Starting phenix.real_space_refine
on Mon Feb 10 23:21:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swn_25476/02_2025/7swn_25476_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swn_25476/02_2025/7swn_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swn_25476/02_2025/7swn_25476.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swn_25476/02_2025/7swn_25476.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swn_25476/02_2025/7swn_25476_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swn_25476/02_2025/7swn_25476_neut.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 2.56, per 1000 atoms: 0.78
  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: 0.83
  Conformation dependent library (CDL) restraints added in 411.6 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: 0.50
  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: 0.81

  Time building geometry restraints manager: 1.00 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:             0.780
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.720
  Find NCS groups from input model:        0.040
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.380
-------------------------------------------------------------------------------
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   3367  Z= 0.482
  Angle     :  1.064  10.040   4577  Z= 0.608
  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 : 41.73
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.042   0.005   TRP H  50 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.059   0.005   PHE H 100F
 TYR   0.038   0.003   TYR L  91 
 ARG   0.012   0.001   ARG H  83 

*********************** 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  : 0.375 
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: 0.7682 (p-90)
REVERT: H   20 VAL cc_start: 0.8821 (t) cc_final: 0.7589 (t)
REVERT: H   35 GLN cc_start: 0.8075 (pt0) cc_final: 0.7730 (pt0)
REVERT: H   50 TRP cc_start: 0.7631 (p-90) cc_final: 0.7377 (p-90)
REVERT: H   52 VAL cc_start: 0.8910 (t) cc_final: 0.8666 (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: 0.4600 (mmt180)
REVERT: L   89 GLN cc_start: 0.8116 (tt0) cc_final: 0.7912 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.2295
  time to fit residues: 26.3146
Evaluate side-chains
  72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0470
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.5684

-------------------------------------------------------------------------------
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 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.091674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.077945 restraints weight = 14241.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.080486 restraints weight = 9042.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.082353 restraints weight = 6340.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3367  Z= 0.240
  Angle     :  0.790  11.794   4577  Z= 0.406
  Chirality :  0.047   0.155    492
  Planarity :  0.006   0.050    592
  Dihedral  :  6.547  20.054    466
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 21.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.36), residues: 416
  helix: -4.57 (0.48), residues: 24
  sheet: -1.70 (0.49), residues: 103
  loop : -3.30 (0.32), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 353 
 HIS   0.001   0.001   HIS H 100C
 PHE   0.027   0.003   PHE H 100F
 TYR   0.014   0.002   TYR A 495 
 ARG   0.006   0.001   ARG A 466 

*********************** 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
  106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8263 (tt0) cc_final: 0.7878 (tt0)
REVERT: A  424 LYS cc_start: 0.9424 (tttm) cc_final: 0.9006 (tmtt)
REVERT: A  454 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8620 (tpp80)
REVERT: H   35 GLN cc_start: 0.8810 (pt0) cc_final: 0.8358 (pt0)
REVERT: H   50 TRP cc_start: 0.8043 (p-90) cc_final: 0.7823 (p-90)
REVERT: H   71 ARG cc_start: 0.8695 (ptt-90) cc_final: 0.8419 (ptt-90)
REVERT: H   80 MET cc_start: 0.8265 (ppp) cc_final: 0.7702 (ppp)
REVERT: H   83 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7871 (tpm170)
REVERT: L   42 GLN cc_start: 0.8828 (mp10) cc_final: 0.8374 (mp10)
REVERT: L   77 ARG cc_start: 0.7035 (mmm160) cc_final: 0.5159 (mpt180)
REVERT: L   89 GLN cc_start: 0.8636 (tt0) cc_final: 0.8052 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2241
  time to fit residues: 27.3921
Evaluate side-chains
  77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0270
   chunk 36 optimal weight:    0.0470
   chunk 32 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 19 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.094689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.081155 restraints weight = 14099.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.083659 restraints weight = 9041.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.085544 restraints weight = 6368.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3670 r_free = 0.3670    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3670 r_free = 0.3670    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3367  Z= 0.188
  Angle     :  0.720   9.256   4577  Z= 0.363
  Chirality :  0.046   0.156    492
  Planarity :  0.006   0.047    592
  Dihedral  :  5.639  18.293    466
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.74 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.99 (0.36), residues: 416
  helix: -4.39 (0.48), residues: 30
  sheet: -1.67 (0.49), residues: 104
  loop : -3.05 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 436 
 HIS   0.001   0.001   HIS H 100C
 PHE   0.018   0.002   PHE A 342 
 TYR   0.022   0.002   TYR L  91 
 ARG   0.008   0.001   ARG A 466 

*********************** 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
  109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.9399 (mm) cc_final: 0.9097 (mm)
REVERT: A  423 TYR cc_start: 0.6032 (t80) cc_final: 0.5621 (t80)
REVERT: A  424 LYS cc_start: 0.9490 (tttm) cc_final: 0.9217 (tmtt)
REVERT: A  425 LEU cc_start: 0.9217 (mp) cc_final: 0.8836 (mt)
REVERT: A  444 LYS cc_start: 0.8791 (tmmt) cc_final: 0.8525 (tptt)
REVERT: A  466 ARG cc_start: 0.7528 (ttp80) cc_final: 0.6797 (ttp80)
REVERT: H   20 VAL cc_start: 0.8995 (t) cc_final: 0.8729 (t)
REVERT: H   35 GLN cc_start: 0.8848 (pt0) cc_final: 0.8463 (pt0)
REVERT: H   67 VAL cc_start: 0.7280 (p) cc_final: 0.7031 (p)
REVERT: H   83 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7904 (tpm170)
REVERT: H  105 GLN cc_start: 0.8116 (pm20) cc_final: 0.7837 (tp-100)
REVERT: L   42 GLN cc_start: 0.8760 (mp10) cc_final: 0.8456 (mp10)
REVERT: L   49 TYR cc_start: 0.8170 (p90) cc_final: 0.7719 (p90)
REVERT: L   77 ARG cc_start: 0.6857 (mmm160) cc_final: 0.5738 (mpt180)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.2018
  time to fit residues: 25.4888
Evaluate side-chains
  78 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3727 r_free = 0.3727 target = 0.087626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.074121 restraints weight = 15096.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.076580 restraints weight = 9637.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.078379 restraints weight = 6812.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3367  Z= 0.308
  Angle     :  0.798   9.294   4577  Z= 0.408
  Chirality :  0.047   0.222    492
  Planarity :  0.006   0.059    592
  Dihedral  :  6.230  21.344    466
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 24.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.30 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.36), residues: 416
  helix: -4.20 (0.54), residues: 30
  sheet: -1.81 (0.48), residues: 106
  loop : -3.11 (0.33), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 353 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.020   0.002   PHE A 342 
 TYR   0.034   0.002   TYR L  91 
 ARG   0.005   0.001   ARG A 408 

*********************** 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
  100 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.416 
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: 0.5873 (t80)
REVERT: A  424 LYS cc_start: 0.9545 (tttm) cc_final: 0.9156 (tmtt)
REVERT: A  471 GLU cc_start: 0.7547 (mp0) cc_final: 0.7282 (mp0)
REVERT: A  498 GLN cc_start: 0.7999 (pt0) cc_final: 0.7789 (pt0)
REVERT: H   20 VAL cc_start: 0.9070 (t) cc_final: 0.8818 (t)
REVERT: H   35 GLN cc_start: 0.8873 (pt0) cc_final: 0.8344 (pt0)
REVERT: H   83 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.7955 (tpm170)
REVERT: H  105 GLN cc_start: 0.8093 (pm20) cc_final: 0.7766 (tp-100)
REVERT: L   42 GLN cc_start: 0.8781 (mp10) cc_final: 0.8371 (mp10)
REVERT: L   71 PHE cc_start: 0.8548 (m-80) cc_final: 0.8252 (m-80)
REVERT: L   77 ARG cc_start: 0.6870 (mmm160) cc_final: 0.5387 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1862
  time to fit residues: 22.1870
Evaluate side-chains
  75 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    0.0370
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.1462

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.090917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.077754 restraints weight = 14973.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.080307 restraints weight = 9352.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.082204 restraints weight = 6487.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    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 = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3367  Z= 0.197
  Angle     :  0.758  13.010   4577  Z= 0.376
  Chirality :  0.047   0.307    492
  Planarity :  0.006   0.057    592
  Dihedral  :  5.645  14.883    466
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 18.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.84 (0.37), residues: 416
  helix: -4.03 (0.60), residues: 30
  sheet: -1.63 (0.48), residues: 106
  loop : -2.94 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 436 
 HIS   0.001   0.000   HIS H 100C
 PHE   0.015   0.002   PHE A 342 
 TYR   0.025   0.002   TYR H  59 
 ARG   0.007   0.001   ARG A 466 

*********************** 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
  104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.380 
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: 0.6148 (t80) cc_final: 0.5780 (t80)
REVERT: A  424 LYS cc_start: 0.9520 (tttm) cc_final: 0.9165 (tmtt)
REVERT: A  471 GLU cc_start: 0.7582 (mp0) cc_final: 0.7272 (mp0)
REVERT: A  498 GLN cc_start: 0.7640 (pt0) cc_final: 0.7412 (pt0)
REVERT: H   35 GLN cc_start: 0.8786 (pt0) cc_final: 0.8356 (pt0)
REVERT: H   83 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.7913 (tpm170)
REVERT: H  105 GLN cc_start: 0.8075 (pm20) cc_final: 0.7790 (tp-100)
REVERT: L   49 TYR cc_start: 0.8348 (p90) cc_final: 0.8031 (p90)
REVERT: L   77 ARG cc_start: 0.6752 (mmm160) cc_final: 0.5337 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1720
  time to fit residues: 21.2441
Evaluate side-chains
  80 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.086802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.073844 restraints weight = 15519.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.076282 restraints weight = 9636.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.078068 restraints weight = 6684.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.4425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3367  Z= 0.298
  Angle     :  0.787   9.041   4577  Z= 0.401
  Chirality :  0.047   0.212    492
  Planarity :  0.006   0.057    592
  Dihedral  :  6.090  16.795    466
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 24.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.22 %
    Favored  : 86.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.76 (0.37), residues: 416
  helix: -4.03 (0.59), residues: 30
  sheet: -1.57 (0.49), residues: 102
  loop : -2.88 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 353 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.017   0.002   PHE H 100F
 TYR   0.030   0.003   TYR L  91 
 ARG   0.008   0.001   ARG A 466 

*********************** 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
  102 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  424 LYS cc_start: 0.9537 (tttm) cc_final: 0.9145 (tmtt)
REVERT: A  425 LEU cc_start: 0.9260 (mp) cc_final: 0.8833 (mp)
REVERT: A  471 GLU cc_start: 0.7720 (mp0) cc_final: 0.7418 (mp0)
REVERT: A  498 GLN cc_start: 0.8058 (pt0) cc_final: 0.7781 (pt0)
REVERT: H   20 VAL cc_start: 0.9040 (t) cc_final: 0.7928 (t)
REVERT: H   35 GLN cc_start: 0.8825 (pt0) cc_final: 0.8363 (pt0)
REVERT: H   67 VAL cc_start: 0.7159 (p) cc_final: 0.6895 (p)
REVERT: H   80 MET cc_start: 0.7993 (ppp) cc_final: 0.7490 (ppp)
REVERT: H   83 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.7938 (tpm170)
REVERT: H  105 GLN cc_start: 0.7901 (pm20) cc_final: 0.7657 (tp-100)
REVERT: L   35 TRP cc_start: 0.7015 (m100) cc_final: 0.6684 (m100)
REVERT: L   42 GLN cc_start: 0.8749 (mp10) cc_final: 0.8353 (mp10)
REVERT: L   49 TYR cc_start: 0.8468 (p90) cc_final: 0.8070 (p90)
REVERT: L   77 ARG cc_start: 0.6781 (mmm160) cc_final: 0.5440 (mpt180)
REVERT: L   88 CYS cc_start: 0.4872 (t) cc_final: 0.4264 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1673
  time to fit residues: 20.3986
Evaluate side-chains
  82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 39 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0030
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.1396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.090751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.078202 restraints weight = 15219.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.080644 restraints weight = 9427.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.082458 restraints weight = 6512.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3623 r_free = 0.3623    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 = 0.3623 r_free = 0.3623    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.4998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3367  Z= 0.194
  Angle     :  0.746  13.855   4577  Z= 0.369
  Chirality :  0.048   0.332    492
  Planarity :  0.006   0.055    592
  Dihedral  :  5.641  21.126    466
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.42 (0.37), residues: 416
  helix: -4.23 (0.57), residues: 24
  sheet: -1.36 (0.49), residues: 100
  loop : -2.62 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 353 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.014   0.002   PHE A 342 
 TYR   0.019   0.002   TYR L  91 
 ARG   0.004   0.001   ARG A 466 

*********************** 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
  107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  424 LYS cc_start: 0.9515 (tttm) cc_final: 0.9185 (tptt)
REVERT: A  471 GLU cc_start: 0.7678 (mp0) cc_final: 0.7336 (mp0)
REVERT: H   20 VAL cc_start: 0.8951 (t) cc_final: 0.7755 (t)
REVERT: H   35 GLN cc_start: 0.8806 (pt0) cc_final: 0.8357 (pt0)
REVERT: H   80 MET cc_start: 0.7960 (ppp) cc_final: 0.7500 (ppp)
REVERT: H   83 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.7971 (tpm170)
REVERT: H  105 GLN cc_start: 0.7969 (pm20) cc_final: 0.7659 (tp-100)
REVERT: L   49 TYR cc_start: 0.8412 (p90) cc_final: 0.8076 (p90)
REVERT: L   77 ARG cc_start: 0.6781 (mmm160) cc_final: 0.5643 (mpt180)
REVERT: L   88 CYS cc_start: 0.5058 (t) cc_final: 0.4170 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1574
  time to fit residues: 20.2793
Evaluate side-chains
  84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0970
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.089756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.077309 restraints weight = 14829.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.079703 restraints weight = 9231.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.081474 restraints weight = 6373.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.5197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3367  Z= 0.204
  Angle     :  0.762  13.631   4577  Z= 0.375
  Chirality :  0.047   0.302    492
  Planarity :  0.006   0.058    592
  Dihedral  :  5.485  16.532    466
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.86 %
    Favored  : 89.90 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.37), residues: 416
  helix: -4.20 (0.56), residues: 24
  sheet: -1.40 (0.49), residues: 106
  loop : -2.57 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP L  35 
 HIS   0.001   0.000   HIS H 100C
 PHE   0.016   0.002   PHE A 486 
 TYR   0.019   0.002   TYR L  91 
 ARG   0.005   0.001   ARG A 466 

*********************** 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
  103 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.8256 (ttt-90) cc_final: 0.8008 (tmt170)
REVERT: A  424 LYS cc_start: 0.9503 (tttm) cc_final: 0.9177 (tmtt)
REVERT: A  471 GLU cc_start: 0.7608 (mp0) cc_final: 0.7258 (mp0)
REVERT: H   20 VAL cc_start: 0.9008 (t) cc_final: 0.7806 (t)
REVERT: H   35 GLN cc_start: 0.8815 (pt0) cc_final: 0.8382 (pt0)
REVERT: H   80 MET cc_start: 0.8079 (ppp) cc_final: 0.7622 (ppp)
REVERT: H   83 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.7998 (tpm170)
REVERT: L   35 TRP cc_start: 0.6609 (m100) cc_final: 0.6166 (m100)
REVERT: L   48 ILE cc_start: 0.8048 (pt) cc_final: 0.7592 (mp)
REVERT: L   49 TYR cc_start: 0.8444 (p90) cc_final: 0.8181 (p90)
REVERT: L   77 ARG cc_start: 0.6822 (mmm160) cc_final: 0.5704 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1664
  time to fit residues: 20.6863
Evaluate side-chains
  80 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 27 optimal weight:    6.9990
   chunk 12 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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**
H 105 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.091545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.078683 restraints weight = 15339.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.081147 restraints weight = 9601.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.082959 restraints weight = 6698.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    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 = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3367  Z= 0.192
  Angle     :  0.758  11.169   4577  Z= 0.377
  Chirality :  0.047   0.260    492
  Planarity :  0.006   0.058    592
  Dihedral  :  5.368  16.061    466
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.28 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.38), residues: 416
  helix: -4.20 (0.54), residues: 24
  sheet: -1.37 (0.47), residues: 106
  loop : -2.48 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 436 
 HIS   0.001   0.000   HIS H 100C
 PHE   0.013   0.001   PHE A 342 
 TYR   0.021   0.002   TYR A 508 
 ARG   0.008   0.001   ARG A 466 

*********************** 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
  106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.417 
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  408 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7743 (tmt170)
REVERT: A  417 LYS cc_start: 0.8485 (tptm) cc_final: 0.8060 (tppt)
REVERT: A  424 LYS cc_start: 0.9497 (tttm) cc_final: 0.9188 (tmtt)
REVERT: A  425 LEU cc_start: 0.9186 (mp) cc_final: 0.8913 (mm)
REVERT: A  471 GLU cc_start: 0.7495 (mp0) cc_final: 0.7102 (mp0)
REVERT: A  472 ILE cc_start: 0.8070 (mm) cc_final: 0.7559 (tp)
REVERT: H   35 GLN cc_start: 0.8949 (pt0) cc_final: 0.8464 (pt0)
REVERT: H   83 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.8065 (tpm170)
REVERT: H  105 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7987 (pm20)
REVERT: L   23 CYS cc_start: 0.5560 (t) cc_final: 0.5360 (t)
REVERT: L   42 GLN cc_start: 0.8470 (mp10) cc_final: 0.8028 (mp10)
REVERT: L   49 TYR cc_start: 0.8483 (p90) cc_final: 0.8170 (p90)
REVERT: L   77 ARG cc_start: 0.6872 (mmm160) cc_final: 0.5895 (mpt180)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1695
  time to fit residues: 21.2886
Evaluate side-chains
  86 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    3.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.085597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.073253 restraints weight = 15251.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.075585 restraints weight = 9710.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.077243 restraints weight = 6781.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3367  Z= 0.336
  Angle     :  0.844  12.401   4577  Z= 0.425
  Chirality :  0.047   0.264    492
  Planarity :  0.007   0.059    592
  Dihedral  :  6.287  24.281    466
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 26.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.22 %
    Favored  : 86.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.37), residues: 416
  helix: -4.24 (0.49), residues: 30
  sheet: -1.49 (0.49), residues: 108
  loop : -2.69 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A 353 
 HIS   0.002   0.001   HIS H 100C
 PHE   0.016   0.003   PHE H 100F
 TYR   0.018   0.003   TYR H  59 
 ARG   0.006   0.001   ARG H  71 

********************** 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
  95 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  424 LYS cc_start: 0.9531 (tttm) cc_final: 0.9127 (tmtt)
REVERT: A  471 GLU cc_start: 0.7697 (mp0) cc_final: 0.7340 (mp0)
REVERT: A  498 GLN cc_start: 0.8142 (pt0) cc_final: 0.7837 (pt0)
REVERT: H   35 GLN cc_start: 0.8858 (pt0) cc_final: 0.8271 (pt0)
REVERT: H   50 TRP cc_start: 0.8002 (p-90) cc_final: 0.7667 (p-90)
REVERT: H   80 MET cc_start: 0.8057 (ppp) cc_final: 0.7549 (ppp)
REVERT: H   83 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.8094 (tpm170)
REVERT: H  105 GLN cc_start: 0.8655 (tp40) cc_final: 0.8141 (pm20)
REVERT: L   42 GLN cc_start: 0.8671 (mp10) cc_final: 0.8252 (mp10)
REVERT: L   49 TYR cc_start: 0.8527 (p90) cc_final: 0.8160 (p90)
REVERT: L   77 ARG cc_start: 0.6817 (mmm160) cc_final: 0.5629 (mpt180)
REVERT: L   82 ASP cc_start: 0.6459 (p0) cc_final: 0.5606 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1757
  time to fit residues: 19.8984
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  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    0.0970
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0570
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.092805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.080484 restraints weight = 15685.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.082899 restraints weight = 9821.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.084649 restraints weight = 6799.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    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 = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.5729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3367  Z= 0.194
  Angle     :  0.773  10.502   4577  Z= 0.382
  Chirality :  0.047   0.232    492
  Planarity :  0.006   0.059    592
  Dihedral  :  5.559  21.429    466
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 18.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.38), residues: 416
  helix: -4.04 (0.65), residues: 24
  sheet: -1.43 (0.47), residues: 112
  loop : -2.49 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP L  35 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.015   0.002   PHE A 342 
 TYR   0.022   0.002   TYR H  59 
 ARG   0.008   0.001   ARG A 466 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1527.33 seconds
wall clock time: 28 minutes 3.22 seconds (1683.22 seconds total)