Starting phenix.real_space_refine
on Tue Mar  3 11:29:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c0y_16375/03_2026/8c0y_16375.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c0y_16375/03_2026/8c0y_16375.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c0y_16375/03_2026/8c0y_16375.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c0y_16375/03_2026/8c0y_16375.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c0y_16375/03_2026/8c0y_16375.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c0y_16375/03_2026/8c0y_16375.map"
  }
  resolution = 2.68
  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=   0.035
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      14      5.16       5
     C    2064      2.51       5
     N     548      2.21       5
     O     611      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3237
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1530
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 11, 'TRANS': 178}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98}
    Chain: "B"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 905
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
  Time building chain proxies: 0.79, per 1000 atoms: 0.24
  Number of scatterers: 3237
  At special positions: 0
  Unit cell: (68.68, 70.7, 85.85, 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      14     16.00
     O     611      8.00
     N     548      7.00
     C    2064      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " 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: 0.15
  Conformation dependent library (CDL) restraints added in 126.4 milliseconds
  

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  748

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      12.1% alpha, 33.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.751A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.882A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 4.059A  pdb=" N   VAL A 367 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.622A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.466A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.513A  pdb=" N   PHE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 86 through 90
      removed outlier: 3.755A  pdb=" N   THR B  90 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 6
      removed outlier: 3.854A  pdb=" N   ASP D  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.410A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   LEU D  33 " --> pdb=" O   PHE D  49 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   PHE D  49 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.738A  pdb=" N   MET B  34 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   VAL B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.962A  pdb=" N   CYS B  95 " --> pdb=" O   TRP B 107 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TRP B 107 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ARG B  97 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)

    110 hydrogen bonds defined for protein.
    258 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: 0.45

  Time building geometry restraints manager: 0.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1042
        1.34 -     1.46: 891
        1.46 -     1.58: 1374
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3323
  Sorted by residual:
  bond pdb=" CB  PRO A 373 "
       pdb=" CG  PRO A 373 "
    ideal  model  delta    sigma   weight residual
    1.492  1.529 -0.037 5.00e-02 4.00e+02 5.48e-01
  bond pdb=" CG1 ILE D   2 "
       pdb=" CD1 ILE D   2 "
    ideal  model  delta    sigma   weight residual
    1.513  1.491  0.022 3.90e-02 6.57e+02 3.11e-01
  bond pdb=" CG  PRO A 479 "
       pdb=" CD  PRO A 479 "
    ideal  model  delta    sigma   weight residual
    1.503  1.484  0.019 3.40e-02 8.65e+02 2.97e-01
  bond pdb=" CG  PHE A 392 "
       pdb=" CD2 PHE A 392 "
    ideal  model  delta    sigma   weight residual
    1.384  1.374  0.010 2.10e-02 2.27e+03 2.20e-01
  bond pdb=" CB  CYS A 480 "
       pdb=" SG  CYS A 480 "
    ideal  model  delta    sigma   weight residual
    1.808  1.793  0.015 3.30e-02 9.18e+02 2.01e-01
  ... (remaining 3318 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 4332
        1.08 -     2.17: 141
        2.17 -     3.25: 27
        3.25 -     4.34: 9
        4.34 -     5.42: 2
  Bond angle restraints: 4511
  Sorted by residual:
  angle pdb=" C   GLY D  50 "
        pdb=" N   ALA D  51 "
        pdb=" CA  ALA D  51 "
      ideal   model   delta    sigma   weight residual
     121.54  125.74   -4.20 1.91e+00 2.74e-01 4.84e+00
  angle pdb=" CB  ARG D  96 "
        pdb=" CG  ARG D  96 "
        pdb=" CD  ARG D  96 "
      ideal   model   delta    sigma   weight residual
     111.30  114.87   -3.57 2.30e+00 1.89e-01 2.41e+00
  angle pdb=" CA  TYR B  33 "
        pdb=" CB  TYR B  33 "
        pdb=" CG  TYR B  33 "
      ideal   model   delta    sigma   weight residual
     113.90  116.52   -2.62 1.80e+00 3.09e-01 2.12e+00
  angle pdb=" N   ARG B  66 "
        pdb=" CA  ARG B  66 "
        pdb=" C   ARG B  66 "
      ideal   model   delta    sigma   weight residual
     114.56  112.80    1.76 1.27e+00 6.20e-01 1.92e+00
  angle pdb=" CG  ARG D  96 "
        pdb=" CD  ARG D  96 "
        pdb=" NE  ARG D  96 "
      ideal   model   delta    sigma   weight residual
     112.00  114.93   -2.93 2.20e+00 2.07e-01 1.77e+00
  ... (remaining 4506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 1718
       16.95 -    33.90: 186
       33.90 -    50.84: 34
       50.84 -    67.79: 6
       67.79 -    84.74: 3
  Dihedral angle restraints: 1947
    sinusoidal: 762
      harmonic: 1185
  Sorted by residual:
  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   59.91   33.09     1      1.00e+01 1.00e-02 1.56e+01
  dihedral pdb=" CA  PHE A 392 "
           pdb=" C   PHE A 392 "
           pdb=" N   THR A 393 "
           pdb=" CA  THR A 393 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.19  -18.81     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ASP D  70 "
           pdb=" CB  ASP D  70 "
           pdb=" CG  ASP D  70 "
           pdb=" OD1 ASP D  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.50   56.50     1      2.00e+01 2.50e-03 1.08e+01
  ... (remaining 1944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 249
       0.026 -    0.052: 134
       0.052 -    0.078: 48
       0.078 -    0.104: 30
       0.104 -    0.130: 13
  Chirality restraints: 474
  Sorted by residual:
  chirality pdb=" CA  VAL B   2 "
            pdb=" N   VAL B   2 "
            pdb=" C   VAL B   2 "
            pdb=" CB  VAL B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  ILE D  48 "
            pdb=" N   ILE D  48 "
            pdb=" C   ILE D  48 "
            pdb=" CB  ILE D  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  chirality pdb=" CA  VAL A 395 "
            pdb=" N   VAL A 395 "
            pdb=" C   VAL A 395 "
            pdb=" CB  VAL A 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 471 not shown)

  Planarity restraints: 587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  96 "    0.298 9.50e-02 1.11e+02   1.34e-01 1.17e+01
        pdb=" NE  ARG D  96 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  96 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  96 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  96 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D  79 "   -0.040 5.00e-02 4.00e+02   6.03e-02 5.82e+00
        pdb=" N   PRO D  80 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO D  80 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D  80 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 346 "   -0.121 9.50e-02 1.11e+02   5.45e-02 2.23e+00
        pdb=" NE  ARG A 346 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 346 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 346 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 346 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 584 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 175
        2.73 -     3.27: 3021
        3.27 -     3.81: 5382
        3.81 -     4.36: 6655
        4.36 -     4.90: 11300
  Nonbonded interactions: 26533
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 359 "
            pdb=" OD1 ASN A 394 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" NH1 ARG D  96 "
            pdb=" OD1 ASP B 101 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OD2 ASP A 420 "
            pdb=" OG  SER B  56 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   ASP D  82 "
            pdb=" OH  TYR D  86 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   LEU A 455 "
            pdb=" OH  TYR B  33 "
     model   vdw
     2.340 3.040
  ... (remaining 26528 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.450
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.830
  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:7.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
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   0.037   3329  Z= 0.111
  Angle     :  0.501   5.419   4523  Z= 0.256
  Chirality :  0.042   0.130    474
  Planarity :  0.007   0.134    587
  Dihedral  : 13.890  84.738   1181
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.43), residues: 404
  helix: -1.86 (1.32), residues: 13
  sheet:  0.91 (0.46), residues: 134
  loop : -0.43 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D  96 
 TYR   0.011   0.001   TYR B  33 
 PHE   0.007   0.001   PHE A 464 
 TRP   0.006   0.001   TRP B 107 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 3323)
  covalent geometry    : angle       0.49941 ( 4511)
  SS BOND              : bond        0.00283 (    6)
  SS BOND              : angle       0.83571 (   12)
  hydrogen bonds       : bond        0.16342 (  105)
  hydrogen bonds       : angle       8.32941 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  364 ASP cc_start: 0.7298 (t0) cc_final: 0.7058 (t70)
REVERT: A  398 ASP cc_start: 0.8075 (m-30) cc_final: 0.7781 (m-30)
REVERT: A  442 ASP cc_start: 0.8997 (m-30) cc_final: 0.8785 (m-30)
REVERT: A  478 LYS cc_start: 0.8988 (mmtp) cc_final: 0.8740 (mmmt)
REVERT: D    2 ILE cc_start: 0.9188 (mp) cc_final: 0.8934 (mp)
REVERT: B    3 HIS cc_start: 0.8637 (m90) cc_final: 0.8409 (m90)
REVERT: B   26 GLU cc_start: 0.8411 (tt0) cc_final: 0.8088 (tm-30)
REVERT: B   59 TYR cc_start: 0.9240 (m-80) cc_final: 0.8878 (m-80)
REVERT: B   75 ARG cc_start: 0.7961 (mpp80) cc_final: 0.7514 (mpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.6077
  time to fit residues: 54.1524
Evaluate side-chains
  52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0770
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0770
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.3296

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.051963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.044806 restraints weight = 14467.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 4.10
r_work: 0.3054 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3329  Z= 0.146
  Angle     :  0.667   7.187   4523  Z= 0.335
  Chirality :  0.046   0.153    474
  Planarity :  0.005   0.053    587
  Dihedral  :  4.438  16.463    462
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.94 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.42), residues: 404
  helix: -4.34 (0.50), residues: 14
  sheet:  1.16 (0.46), residues: 134
  loop : -0.49 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  24 
 TYR   0.008   0.001   TYR B  94 
 PHE   0.011   0.001   PHE A 392 
 TRP   0.008   0.001   TRP B 107 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3323)
  covalent geometry    : angle       0.66479 ( 4511)
  SS BOND              : bond        0.00230 (    6)
  SS BOND              : angle       1.31750 (   12)
  hydrogen bonds       : bond        0.03553 (  105)
  hydrogen bonds       : angle       6.17643 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8118 (p) cc_final: 0.7812 (t)
REVERT: A  391 CYS cc_start: 0.7859 (t) cc_final: 0.7614 (m)
REVERT: A  406 GLU cc_start: 0.8805 (mp0) cc_final: 0.8336 (pm20)
REVERT: A  442 ASP cc_start: 0.9099 (m-30) cc_final: 0.8837 (m-30)
REVERT: A  478 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8805 (mmmt)
REVERT: D   39 LYS cc_start: 0.9156 (tppp) cc_final: 0.8729 (mmtm)
REVERT: D   42 GLN cc_start: 0.8629 (mt0) cc_final: 0.8407 (mt0)
REVERT: D   79 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7806 (mm-30)
REVERT: B    3 HIS cc_start: 0.8662 (m90) cc_final: 0.8367 (m90)
REVERT: B   26 GLU cc_start: 0.8557 (tt0) cc_final: 0.8202 (tp30)
REVERT: B  106 TYR cc_start: 0.8931 (m-80) cc_final: 0.8701 (m-80)
REVERT: B  109 GLN cc_start: 0.9017 (mp10) cc_final: 0.8743 (pm20)
  outliers start: 4
  outliers final: 0
  residues processed: 66
  average time/residue: 0.7043
  time to fit residues: 47.5088
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   chunk 18 optimal weight:    0.4980
   chunk 37 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0770
   chunk 1 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.3738

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.051174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.043906 restraints weight = 14310.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 4.12
r_work: 0.3039 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3329  Z= 0.151
  Angle     :  0.643   9.139   4523  Z= 0.319
  Chirality :  0.046   0.164    474
  Planarity :  0.004   0.044    587
  Dihedral  :  4.251  15.478    462
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.94 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.42), residues: 404
  helix: -4.43 (0.46), residues: 14
  sheet:  1.07 (0.46), residues: 136
  loop : -0.52 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  24 
 TYR   0.008   0.001   TYR B  33 
 PHE   0.007   0.001   PHE A 464 
 TRP   0.005   0.001   TRP B 107 
 HIS   0.001   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3323)
  covalent geometry    : angle       0.64215 ( 4511)
  SS BOND              : bond        0.00182 (    6)
  SS BOND              : angle       0.97678 (   12)
  hydrogen bonds       : bond        0.03124 (  105)
  hydrogen bonds       : angle       5.70553 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8213 (p) cc_final: 0.7986 (t)
REVERT: A  406 GLU cc_start: 0.8914 (mp0) cc_final: 0.8455 (pm20)
REVERT: A  442 ASP cc_start: 0.9135 (m-30) cc_final: 0.8852 (m-30)
REVERT: A  478 LYS cc_start: 0.9009 (mmtp) cc_final: 0.8778 (mmmt)
REVERT: A  525 CYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7656 (p)
REVERT: D   39 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8794 (mmmm)
REVERT: D   42 GLN cc_start: 0.8653 (mt0) cc_final: 0.8406 (mt0)
REVERT: D   79 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7955 (mm-30)
REVERT: B    3 HIS cc_start: 0.8736 (m90) cc_final: 0.8471 (m90)
REVERT: B   26 GLU cc_start: 0.8598 (tt0) cc_final: 0.8188 (tp30)
REVERT: B   75 ARG cc_start: 0.8357 (mpp80) cc_final: 0.7961 (mpp80)
REVERT: B  106 TYR cc_start: 0.8956 (m-80) cc_final: 0.8676 (m-80)
  outliers start: 9
  outliers final: 1
  residues processed: 62
  average time/residue: 0.7837
  time to fit residues: 49.5824
Evaluate side-chains
  55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain B residue   73 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 31 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0070
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.3598

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.050994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.043829 restraints weight = 14427.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 4.12
r_work: 0.3039 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3329  Z= 0.149
  Angle     :  0.649   9.081   4523  Z= 0.321
  Chirality :  0.046   0.160    474
  Planarity :  0.004   0.039    587
  Dihedral  :  4.207  15.330    462
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.67 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.41), residues: 404
  helix: -4.31 (0.48), residues: 14
  sheet:  1.02 (0.46), residues: 135
  loop : -0.60 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  24 
 TYR   0.008   0.001   TYR B  33 
 PHE   0.007   0.001   PHE A 464 
 TRP   0.007   0.001   TRP B 107 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3323)
  covalent geometry    : angle       0.64881 ( 4511)
  SS BOND              : bond        0.00188 (    6)
  SS BOND              : angle       0.85301 (   12)
  hydrogen bonds       : bond        0.03018 (  105)
  hydrogen bonds       : angle       5.44520 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8239 (p) cc_final: 0.7993 (t)
REVERT: A  406 GLU cc_start: 0.8903 (mp0) cc_final: 0.8397 (pm20)
REVERT: A  442 ASP cc_start: 0.9155 (m-30) cc_final: 0.8888 (m-30)
REVERT: A  478 LYS cc_start: 0.9045 (mmtp) cc_final: 0.8805 (mmmt)
REVERT: A  525 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7543 (p)
REVERT: D   39 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8780 (mmtm)
REVERT: D   42 GLN cc_start: 0.8668 (mt0) cc_final: 0.8419 (mt0)
REVERT: D   79 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7888 (mm-30)
REVERT: D  105 GLU cc_start: 0.6388 (tp30) cc_final: 0.6136 (tt0)
REVERT: B    3 HIS cc_start: 0.8762 (m90) cc_final: 0.8502 (m90)
REVERT: B   26 GLU cc_start: 0.8632 (tt0) cc_final: 0.8171 (tp30)
REVERT: B   75 ARG cc_start: 0.8433 (mpp80) cc_final: 0.8009 (mpp80)
REVERT: B  106 TYR cc_start: 0.8976 (m-80) cc_final: 0.8646 (m-80)
REVERT: B  109 GLN cc_start: 0.9040 (mp10) cc_final: 0.8746 (pm20)
  outliers start: 11
  outliers final: 5
  residues processed: 66
  average time/residue: 0.6835
  time to fit residues: 46.0683
Evaluate side-chains
  58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain B residue   73 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0770
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.049786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.042731 restraints weight = 14797.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 4.08
r_work: 0.3005 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3329  Z= 0.212
  Angle     :  0.700  12.616   4523  Z= 0.345
  Chirality :  0.047   0.168    474
  Planarity :  0.004   0.044    587
  Dihedral  :  4.384  16.834    462
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.53 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.41), residues: 404
  helix: -4.17 (0.62), residues: 14
  sheet:  0.97 (0.46), residues: 136
  loop : -0.65 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  24 
 TYR   0.012   0.001   TYR A 396 
 PHE   0.010   0.001   PHE B 104 
 TRP   0.005   0.001   TRP B 107 
 HIS   0.001   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 3323)
  covalent geometry    : angle       0.69907 ( 4511)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       1.05208 (   12)
  hydrogen bonds       : bond        0.03287 (  105)
  hydrogen bonds       : angle       5.49620 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8114 (p) cc_final: 0.7862 (t)
REVERT: A  406 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8486 (pm20)
REVERT: A  442 ASP cc_start: 0.9178 (m-30) cc_final: 0.8898 (m-30)
REVERT: A  478 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8817 (mmmt)
REVERT: A  525 CYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7651 (p)
REVERT: D   79 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8055 (mm-30)
REVERT: D  105 GLU cc_start: 0.6400 (tp30) cc_final: 0.6115 (tt0)
REVERT: B    3 HIS cc_start: 0.8665 (m90) cc_final: 0.8441 (m90)
REVERT: B   26 GLU cc_start: 0.8643 (tt0) cc_final: 0.8201 (tp30)
REVERT: B   46 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.9069 (pt0)
REVERT: B   75 ARG cc_start: 0.8410 (mpp80) cc_final: 0.7963 (mpp80)
REVERT: B  109 GLN cc_start: 0.8987 (mp10) cc_final: 0.8596 (pm20)
  outliers start: 11
  outliers final: 3
  residues processed: 58
  average time/residue: 0.7114
  time to fit residues: 42.2014
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain B residue   46 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.049397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.042236 restraints weight = 14801.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 4.09
r_work: 0.2992 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3329  Z= 0.232
  Angle     :  0.716  12.802   4523  Z= 0.352
  Chirality :  0.047   0.165    474
  Planarity :  0.005   0.049    587
  Dihedral  :  4.438  17.331    462
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.97 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.42), residues: 404
  helix: -4.08 (0.72), residues: 14
  sheet:  0.87 (0.45), residues: 146
  loop : -0.67 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  24 
 TYR   0.010   0.001   TYR B  33 
 PHE   0.010   0.001   PHE B 104 
 TRP   0.007   0.001   TRP B  47 
 HIS   0.001   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 3323)
  covalent geometry    : angle       0.71543 ( 4511)
  SS BOND              : bond        0.00180 (    6)
  SS BOND              : angle       0.98188 (   12)
  hydrogen bonds       : bond        0.03261 (  105)
  hydrogen bonds       : angle       5.47515 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8220 (p) cc_final: 0.7980 (t)
REVERT: A  406 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8386 (pm20)
REVERT: A  442 ASP cc_start: 0.9243 (m-30) cc_final: 0.8972 (m-30)
REVERT: D   42 GLN cc_start: 0.8667 (mt0) cc_final: 0.8155 (mp10)
REVERT: D   79 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8034 (mm-30)
REVERT: D  105 GLU cc_start: 0.6358 (tp30) cc_final: 0.6067 (tt0)
REVERT: B    3 HIS cc_start: 0.8751 (m90) cc_final: 0.8548 (m90)
REVERT: B   26 GLU cc_start: 0.8678 (tt0) cc_final: 0.8067 (tm-30)
REVERT: B   46 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.9019 (pt0)
REVERT: B   64 LYS cc_start: 0.9334 (ptpp) cc_final: 0.8996 (ptpp)
  outliers start: 11
  outliers final: 5
  residues processed: 58
  average time/residue: 0.7509
  time to fit residues: 44.4575
Evaluate side-chains
  56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   46 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 2 optimal weight:    0.2980
   chunk 28 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0670
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.049715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.042500 restraints weight = 15024.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 4.15
r_work: 0.3000 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3329  Z= 0.178
  Angle     :  0.733  11.034   4523  Z= 0.361
  Chirality :  0.046   0.141    474
  Planarity :  0.004   0.052    587
  Dihedral  :  4.349  16.332    462
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 19.54 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.42), residues: 404
  helix: -4.08 (0.71), residues: 14
  sheet:  0.86 (0.45), residues: 146
  loop : -0.62 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  24 
 TYR   0.010   0.001   TYR B  33 
 PHE   0.008   0.001   PHE B 104 
 TRP   0.008   0.001   TRP B 107 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 3323)
  covalent geometry    : angle       0.73317 ( 4511)
  SS BOND              : bond        0.00164 (    6)
  SS BOND              : angle       0.84157 (   12)
  hydrogen bonds       : bond        0.03070 (  105)
  hydrogen bonds       : angle       5.35186 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8171 (p) cc_final: 0.7917 (t)
REVERT: A  406 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8424 (pm20)
REVERT: A  442 ASP cc_start: 0.9188 (m-30) cc_final: 0.8939 (m-30)
REVERT: D   42 GLN cc_start: 0.8561 (mt0) cc_final: 0.8130 (mp10)
REVERT: D   79 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8060 (mm-30)
REVERT: D  105 GLU cc_start: 0.6358 (tp30) cc_final: 0.6000 (tt0)
REVERT: B   26 GLU cc_start: 0.8647 (tt0) cc_final: 0.8228 (tp30)
REVERT: B   46 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.9062 (pt0)
REVERT: B   64 LYS cc_start: 0.9308 (ptpp) cc_final: 0.9049 (ptpp)
REVERT: B   75 ARG cc_start: 0.8468 (mpp80) cc_final: 0.7982 (mpp80)
REVERT: B  109 GLN cc_start: 0.9084 (mp10) cc_final: 0.8804 (pm20)
  outliers start: 11
  outliers final: 3
  residues processed: 62
  average time/residue: 0.7058
  time to fit residues: 44.7210
Evaluate side-chains
  55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain B residue   46 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.0970
   chunk 20 optimal weight:    0.0020
   chunk 35 optimal weight:    0.4980
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0870
   chunk 26 optimal weight:    0.3980
   chunk 37 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0010
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.0970

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
B  46 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.051319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.044207 restraints weight = 14924.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 4.17
r_work: 0.3058 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3329  Z= 0.129
  Angle     :  0.737   9.148   4523  Z= 0.363
  Chirality :  0.046   0.142    474
  Planarity :  0.004   0.050    587
  Dihedral  :  4.088  15.031    462
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 21.26 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.42), residues: 404
  helix: -4.22 (0.47), residues: 20
  sheet:  1.17 (0.47), residues: 133
  loop : -0.53 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D  24 
 TYR   0.009   0.001   TYR A 396 
 PHE   0.006   0.001   PHE A 377 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.000   0.000   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3323)
  covalent geometry    : angle       0.73644 ( 4511)
  SS BOND              : bond        0.00260 (    6)
  SS BOND              : angle       0.95986 (   12)
  hydrogen bonds       : bond        0.02789 (  105)
  hydrogen bonds       : angle       5.11116 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8251 (p) cc_final: 0.7999 (t)
REVERT: A  406 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8471 (pm20)
REVERT: A  442 ASP cc_start: 0.9108 (m-30) cc_final: 0.8876 (m-30)
REVERT: D   39 LYS cc_start: 0.9146 (tppp) cc_final: 0.8716 (mmtm)
REVERT: D   42 GLN cc_start: 0.8551 (mt0) cc_final: 0.8147 (mp10)
REVERT: D   79 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7795 (mm-30)
REVERT: D  103 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8614 (ttpp)
REVERT: B   26 GLU cc_start: 0.8582 (tt0) cc_final: 0.8174 (tp30)
REVERT: B   43 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8757 (mp0)
REVERT: B   75 ARG cc_start: 0.8459 (mpp80) cc_final: 0.8025 (mpp80)
REVERT: B  106 TYR cc_start: 0.8937 (m-80) cc_final: 0.8722 (m-80)
  outliers start: 7
  outliers final: 2
  residues processed: 63
  average time/residue: 0.6932
  time to fit residues: 44.7212
Evaluate side-chains
  56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain D residue    4 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0010
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   chunk 28 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0170
   overall best weight:    0.4024

-------------------------------------------------------------------------------
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 = 0.3349 r_free = 0.3349 target = 0.050076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.042868 restraints weight = 14524.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 4.11
r_work: 0.3013 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3329  Z= 0.174
  Angle     :  0.796   9.323   4523  Z= 0.392
  Chirality :  0.046   0.150    474
  Planarity :  0.004   0.058    587
  Dihedral  :  4.245  16.136    462
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 23.56 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.42), residues: 404
  helix: -4.10 (0.65), residues: 14
  sheet:  0.98 (0.47), residues: 135
  loop : -0.51 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  24 
 TYR   0.010   0.001   TYR B  33 
 PHE   0.007   0.001   PHE B 104 
 TRP   0.008   0.001   TRP B 107 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 3323)
  covalent geometry    : angle       0.79564 ( 4511)
  SS BOND              : bond        0.00205 (    6)
  SS BOND              : angle       1.05789 (   12)
  hydrogen bonds       : bond        0.02861 (  105)
  hydrogen bonds       : angle       5.12550 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8317 (p) cc_final: 0.7821 (t)
REVERT: A  386 LYS cc_start: 0.8443 (mptt) cc_final: 0.8209 (mppt)
REVERT: A  406 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8467 (pm20)
REVERT: A  442 ASP cc_start: 0.9201 (m-30) cc_final: 0.8973 (m-30)
REVERT: D   39 LYS cc_start: 0.9153 (tppp) cc_final: 0.8765 (mmtm)
REVERT: D   42 GLN cc_start: 0.8491 (mt0) cc_final: 0.8101 (mp10)
REVERT: D   79 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7981 (mm-30)
REVERT: D  103 LYS cc_start: 0.9012 (tmtt) cc_final: 0.8530 (ttpp)
REVERT: B   26 GLU cc_start: 0.8598 (tt0) cc_final: 0.8209 (tp30)
REVERT: B   43 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8689 (mp0)
  outliers start: 4
  outliers final: 1
  residues processed: 53
  average time/residue: 0.7002
  time to fit residues: 37.9294
Evaluate side-chains
  50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.048882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.041647 restraints weight = 14956.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 4.11
r_work: 0.2980 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3329  Z= 0.258
  Angle     :  0.849  12.770   4523  Z= 0.417
  Chirality :  0.047   0.135    474
  Planarity :  0.005   0.068    587
  Dihedral  :  4.603  17.111    462
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 24.43 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.44), residues: 404
  helix: -3.89 (0.73), residues: 14
  sheet:  0.71 (0.44), residues: 157
  loop : -0.53 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  24 
 TYR   0.013   0.001   TYR B  33 
 PHE   0.011   0.001   PHE B 104 
 TRP   0.010   0.001   TRP B 107 
 HIS   0.002   0.001   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 3323)
  covalent geometry    : angle       0.84747 ( 4511)
  SS BOND              : bond        0.00203 (    6)
  SS BOND              : angle       1.19230 (   12)
  hydrogen bonds       : bond        0.03231 (  105)
  hydrogen bonds       : angle       5.41514 (  258)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 THR cc_start: 0.8253 (p) cc_final: 0.7976 (t)
REVERT: A  406 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8398 (pm20)
REVERT: A  442 ASP cc_start: 0.9271 (m-30) cc_final: 0.9013 (m-30)
REVERT: D   42 GLN cc_start: 0.8648 (mt0) cc_final: 0.8206 (mp10)
REVERT: D   79 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7957 (mm-30)
REVERT: D  103 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8753 (ttpp)
REVERT: B   26 GLU cc_start: 0.8694 (tt0) cc_final: 0.8113 (tm-30)
REVERT: B   75 ARG cc_start: 0.8467 (mpp80) cc_final: 0.7977 (mpp80)
  outliers start: 3
  outliers final: 1
  residues processed: 48
  average time/residue: 0.7790
  time to fit residues: 38.2250
Evaluate side-chains
  46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0870
   chunk 23 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.050111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.042879 restraints weight = 15078.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 4.14
r_work: 0.3014 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3329  Z= 0.175
  Angle     :  0.841   9.926   4523  Z= 0.415
  Chirality :  0.046   0.157    474
  Planarity :  0.005   0.064    587
  Dihedral  :  4.480  15.452    462
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 23.85 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.43), residues: 404
  helix: -4.16 (0.59), residues: 14
  sheet:  0.93 (0.48), residues: 135
  loop : -0.48 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  24 
 TYR   0.012   0.001   TYR B  33 
 PHE   0.007   0.001   PHE B 104 
 TRP   0.011   0.001   TRP B 107 
 HIS   0.002   0.001   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3323)
  covalent geometry    : angle       0.83995 ( 4511)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       1.08196 (   12)
  hydrogen bonds       : bond        0.03015 (  105)
  hydrogen bonds       : angle       5.42402 (  258)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1919.11 seconds
wall clock time: 33 minutes 26.11 seconds (2006.11 seconds total)