to " O   PRO A 198 " =    1.323
peak=   -3.737 closest distance to " OE2 GLU A   2 " =    1.579
peak=   -3.734 closest distance to " O   GLY A 118 " =    2.288
peak=   -3.725 closest distance to " C   ALA A 158 " =    1.223
peak=   -3.717 closest distance to " O   HOH Z 151 " =    1.458
peak=   -3.708 closest distance to " O   HOH Z  92 " =    1.540
peak=   -3.702 closest distance to " O   HOH Z 377 " =    1.159
peak=   -3.700 closest distance to " O   HOH Z  19 " =    2.086
peak=   -3.698 closest distance to " O   HOH Z 396 " =    1.580
peak=   -3.694 closest distance to " O   HOH Z  93 " =    1.313
peak=   -3.693 closest distance to " N   SER A 276 " =    1.399
peak=   -3.691 closest distance to " O   HOH Z  76 " =    2.093
peak=   -3.686 closest distance to " CD2 LEU A 237 " =    2.648
peak=   -3.681 closest distance to " ND2 ASN A 187 " =    1.508
peak=   -3.676 closest distance to " O   HOH Z 221 " =    1.170
peak=   -3.674 closest distance to " O   HOH Z 311 " =    3.580
peak=   -3.658 closest distance to " O   SER A 210 " =    1.843
peak=   -3.655 closest distance to " CD1 LEU A 228 " =    2.351
peak=   -3.652 closest distance to " OG BSER A 134 " =    1.771
peak=   -3.642 closest distance to " CG  ASP A  50 " =    2.405
peak=   -3.640 closest distance to " O   GLY A 196 " =    1.112
peak=   -3.639 closest distance to " CB  CYS A 254 " =    2.489
peak=   -3.637 closest distance to " CE  MET A  93 " =    1.181
peak=   -3.625 closest distance to " CB  TYR A  15 " =    2.228
peak=   -3.616 closest distance to " NH1 ARG A 195 " =    2.543
peak=   -3.615 closest distance to " CG  GLU A  53 " =    1.522
peak=   -3.612 closest distance to " CE  MET A 105 " =    1.873
peak=   -3.611 closest distance to " CD1 PHE A  59 " =    1.925
peak=   -3.600 closest distance to " CB  ASN A  39 " =    2.272
peak=   -3.596 closest distance to " CB  SER A 258 " =    1.993
peak=   -3.596 closest distance to " O   HOH Z  98 " =    1.867
peak=   -3.595 closest distance to " NH2 ARG A  79 " =    1.889
peak=   -3.595 closest distance to " CB  PRO A 243 " =    2.596
peak=   -3.592 closest distance to " O   HOH Z 313 " =    1.022
peak=   -3.580 closest distance to " CG  LEU A  83 " =    2.011
peak=   -3.579 closest distance to " SG  CYS A 254 " =    3.205
peak=   -3.571 closest distance to " O   VAL A 125 " =    2.093
peak=   -3.563 closest distance to " CG  ASP A 231 " =    0.774
peak=   -3.563 closest distance to " O   HOH Z 388 " =    2.130
peak=   -3.558 closest distance to " OG  SER A  62 " =    1.400
peak=   -3.539 closest distance to " OE1 GLN A  77 " =    1.613
peak=   -3.533 closest distance to " O   HOH Z 165 " =    2.087
peak=   -3.533 closest distance to " O   ALA A 256 " =    1.535
peak=   -3.526 closest distance to " O   HOH Z 118 " =    3.031
peak=   -3.525 closest distance to " N   ALA A  43 " =    2.572
peak=   -3.517 closest distance to " OD1 ASN A 148 " =    1.697
peak=   -3.514 closest distance to " SG ACYS A 201 " =    2.265
peak=   -3.513 closest distance to " CD1 PHE A 130 " =    2.258
peak=   -3.509 closest distance to " CD2 PHE A  59 " =    2.435
peak=   -3.508 closest distance to " ND2 ASN A  45 " =    0.991
peak=   -3.505 closest distance to " CB  LEU A 167 " =    2.166
peak=   -3.493 closest distance to " ND2 ASN A  60 " =    1.465
peak=   -3.491 closest distance to " O   HOH Z  38 " =    1.372
peak=   -3.482 closest distance to " NH2 ARG A  66 " =    4.981
peak=   -3.473 closest distance to " O   HOH Z 236 " =    1.296
peak=   -3.472 closest distance to " CG  GLN A  58 " =    1.304
peak=   -3.470 closest distance to " O   HOH Z 196 " =    2.195
peak=   -3.452 closest distance to " OG  SER A  26 " =    1.190
peak=   -3.447 closest distance to " CZ  TYR A 169 " =    1.817
peak=   -3.431 closest distance to " CB  PRO A 163 " =    2.762
peak=   -3.430 closest distance to " O   TRP A  92 " =    1.875
peak=   -3.427 closest distance to " CD  GLN A  88 " =    2.100
peak=   -3.424 closest distance to " N   MET A 188 " =    1.848
peak=   -3.415 closest distance to " O   HOH Z 418 " =    1.388
peak=   -3.407 closest distance to " CD1 PHE A  16 " =    2.687
peak=   -3.391 closest distance to " O   ASN A  45 " =    1.901
peak=   -3.386 closest distance to " OG BSER A 134 " =    1.294
peak=   -3.384 closest distance to " OD2 ASP A 171 " =    2.379
peak=   -3.383 closest distance to " O   HOH Z  71 " =    1.174
peak=   -3.374 closest distance to " CG  LYS A 193 " =    2.533
peak=   -3.374 closest distance to " N   ALA A 226 " =    2.039
peak=   -3.369 closest distance to " O   HOH Z 423 " =    2.373
peak=   -3.368 closest distance to " NH2AARG A 275 " =    5.311
peak=   -3.346 closest distance to " O   VAL A 174 " =    2.049
peak=   -3.339 closest distance to " SD  MET A 188 " =    2.208
peak=   -3.334 closest distance to " OG  SER A  87 " =    1.327
peak=   -3.332 closest distance to " CG  GLU A  44 " =    2.135
peak=   -3.328 closest distance to " O   HOH Z 266 " =    4.673
peak=   -3.326 closest distance to " CB  ASP A 132 " =    2.339
peak=   -3.324 closest distance to " O   HOH Z 198 " =    2.485
peak=   -3.323 closest distance to " O   HOH Z 241 " =    1.288
peak=   -3.322 closest distance to " O   HOH Z 427 " =    1.433
peak=   -3.314 closest distance to " O   HOH Z 385 " =    2.073
peak=   -3.307 closest distance to " C   LEU A 143 " =    1.241
peak=   -3.302 closest distance to " N   GLY A 133 " =    1.799
peak=   -3.299 closest distance to " O   ALA A 160 " =    1.534
peak=   -3.298 closest distance to " NH2 ARG A 159 " =    2.375
peak=   -3.298 closest distance to " O   HOH Z 417 " =    2.531
peak=   -3.296 closest distance to " OD1 ASP A 191 " =    1.726
peak=   -3.290 closest distance to " CG2 VAL A 189 " =    2.208
peak=   -3.286 closest distance to " CG1AVAL A  41 " =    2.664
peak=   -3.285 closest distance to " CB  PHE A 208 " =    2.236
peak=   -3.285 closest distance to " N   GLN A 122 " =    1.657
peak=   -3.284 closest distance to " O   HOH Z 265 " =    1.946
peak=   -3.279 closest distance to " O   PHE A 218 " =    1.517
peak=   -3.274 closest distance to " CZ  ARG A  66 " =    1.034
peak=   -3.273 closest distance to " CE3 TRP A 150 " =    1.946
peak=   -3.272 closest distance to " O   HOH Z 185 " =    2.298
peak=   -3.270 closest distance to " O   ASP A 191 " =    1.391
peak=   -3.266 closest distance to " CG  ARG A  66 " =    2.369
peak=   -3.266 closest distance to " ND2 ASN A 249 " =    2.172
peak=   -3.265 closest distance to " N   ALA A 248 " =    1.746
peak=   -3.264 closest distance to " O   HOH Z 213 " =    1.250
peak=   -3.264 closest distance to " C   SER A 206 " =    1.547
peak=   -3.259 closest distance to " ND2 ASN A  45 " =    1.190
peak=   -3.252 closest distance to " OD2 ASP A 171 " =    2.541
peak=   -3.252 closest distance to " O   HOH Z 412 " =    4.856
peak=   -3.249 closest distance to " O   ASN A 187 " =    1.458
peak=   -3.249 closest distance to " CA  GLY A 241 " =    2.266
peak=   -3.248 closest distance to " O   HOH Z 128 " =    2.506
peak=   -3.247 closest distance to " CD  ARG A 195 " =    5.161
peak=   -3.247 closest distance to " O   HOH Z  88 " =    1.840
peak=   -3.246 closest distance to " O   HOH Z 361 " =    3.417
peak=   -3.245 closest distance to " O   LEU A 167 " =    1.587
peak=   -3.245 closest distance to " C   ASN A 285 " =    2.492
peak=   -3.244 closest distance to " CD2 TYR A 293 " =    2.103
peak=   -3.243 closest distance to " OE1 GLN A 223 " =    2.270
peak=   -3.239 closest distance to " N   VAL A 189 " =    1.761
peak=   -3.238 closest distance to " O   HOH Z  20 " =    1.397
peak=   -3.237 closest distance to " CD1 ILE A 109 " =    2.541
peak=   -3.237 closest distance to " O   HOH Z   6 " =    1.671
peak=   -3.236 closest distance to " O   HOH Z  90 " =    3.083
peak=   -3.236 closest distance to " OD1 ASP A 171 " =    1.610
peak=   -3.236 closest distance to " O   HOH Z 283 " =    1.810
peak=   -3.235 closest distance to " O   PRO A 198 " =    1.311
peak=   -3.235 closest distance to " CD  GLN A  58 " =    1.367
peak=   -3.231 closest distance to " O   HOH Z 435 " =    2.528
peak=   -3.229 closest distance to " CD2 LEU A 167 " =    1.687
peak=   -3.226 closest distance to " O   HOH Z 350 " =    1.571
peak=   -3.221 closest distance to " O   HOH Z  98 " =    1.628
peak=   -3.221 closest distance to " O   HOH Z 264 " =    1.879
peak=   -3.219 closest distance to " O   HOH Z 384 " =    2.320
peak=   -3.214 closest distance to " OH  TYR A 172 " =    1.676
peak=   -3.211 closest distance to " CB  TRP A  85 " =    2.505
peak=   -3.203 closest distance to " OD1 ASN A 176 " =    1.094
peak=   -3.202 closest distance to " CD  LYS A 289 " =    2.510
peak=   -3.191 closest distance to " O   SER A 146 " =    0.952
peak=   -3.187 closest distance to " CB  ALA A 248 " =    1.951
peak=   -3.180 closest distance to " ND2 ASN A  60 " =    1.640
peak=   -3.175 closest distance to " CG  ARG A 269 " =    2.240
peak=   -3.172 closest distance to " N   THR A 157 " =    1.650
peak=   -3.167 closest distance to " O   HOH Z 385 " =    3.668
peak=   -3.166 closest distance to " O   PRO A 198 " =    2.284
peak=   -3.165 closest distance to " O   PRO A 198 " =    1.737
peak=   -3.158 closest distance to " O   HOH Z  90 " =    1.984
peak=   -3.157 closest distance to " CE1 TYR A 169 " =    2.325
peak=   -3.156 closest distance to " CG  LYS A 119 " =    2.880
peak=   -3.150 closest distance to " NE2 GLN A 103 " =    1.547
peak=   -3.149 closest distance to " CB  ASP A 286 " =    2.320
peak=   -3.146 closest distance to " O   HOH Z 424 " =    2.944
peak=   -3.141 closest distance to " CA  TRP A 274 " =    1.660
peak=   -3.139 closest distance to " CG  PRO A 163 " =    2.534
peak=   -3.135 closest distance to " CA  VAL A 197 " =    0.955
peak=   -3.132 closest distance to " CB  PHE A 192 " =    1.885
peak=   -3.127 closest distance to " O   HOH Z 310 " =    3.616
peak=   -3.126 closest distance to " CZ  ARG A 259 " =    0.810
peak=   -3.123 closest distance to " ND2 ASN A  39 " =    1.367
peak=   -3.121 closest distance to " CG2AVAL A  41 " =    2.780
peak=   -3.117 closest distance to " OG  SER A 206 " =    1.818
peak=   -3.110 closest distance to " O   HOH Z 242 " =    1.612
peak=   -3.109 closest distance to " O   HOH Z 148 " =    3.487
peak=   -3.099 closest distance to " CD2 LEU A 237 " =    2.655
peak=   -3.096 closest distance to " CB  ASP A 124 " =    2.144
peak=   -3.092 closest distance to " O   HOH Z 132 " =    1.308
peak=   -3.087 closest distance to " CA  ASP A 298 " =    1.114
peak=   -3.082 closest distance to " SG  CYS A 168 " =    1.075
peak=   -3.077 closest distance to " OD2 ASP A 171 " =    1.741
peak=   -3.053 closest distance to " CD1 TYR A 247 " =    2.394
peak=   -3.046 closest distance to " CD1 ILE A 263 " =    2.435
peak=   -3.043 closest distance to " O   HOH Z 421 " =    2.969
peak=   -3.037 closest distance to " CG  GLU A 152 " =    1.184
peak=   -3.025 closest distance to " O   ASN A 301 " =    1.379

================= 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    :  0.4387 0.4335   6.248997e+00   6.243362e+00
   1_bss:  0.4280 0.4216   6.241048e+00   6.226646e+00
   1_xyz:  0.3333 0.3617   6.053776e+00   6.117849e+00
   1_adp:  0.3046 0.3734   6.007399e+00   6.137970e+00
   1_occ:  0.3045 0.3740   6.006339e+00   6.137321e+00
   2_bss:  0.3033 0.3725   6.005950e+00   6.136435e+00
   2_xyz:  0.2131 0.2670   5.696865e+00   5.881278e+00
   2_adp:  0.1847 0.2406   5.573395e+00   5.778147e+00
   2_occ:  0.1844 0.2406   5.573166e+00   5.777865e+00
   3_bss:  0.1831 0.2397   5.568442e+00   5.773095e+00
   3_xyz:  0.1414 0.1895   5.338561e+00   5.564684e+00
   3_adp:  0.1333 0.1821   5.292850e+00   5.523986e+00
   3_occ:  0.1331 0.1822   5.292368e+00   5.524185e+00
   4_bss:  0.1334 0.1822   5.294625e+00   5.525446e+00
   4_xyz:  0.1276 0.1750   5.256230e+00   5.485290e+00
   4_adp:  0.1217 0.1680   5.217449e+00   5.445501e+00
   4_occ:  0.1216 0.1679   5.217153e+00   5.445555e+00
   5_bss:  0.1216 0.1679   5.216950e+00   5.445385e+00
   5_xyz:  0.1115 0.1618   5.157907e+00   5.406036e+00
   5_adp:  0.1114 0.1597   5.152560e+00   5.395513e+00
   5_occ:  0.1112 0.1596   5.152160e+00   5.395541e+00
   5_bss:  0.1112 0.1596   5.152160e+00   5.395541e+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:  0.329  50.000  -2.879   2.129   2.343   0.000   0.000   0.000
   1_xyz:  0.329  50.000  -2.879   2.129   2.343   0.000   0.000   0.000
   1_adp:  0.329  50.000  -2.879   2.129   2.343   0.000   0.000   0.000
   1_occ:  0.329  50.000  -2.879   2.129   2.343   0.000   0.000   0.000
   2_bss:  0.321  50.000  -2.034   0.649   0.486   0.000   0.000   0.000
   2_xyz:  0.321  50.000  -2.034   0.649   0.486   0.000   0.000   0.000
   2_adp:  0.321  50.000  -2.034   0.649   0.486   0.000   0.000   0.000
   2_occ:  0.321  50.000  -2.034   0.649   0.486   0.000   0.000   0.000
   3_bss:  0.309  49.993  -2.286  -1.085  -1.328  -0.000  -0.000  -0.000
   3_xyz:  0.309  49.993  -2.286  -1.085  -1.328  -0.000  -0.000  -0.000
   3_adp:  0.309  49.993  -2.286  -1.085  -1.328  -0.000  -0.000  -0.000
   3_occ:  0.309  49.993  -2.286  -1.085  -1.328  -0.000  -0.000  -0.000
   4_bss:  0.319  49.039  -2.547  -1.631  -1.838  -0.000  -0.000  -0.000
   4_xyz:  0.319  49.039  -2.547  -1.631  -1.838  -0.000  -0.000  -0.000
   4_adp:  0.319  49.039  -2.547  -1.631  -1.838  -0.000  -0.000  -0.000
   4_occ:  0.319  49.039  -2.547  -1.631  -1.838  -0.000  -0.000  -0.000
   5_bss:  0.320  49.038  -2.594  -1.882  -2.083  -0.000  -0.000  -0.000
   5_xyz:  0.320  49.038  -2.594  -1.882  -2.083  -0.000  -0.000  -0.000
   5_adp:  0.320  49.038  -2.594  -1.882  -2.083  -0.000  -0.000  -0.000
   5_occ:  0.320  49.038  -2.594  -1.882  -2.083  -0.000  -0.000  -0.000
   5_bss:  0.320  48.942  -2.498  -1.786  -1.987  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.963 0.4697  0.6262    60976.759
   1_bss:  51.919 0.4939  0.6726    56442.739
   1_xyz:  39.759 0.6449  0.8598    37006.020
   1_adp:  41.601 0.6218  0.8420    39620.444
   1_occ:  41.556 0.6223  0.8405    39538.041
   2_bss:  41.307 0.6254  0.8229    39276.479
   2_xyz:  27.934 0.7786  0.9833    19185.005
   2_adp:  23.986 0.8214  1.0038    15057.666
   2_occ:  24.006 0.8212  1.0033    15065.245
   3_bss:  23.784 0.8233  0.9610    14830.382
   3_xyz:  18.177 0.8777  0.9918     9134.117
   3_adp:  17.163 0.8874  0.9946     8504.747
   3_occ:  17.165 0.8875  0.9946     8510.984
   4_bss:  17.198 0.8872  0.9790     8569.825
   4_xyz:  16.211 0.8962  0.9839     7825.256
   4_adp:  15.388 0.9035  0.9825     7232.862
   4_occ:  15.385 0.9035  0.9824     7235.976
   5_bss:  15.378 0.9035  0.9763     7236.142
   5_xyz:  14.621 0.9097  0.9780     6668.234
   5_adp:  14.354 0.9121  0.9745     6549.814
   5_occ:  14.349 0.9122  0.9744     6551.587
   5_bss:  14.349 0.9122  0.9744     6551.587
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8796e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8796e-01
   1_xyz:   1.368  0.011  0.082 15.633  0.005  4.112   1.0367e-01
   1_adp:   1.368  0.011  0.082 15.633  0.005  4.112   1.0367e-01
   1_occ:   1.368  0.011  0.082 15.633  0.005  4.112   1.0367e-01
   2_bss:   1.368  0.011  0.082 15.633  0.005  4.112   1.0367e-01
   2_xyz:   1.287  0.009  0.086 14.809  0.004  4.112   8.9331e-02
   2_adp:   1.287  0.009  0.086 14.809  0.004  4.112   8.9331e-02
   2_occ:   1.287  0.009  0.086 14.809  0.004  4.112   8.9331e-02
   3_bss:   1.287  0.009  0.086 14.809  0.004  4.112   8.9331e-02
   3_xyz:   1.075  0.008  0.073 14.603  0.004  4.123   6.7064e-02
   3_adp:   1.075  0.008  0.073 14.603  0.004  4.123   6.7064e-02
   3_occ:   1.075  0.008  0.073 14.603  0.004  4.123   6.7064e-02
   4_bss:   1.075  0.008  0.073 14.603  0.004  4.123   6.7064e-02
   4_xyz:   0.952  0.006  0.068 14.308  0.003  4.126   5.3146e-02
   4_adp:   0.952  0.006  0.068 14.308  0.003  4.126   5.3146e-02
   4_occ:   0.952  0.006  0.068 14.308  0.003  4.126   5.3146e-02
   5_bss:   0.952  0.006  0.068 14.308  0.003  4.126   5.3146e-02
   5_xyz:   1.165  0.010  0.082 14.860  0.005  4.114   7.5972e-02
   5_adp:   1.165  0.010  0.082 14.860  0.005  4.114   7.5972e-02
   5_occ:   1.165  0.010  0.082 14.860  0.005  4.114   7.5972e-02
   5_bss:   1.165  0.010  0.082 14.860  0.005  4.114   7.5972e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.455   2.4143e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.455   2.4143e-01
   1_xyz:   9.359  0.063  0.396 86.544  0.032  2.026   9.3322e-02
   1_adp:   9.359  0.063  0.396 86.544  0.032  2.026   9.3322e-02
   1_occ:   9.359  0.063  0.396 86.544  0.032  2.026   9.3322e-02
   2_bss:   9.359  0.063  0.396 86.544  0.032  2.026   9.3322e-02
   2_xyz:   8.041  0.066  0.284 87.141  0.025  2.203   1.2765e-01
   2_adp:   8.041  0.066  0.284 87.141  0.025  2.203   1.2765e-01
   2_occ:   8.041  0.066  0.284 87.141  0.025  2.203   1.2765e-01
   3_bss:   8.041  0.066  0.284 87.141  0.025  2.203   1.2765e-01
   3_xyz:   7.103  0.055  0.265 81.965  0.033  2.326   5.7637e-02
   3_adp:   7.103  0.055  0.265 81.965  0.033  2.326   5.7637e-02
   3_occ:   7.103  0.055  0.265 81.965  0.033  2.326   5.7637e-02
   4_bss:   7.103  0.055  0.265 81.965  0.033  2.326   5.7637e-02
   4_xyz:   6.555  0.040  0.222 82.673  0.027  2.379   3.4891e-02
   4_adp:   6.555  0.040  0.222 82.673  0.027  2.379   3.4891e-02
   4_occ:   6.555  0.040  0.222 82.673  0.027  2.379   3.4891e-02
   5_bss:   6.555  0.040  0.222 82.673  0.027  2.379   3.4891e-02
   5_xyz:   7.612  0.054  0.252 82.117  0.031  2.231   6.7931e-02
   5_adp:   7.612  0.054  0.252 82.117  0.031  2.231   6.7931e-02
   5_occ:   7.612  0.054  0.252 82.117  0.031  2.231   6.7931e-02
   5_bss:   7.612  0.054  0.252 82.117  0.031  2.231   6.7931e-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:  92.96   0.00  18.82  92.96   0.00  15.02  90.80   0.59  39.57
   1_occ:  92.96   0.00  18.82  92.96   0.00  15.02  90.80   0.59  39.57
   2_bss:  92.96   0.00  18.82  92.96   0.00  15.02  90.80   0.59  39.57
   2_xyz:  92.96   0.00  18.82  92.96   0.00  15.02  90.80   0.59  39.57
   2_adp:  91.55   0.00  18.38  91.55   0.00  13.92  87.30   5.91  42.66
   2_occ:  91.55   0.00  18.38  91.55   0.00  13.92  87.30   5.91  42.66
   3_bss:  91.55   0.00  18.38  91.55   0.00  13.92  87.30   5.91  42.66
   3_xyz:  91.55   0.00  18.38  91.55   0.00  13.92  87.30   5.91  42.66
   3_adp:  90.93   0.00  18.23  90.93   0.00  13.72  87.31   5.88  42.81
   3_occ:  90.93   0.00  18.23  90.93   0.00  13.72  87.31   5.88  42.81
   4_bss:  90.93   0.00  18.23  90.93   0.00  13.72  87.31   5.88  42.81
   4_xyz:  90.93   0.00  18.23  90.93   0.00  13.72  87.31   5.88  42.81
   4_adp:  92.46   1.77  17.87  92.46   1.77  13.31  87.05   5.37  42.66
   4_occ:  92.46   1.77  17.87  92.46   1.77  13.31  87.05   5.37  42.66
   5_bss:  92.46   1.77  17.87  92.46   1.77  13.31  87.05   5.37  42.66
   5_xyz:  92.46   1.77  17.87  92.46   1.77  13.31  87.05   5.37  42.66
   5_adp:  89.31   2.64  17.17  89.31   2.64  13.01  82.94   5.45  39.81
   5_occ:  89.31   2.64  17.17  89.31   2.64  13.01  82.94   5.45  39.81
   5_bss:  89.21   2.55  17.08  89.21   2.55  12.92  82.85   5.36  39.72
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.877    0.020    0.308
   1_adp:    1.877    0.020    0.308
   1_occ:    1.877    0.020    0.308
   2_bss:    1.877    0.020    0.308
   2_xyz:    1.470    0.058    0.588
   2_adp:    1.470    0.058    0.588
   2_occ:    1.470    0.058    0.588
   3_bss:    1.470    0.058    0.588
   3_xyz:    1.517    0.060    0.659
   3_adp:    1.517    0.060    0.659
   3_occ:    1.517    0.060    0.659
   4_bss:    1.517    0.060    0.659
   4_xyz:    1.582    0.079    0.682
   4_adp:    1.582    0.079    0.682
   4_occ:    1.582    0.079    0.682
   5_bss:    1.582    0.079    0.682
   5_xyz:    1.713    0.089    0.706
   5_adp:    1.713    0.089    0.706
   5_occ:    1.713    0.089    0.706
   5_bss:    1.713    0.089    0.706
------------------------------------------------------------------------

CPU time actual refinement: 342.66


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_814/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_814/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_814/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_814/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_814/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.50 
  Macro-tasks:
    bulk solvent and scale       = 36.16  
    individual site refinement   = 142.84 
    weights calculation          = 28.48  
    collect and process          = 5.98   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.57 
  Micro-tasks:
    mask                            = 1.88   
    f_calc                          = 115.41 
    alpha_beta                      = 8.05   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 122.71 
    fmodel                         = 6.40   
    r_factors                      = 0.18   
    phase_errors                   = 10.70  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 266.80 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.907 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    638 calls, 115.07 s
gradients_fft:          583 calls, 109.87 s

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

# Date 2008-01-16 Time 05:43:16 PST -0800 (1200490996.82 s)
Start R-work = 0.4387, R-free = 0.4335 (no bulk solvent and anisotropic scale)
Final R-work = 0.1362, R-free = 0.1811 (no bulk solvent and anisotropic scale)

Start R-work = 0.4280, R-free = 0.4216
Final R-work = 0.1112, R-free = 0.1596