Starting phenix.real_space_refine
on Tue Feb  3 14:43:13 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9ne5_49295/02_2026/9ne5_49295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ne5_49295/02_2026/9ne5_49295.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ne5_49295/02_2026/9ne5_49295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ne5_49295/02_2026/9ne5_49295.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ne5_49295/02_2026/9ne5_49295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ne5_49295/02_2026/9ne5_49295.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    2467      2.51       5
     N     636      2.21       5
     O     698      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3826
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 3826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3826
          Classifications: {'peptide': 468}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 442}
          Chain breaks: 2
  Time building chain proxies: 0.77, per 1000 atoms: 0.20
  Number of scatterers: 3826
  At special positions: 0
  Unit cell: (109.026, 67.8384, 86.0094, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O     698      8.00
     N     636      7.00
     C    2467      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 81.3 milliseconds
  

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  884

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 1 sheets defined
      55.3% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'B' and resid 74 through 88
    Processing helix  chain 'B' and resid 112 through 129
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 3.835A  pdb=" N   LEU B 141 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 164
      removed outlier: 3.673A  pdb=" N   VAL B 151 " --> pdb=" O   ASN B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 190 through 206
    Processing helix  chain 'B' and resid 220 through 224
    Processing helix  chain 'B' and resid 231 through 241
    Processing helix  chain 'B' and resid 260 through 272
      removed outlier: 3.985A  pdb=" N   ILE B 264 " --> pdb=" O   PRO B 260 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE B 270 " --> pdb=" O   GLU B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 307
      removed outlier: 4.396A  pdb=" N   ARG B 306 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 320
    Processing helix  chain 'B' and resid 321 through 334
    Processing helix  chain 'B' and resid 375 through 389
      removed outlier: 4.049A  pdb=" N   GLN B 389 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 392
      No H-bonds generated for 'chain 'B' and resid 390 through 392'
    Processing helix  chain 'B' and resid 554 through 565
    Processing helix  chain 'B' and resid 572 through 588
    Processing helix  chain 'B' and resid 589 through 592
    Processing helix  chain 'B' and resid 600 through 629
    Processing helix  chain 'B' and resid 634 through 639
    Processing helix  chain 'B' and resid 640 through 663
      removed outlier: 3.714A  pdb=" N   VAL B 644 " --> pdb=" O   MET B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 683 through 692
      removed outlier: 3.661A  pdb=" N   LEU B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 61 through 66
      removed outlier: 5.893A  pdb=" N   CYS B  62 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   LEU B  94 " --> pdb=" O   CYS B  62 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL B  64 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   PHE B 133 " --> pdb=" O   SER B 168 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   TYR B 135 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   LEU B 172 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ILE B 137 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   PHE B 212 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   LEU B 248 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   PHE B 214 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL B 247 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   TRP B 278 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   TRP B 249 " --> pdb=" O   TRP B 278 " (cutoff:3.500A)

    183 hydrogen bonds defined for protein.
    525 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.43

  Time building geometry restraints manager: 0.24 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 1216
        1.34 -     1.46: 855
        1.46 -     1.57: 1820
        1.57 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 3930
  Sorted by residual:
  bond pdb=" CA  ILE B 270 "
       pdb=" CB  ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.545  1.535  0.011 1.05e-02 9.07e+03 1.02e+00
  bond pdb=" C   ILE B 304 "
       pdb=" N   PRO B 305 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.28e-02 6.10e+03 7.99e-01
  bond pdb=" CA  THR B 327 "
       pdb=" C   THR B 327 "
    ideal  model  delta    sigma   weight residual
    1.523  1.512  0.011 1.30e-02 5.92e+03 7.08e-01
  bond pdb=" CA  ILE B 304 "
       pdb=" CB  ILE B 304 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 6.27e-01
  bond pdb=" CA  VAL B 323 "
       pdb=" C   VAL B 323 "
    ideal  model  delta    sigma   weight residual
    1.524  1.514  0.009 1.22e-02 6.72e+03 5.80e-01
  ... (remaining 3925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 5016
        0.91 -     1.83: 244
        1.83 -     2.74: 38
        2.74 -     3.65: 18
        3.65 -     4.57: 4
  Bond angle restraints: 5320
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     111.67  109.14    2.53 9.50e-01 1.11e+00 7.11e+00
  angle pdb=" C   ASN B  91 "
        pdb=" N   THR B  92 "
        pdb=" CA  THR B  92 "
      ideal   model   delta    sigma   weight residual
     122.74  118.79    3.95 1.54e+00 4.22e-01 6.58e+00
  angle pdb=" C   THR B 554 "
        pdb=" N   LEU B 555 "
        pdb=" CA  LEU B 555 "
      ideal   model   delta    sigma   weight residual
     120.38  123.82   -3.44 1.37e+00 5.33e-01 6.32e+00
  angle pdb=" C   ARG B 273 "
        pdb=" N   ALA B 274 "
        pdb=" CA  ALA B 274 "
      ideal   model   delta    sigma   weight residual
     120.67  117.61    3.06 1.34e+00 5.57e-01 5.22e+00
  angle pdb=" N   GLY B 674 "
        pdb=" CA  GLY B 674 "
        pdb=" C   GLY B 674 "
      ideal   model   delta    sigma   weight residual
     113.18  108.78    4.40 2.37e+00 1.78e-01 3.44e+00
  ... (remaining 5315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 2276
       17.78 -    35.56: 52
       35.56 -    53.34: 9
       53.34 -    71.13: 3
       71.13 -    88.91: 2
  Dihedral angle restraints: 2342
    sinusoidal: 969
      harmonic: 1373
  Sorted by residual:
  dihedral pdb=" CA  GLY B  63 "
           pdb=" C   GLY B  63 "
           pdb=" N   VAL B  64 "
           pdb=" CA  VAL B  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.93  -16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CA  PHE B 565 "
           pdb=" C   PHE B 565 "
           pdb=" N   TYR B 566 "
           pdb=" CA  TYR B 566 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.18  -15.82     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CA  TYR B 286 "
           pdb=" C   TYR B 286 "
           pdb=" N   ASP B 287 "
           pdb=" CA  ASP B 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.28   15.72     0      5.00e+00 4.00e-02 9.89e+00
  ... (remaining 2339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 327
       0.026 -    0.052: 137
       0.052 -    0.078: 56
       0.078 -    0.104: 20
       0.104 -    0.131: 17
  Chirality restraints: 557
  Sorted by residual:
  chirality pdb=" CA  VAL B 393 "
            pdb=" N   VAL B 393 "
            pdb=" C   VAL B 393 "
            pdb=" CB  VAL B 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE B 673 "
            pdb=" N   ILE B 673 "
            pdb=" C   ILE B 673 "
            pdb=" CB  ILE B 673 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.68e-01
  chirality pdb=" CA  VAL B  64 "
            pdb=" N   VAL B  64 "
            pdb=" C   VAL B  64 "
            pdb=" CB  VAL B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.67e-01
  ... (remaining 554 not shown)

  Planarity restraints: 681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 327 "   -0.010 2.00e-02 2.50e+03   1.90e-02 3.62e+00
        pdb=" C   THR B 327 "    0.033 2.00e-02 2.50e+03
        pdb=" O   THR B 327 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU B 328 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 324 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.14e+00
        pdb=" C   ALA B 324 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ALA B 324 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE B 325 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 323 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.12e+00
        pdb=" C   VAL B 323 "    0.031 2.00e-02 2.50e+03
        pdb=" O   VAL B 323 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA B 324 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 678 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 884
        2.78 -     3.31: 3575
        3.31 -     3.84: 6271
        3.84 -     4.37: 7127
        4.37 -     4.90: 12070
  Nonbonded interactions: 29927
  Sorted by model distance:
  nonbonded pdb=" N   ASN B 315 "
            pdb=" OD1 ASN B 321 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OH  TYR B 111 "
            pdb=" OH  TYR B 135 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   ALA B 324 "
            pdb=" OG1 THR B 327 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" OE1 GLU B  66 "
            pdb=" OH  TYR B  93 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OH  TYR B 548 "
            pdb=" OD1 ASN B 630 "
     model   vdw
     2.357 3.040
  ... (remaining 29922 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.200
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5497
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3930  Z= 0.145
  Angle     :  0.497   4.566   5320  Z= 0.289
  Chirality :  0.040   0.131    557
  Planarity :  0.004   0.027    681
  Dihedral  :  9.486  88.908   1458
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.39), residues: 462
  helix:  2.39 (0.35), residues: 228
  sheet: -0.39 (0.81), residues: 44
  loop : -0.01 (0.42), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 608 
 TYR   0.010   0.001   TYR B 296 
 PHE   0.016   0.001   PHE B 191 
 TRP   0.012   0.001   TRP B 278 
 HIS   0.002   0.001   HIS B 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3930)
  covalent geometry    : angle       0.49668 ( 5320)
  hydrogen bonds       : bond        0.13884 (  183)
  hydrogen bonds       : angle       5.37823 (  525)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 ARG cc_start: 0.7500 (ttp80) cc_final: 0.6595 (mtt90)
REVERT: B  239 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6589 (tm-30)
REVERT: B  651 MET cc_start: 0.8265 (mmt) cc_final: 0.7930 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0800
  time to fit residues: 11.4069
Evaluate side-chains
  71 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.0000
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0010
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.4192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.180739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.158543 restraints weight = 8572.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.4182 rms_B_bonded: 4.33
r_work: 0.4096 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3930  Z= 0.126
  Angle     :  0.542   4.729   5320  Z= 0.286
  Chirality :  0.043   0.153    557
  Planarity :  0.004   0.040    681
  Dihedral  :  4.390  13.984    515
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  :  7.71 %
    Favored  : 89.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.39), residues: 462
  helix:  2.23 (0.33), residues: 232
  sheet: -0.37 (0.80), residues: 44
  loop :  0.01 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 167 
 TYR   0.012   0.002   TYR B 638 
 PHE   0.020   0.002   PHE B 191 
 TRP   0.021   0.001   TRP B 660 
 HIS   0.004   0.001   HIS B 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3930)
  covalent geometry    : angle       0.54158 ( 5320)
  hydrogen bonds       : bond        0.04214 (  183)
  hydrogen bonds       : angle       4.38077 (  525)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 PHE cc_start: 0.7386 (t80) cc_final: 0.7097 (t80)
REVERT: B   83 ARG cc_start: 0.7795 (ttp80) cc_final: 0.6689 (mtt-85)
REVERT: B  100 ASP cc_start: 0.7325 (t0) cc_final: 0.6828 (t70)
REVERT: B  185 LYS cc_start: 0.5632 (mtmt) cc_final: 0.4792 (tptp)
REVERT: B  332 TYR cc_start: 0.7292 (t80) cc_final: 0.7016 (t80)
REVERT: B  639 ASP cc_start: 0.7710 (m-30) cc_final: 0.6251 (m-30)
REVERT: B  651 MET cc_start: 0.8677 (mmt) cc_final: 0.8250 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0534
  time to fit residues: 5.3553
Evaluate side-chains
  64 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  638 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0270
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0270
   overall best weight:    0.3896

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 559 GLN
B 666 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.179202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.157596 restraints weight = 8666.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 4.20
r_work: 0.4091 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3930  Z= 0.113
  Angle     :  0.512   7.679   5320  Z= 0.267
  Chirality :  0.041   0.157    557
  Planarity :  0.004   0.034    681
  Dihedral  :  4.132  14.350    515
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  8.92 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.39), residues: 462
  helix:  2.39 (0.33), residues: 232
  sheet: -0.40 (0.79), residues: 44
  loop : -0.11 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 167 
 TYR   0.009   0.001   TYR B 296 
 PHE   0.014   0.001   PHE B 191 
 TRP   0.008   0.001   TRP B 278 
 HIS   0.003   0.001   HIS B 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3930)
  covalent geometry    : angle       0.51175 ( 5320)
  hydrogen bonds       : bond        0.03630 (  183)
  hydrogen bonds       : angle       4.11512 (  525)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 ARG cc_start: 0.7845 (ttp80) cc_final: 0.6574 (mtt-85)
REVERT: B  100 ASP cc_start: 0.7511 (t0) cc_final: 0.7092 (t70)
REVERT: B  142 ASP cc_start: 0.7695 (p0) cc_final: 0.7452 (p0)
REVERT: B  180 MET cc_start: 0.5917 (mtm) cc_final: 0.5575 (mtp)
REVERT: B  185 LYS cc_start: 0.5627 (mtmt) cc_final: 0.5200 (ptpt)
REVERT: B  638 TYR cc_start: 0.8307 (m-10) cc_final: 0.8002 (m-10)
REVERT: B  651 MET cc_start: 0.8734 (mmt) cc_final: 0.7768 (mmm)
  outliers start: 8
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0510
  time to fit residues: 4.5302
Evaluate side-chains
  63 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  629 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 26 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0050
   chunk 20 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0370
   chunk 12 optimal weight:    0.0870
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   overall best weight:    0.1450

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.178837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.157095 restraints weight = 8437.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 4.26
r_work: 0.4090 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6554
moved from start:          0.4233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3930  Z= 0.093
  Angle     :  0.466   5.160   5320  Z= 0.243
  Chirality :  0.039   0.145    557
  Planarity :  0.003   0.019    681
  Dihedral  :  3.890  14.020    515
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.36 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.39), residues: 462
  helix:  2.51 (0.33), residues: 233
  sheet: -0.22 (0.81), residues: 44
  loop : -0.07 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 167 
 TYR   0.016   0.001   TYR B 225 
 PHE   0.012   0.001   PHE B  60 
 TRP   0.007   0.001   TRP B 278 
 HIS   0.002   0.001   HIS B 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 3930)
  covalent geometry    : angle       0.46619 ( 5320)
  hydrogen bonds       : bond        0.03204 (  183)
  hydrogen bonds       : angle       3.93161 (  525)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 ARG cc_start: 0.7684 (ttp80) cc_final: 0.6571 (mtt90)
REVERT: B  100 ASP cc_start: 0.7672 (t0) cc_final: 0.7057 (t70)
REVERT: B  142 ASP cc_start: 0.7704 (p0) cc_final: 0.7424 (p0)
REVERT: B  180 MET cc_start: 0.5918 (mtm) cc_final: 0.5583 (mtp)
REVERT: B  185 LYS cc_start: 0.5553 (mtmt) cc_final: 0.5124 (ptpt)
REVERT: B  579 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8596 (tt)
REVERT: B  651 MET cc_start: 0.8756 (mmt) cc_final: 0.8425 (mmm)
  outliers start: 9
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0644
  time to fit residues: 5.0949
Evaluate side-chains
  63 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  618 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0770
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 666 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.175751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.153669 restraints weight = 8386.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 4.09
r_work: 0.4046 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start:          0.4898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3930  Z= 0.122
  Angle     :  0.507   4.993   5320  Z= 0.268
  Chirality :  0.041   0.140    557
  Planarity :  0.004   0.025    681
  Dihedral  :  3.951  12.313    515
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.84 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.38), residues: 462
  helix:  2.43 (0.32), residues: 233
  sheet: -0.39 (0.79), residues: 44
  loop : -0.38 (0.44), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 290 
 TYR   0.013   0.001   TYR B 225 
 PHE   0.012   0.001   PHE B  60 
 TRP   0.008   0.001   TRP B 278 
 HIS   0.004   0.001   HIS B 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3930)
  covalent geometry    : angle       0.50662 ( 5320)
  hydrogen bonds       : bond        0.03435 (  183)
  hydrogen bonds       : angle       3.98566 (  525)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 ARG cc_start: 0.7725 (ttp80) cc_final: 0.6632 (mtt-85)
REVERT: B  100 ASP cc_start: 0.7876 (t0) cc_final: 0.7429 (t70)
REVERT: B  101 TYR cc_start: 0.8564 (m-80) cc_final: 0.8308 (m-80)
REVERT: B  115 GLU cc_start: 0.5137 (OUTLIER) cc_final: 0.4934 (mp0)
REVERT: B  142 ASP cc_start: 0.7890 (p0) cc_final: 0.7573 (p0)
REVERT: B  180 MET cc_start: 0.6093 (mtm) cc_final: 0.5824 (mtp)
REVERT: B  245 ILE cc_start: 0.8575 (mt) cc_final: 0.8219 (tt)
REVERT: B  290 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8070 (mtp180)
REVERT: B  622 MET cc_start: 0.6924 (mpp) cc_final: 0.6027 (mpp)
REVERT: B  651 MET cc_start: 0.8866 (mmt) cc_final: 0.7952 (mmm)
  outliers start: 10
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0517
  time to fit residues: 4.1946
Evaluate side-chains
  61 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  115 GLU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  629 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0980
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.175850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.153323 restraints weight = 8174.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.4132 rms_B_bonded: 4.00
r_work: 0.4048 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6761
moved from start:          0.5403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3930  Z= 0.112
  Angle     :  0.481   4.999   5320  Z= 0.256
  Chirality :  0.040   0.139    557
  Planarity :  0.003   0.020    681
  Dihedral  :  3.882  12.494    515
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  :  9.88 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.39), residues: 462
  helix:  2.40 (0.32), residues: 233
  sheet: -0.54 (0.78), residues: 44
  loop : -0.44 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 235 
 TYR   0.008   0.001   TYR B 296 
 PHE   0.010   0.001   PHE B  60 
 TRP   0.007   0.001   TRP B 278 
 HIS   0.004   0.001   HIS B 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3930)
  covalent geometry    : angle       0.48089 ( 5320)
  hydrogen bonds       : bond        0.03195 (  183)
  hydrogen bonds       : angle       3.96034 (  525)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.102 
Fit side-chains
REVERT: B   83 ARG cc_start: 0.7822 (ttp80) cc_final: 0.6611 (mtt-85)
REVERT: B  142 ASP cc_start: 0.7898 (p0) cc_final: 0.7663 (p0)
REVERT: B  180 MET cc_start: 0.6113 (mtm) cc_final: 0.5846 (mtp)
REVERT: B  185 LYS cc_start: 0.6033 (ptpt) cc_final: 0.5408 (ptmm)
REVERT: B  245 ILE cc_start: 0.8551 (mt) cc_final: 0.8180 (tt)
REVERT: B  578 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8339 (mmm)
REVERT: B  629 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8775 (m)
REVERT: B  651 MET cc_start: 0.8844 (mmt) cc_final: 0.8394 (mmm)
  outliers start: 16
  outliers final: 11
  residues processed: 69
  average time/residue: 0.0382
  time to fit residues: 3.4878
Evaluate side-chains
  64 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  590 SER
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  647 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.173012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.150643 restraints weight = 8274.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.4090 rms_B_bonded: 4.05
r_work: 0.4003 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.5966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3930  Z= 0.149
  Angle     :  0.538   5.138   5320  Z= 0.285
  Chirality :  0.042   0.129    557
  Planarity :  0.003   0.021    681
  Dihedral  :  4.099  14.252    515
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 11.81 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.38), residues: 462
  helix:  2.15 (0.32), residues: 233
  sheet: -0.62 (0.76), residues: 44
  loop : -0.58 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 664 
 TYR   0.012   0.001   TYR B 225 
 PHE   0.011   0.002   PHE B 145 
 TRP   0.011   0.001   TRP B 584 
 HIS   0.002   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 3930)
  covalent geometry    : angle       0.53839 ( 5320)
  hydrogen bonds       : bond        0.03539 (  183)
  hydrogen bonds       : angle       4.09671 (  525)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.163 
Fit side-chains
REVERT: B   83 ARG cc_start: 0.7851 (ttp80) cc_final: 0.6596 (mtt-85)
REVERT: B  142 ASP cc_start: 0.8250 (p0) cc_final: 0.7942 (p0)
REVERT: B  180 MET cc_start: 0.6329 (mtm) cc_final: 0.6025 (mtp)
REVERT: B  245 ILE cc_start: 0.8647 (mt) cc_final: 0.8206 (tt)
REVERT: B  622 MET cc_start: 0.7029 (mpp) cc_final: 0.6122 (mpp)
REVERT: B  629 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8773 (m)
REVERT: B  651 MET cc_start: 0.8889 (mmt) cc_final: 0.8658 (mmm)
REVERT: B  660 TRP cc_start: 0.7163 (m100) cc_final: 0.6614 (m100)
  outliers start: 14
  outliers final: 12
  residues processed: 63
  average time/residue: 0.0454
  time to fit residues: 3.7780
Evaluate side-chains
  64 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  647 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.172485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.150001 restraints weight = 8267.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 4.05
r_work: 0.3995 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.6448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3930  Z= 0.153
  Angle     :  0.560   5.836   5320  Z= 0.299
  Chirality :  0.041   0.128    557
  Planarity :  0.004   0.024    681
  Dihedral  :  4.228  15.347    515
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 11.57 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.38), residues: 462
  helix:  1.89 (0.32), residues: 234
  sheet: -0.56 (0.77), residues: 44
  loop : -0.65 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 664 
 TYR   0.010   0.001   TYR B 641 
 PHE   0.013   0.002   PHE B  60 
 TRP   0.012   0.001   TRP B 584 
 HIS   0.003   0.001   HIS B 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3930)
  covalent geometry    : angle       0.55966 ( 5320)
  hydrogen bonds       : bond        0.03665 (  183)
  hydrogen bonds       : angle       4.19546 (  525)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: B  142 ASP cc_start: 0.8247 (p0) cc_final: 0.7963 (p0)
REVERT: B  180 MET cc_start: 0.6398 (mtm) cc_final: 0.6095 (mtp)
REVERT: B  245 ILE cc_start: 0.8651 (mt) cc_final: 0.8216 (tt)
REVERT: B  622 MET cc_start: 0.6965 (mpp) cc_final: 0.6087 (mpp)
REVERT: B  629 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8771 (m)
REVERT: B  651 MET cc_start: 0.9005 (mmt) cc_final: 0.8752 (mmm)
REVERT: B  660 TRP cc_start: 0.6983 (m100) cc_final: 0.6353 (m100)
REVERT: B  688 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7617 (mm-30)
  outliers start: 15
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0395
  time to fit residues: 3.3880
Evaluate side-chains
  63 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  647 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0030
   overall best weight:    0.5790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.172330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.149545 restraints weight = 8403.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.4070 rms_B_bonded: 4.18
r_work: 0.3982 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.6612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3930  Z= 0.119
  Angle     :  0.507   5.047   5320  Z= 0.269
  Chirality :  0.040   0.177    557
  Planarity :  0.003   0.023    681
  Dihedral  :  4.115  15.173    515
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.29 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.39), residues: 462
  helix:  1.97 (0.32), residues: 234
  sheet: -0.48 (0.77), residues: 44
  loop : -0.54 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 664 
 TYR   0.007   0.001   TYR B 296 
 PHE   0.017   0.001   PHE B 657 
 TRP   0.015   0.001   TRP B 584 
 HIS   0.002   0.001   HIS B 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3930)
  covalent geometry    : angle       0.50657 ( 5320)
  hydrogen bonds       : bond        0.03455 (  183)
  hydrogen bonds       : angle       4.10543 (  525)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.088 
Fit side-chains
REVERT: B  142 ASP cc_start: 0.8235 (p0) cc_final: 0.7920 (p0)
REVERT: B  180 MET cc_start: 0.6238 (mtm) cc_final: 0.5962 (mtp)
REVERT: B  245 ILE cc_start: 0.8580 (mt) cc_final: 0.8136 (tt)
REVERT: B  319 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7670 (mp0)
REVERT: B  578 MET cc_start: 0.9254 (tpp) cc_final: 0.9039 (mmt)
REVERT: B  629 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8782 (m)
REVERT: B  651 MET cc_start: 0.8997 (mmt) cc_final: 0.8695 (mmm)
REVERT: B  660 TRP cc_start: 0.6998 (m100) cc_final: 0.6342 (m100)
REVERT: B  688 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7648 (mm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 61
  average time/residue: 0.0322
  time to fit residues: 2.6691
Evaluate side-chains
  60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  647 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0070
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.6800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.171693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.148886 restraints weight = 8389.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 4.15
r_work: 0.3979 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.6956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3930  Z= 0.128
  Angle     :  0.530   5.062   5320  Z= 0.281
  Chirality :  0.041   0.143    557
  Planarity :  0.003   0.023    681
  Dihedral  :  4.151  15.784    515
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 11.57 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.39), residues: 462
  helix:  1.96 (0.33), residues: 234
  sheet: -0.57 (0.75), residues: 44
  loop : -0.62 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 664 
 TYR   0.010   0.001   TYR B 135 
 PHE   0.010   0.001   PHE B  60 
 TRP   0.016   0.001   TRP B 584 
 HIS   0.002   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3930)
  covalent geometry    : angle       0.53010 ( 5320)
  hydrogen bonds       : bond        0.03565 (  183)
  hydrogen bonds       : angle       4.12124 (  525)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.141 
Fit side-chains
REVERT: B  142 ASP cc_start: 0.8296 (p0) cc_final: 0.8017 (p0)
REVERT: B  180 MET cc_start: 0.6213 (mtm) cc_final: 0.5929 (mtp)
REVERT: B  245 ILE cc_start: 0.8579 (mt) cc_final: 0.8098 (tt)
REVERT: B  578 MET cc_start: 0.9235 (tpp) cc_final: 0.8705 (mmt)
REVERT: B  622 MET cc_start: 0.7119 (mpp) cc_final: 0.6781 (mpp)
REVERT: B  629 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8739 (m)
REVERT: B  651 MET cc_start: 0.8985 (mmt) cc_final: 0.8710 (mmm)
REVERT: B  660 TRP cc_start: 0.6808 (m100) cc_final: 0.6161 (m100)
REVERT: B  688 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7651 (mm-30)
  outliers start: 12
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0465
  time to fit residues: 3.7316
Evaluate side-chains
  57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  590 SER
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  647 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0870
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.7158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.171489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.149070 restraints weight = 8467.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 4.27
r_work: 0.3981 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.7130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3930  Z= 0.129
  Angle     :  0.529   5.441   5320  Z= 0.280
  Chirality :  0.041   0.148    557
  Planarity :  0.003   0.023    681
  Dihedral  :  4.172  15.938    515
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.73 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.38), residues: 462
  helix:  1.87 (0.33), residues: 234
  sheet: -0.52 (0.75), residues: 44
  loop : -0.53 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 634 
 TYR   0.009   0.001   TYR B 566 
 PHE   0.017   0.001   PHE B 657 
 TRP   0.014   0.001   TRP B 584 
 HIS   0.002   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3930)
  covalent geometry    : angle       0.52877 ( 5320)
  hydrogen bonds       : bond        0.03516 (  183)
  hydrogen bonds       : angle       4.20749 (  525)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1071.26 seconds
wall clock time: 18 minutes 59.13 seconds (1139.13 seconds total)