Starting phenix.real_space_refine
on Wed Sep 17 02:59:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9isi_60836/09_2025/9isi_60836_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9isi_60836/09_2025/9isi_60836.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9isi_60836/09_2025/9isi_60836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9isi_60836/09_2025/9isi_60836.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9isi_60836/09_2025/9isi_60836_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9isi_60836/09_2025/9isi_60836_neut.cif"
  }
  resolution = 3.56
  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=  -0.001 sd=   0.005
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      21      5.16       5
     C    1310      2.51       5
     N     311      2.21       5
     O     313      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1955
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1955
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 12, 'TRANS': 239}
          Chain breaks: 4
  Time building chain proxies: 0.51, per 1000 atoms: 0.26
  Number of scatterers: 1955
  At special positions: 0
  Unit cell: (52.576, 72.928, 78.016, 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      21     16.00
     O     313      8.00
     N     311      7.00
     C    1310      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: 0.09
  Conformation dependent library (CDL) restraints added in 43.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  480

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      91.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.03
  Creating SS restraints...
    Processing helix  chain 'B' and resid 22 through 36
    Processing helix  chain 'B' and resid 37 through 50
    Processing helix  chain 'B' and resid 57 through 73
      removed outlier: 3.913A  pdb=" N   PHE B  61 " --> pdb=" O   ASN B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 85
      removed outlier: 3.621A  pdb=" N   SER B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 97
    Processing helix  chain 'B' and resid 99 through 124
      removed outlier: 4.154A  pdb=" N   VAL B 103 " --> pdb=" O   PRO B  99 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL B 124 " --> pdb=" O   ARG B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 130
      removed outlier: 3.581A  pdb=" N   TRP B 129 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 153
      removed outlier: 3.614A  pdb=" N   MET B 153 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 159
    Processing helix  chain 'B' and resid 332 through 345
      removed outlier: 3.758A  pdb=" N   THR B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ILE B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 365
      removed outlier: 3.536A  pdb=" N   SER B 349 " --> pdb=" O   PHE B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 403
      removed outlier: 3.706A  pdb=" N   ALA B 379 " --> pdb=" O   THR B 375 " (cutoff:3.500A)
      Proline residue:  B 392  - end of helix
    Processing helix  chain 'B' and resid 407 through 438
      removed outlier: 4.413A  pdb=" N   HIS B 418 " --> pdb=" O   MET B 414 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   VAL B 419 " --> pdb=" O   SER B 415 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   SER B 428 " --> pdb=" O   ALA B 424 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   CYS B 429 " --> pdb=" O   SER B 425 " (cutoff:3.500A)
      Proline residue:  B 432  - end of helix
      removed outlier: 4.058A  pdb=" N   TYR B 435 " --> pdb=" O   ASN B 431 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ALA B 436 " --> pdb=" O   PRO B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 459
      removed outlier: 3.903A  pdb=" N   ALA B 456 " --> pdb=" O   GLY B 452 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ALA B 457 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   PHE B 458 " --> pdb=" O   LEU B 454 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   SER B 459 " --> pdb=" O   GLU B 455 " (cutoff:3.500A)

    149 hydrogen bonds defined for protein.
    444 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: 0.15

  Time building geometry restraints manager: 0.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 451
        1.34 -     1.45: 381
        1.45 -     1.57: 1142
        1.57 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 2003
  Sorted by residual:
  bond pdb=" C   THR B 339 "
       pdb=" N   ARG B 340 "
    ideal  model  delta    sigma   weight residual
    1.334  1.290  0.045 1.27e-02 6.20e+03 1.25e+01
  bond pdb=" C   ARG B 340 "
       pdb=" N   LEU B 341 "
    ideal  model  delta    sigma   weight residual
    1.335  1.379 -0.044 1.31e-02 5.83e+03 1.15e+01
  bond pdb=" N   LEU B  50 "
       pdb=" CA  LEU B  50 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.16e-02 7.43e+03 1.03e+01
  bond pdb=" N   LEU B  97 "
       pdb=" CA  LEU B  97 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.30e-02 5.92e+03 7.00e+00
  bond pdb=" N   LEU B 413 "
       pdb=" CA  LEU B 413 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.23e-02 6.61e+03 6.00e+00
  ... (remaining 1998 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 2514
        1.06 -     2.11: 150
        2.11 -     3.17: 48
        3.17 -     4.22: 13
        4.22 -     5.28: 5
  Bond angle restraints: 2730
  Sorted by residual:
  angle pdb=" O   ARG B 340 "
        pdb=" C   ARG B 340 "
        pdb=" N   LEU B 341 "
      ideal   model   delta    sigma   weight residual
     122.07  125.50   -3.43 1.03e+00 9.43e-01 1.11e+01
  angle pdb=" CA  LEU B 413 "
        pdb=" C   LEU B 413 "
        pdb=" O   LEU B 413 "
      ideal   model   delta    sigma   weight residual
     120.42  117.20    3.22 1.06e+00 8.90e-01 9.23e+00
  angle pdb=" N   PRO B  99 "
        pdb=" CA  PRO B  99 "
        pdb=" C   PRO B  99 "
      ideal   model   delta    sigma   weight residual
     114.18  109.96    4.22 1.39e+00 5.18e-01 9.22e+00
  angle pdb=" C   PRO B 432 "
        pdb=" CA  PRO B 432 "
        pdb=" CB  PRO B 432 "
      ideal   model   delta    sigma   weight residual
     111.85  108.07    3.78 1.42e+00 4.96e-01 7.08e+00
  angle pdb=" N   MET B 138 "
        pdb=" CA  MET B 138 "
        pdb=" C   MET B 138 "
      ideal   model   delta    sigma   weight residual
     111.28  108.44    2.84 1.09e+00 8.42e-01 6.80e+00
  ... (remaining 2725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.83: 952
       10.83 -    21.66: 121
       21.66 -    32.50: 64
       32.50 -    43.33: 25
       43.33 -    54.16: 6
  Dihedral angle restraints: 1168
    sinusoidal: 436
      harmonic: 732
  Sorted by residual:
  dihedral pdb=" N   MET B 363 "
           pdb=" CA  MET B 363 "
           pdb=" CB  MET B 363 "
           pdb=" CG  MET B 363 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -129.25  -50.75     3      1.50e+01 4.44e-03 8.94e+00
  dihedral pdb=" CA  LEU B  70 "
           pdb=" CB  LEU B  70 "
           pdb=" CG  LEU B  70 "
           pdb=" CD1 LEU B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  130.32   49.68     3      1.50e+01 4.44e-03 8.81e+00
  dihedral pdb=" CA  GLN B  85 "
           pdb=" CB  GLN B  85 "
           pdb=" CG  GLN B  85 "
           pdb=" CD  GLN B  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -105.90   45.90     3      1.50e+01 4.44e-03 8.25e+00
  ... (remaining 1165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 230
       0.036 -    0.072: 85
       0.072 -    0.107: 19
       0.107 -    0.143: 6
       0.143 -    0.179: 3
  Chirality restraints: 343
  Sorted by residual:
  chirality pdb=" CA  THR B 391 "
            pdb=" N   THR B 391 "
            pdb=" C   THR B 391 "
            pdb=" CB  THR B 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 8.01e-01
  chirality pdb=" CA  MET B 138 "
            pdb=" N   MET B 138 "
            pdb=" C   MET B 138 "
            pdb=" CB  MET B 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.70e-01
  chirality pdb=" CA  MET B 106 "
            pdb=" N   MET B 106 "
            pdb=" C   MET B 106 "
            pdb=" CB  MET B 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.26e-01
  ... (remaining 340 not shown)

  Planarity restraints: 319
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  98 "    0.006 2.00e-02 2.50e+03   1.10e-02 1.20e+00
        pdb=" C   ILE B  98 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE B  98 "    0.007 2.00e-02 2.50e+03
        pdb=" N   PRO B  99 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 404 "    0.015 5.00e-02 4.00e+02   2.33e-02 8.70e-01
        pdb=" N   PRO B 405 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO B 405 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 405 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  34 "    0.008 2.00e-02 2.50e+03   6.97e-03 8.50e-01
        pdb=" CG  PHE B  34 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  34 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  34 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  34 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  34 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  34 "    0.000 2.00e-02 2.50e+03
  ... (remaining 316 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 772
        2.90 -     3.40: 2096
        3.40 -     3.90: 3105
        3.90 -     4.40: 3132
        4.40 -     4.90: 5488
  Nonbonded interactions: 14593
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 105 "
            pdb=" N   MET B 106 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" O   LYS B 411 "
            pdb=" OG  SER B 415 "
     model   vdw
     2.414 3.040
  nonbonded pdb=" O   LEU B 409 "
            pdb=" OG1 THR B 412 "
     model   vdw
     2.448 3.040
  nonbonded pdb=" O   VAL B  23 "
            pdb=" OG  SER B  26 "
     model   vdw
     2.470 3.040
  nonbonded pdb=" O   ILE B 102 "
            pdb=" OD1 ASN B 105 "
     model   vdw
     2.508 3.040
  ... (remaining 14588 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 group one per residue
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:             2.410
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.550
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
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      :  0.005   0.045   2003  Z= 0.292
  Angle     :  0.666   5.277   2730  Z= 0.421
  Chirality :  0.043   0.179    343
  Planarity :  0.003   0.023    319
  Dihedral  : 14.084  54.158    688
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.62 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.49 (0.57), residues: 242
  helix:  1.70 (0.38), residues: 198
  sheet:  None (None), residues: 0
  loop : -2.37 (0.94), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 340 
 TYR   0.007   0.001   TYR B 393 
 PHE   0.016   0.001   PHE B  34 
 TRP   0.004   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 2003)
  covalent geometry    : angle       0.66597 ( 2730)
  hydrogen bonds       : bond        0.10151 (  149)
  hydrogen bonds       : angle       5.33603 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.038 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0555
  time to fit residues: 1.9807
Evaluate side-chains
  31 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0970
   chunk 16 optimal weight:    0.0980
   chunk 15 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.1980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.2378

-------------------------------------------------------------------------------
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 = 0.4410 r_free = 0.4410 target = 0.220568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.167885 restraints weight = 2401.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.171203 restraints weight = 1805.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.173045 restraints weight = 1526.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.174642 restraints weight = 1385.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.175161 restraints weight = 1304.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2003  Z= 0.122
  Angle     :  0.563   7.238   2730  Z= 0.277
  Chirality :  0.040   0.168    343
  Planarity :  0.004   0.023    319
  Dihedral  :  3.423  11.386    260
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.37 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.21 (0.55), residues: 242
  helix:  2.01 (0.36), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.07 (1.01), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 365 
 TYR   0.008   0.001   TYR B 160 
 PHE   0.014   0.001   PHE B  34 
 TRP   0.004   0.001   TRP B  46 
 HIS   0.001   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 2003)
  covalent geometry    : angle       0.56346 ( 2730)
  hydrogen bonds       : bond        0.03627 (  149)
  hydrogen bonds       : angle       4.19891 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.067 
Fit side-chains
REVERT: B   50 LEU cc_start: 0.7396 (mp) cc_final: 0.7082 (tt)
  outliers start: 5
  outliers final: 3
  residues processed: 38
  average time/residue: 0.1086
  time to fit residues: 4.5626
Evaluate side-chains
  37 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 18 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.220409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.168846 restraints weight = 2454.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.170012 restraints weight = 2097.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.171466 restraints weight = 1921.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.172209 restraints weight = 1819.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.172210 restraints weight = 1740.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2003  Z= 0.155
  Angle     :  0.600   7.265   2730  Z= 0.295
  Chirality :  0.041   0.167    343
  Planarity :  0.004   0.023    319
  Dihedral  :  3.486  11.648    260
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 19.37 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.92 (0.54), residues: 242
  helix:  1.85 (0.36), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.51 (0.96), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 134 
 TYR   0.010   0.002   TYR B 356 
 PHE   0.015   0.002   PHE B  34 
 TRP   0.005   0.001   TRP B 147 
 HIS   0.003   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 2003)
  covalent geometry    : angle       0.59984 ( 2730)
  hydrogen bonds       : bond        0.04310 (  149)
  hydrogen bonds       : angle       4.18307 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.053 
Fit side-chains
REVERT: B   85 GLN cc_start: 0.4796 (tm-30) cc_final: 0.4411 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 39
  average time/residue: 0.0849
  time to fit residues: 3.7035
Evaluate side-chains
  38 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0470
   chunk 24 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 7 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.3678

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.221429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.170705 restraints weight = 2416.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.172693 restraints weight = 2043.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.173458 restraints weight = 1846.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.174158 restraints weight = 1747.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.174158 restraints weight = 1690.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2003  Z= 0.132
  Angle     :  0.572   7.558   2730  Z= 0.279
  Chirality :  0.040   0.165    343
  Planarity :  0.004   0.023    319
  Dihedral  :  3.431  11.414    260
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 20.72 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.99 (0.55), residues: 242
  helix:  1.90 (0.36), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.59 (0.98), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 362 
 TYR   0.007   0.001   TYR B 356 
 PHE   0.014   0.001   PHE B  34 
 TRP   0.004   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 2003)
  covalent geometry    : angle       0.57183 ( 2730)
  hydrogen bonds       : bond        0.03825 (  149)
  hydrogen bonds       : angle       4.05475 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.068 
Fit side-chains
REVERT: B   85 GLN cc_start: 0.4814 (tm-30) cc_final: 0.4421 (tm-30)
REVERT: B  105 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7448 (p0)
  outliers start: 9
  outliers final: 6
  residues processed: 35
  average time/residue: 0.0958
  time to fit residues: 3.7824
Evaluate side-chains
  37 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 13 optimal weight:    0.0010
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.2980
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 8 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.221458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.170885 restraints weight = 2427.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.172290 restraints weight = 2060.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.173985 restraints weight = 1876.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.173985 restraints weight = 1762.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.174656 restraints weight = 1762.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2003  Z= 0.132
  Angle     :  0.584   7.507   2730  Z= 0.280
  Chirality :  0.041   0.164    343
  Planarity :  0.004   0.023    319
  Dihedral  :  3.425  11.311    260
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 19.37 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.00 (0.55), residues: 242
  helix:  1.91 (0.36), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.59 (0.97), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 362 
 TYR   0.007   0.001   TYR B 356 
 PHE   0.014   0.001   PHE B 376 
 TRP   0.004   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 2003)
  covalent geometry    : angle       0.58428 ( 2730)
  hydrogen bonds       : bond        0.03742 (  149)
  hydrogen bonds       : angle       4.02836 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.088 
Fit side-chains
REVERT: B   27 MET cc_start: 0.7539 (tpp) cc_final: 0.7255 (mmm)
REVERT: B   85 GLN cc_start: 0.4709 (tm-30) cc_final: 0.4307 (tm-30)
REVERT: B  105 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7307 (p0)
  outliers start: 11
  outliers final: 7
  residues processed: 38
  average time/residue: 0.0888
  time to fit residues: 3.8302
Evaluate side-chains
  38 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0770
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   chunk 7 optimal weight:    0.2980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.2738

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.222571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.172130 restraints weight = 2475.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.173776 restraints weight = 2097.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.174317 restraints weight = 1890.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.175973 restraints weight = 1806.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.176162 restraints weight = 1719.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2003  Z= 0.121
  Angle     :  0.581   7.551   2730  Z= 0.278
  Chirality :  0.040   0.167    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.387  11.437    260
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 19.82 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.15 (0.55), residues: 242
  helix:  2.01 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.52 (0.97), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 362 
 TYR   0.006   0.001   TYR B 356 
 PHE   0.014   0.001   PHE B  34 
 TRP   0.003   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 2003)
  covalent geometry    : angle       0.58060 ( 2730)
  hydrogen bonds       : bond        0.03462 (  149)
  hydrogen bonds       : angle       3.93073 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.077 
Fit side-chains
REVERT: B   27 MET cc_start: 0.7436 (tpp) cc_final: 0.7179 (mmm)
REVERT: B   85 GLN cc_start: 0.4756 (tm-30) cc_final: 0.4289 (tm-30)
REVERT: B  105 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7318 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 38
  average time/residue: 0.0800
  time to fit residues: 3.4554
Evaluate side-chains
  38 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  429 CYS
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0970
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    0.2980
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0970
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.221325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.170733 restraints weight = 2444.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.172659 restraints weight = 2076.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173165 restraints weight = 1878.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173165 restraints weight = 1799.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173165 restraints weight = 1799.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2003  Z= 0.134
  Angle     :  0.594   7.545   2730  Z= 0.284
  Chirality :  0.041   0.166    343
  Planarity :  0.004   0.022    319
  Dihedral  :  3.396  11.295    260
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 19.37 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.13 (0.55), residues: 242
  helix:  2.00 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.51 (0.97), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 362 
 TYR   0.008   0.001   TYR B 356 
 PHE   0.015   0.001   PHE B  34 
 TRP   0.004   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2003)
  covalent geometry    : angle       0.59360 ( 2730)
  hydrogen bonds       : bond        0.03666 (  149)
  hydrogen bonds       : angle       3.95577 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.072 
Fit side-chains
REVERT: B   27 MET cc_start: 0.7425 (tpp) cc_final: 0.7079 (mmm)
REVERT: B  105 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7372 (p0)
  outliers start: 14
  outliers final: 10
  residues processed: 37
  average time/residue: 0.0878
  time to fit residues: 3.6533
Evaluate side-chains
  40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 29
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  429 CYS
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 16 optimal weight:    0.1980
   chunk 14 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0010
   chunk 9 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.220436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.169927 restraints weight = 2465.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.171539 restraints weight = 2126.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.172317 restraints weight = 1909.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.172318 restraints weight = 1813.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.172318 restraints weight = 1813.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2003  Z= 0.144
  Angle     :  0.604   7.548   2730  Z= 0.290
  Chirality :  0.041   0.164    343
  Planarity :  0.004   0.023    319
  Dihedral  :  3.434  11.632    260
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 19.82 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.06 (0.55), residues: 242
  helix:  1.94 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.50 (0.97), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 362 
 TYR   0.008   0.001   TYR B 356 
 PHE   0.016   0.001   PHE B 376 
 TRP   0.004   0.001   TRP B 147 
 HIS   0.003   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 2003)
  covalent geometry    : angle       0.60443 ( 2730)
  hydrogen bonds       : bond        0.03815 (  149)
  hydrogen bonds       : angle       3.99411 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 32
  time to evaluate  : 0.074 
Fit side-chains
REVERT: B   27 MET cc_start: 0.7313 (tpp) cc_final: 0.6932 (mmm)
REVERT: B  105 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7364 (p0)
  outliers start: 14
  outliers final: 11
  residues processed: 40
  average time/residue: 0.0811
  time to fit residues: 3.6598
Evaluate side-chains
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  429 CYS
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 6 optimal weight:    0.0870
   chunk 9 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0970
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 0 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.3156

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.220979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.171244 restraints weight = 2445.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.172860 restraints weight = 2072.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.174277 restraints weight = 1866.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.174276 restraints weight = 1768.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.174276 restraints weight = 1768.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2003  Z= 0.126
  Angle     :  0.595   7.594   2730  Z= 0.284
  Chirality :  0.040   0.167    343
  Planarity :  0.004   0.025    319
  Dihedral  :  3.415  11.391    260
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 21.62 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.16 (0.55), residues: 242
  helix:  2.01 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.48 (0.97), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 362 
 TYR   0.007   0.001   TYR B 356 
 PHE   0.015   0.001   PHE B  34 
 TRP   0.003   0.000   TRP B 147 
 HIS   0.002   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 2003)
  covalent geometry    : angle       0.59549 ( 2730)
  hydrogen bonds       : bond        0.03544 (  149)
  hydrogen bonds       : angle       3.94162 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.071 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7322 (p0)
  outliers start: 11
  outliers final: 9
  residues processed: 39
  average time/residue: 0.0757
  time to fit residues: 3.3548
Evaluate side-chains
  41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  429 CYS
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0020
   chunk 9 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN
B 394 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.220991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.170885 restraints weight = 2525.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.173125 restraints weight = 2107.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.174312 restraints weight = 1887.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.174624 restraints weight = 1765.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.176027 restraints weight = 1719.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2003  Z= 0.124
  Angle     :  0.583   7.603   2730  Z= 0.278
  Chirality :  0.040   0.168    343
  Planarity :  0.004   0.025    319
  Dihedral  :  3.369  11.311    260
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 20.72 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.25 (0.55), residues: 242
  helix:  2.08 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.49 (0.96), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 362 
 TYR   0.007   0.001   TYR B 356 
 PHE   0.015   0.001   PHE B  34 
 TRP   0.003   0.000   TRP B 147 
 HIS   0.002   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2003)
  covalent geometry    : angle       0.58292 ( 2730)
  hydrogen bonds       : bond        0.03435 (  149)
  hydrogen bonds       : angle       3.88439 (  444)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.064 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7295 (p0)
  outliers start: 11
  outliers final: 9
  residues processed: 38
  average time/residue: 0.0740
  time to fit residues: 3.2255
Evaluate side-chains
  41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  429 CYS
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 15 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0980
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.220188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.170843 restraints weight = 2501.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.172497 restraints weight = 2135.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.173924 restraints weight = 1930.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173973 restraints weight = 1787.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173973 restraints weight = 1776.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2003  Z= 0.142
  Angle     :  0.604   7.579   2730  Z= 0.289
  Chirality :  0.041   0.168    343
  Planarity :  0.004   0.026    319
  Dihedral  :  3.386  11.623    260
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 21.62 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.27 (0.55), residues: 242
  helix:  2.09 (0.36), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.50 (0.97), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 134 
 TYR   0.008   0.001   TYR B 356 
 PHE   0.016   0.001   PHE B 376 
 TRP   0.004   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2003)
  covalent geometry    : angle       0.60445 ( 2730)
  hydrogen bonds       : bond        0.03701 (  149)
  hydrogen bonds       : angle       3.94788 (  444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 678.14 seconds
wall clock time: 12 minutes 25.02 seconds (745.02 seconds total)