Starting phenix.real_space_refine
on Tue Mar  3 11:27:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swn_25476/03_2026/7swn_25476_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swn_25476/03_2026/7swn_25476.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swn_25476/03_2026/7swn_25476_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swn_25476/03_2026/7swn_25476_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swn_25476/03_2026/7swn_25476.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swn_25476/03_2026/7swn_25476.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      17      5.16       5
     C    2080      2.51       5
     N     554      2.21       5
     O     632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  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: 3283
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "H"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 120, 924
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 108, 823
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100}
  Time building chain proxies: 0.66, per 1000 atoms: 0.20
  Number of scatterers: 3283
  At special positions: 0
  Unit cell: (100.65, 70.95, 75.075, 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      17     16.00
     O     632      8.00
     N     554      7.00
     C    2080      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, 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=2.04
    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 H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  97 " - pdb=" SG  CYS H 100B" distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.05

  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: 0.20
  Conformation dependent library (CDL) restraints added in 78.2 milliseconds
  

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      8.3% alpha, 26.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 386 through 389
    Processing helix  chain 'A' and resid 405 through 410
    Processing helix  chain 'H' and resid 28 through 31
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 4.034A  pdb=" N   GLN H  64 " --> pdb=" O   GLN H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.551A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.319A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.864A  pdb=" N   THR H 107 " --> pdb=" O   TYR H  90 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   TRP H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.864A  pdb=" N   THR H 107 " --> pdb=" O   TYR H  90 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE H 102 " --> pdb=" O   ALA H  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 97 through 98
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11
      removed outlier: 6.398A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11
    Processing sheet with id=AA9, first strand: chain 'L' and resid 20 through 23

    83 hydrogen bonds defined for protein.
    186 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: 0.39

  Time building geometry restraints manager: 0.28 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: 1043
        1.34 -     1.46: 862
        1.46 -     1.58: 1442
        1.58 -     1.71: 0
        1.71 -     1.83: 20
  Bond restraints: 3367
  Sorted by residual:
  bond pdb=" N   VAL H  67 "
       pdb=" CA  VAL H  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.22e+00
  bond pdb=" N   VAL H  89 "
       pdb=" CA  VAL H  89 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.22e-02 6.72e+03 8.12e+00
  bond pdb=" N   VAL L 104 "
       pdb=" CA  VAL L 104 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.22e-02 6.72e+03 7.79e+00
  bond pdb=" N   ARG H  71 "
       pdb=" CA  ARG H  71 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.035 1.29e-02 6.01e+03 7.54e+00
  bond pdb=" N   ASN A 450 "
       pdb=" CA  ASN A 450 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.32e-02 5.74e+03 7.12e+00
  ... (remaining 3362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 4286
        2.01 -     4.02: 250
        4.02 -     6.02: 34
        6.02 -     8.03: 4
        8.03 -    10.04: 3
  Bond angle restraints: 4577
  Sorted by residual:
  angle pdb=" N   VAL H  89 "
        pdb=" CA  VAL H  89 "
        pdb=" C   VAL H  89 "
      ideal   model   delta    sigma   weight residual
     106.88   97.68    9.20 1.52e+00 4.33e-01 3.66e+01
  angle pdb=" N   PRO L  59 "
        pdb=" CA  PRO L  59 "
        pdb=" C   PRO L  59 "
      ideal   model   delta    sigma   weight residual
     111.15  118.00   -6.85 1.58e+00 4.01e-01 1.88e+01
  angle pdb=" C   ILE L  58 "
        pdb=" N   PRO L  59 "
        pdb=" CA  PRO L  59 "
      ideal   model   delta    sigma   weight residual
     119.90  124.22   -4.32 1.02e+00 9.61e-01 1.80e+01
  angle pdb=" N   SER H  74 "
        pdb=" CA  SER H  74 "
        pdb=" C   SER H  74 "
      ideal   model   delta    sigma   weight residual
     112.68  107.38    5.30 1.33e+00 5.65e-01 1.59e+01
  angle pdb=" N   ARG L  61 "
        pdb=" CA  ARG L  61 "
        pdb=" C   ARG L  61 "
      ideal   model   delta    sigma   weight residual
     113.31  105.45    7.86 2.04e+00 2.40e-01 1.48e+01
  ... (remaining 4572 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.34: 1754
       16.34 -    32.68: 182
       32.68 -    49.01: 42
       49.01 -    65.35: 8
       65.35 -    81.69: 4
  Dihedral angle restraints: 1990
    sinusoidal: 771
      harmonic: 1219
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  92 "
           pdb=" CB  CYS H  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.47   41.47     1      1.00e+01 1.00e-02 2.41e+01
  dihedral pdb=" CA  VAL A 401 "
           pdb=" C   VAL A 401 "
           pdb=" N   ILE A 402 "
           pdb=" CA  ILE A 402 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.37  -19.63     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ALA A 522 "
           pdb=" C   ALA A 522 "
           pdb=" N   THR A 523 "
           pdb=" CA  THR A 523 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.19  -18.81     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 1987 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 407
       0.072 -    0.144: 78
       0.144 -    0.216: 6
       0.216 -    0.288: 0
       0.288 -    0.360: 1
  Chirality restraints: 492
  Sorted by residual:
  chirality pdb=" CA  VAL H  89 "
            pdb=" N   VAL H  89 "
            pdb=" C   VAL H  89 "
            pdb=" CB  VAL H  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.80   -0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CA  VAL L 104 "
            pdb=" N   VAL L 104 "
            pdb=" C   VAL L 104 "
            pdb=" CB  VAL L 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  VAL A 407 "
            pdb=" CA  VAL A 407 "
            pdb=" CG1 VAL A 407 "
            pdb=" CG2 VAL A 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 489 not shown)

  Planarity restraints: 592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H 100F"    0.023 2.00e-02 2.50e+03   2.63e-02 1.21e+01
        pdb=" CG  PHE H 100F"   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE H 100F"    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE H 100F"    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE H 100F"   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE H 100F"    0.016 2.00e-02 2.50e+03
        pdb=" CZ  PHE H 100F"   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  50 "    0.016 2.00e-02 2.50e+03   1.63e-02 6.64e+00
        pdb=" CG  TRP H  50 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  50 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  50 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  50 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  50 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 425 "    0.039 5.00e-02 4.00e+02   5.83e-02 5.44e+00
        pdb=" N   PRO A 426 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 426 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 426 "    0.032 5.00e-02 4.00e+02
  ... (remaining 589 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 478
        2.74 -     3.28: 3571
        3.28 -     3.82: 5496
        3.82 -     4.36: 6691
        4.36 -     4.90: 10807
  Nonbonded interactions: 27043
  Sorted by model distance:
  nonbonded pdb=" O   LEU L   4 "
            pdb=" NE2 GLN L 100 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OH  TYR A 451 "
            pdb=" O   PHE A 497 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   LYS H  12 "
            pdb=" N   SER H 112 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   PHE H  63 "
            pdb=" CG1 VAL H  67 "
     model   vdw
     2.238 3.460
  nonbonded pdb=" O   LYS H  62 "
            pdb=" NH2 ARG H  66 "
     model   vdw
     2.241 3.120
  ... (remaining 27038 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:             0.470
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.890
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
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      :  0.007   0.069   3374  Z= 0.369
  Angle     :  1.068  10.040   4591  Z= 0.609
  Chirality :  0.058   0.360    492
  Planarity :  0.007   0.058    592
  Dihedral  : 14.582  81.689   1195
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 41.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.88 %
    Favored  : 78.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -4.82 (0.35), residues: 416
  helix: -4.85 (0.38), residues: 30
  sheet: -2.02 (0.52), residues: 102
  loop : -3.75 (0.30), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  83 
 TYR   0.038   0.003   TYR L  91 
 PHE   0.059   0.005   PHE H 100F
 TRP   0.042   0.005   TRP H  50 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00724 ( 3367)
  covalent geometry    : angle       1.06390 ( 4577)
  SS BOND              : bond        0.00740 (    7)
  SS BOND              : angle       1.92999 (   14)
  hydrogen bonds       : bond        0.18755 (   76)
  hydrogen bonds       : angle      11.65780 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.7819 (tt0) cc_final: 0.7602 (tt0)
REVERT: A  424 LYS cc_start: 0.9304 (tttm) cc_final: 0.9070 (tmtt)
REVERT: A  436 TRP cc_start: 0.7984 (p-90) cc_final: 0.7681 (p-90)
REVERT: H   20 VAL cc_start: 0.8821 (t) cc_final: 0.7586 (t)
REVERT: H   35 GLN cc_start: 0.8075 (pt0) cc_final: 0.7729 (pt0)
REVERT: H   50 TRP cc_start: 0.7631 (p-90) cc_final: 0.7376 (p-90)
REVERT: H   52 VAL cc_start: 0.8910 (t) cc_final: 0.8665 (t)
REVERT: H   83 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7959 (tpm170)
REVERT: L   77 ARG cc_start: 0.6410 (mmm160) cc_final: 0.4596 (mmt180)
REVERT: L   89 GLN cc_start: 0.8116 (tt0) cc_final: 0.7910 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0976
  time to fit residues: 11.1630
Evaluate side-chains
  71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.091883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.077993 restraints weight = 14485.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.080567 restraints weight = 9195.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.082422 restraints weight = 6439.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.083803 restraints weight = 4826.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.084764 restraints weight = 3803.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3374  Z= 0.161
  Angle     :  0.778   9.342   4591  Z= 0.401
  Chirality :  0.047   0.158    492
  Planarity :  0.006   0.049    592
  Dihedral  :  6.462  20.139    466
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 20.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.30 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  6.41 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -4.18 (0.36), residues: 416
  helix: -4.54 (0.49), residues: 24
  sheet: -1.60 (0.49), residues: 101
  loop : -3.31 (0.32), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 466 
 TYR   0.015   0.002   TYR A 495 
 PHE   0.025   0.003   PHE H 100F
 TRP   0.012   0.002   TRP A 353 
 HIS   0.001   0.001   HIS H 100C

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3367)
  covalent geometry    : angle       0.77584 ( 4577)
  SS BOND              : bond        0.00537 (    7)
  SS BOND              : angle       1.22482 (   14)
  hydrogen bonds       : bond        0.03868 (   76)
  hydrogen bonds       : angle       9.32863 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8310 (tt0) cc_final: 0.7903 (tt0)
REVERT: A  417 LYS cc_start: 0.8781 (tptm) cc_final: 0.8534 (tptm)
REVERT: A  424 LYS cc_start: 0.9419 (tttm) cc_final: 0.9021 (tmtt)
REVERT: H   35 GLN cc_start: 0.8824 (pt0) cc_final: 0.8394 (pt0)
REVERT: H   50 TRP cc_start: 0.8101 (p-90) cc_final: 0.7855 (p-90)
REVERT: H   71 ARG cc_start: 0.8692 (ptt-90) cc_final: 0.8445 (ptt-90)
REVERT: H   80 MET cc_start: 0.8304 (ppp) cc_final: 0.7723 (ppp)
REVERT: H   83 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.7850 (tpm170)
REVERT: L   13 LEU cc_start: 0.9042 (mp) cc_final: 0.8832 (tp)
REVERT: L   42 GLN cc_start: 0.8809 (mp10) cc_final: 0.8383 (mp10)
REVERT: L   77 ARG cc_start: 0.6912 (mmm160) cc_final: 0.5065 (mpt180)
REVERT: L  106 ILE cc_start: 0.7382 (mm) cc_final: 0.7021 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 107
  average time/residue: 0.0888
  time to fit residues: 10.9265
Evaluate side-chains
  79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.0470
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0470
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.2180

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.092095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.078201 restraints weight = 14329.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.080778 restraints weight = 9162.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.082639 restraints weight = 6465.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.084007 restraints weight = 4859.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.085079 restraints weight = 3843.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3374  Z= 0.138
  Angle     :  0.725   9.445   4591  Z= 0.367
  Chirality :  0.046   0.152    492
  Planarity :  0.006   0.048    592
  Dihedral  :  5.828  18.133    466
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -4.09 (0.36), residues: 416
  helix: -4.51 (0.43), residues: 30
  sheet: -1.50 (0.50), residues: 102
  loop : -3.21 (0.32), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 466 
 TYR   0.022   0.002   TYR L  91 
 PHE   0.019   0.002   PHE A 342 
 TRP   0.026   0.002   TRP A 436 
 HIS   0.001   0.001   HIS H 100C

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3367)
  covalent geometry    : angle       0.72382 ( 4577)
  SS BOND              : bond        0.00446 (    7)
  SS BOND              : angle       1.01373 (   14)
  hydrogen bonds       : bond        0.03277 (   76)
  hydrogen bonds       : angle       8.65926 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.9393 (mm) cc_final: 0.9049 (mm)
REVERT: A  423 TYR cc_start: 0.6119 (t80) cc_final: 0.5739 (t80)
REVERT: A  424 LYS cc_start: 0.9415 (tttm) cc_final: 0.9007 (tmtt)
REVERT: A  425 LEU cc_start: 0.9227 (mp) cc_final: 0.8815 (mt)
REVERT: A  444 LYS cc_start: 0.8906 (tmmt) cc_final: 0.8615 (tptt)
REVERT: A  466 ARG cc_start: 0.7600 (ttp80) cc_final: 0.6828 (ttp80)
REVERT: A  471 GLU cc_start: 0.7490 (mp0) cc_final: 0.7124 (mp0)
REVERT: H   20 VAL cc_start: 0.9029 (t) cc_final: 0.8772 (t)
REVERT: H   35 GLN cc_start: 0.8796 (pt0) cc_final: 0.8393 (pt0)
REVERT: H   83 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7906 (tpm170)
REVERT: H  105 GLN cc_start: 0.8097 (pm20) cc_final: 0.7762 (tp-100)
REVERT: L   13 LEU cc_start: 0.8997 (mp) cc_final: 0.8750 (tp)
REVERT: L   42 GLN cc_start: 0.8751 (mp10) cc_final: 0.8387 (mp10)
REVERT: L   49 TYR cc_start: 0.8169 (p90) cc_final: 0.7723 (p90)
REVERT: L   77 ARG cc_start: 0.6768 (mmm160) cc_final: 0.5693 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0837
  time to fit residues: 10.2566
Evaluate side-chains
  76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 13 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 ASN
A 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.089068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.075800 restraints weight = 14386.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.078241 restraints weight = 9259.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.080076 restraints weight = 6543.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.081387 restraints weight = 4911.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.082354 restraints weight = 3866.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3374  Z= 0.176
  Angle     :  0.753   9.292   4591  Z= 0.382
  Chirality :  0.047   0.266    492
  Planarity :  0.006   0.056    592
  Dihedral  :  5.967  17.012    466
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 22.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -4.02 (0.37), residues: 416
  helix: -4.33 (0.48), residues: 30
  sheet: -1.50 (0.50), residues: 103
  loop : -3.15 (0.33), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 457 
 TYR   0.032   0.002   TYR L  91 
 PHE   0.022   0.003   PHE A 347 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 3367)
  covalent geometry    : angle       0.75067 ( 4577)
  SS BOND              : bond        0.00496 (    7)
  SS BOND              : angle       1.36442 (   14)
  hydrogen bonds       : bond        0.03620 (   76)
  hydrogen bonds       : angle       8.40805 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.6205 (t80) cc_final: 0.5895 (t80)
REVERT: A  424 LYS cc_start: 0.9535 (tttm) cc_final: 0.9169 (tmtt)
REVERT: A  471 GLU cc_start: 0.7485 (mp0) cc_final: 0.7168 (mp0)
REVERT: H   20 VAL cc_start: 0.9025 (t) cc_final: 0.7788 (t)
REVERT: H   35 GLN cc_start: 0.8895 (pt0) cc_final: 0.8400 (pt0)
REVERT: H   80 MET cc_start: 0.8193 (ppp) cc_final: 0.7664 (ppp)
REVERT: H   83 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.7944 (tpm170)
REVERT: H  105 GLN cc_start: 0.8064 (pm20) cc_final: 0.7754 (tp-100)
REVERT: L   13 LEU cc_start: 0.9012 (mp) cc_final: 0.8784 (tp)
REVERT: L   42 GLN cc_start: 0.8727 (mp10) cc_final: 0.8339 (mp10)
REVERT: L   49 TYR cc_start: 0.8293 (p90) cc_final: 0.7752 (p90)
REVERT: L   77 ARG cc_start: 0.6773 (mmm160) cc_final: 0.5235 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0715
  time to fit residues: 8.2831
Evaluate side-chains
  74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0870
   chunk 34 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.4962

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.089935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.076833 restraints weight = 14990.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.079312 restraints weight = 9613.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.081066 restraints weight = 6784.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.082381 restraints weight = 5093.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.083380 restraints weight = 4019.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3374  Z= 0.142
  Angle     :  0.750  12.152   4591  Z= 0.373
  Chirality :  0.046   0.261    492
  Planarity :  0.006   0.059    592
  Dihedral  :  5.642  16.143    466
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 20.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.02 %
    Favored  : 87.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.96 (0.37), residues: 416
  helix: -4.23 (0.52), residues: 30
  sheet: -1.67 (0.48), residues: 106
  loop : -3.03 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 466 
 TYR   0.022   0.002   TYR A 508 
 PHE   0.017   0.002   PHE A 342 
 TRP   0.026   0.002   TRP A 436 
 HIS   0.001   0.000   HIS H 100C

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3367)
  covalent geometry    : angle       0.74873 ( 4577)
  SS BOND              : bond        0.00456 (    7)
  SS BOND              : angle       1.13961 (   14)
  hydrogen bonds       : bond        0.03338 (   76)
  hydrogen bonds       : angle       8.05421 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.6199 (t80) cc_final: 0.5757 (t80)
REVERT: A  424 LYS cc_start: 0.9524 (tttm) cc_final: 0.9147 (tmtt)
REVERT: A  471 GLU cc_start: 0.7456 (mp0) cc_final: 0.7122 (mp0)
REVERT: A  498 GLN cc_start: 0.7741 (pt0) cc_final: 0.7506 (pt0)
REVERT: H   20 VAL cc_start: 0.9047 (t) cc_final: 0.7854 (t)
REVERT: H   35 GLN cc_start: 0.8901 (pt0) cc_final: 0.8417 (pt0)
REVERT: H   67 VAL cc_start: 0.7137 (p) cc_final: 0.6907 (p)
REVERT: H   73 MET cc_start: 0.6981 (mmp) cc_final: 0.6750 (mmp)
REVERT: H   80 MET cc_start: 0.8142 (ppp) cc_final: 0.7632 (ppp)
REVERT: H   83 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.7976 (tpm170)
REVERT: H  105 GLN cc_start: 0.8065 (pm20) cc_final: 0.7822 (tp-100)
REVERT: H  108 MET cc_start: 0.8559 (mtt) cc_final: 0.8333 (mtp)
REVERT: L   13 LEU cc_start: 0.8983 (mp) cc_final: 0.8732 (tp)
REVERT: L   42 GLN cc_start: 0.8713 (mp10) cc_final: 0.8341 (mp10)
REVERT: L   49 TYR cc_start: 0.8367 (p90) cc_final: 0.7858 (p90)
REVERT: L   77 ARG cc_start: 0.6499 (mmm160) cc_final: 0.5335 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0682
  time to fit residues: 8.7010
Evaluate side-chains
  73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.087676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.074147 restraints weight = 14948.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.076596 restraints weight = 9548.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.078369 restraints weight = 6765.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.079679 restraints weight = 5118.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.080677 restraints weight = 4056.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.4493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3374  Z= 0.168
  Angle     :  0.745   8.884   4591  Z= 0.378
  Chirality :  0.045   0.182    492
  Planarity :  0.006   0.058    592
  Dihedral  :  5.838  22.275    466
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 21.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.89 (0.36), residues: 416
  helix: -4.26 (0.53), residues: 30
  sheet: -1.78 (0.47), residues: 106
  loop : -2.90 (0.33), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 509 
 TYR   0.022   0.002   TYR A 453 
 PHE   0.016   0.002   PHE A 486 
 TRP   0.015   0.002   TRP A 353 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3367)
  covalent geometry    : angle       0.74141 ( 4577)
  SS BOND              : bond        0.00511 (    7)
  SS BOND              : angle       1.52288 (   14)
  hydrogen bonds       : bond        0.03638 (   76)
  hydrogen bonds       : angle       8.02896 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.6194 (t80) cc_final: 0.5784 (t80)
REVERT: A  424 LYS cc_start: 0.9528 (tttm) cc_final: 0.9127 (tmtt)
REVERT: A  471 GLU cc_start: 0.7502 (mp0) cc_final: 0.7152 (mp0)
REVERT: H   20 VAL cc_start: 0.9095 (t) cc_final: 0.8764 (t)
REVERT: H   35 GLN cc_start: 0.8917 (pt0) cc_final: 0.8444 (pt0)
REVERT: H   80 MET cc_start: 0.8232 (ppp) cc_final: 0.7975 (ppp)
REVERT: H   83 ARG cc_start: 0.8456 (ttp-110) cc_final: 0.7992 (tpm170)
REVERT: L   13 LEU cc_start: 0.9014 (mp) cc_final: 0.8735 (tp)
REVERT: L   42 GLN cc_start: 0.8690 (mp10) cc_final: 0.8329 (mp10)
REVERT: L   49 TYR cc_start: 0.8485 (p90) cc_final: 0.8108 (p90)
REVERT: L   77 ARG cc_start: 0.6752 (mmm160) cc_final: 0.5538 (mpt180)
REVERT: L   88 CYS cc_start: 0.5065 (t) cc_final: 0.4218 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0688
  time to fit residues: 8.3765
Evaluate side-chains
  78 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 32 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0010
   overall best weight:    1.2992

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 474 GLN
A 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.090489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.077902 restraints weight = 15814.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.080327 restraints weight = 9883.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.082092 restraints weight = 6839.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.083351 restraints weight = 5056.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.084292 restraints weight = 3950.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.5035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3374  Z= 0.141
  Angle     :  0.767  13.200   4591  Z= 0.383
  Chirality :  0.047   0.286    492
  Planarity :  0.006   0.060    592
  Dihedral  :  5.663  22.355    466
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 18.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.74 %
    Favored  : 87.26 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  2.23 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.76 (0.37), residues: 416
  helix: -4.21 (0.57), residues: 30
  sheet: -1.65 (0.48), residues: 105
  loop : -2.81 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 509 
 TYR   0.029   0.002   TYR L  91 
 PHE   0.014   0.002   PHE A 342 
 TRP   0.042   0.003   TRP A 436 
 HIS   0.001   0.000   HIS H 100C

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3367)
  covalent geometry    : angle       0.76528 ( 4577)
  SS BOND              : bond        0.00530 (    7)
  SS BOND              : angle       1.25304 (   14)
  hydrogen bonds       : bond        0.03483 (   76)
  hydrogen bonds       : angle       7.72011 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.6079 (t80) cc_final: 0.5746 (t80)
REVERT: A  424 LYS cc_start: 0.9523 (tttm) cc_final: 0.9194 (tmtt)
REVERT: A  425 LEU cc_start: 0.9257 (mp) cc_final: 0.8963 (mm)
REVERT: A  471 GLU cc_start: 0.7550 (mp0) cc_final: 0.7161 (mp0)
REVERT: H   20 VAL cc_start: 0.9057 (t) cc_final: 0.7668 (t)
REVERT: H   80 MET cc_start: 0.8241 (ppp) cc_final: 0.7613 (ppp)
REVERT: H   81 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7183 (tm-30)
REVERT: H   83 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8020 (tpm170)
REVERT: L   13 LEU cc_start: 0.9018 (mp) cc_final: 0.8746 (tp)
REVERT: L   49 TYR cc_start: 0.8437 (p90) cc_final: 0.8179 (p90)
REVERT: L   77 ARG cc_start: 0.6436 (mmm160) cc_final: 0.5485 (mpt180)
  outliers start: 2
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0684
  time to fit residues: 9.1824
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 35 optimal weight:    0.1980
   chunk 13 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0970
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 493 GLN
H 105 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.091745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.078875 restraints weight = 15493.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.081363 restraints weight = 9704.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.083112 restraints weight = 6738.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.084369 restraints weight = 5010.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.085356 restraints weight = 3926.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3374  Z= 0.134
  Angle     :  0.754  10.669   4591  Z= 0.374
  Chirality :  0.047   0.243    492
  Planarity :  0.006   0.054    592
  Dihedral  :  5.500  21.707    466
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  2.23 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.69 (0.37), residues: 416
  helix: -4.17 (0.56), residues: 30
  sheet: -1.74 (0.47), residues: 108
  loop : -2.70 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 466 
 TYR   0.020   0.002   TYR H  59 
 PHE   0.017   0.002   PHE A 486 
 TRP   0.022   0.002   TRP L  35 
 HIS   0.001   0.000   HIS H 100C

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3367)
  covalent geometry    : angle       0.75246 ( 4577)
  SS BOND              : bond        0.00522 (    7)
  SS BOND              : angle       1.22933 (   14)
  hydrogen bonds       : bond        0.03435 (   76)
  hydrogen bonds       : angle       7.43971 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 THR cc_start: 0.7933 (m) cc_final: 0.7717 (p)
REVERT: A  423 TYR cc_start: 0.5982 (t80) cc_final: 0.5659 (t80)
REVERT: A  424 LYS cc_start: 0.9499 (tttm) cc_final: 0.9199 (tmtt)
REVERT: A  425 LEU cc_start: 0.9268 (mp) cc_final: 0.8989 (mm)
REVERT: A  471 GLU cc_start: 0.7535 (mp0) cc_final: 0.7124 (mp0)
REVERT: H   20 VAL cc_start: 0.9048 (t) cc_final: 0.8748 (t)
REVERT: H   35 GLN cc_start: 0.8876 (pt0) cc_final: 0.8538 (pt0)
REVERT: H   80 MET cc_start: 0.8262 (ppp) cc_final: 0.8023 (ppp)
REVERT: H   83 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.8029 (tpm170)
REVERT: L   13 LEU cc_start: 0.9025 (mp) cc_final: 0.8708 (tp)
REVERT: L   49 TYR cc_start: 0.8467 (p90) cc_final: 0.8244 (p90)
REVERT: L   77 ARG cc_start: 0.6258 (mmm160) cc_final: 0.5526 (mpt180)
  outliers start: 2
  outliers final: 1
  residues processed: 110
  average time/residue: 0.0758
  time to fit residues: 10.0140
Evaluate side-chains
  87 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 1 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0570
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 9 optimal weight:    0.2980
   chunk 7 optimal weight:    0.2980
   overall best weight:    0.2896

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
H 105 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.095523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.083332 restraints weight = 15589.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.085733 restraints weight = 9892.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.087442 restraints weight = 6894.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.088641 restraints weight = 5132.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.089613 restraints weight = 4029.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.5899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3374  Z= 0.125
  Angle     :  0.752  13.528   4591  Z= 0.373
  Chirality :  0.048   0.303    492
  Planarity :  0.006   0.056    592
  Dihedral  :  5.311  21.557    466
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 18.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.26 %
    Favored  : 87.74 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.56 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.56 (0.37), residues: 416
  helix: -4.27 (0.52), residues: 30
  sheet: -1.51 (0.46), residues: 114
  loop : -2.66 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 466 
 TYR   0.020   0.002   TYR L  91 
 PHE   0.019   0.002   PHE A 486 
 TRP   0.048   0.004   TRP A 436 
 HIS   0.001   0.000   HIS H 100C

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3367)
  covalent geometry    : angle       0.74995 ( 4577)
  SS BOND              : bond        0.00489 (    7)
  SS BOND              : angle       1.15153 (   14)
  hydrogen bonds       : bond        0.03336 (   76)
  hydrogen bonds       : angle       7.07685 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 THR cc_start: 0.7824 (m) cc_final: 0.7600 (p)
REVERT: A  423 TYR cc_start: 0.5699 (t80) cc_final: 0.5434 (t80)
REVERT: A  424 LYS cc_start: 0.9452 (tttm) cc_final: 0.9200 (tmtt)
REVERT: A  425 LEU cc_start: 0.9104 (mp) cc_final: 0.8820 (mm)
REVERT: A  471 GLU cc_start: 0.7621 (mp0) cc_final: 0.7155 (mp0)
REVERT: H   20 VAL cc_start: 0.9001 (t) cc_final: 0.8612 (t)
REVERT: H   35 GLN cc_start: 0.8817 (pt0) cc_final: 0.8556 (pt0)
REVERT: H   79 TYR cc_start: 0.8246 (m-80) cc_final: 0.8000 (m-80)
REVERT: H   80 MET cc_start: 0.8238 (ppp) cc_final: 0.7996 (ppp)
REVERT: H  105 GLN cc_start: 0.8530 (tp40) cc_final: 0.7865 (pm20)
REVERT: L   49 TYR cc_start: 0.8335 (p90) cc_final: 0.8058 (p90)
REVERT: L   71 PHE cc_start: 0.8338 (m-80) cc_final: 0.8034 (m-80)
REVERT: L   77 ARG cc_start: 0.6118 (mmm160) cc_final: 0.5606 (mpt180)
  outliers start: 1
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0587
  time to fit residues: 8.0810
Evaluate side-chains
  85 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0980
   chunk 33 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 24 optimal weight:    0.4980
   chunk 30 optimal weight:    0.5980
   chunk 1 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 409 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.095552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.082608 restraints weight = 15436.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.085164 restraints weight = 9755.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.087038 restraints weight = 6793.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.088374 restraints weight = 5035.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.089343 restraints weight = 3917.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.6173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3374  Z= 0.125
  Angle     :  0.750  12.335   4591  Z= 0.373
  Chirality :  0.048   0.296    492
  Planarity :  0.006   0.061    592
  Dihedral  :  5.350  25.854    466
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  0.84 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.49 (0.37), residues: 416
  helix: -4.37 (0.47), residues: 30
  sheet: -1.68 (0.44), residues: 126
  loop : -2.49 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 466 
 TYR   0.018   0.002   TYR L  91 
 PHE   0.018   0.002   PHE A 486 
 TRP   0.021   0.003   TRP H  36 
 HIS   0.001   0.000   HIS H 100C

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3367)
  covalent geometry    : angle       0.74917 ( 4577)
  SS BOND              : bond        0.00439 (    7)
  SS BOND              : angle       1.04632 (   14)
  hydrogen bonds       : bond        0.03539 (   76)
  hydrogen bonds       : angle       6.99506 (  186)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 THR cc_start: 0.8016 (m) cc_final: 0.7776 (p)
REVERT: A  423 TYR cc_start: 0.5740 (t80) cc_final: 0.5505 (t80)
REVERT: A  424 LYS cc_start: 0.9444 (tttm) cc_final: 0.9174 (tmtt)
REVERT: A  425 LEU cc_start: 0.9058 (mp) cc_final: 0.8770 (mm)
REVERT: A  471 GLU cc_start: 0.7515 (mp0) cc_final: 0.7048 (mp0)
REVERT: H   20 VAL cc_start: 0.9100 (t) cc_final: 0.8664 (t)
REVERT: H   35 GLN cc_start: 0.8908 (pt0) cc_final: 0.8580 (pt0)
REVERT: H   80 MET cc_start: 0.8326 (ppp) cc_final: 0.8015 (ppp)
REVERT: H  105 GLN cc_start: 0.8654 (tp40) cc_final: 0.8174 (pm20)
REVERT: L   33 LEU cc_start: 0.9155 (tt) cc_final: 0.8951 (tt)
REVERT: L   49 TYR cc_start: 0.8406 (p90) cc_final: 0.8136 (p90)
REVERT: L   71 PHE cc_start: 0.8290 (m-80) cc_final: 0.7884 (m-10)
REVERT: L   77 ARG cc_start: 0.6415 (mmm160) cc_final: 0.5841 (mpt180)
  outliers start: 2
  outliers final: 1
  residues processed: 103
  average time/residue: 0.0689
  time to fit residues: 8.5946
Evaluate side-chains
  79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0870
   overall best weight:    1.8164

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.091862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.078622 restraints weight = 15440.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.081196 restraints weight = 9838.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.083025 restraints weight = 6881.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.084396 restraints weight = 5157.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.085443 restraints weight = 4045.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.6027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3374  Z= 0.161
  Angle     :  0.791  13.051   4591  Z= 0.394
  Chirality :  0.047   0.293    492
  Planarity :  0.006   0.062    592
  Dihedral  :  5.568  21.234    466
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 21.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.61 (0.38), residues: 416
  helix: -4.30 (0.46), residues: 30
  sheet: -2.02 (0.42), residues: 134
  loop : -2.43 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 466 
 TYR   0.020   0.002   TYR H  59 
 PHE   0.015   0.002   PHE A 374 
 TRP   0.048   0.004   TRP A 436 
 HIS   0.001   0.001   HIS H 100C

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3367)
  covalent geometry    : angle       0.79001 ( 4577)
  SS BOND              : bond        0.00482 (    7)
  SS BOND              : angle       1.16369 (   14)
  hydrogen bonds       : bond        0.03598 (   76)
  hydrogen bonds       : angle       7.26707 (  186)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 821.72 seconds
wall clock time: 14 minutes 47.23 seconds (887.23 seconds total)