Starting phenix.real_space_refine
on Wed Sep 17 03:33:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9js4_61766/09_2025/9js4_61766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9js4_61766/09_2025/9js4_61766.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9js4_61766/09_2025/9js4_61766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9js4_61766/09_2025/9js4_61766.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9js4_61766/09_2025/9js4_61766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9js4_61766/09_2025/9js4_61766.map"
  }
  resolution = 3.8
  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=  -0.002 sd=   0.057
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      15      5.16       5
     C    2065      2.51       5
     N     544      2.21       5
     O     620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  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: 3244
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 816
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 8, 'TRANS': 98}
    Chain: "B"
      Number of atoms: 854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 854
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 5, 'TRANS': 108}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1574
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 12, 'TRANS': 183}
  Time building chain proxies: 1.04, per 1000 atoms: 0.32
  Number of scatterers: 3244
  At special positions: 0
  Unit cell: (66, 73.7, 101.2, 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      15     16.00
     O     620      8.00
     N     544      7.00
     C    2065      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03

  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: 0.16
  Conformation dependent library (CDL) restraints added in 92.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  762

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      9.6% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 3.588A  pdb=" N   ILE A  83 " --> pdb=" O   PRO A  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.509A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 372
      removed outlier: 4.562A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ALA C 372 " --> pdb=" O   LEU C 368 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 3.619A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 408
      removed outlier: 3.957A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 405 through 408'
    Processing helix  chain 'C' and resid 417 through 422
    Processing helix  chain 'C' and resid 438 through 443
      removed outlier: 3.905A  pdb=" N   ASP C 442 " --> pdb=" O   SER C 438 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER C 443 " --> pdb=" O   ASN C 439 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 438 through 443'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6
      removed outlier: 4.019A  pdb=" N   THR A   5 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
    Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 90
      removed outlier: 3.589A  pdb=" N   HIS A  90 " --> pdb=" O   THR A 100 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   THR A 100 " --> pdb=" O   HIS A  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 22
      removed outlier: 3.679A  pdb=" N   THR B  68 " --> pdb=" O   GLU B  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59
      removed outlier: 3.832A  pdb=" N   TYR B  58 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL B  50 " --> pdb=" O   TYR B  58 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL B  92 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358
      removed outlier: 4.111A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   SER C 399 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA C 435 " --> pdb=" O   THR C 376 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR C 376 " --> pdb=" O   ALA C 435 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474
      removed outlier: 3.692A  pdb=" N   TYR C 473 " --> pdb=" O   TYR C 489 " (cutoff:3.500A)

    59 hydrogen bonds defined for protein.
    147 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: 0.42

  Time building geometry restraints manager: 0.22 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: 1041
        1.34 -     1.46: 861
        1.46 -     1.58: 1409
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3329
  Sorted by residual:
  bond pdb=" CA  VAL B  63 "
       pdb=" CB  VAL B  63 "
    ideal  model  delta    sigma   weight residual
    1.527  1.540 -0.013 1.31e-02 5.83e+03 1.04e+00
  bond pdb=" CG  PRO C 384 "
       pdb=" CD  PRO C 384 "
    ideal  model  delta    sigma   weight residual
    1.503  1.533 -0.030 3.40e-02 8.65e+02 7.77e-01
  bond pdb=" CB  ASP C 428 "
       pdb=" CG  ASP C 428 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.62e-01
  bond pdb=" CB  ASN A  31 "
       pdb=" CG  ASN A  31 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.29e-01
  bond pdb=" CA  ASN A  31 "
       pdb=" CB  ASN A  31 "
    ideal  model  delta    sigma   weight residual
    1.533  1.546 -0.013 1.66e-02 3.63e+03 5.73e-01
  ... (remaining 3324 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 4289
        1.22 -     2.44: 191
        2.44 -     3.67: 41
        3.67 -     4.89: 11
        4.89 -     6.11: 2
  Bond angle restraints: 4534
  Sorted by residual:
  angle pdb=" CA  CYS C 361 "
        pdb=" CB  CYS C 361 "
        pdb=" SG  CYS C 361 "
      ideal   model   delta    sigma   weight residual
     114.40  120.51   -6.11 2.30e+00 1.89e-01 7.06e+00
  angle pdb=" CA  TYR A  91 "
        pdb=" CB  TYR A  91 "
        pdb=" CG  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     113.90  118.45   -4.55 1.80e+00 3.09e-01 6.39e+00
  angle pdb=" C   SER A  30 "
        pdb=" N   ASN A  31 "
        pdb=" CA  ASN A  31 "
      ideal   model   delta    sigma   weight residual
     123.91  127.83   -3.92 1.66e+00 3.63e-01 5.56e+00
  angle pdb=" N   GLY C 526 "
        pdb=" CA  GLY C 526 "
        pdb=" C   GLY C 526 "
      ideal   model   delta    sigma   weight residual
     112.34  116.81   -4.47 2.04e+00 2.40e-01 4.80e+00
  angle pdb=" CA  ASN A  31 "
        pdb=" CB  ASN A  31 "
        pdb=" CG  ASN A  31 "
      ideal   model   delta    sigma   weight residual
     112.60  114.76   -2.16 1.00e+00 1.00e+00 4.65e+00
  ... (remaining 4529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.78: 1728
       14.78 -    29.56: 174
       29.56 -    44.34: 51
       44.34 -    59.12: 6
       59.12 -    73.90: 5
  Dihedral angle restraints: 1964
    sinusoidal: 760
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.90  -73.90     1      1.00e+01 1.00e-02 6.94e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.36  -70.36     1      1.00e+01 1.00e-02 6.37e+01
  dihedral pdb=" CA  CYS C 361 "
           pdb=" C   CYS C 361 "
           pdb=" N   VAL C 362 "
           pdb=" CA  VAL C 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.04   31.96     0      5.00e+00 4.00e-02 4.09e+01
  ... (remaining 1961 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 262
       0.027 -    0.054: 129
       0.054 -    0.080: 57
       0.080 -    0.107: 30
       0.107 -    0.134: 12
  Chirality restraints: 490
  Sorted by residual:
  chirality pdb=" CA  VAL B  50 "
            pdb=" N   VAL B  50 "
            pdb=" C   VAL B  50 "
            pdb=" CB  VAL B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  ASN A  31 "
            pdb=" N   ASN A  31 "
            pdb=" C   ASN A  31 "
            pdb=" CB  ASN A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  ILE A  75 "
            pdb=" N   ILE A  75 "
            pdb=" C   ILE A  75 "
            pdb=" CB  ILE A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 487 not shown)

  Planarity restraints: 589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 383 "   -0.059 5.00e-02 4.00e+02   8.93e-02 1.28e+01
        pdb=" N   PRO C 384 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO C 384 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO C 384 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 462 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO C 463 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B  52 "    0.022 5.00e-02 4.00e+02   3.36e-02 1.81e+00
        pdb=" N   PRO B  53 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B  53 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  53 "    0.019 5.00e-02 4.00e+02
  ... (remaining 586 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 913
        2.81 -     3.33: 2664
        3.33 -     3.85: 4632
        3.85 -     4.38: 4990
        4.38 -     4.90: 9122
  Nonbonded interactions: 22321
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  28 "
            pdb=" O   ALA C 475 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" ND2 ASN A  96 "
            pdb=" OD2 ASP C 405 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" NE2 GLN A  38 "
            pdb=" O   LYS A  39 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" NH1 ARG B  38 "
            pdb=" OD1 ASP B  89 "
     model   vdw
     2.403 3.120
  nonbonded pdb=" NH2 ARG C 454 "
            pdb=" OD2 ASP C 467 "
     model   vdw
     2.418 3.120
  ... (remaining 22316 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             5.660
  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:                     4.470
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
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      :  0.002   0.030   3335  Z= 0.118
  Angle     :  0.624   6.111   4546  Z= 0.333
  Chirality :  0.044   0.134    490
  Planarity :  0.006   0.089    589
  Dihedral  : 12.564  73.350   1184
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -1.81 (0.38), residues: 409
  helix: -3.08 (0.79), residues: 20
  sheet: -0.42 (0.47), residues: 120
  loop : -1.48 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.014   0.001   TYR C 501 
 PHE   0.010   0.001   PHE B  67 
 TRP   0.010   0.001   TRP C 436 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 3329)
  covalent geometry    : angle       0.61521 ( 4534)
  SS BOND              : bond        0.00454 (    6)
  SS BOND              : angle       2.16759 (   12)
  hydrogen bonds       : bond        0.18371 (   59)
  hydrogen bonds       : angle       8.83364 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.121 
Fit side-chains
REVERT: B   84 SER cc_start: 0.7991 (t) cc_final: 0.7750 (t)
REVERT: C  405 ASP cc_start: 0.7173 (t70) cc_final: 0.6891 (t0)
REVERT: C  489 TYR cc_start: 0.6868 (m-10) cc_final: 0.6433 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0454
  time to fit residues: 3.4461
Evaluate side-chains
  47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 26 optimal weight:    0.0970
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.4076 r_free = 0.4076 target = 0.171918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.157834 restraints weight = 6558.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.160325 restraints weight = 4479.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.162139 restraints weight = 3341.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.163501 restraints weight = 2645.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.164504 restraints weight = 2178.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3335  Z= 0.114
  Angle     :  0.599   4.979   4546  Z= 0.316
  Chirality :  0.045   0.166    490
  Planarity :  0.005   0.060    589
  Dihedral  :  5.280  27.427    461
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.01 %
    Favored  : 89.58 %
  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: -1.75 (0.38), residues: 409
  helix: -2.89 (0.87), residues: 20
  sheet: -0.32 (0.48), residues: 113
  loop : -1.46 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  19 
 TYR   0.014   0.001   TYR C 489 
 PHE   0.010   0.001   PHE B  67 
 TRP   0.013   0.001   TRP C 436 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 3329)
  covalent geometry    : angle       0.59085 ( 4534)
  SS BOND              : bond        0.00492 (    6)
  SS BOND              : angle       2.00888 (   12)
  hydrogen bonds       : bond        0.04341 (   59)
  hydrogen bonds       : angle       7.33059 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.105 
Fit side-chains
REVERT: B   84 SER cc_start: 0.7982 (t) cc_final: 0.7733 (t)
REVERT: C  465 GLU cc_start: 0.5228 (pm20) cc_final: 0.5026 (pm20)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 0.0525
  time to fit residues: 3.9352
Evaluate side-chains
  47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain C residue  333 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.171223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.156768 restraints weight = 6530.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.159295 restraints weight = 4438.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.161132 restraints weight = 3310.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.162571 restraints weight = 2627.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.163621 restraints weight = 2158.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3335  Z= 0.120
  Angle     :  0.580   5.733   4546  Z= 0.308
  Chirality :  0.045   0.165    490
  Planarity :  0.005   0.049    589
  Dihedral  :  5.148  19.282    461
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.27 %
    Favored  : 86.76 %
  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: -1.63 (0.40), residues: 409
  helix: -2.45 (0.97), residues: 20
  sheet: -0.36 (0.49), residues: 116
  loop : -1.36 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.012   0.001   TYR C 501 
 PHE   0.013   0.001   PHE B  67 
 TRP   0.012   0.001   TRP C 436 
 HIS   0.004   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3329)
  covalent geometry    : angle       0.57750 ( 4534)
  SS BOND              : bond        0.00398 (    6)
  SS BOND              : angle       1.18412 (   12)
  hydrogen bonds       : bond        0.04078 (   59)
  hydrogen bonds       : angle       6.98325 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.125 
Fit side-chains
REVERT: B   84 SER cc_start: 0.7954 (t) cc_final: 0.7714 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 50
  average time/residue: 0.0379
  time to fit residues: 2.6260
Evaluate side-chains
  44 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain C residue  333 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 13 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.165163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.150576 restraints weight = 6422.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.152960 restraints weight = 4461.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.154839 restraints weight = 3389.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.156219 restraints weight = 2686.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.157163 restraints weight = 2226.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3335  Z= 0.197
  Angle     :  0.683   6.008   4546  Z= 0.369
  Chirality :  0.048   0.166    490
  Planarity :  0.005   0.044    589
  Dihedral  :  5.964  22.285    461
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 10.70 %
    Favored  : 86.48 %
  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: -1.94 (0.39), residues: 409
  helix: -2.59 (1.02), residues: 20
  sheet: -0.44 (0.51), residues: 110
  loop : -1.63 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.019   0.002   TYR A  49 
 PHE   0.016   0.002   PHE C 400 
 TRP   0.014   0.002   TRP C 436 
 HIS   0.005   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 3329)
  covalent geometry    : angle       0.67823 ( 4534)
  SS BOND              : bond        0.00423 (    6)
  SS BOND              : angle       1.68218 (   12)
  hydrogen bonds       : bond        0.05193 (   59)
  hydrogen bonds       : angle       7.31521 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.107 
Fit side-chains
REVERT: C  375 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6634 (t80)
REVERT: C  405 ASP cc_start: 0.7581 (t0) cc_final: 0.7353 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 49
  average time/residue: 0.0387
  time to fit residues: 2.6340
Evaluate side-chains
  47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  375 PHE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  438 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0670
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.168386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.153333 restraints weight = 6382.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.155989 restraints weight = 4257.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.157937 restraints weight = 3132.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.159439 restraints weight = 2463.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.160546 restraints weight = 2017.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3335  Z= 0.125
  Angle     :  0.608   6.887   4546  Z= 0.319
  Chirality :  0.046   0.163    490
  Planarity :  0.004   0.041    589
  Dihedral  :  5.534  20.989    461
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.96 %
    Favored  : 85.07 %
  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: -1.85 (0.40), residues: 409
  helix: -2.53 (1.04), residues: 20
  sheet: -0.62 (0.50), residues: 112
  loop : -1.45 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.011   0.001   TYR A  49 
 PHE   0.009   0.001   PHE C 400 
 TRP   0.012   0.001   TRP C 436 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3329)
  covalent geometry    : angle       0.60267 ( 4534)
  SS BOND              : bond        0.00327 (    6)
  SS BOND              : angle       1.67519 (   12)
  hydrogen bonds       : bond        0.03961 (   59)
  hydrogen bonds       : angle       6.99641 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.123 
Fit side-chains
REVERT: B   84 SER cc_start: 0.7987 (t) cc_final: 0.7761 (t)
REVERT: B  106 MET cc_start: 0.8253 (mmt) cc_final: 0.7976 (mmt)
REVERT: C  375 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6703 (t80)
REVERT: C  405 ASP cc_start: 0.7647 (t0) cc_final: 0.7381 (t0)
REVERT: C  489 TYR cc_start: 0.7204 (m-10) cc_final: 0.6991 (m-80)
  outliers start: 7
  outliers final: 6
  residues processed: 49
  average time/residue: 0.0445
  time to fit residues: 2.9388
Evaluate side-chains
  48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  375 PHE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  438 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.166937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.152636 restraints weight = 6467.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.155146 restraints weight = 4405.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.157027 restraints weight = 3265.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.158345 restraints weight = 2573.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.159387 restraints weight = 2127.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3335  Z= 0.143
  Angle     :  0.631   6.550   4546  Z= 0.333
  Chirality :  0.046   0.164    490
  Planarity :  0.005   0.041    589
  Dihedral  :  5.552  20.629    461
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.65 %
    Favored  : 82.82 %
  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: -1.91 (0.40), residues: 409
  helix: -2.84 (0.96), residues: 20
  sheet: -0.66 (0.50), residues: 113
  loop : -1.47 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.013   0.002   TYR C 501 
 PHE   0.011   0.001   PHE C 429 
 TRP   0.012   0.001   TRP C 436 
 HIS   0.005   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3329)
  covalent geometry    : angle       0.62537 ( 4534)
  SS BOND              : bond        0.00482 (    6)
  SS BOND              : angle       1.71175 (   12)
  hydrogen bonds       : bond        0.04200 (   59)
  hydrogen bonds       : angle       6.92015 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 SER cc_start: 0.7967 (t) cc_final: 0.7748 (t)
REVERT: C  375 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6591 (t80)
REVERT: C  405 ASP cc_start: 0.7480 (t0) cc_final: 0.7194 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0380
  time to fit residues: 2.6250
Evaluate side-chains
  48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  375 PHE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  438 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.167024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.152143 restraints weight = 6513.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.154805 restraints weight = 4347.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.156798 restraints weight = 3184.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.158280 restraints weight = 2482.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.159383 restraints weight = 2030.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3335  Z= 0.145
  Angle     :  0.643   6.445   4546  Z= 0.341
  Chirality :  0.046   0.162    490
  Planarity :  0.005   0.041    589
  Dihedral  :  5.622  21.759    461
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.93 %
    Favored  : 81.69 %
  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: -1.97 (0.40), residues: 409
  helix: -3.10 (0.88), residues: 20
  sheet: -0.72 (0.50), residues: 112
  loop : -1.48 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.013   0.002   TYR C 501 
 PHE   0.013   0.001   PHE C 429 
 TRP   0.011   0.001   TRP C 436 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3329)
  covalent geometry    : angle       0.63639 ( 4534)
  SS BOND              : bond        0.00391 (    6)
  SS BOND              : angle       1.95898 (   12)
  hydrogen bonds       : bond        0.04153 (   59)
  hydrogen bonds       : angle       6.87320 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 SER cc_start: 0.8016 (t) cc_final: 0.7783 (t)
REVERT: C  375 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6554 (t80)
REVERT: C  386 LYS cc_start: 0.3269 (mmtt) cc_final: 0.2119 (ttpt)
REVERT: C  405 ASP cc_start: 0.7369 (t0) cc_final: 0.7047 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0415
  time to fit residues: 2.9070
Evaluate side-chains
  51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  375 PHE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  438 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.167713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.153851 restraints weight = 6609.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.156266 restraints weight = 4483.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.158136 restraints weight = 3336.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.159300 restraints weight = 2621.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.160435 restraints weight = 2187.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3335  Z= 0.134
  Angle     :  0.642   6.534   4546  Z= 0.337
  Chirality :  0.045   0.161    490
  Planarity :  0.005   0.043    589
  Dihedral  :  5.533  20.174    461
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.21 %
    Favored  : 81.97 %
  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: -1.94 (0.40), residues: 409
  helix: -3.25 (0.86), residues: 21
  sheet: -0.73 (0.50), residues: 112
  loop : -1.42 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.014   0.001   TYR C 501 
 PHE   0.012   0.001   PHE C 429 
 TRP   0.011   0.001   TRP C 436 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3329)
  covalent geometry    : angle       0.63452 ( 4534)
  SS BOND              : bond        0.00424 (    6)
  SS BOND              : angle       2.02378 (   12)
  hydrogen bonds       : bond        0.03974 (   59)
  hydrogen bonds       : angle       6.78435 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.121 
Fit side-chains
REVERT: B   84 SER cc_start: 0.7949 (t) cc_final: 0.7721 (t)
REVERT: C  375 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.6537 (t80)
REVERT: C  386 LYS cc_start: 0.3262 (mmtt) cc_final: 0.2211 (ttmt)
  outliers start: 10
  outliers final: 9
  residues processed: 48
  average time/residue: 0.0397
  time to fit residues: 2.6371
Evaluate side-chains
  51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  375 PHE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  438 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0870
   chunk 36 optimal weight:    0.3980
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.168740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.154633 restraints weight = 6515.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.157157 restraints weight = 4353.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.159036 restraints weight = 3211.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.160447 restraints weight = 2524.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.161364 restraints weight = 2063.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3335  Z= 0.122
  Angle     :  0.617   6.061   4546  Z= 0.326
  Chirality :  0.045   0.160    490
  Planarity :  0.004   0.043    589
  Dihedral  :  5.481  20.911    461
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.49 %
    Favored  : 81.97 %
  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: -1.84 (0.40), residues: 409
  helix: -2.75 (1.14), residues: 15
  sheet: -0.74 (0.50), residues: 112
  loop : -1.40 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.016   0.001   TYR C 489 
 PHE   0.011   0.001   PHE C 429 
 TRP   0.011   0.001   TRP C 436 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3329)
  covalent geometry    : angle       0.60964 ( 4534)
  SS BOND              : bond        0.00304 (    6)
  SS BOND              : angle       1.88755 (   12)
  hydrogen bonds       : bond        0.03743 (   59)
  hydrogen bonds       : angle       6.64467 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.080 
Fit side-chains
REVERT: B   84 SER cc_start: 0.7960 (t) cc_final: 0.7731 (t)
REVERT: C  375 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6576 (t80)
REVERT: C  386 LYS cc_start: 0.3255 (mmtt) cc_final: 0.2212 (ttmt)
REVERT: C  405 ASP cc_start: 0.7309 (t0) cc_final: 0.7001 (t0)
REVERT: C  420 ASP cc_start: 0.8394 (t70) cc_final: 0.8133 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0407
  time to fit residues: 2.7960
Evaluate side-chains
  51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  375 PHE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  438 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0970
   chunk 9 optimal weight:    0.0570
   chunk 5 optimal weight:    0.0020
   chunk 33 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.2904

-------------------------------------------------------------------------------
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 = 0.4064 r_free = 0.4064 target = 0.172208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.159010 restraints weight = 6454.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.161392 restraints weight = 4380.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.163226 restraints weight = 3268.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.164398 restraints weight = 2570.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.165505 restraints weight = 2129.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3335  Z= 0.099
  Angle     :  0.594   6.373   4546  Z= 0.310
  Chirality :  0.044   0.185    490
  Planarity :  0.004   0.044    589
  Dihedral  :  5.141  20.384    461
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.62 %
    Favored  : 81.69 %
  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: -1.77 (0.40), residues: 409
  helix: -2.54 (1.21), residues: 15
  sheet: -0.57 (0.53), residues: 101
  loop : -1.39 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  66 
 TYR   0.012   0.001   TYR C 489 
 PHE   0.008   0.001   PHE C 429 
 TRP   0.010   0.001   TRP C 436 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 3329)
  covalent geometry    : angle       0.58812 ( 4534)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       1.75210 (   12)
  hydrogen bonds       : bond        0.03142 (   59)
  hydrogen bonds       : angle       6.36445 (  147)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.120 
Fit side-chains
REVERT: B   84 SER cc_start: 0.7989 (t) cc_final: 0.7767 (t)
REVERT: C  371 LEU cc_start: 0.5034 (tp) cc_final: 0.4722 (tp)
REVERT: C  375 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6645 (t80)
REVERT: C  386 LYS cc_start: 0.3605 (mmtt) cc_final: 0.2466 (ttpt)
REVERT: C  405 ASP cc_start: 0.7221 (t0) cc_final: 0.6928 (t0)
REVERT: C  420 ASP cc_start: 0.8306 (t70) cc_final: 0.7975 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0405
  time to fit residues: 2.7789
Evaluate side-chains
  51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  375 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0870
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.170579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.156378 restraints weight = 6595.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.158975 restraints weight = 4372.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.160931 restraints weight = 3211.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.162372 restraints weight = 2497.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.163311 restraints weight = 2032.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3335  Z= 0.116
  Angle     :  0.619   5.912   4546  Z= 0.323
  Chirality :  0.045   0.188    490
  Planarity :  0.004   0.044    589
  Dihedral  :  5.165  20.294    461
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.34 %
    Favored  : 81.69 %
  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: -1.78 (0.40), residues: 409
  helix: -2.66 (1.16), residues: 15
  sheet: -0.58 (0.52), residues: 103
  loop : -1.40 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.015   0.001   TYR C 501 
 PHE   0.011   0.001   PHE C 429 
 TRP   0.011   0.001   TRP C 436 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 3329)
  covalent geometry    : angle       0.61258 ( 4534)
  SS BOND              : bond        0.00347 (    6)
  SS BOND              : angle       1.79291 (   12)
  hydrogen bonds       : bond        0.03483 (   59)
  hydrogen bonds       : angle       6.38729 (  147)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 752.83 seconds
wall clock time: 13 minutes 40.92 seconds (820.92 seconds total)