Starting phenix.real_space_refine
on Wed Mar  5 18:23:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swn_25476/03_2025/7swn_25476_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swn_25476/03_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_25476/03_2025/7swn_25476.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swn_25476/03_2025/7swn_25476.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swn_25476/03_2025/7swn_25476_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swn_25476/03_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-5624/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: 2.71, per 1000 atoms: 0.83
  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: 0.82
  Conformation dependent library (CDL) restraints added in 407.8 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: 0.46
  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: 0.97 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:             0.870
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.960
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.030
-------------------------------------------------------------------------------
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  : 0.363 
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: 0.2232
  time to fit residues: 25.5957
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  : 0.365 
-------------------------------------------------------------------------------
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 = 38)----------------|
| 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 = 0.080510 restraints weight = 9042.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.082345 restraints weight = 6321.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    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 = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3593
-------------------------------------------------------------------------------
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  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8267 (tt0) cc_final: 0.7880 (tt0)
REVERT: A  424 LYS cc_start: 0.9425 (tttm) cc_final: 0.9007 (tmtt)
REVERT: A  454 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8622 (tpp80)
REVERT: H   35 GLN cc_start: 0.8811 (pt0) cc_final: 0.8357 (pt0)
REVERT: H   50 TRP cc_start: 0.8031 (p-90) cc_final: 0.7814 (p-90)
REVERT: H   71 ARG cc_start: 0.8699 (ptt-90) cc_final: 0.8424 (ptt-90)
REVERT: H   80 MET cc_start: 0.8276 (ppp) cc_final: 0.7707 (ppp)
REVERT: H   83 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7874 (tpm170)
REVERT: L   42 GLN cc_start: 0.8833 (mp10) cc_final: 0.8383 (mp10)
REVERT: L   77 ARG cc_start: 0.7076 (mmm160) cc_final: 0.5199 (mpt180)
REVERT: L   89 GLN cc_start: 0.8638 (tt0) cc_final: 0.8052 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2162
  time to fit residues: 26.4123
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  : 0.376 
-------------------------------------------------------------------------------
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:    8.9990
   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 = 0.3840 r_free = 0.3840 target = 0.094724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.081563 restraints weight = 14054.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.084060 restraints weight = 8951.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.085907 restraints weight = 6265.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.086         |
| 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: 0.6952
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3367  Z= 0.189
  Angle     :  0.719   9.223   4577  Z= 0.363
  Chirality :  0.046   0.156    492
  Planarity :  0.006   0.047    592
  Dihedral  :  5.613  18.157    466
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 16.53
  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: -4.38 (0.48), residues: 30
  sheet: -1.66 (0.49), residues: 104
  loop : -3.04 (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  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.9395 (mm) cc_final: 0.9109 (mm)
REVERT: A  423 TYR cc_start: 0.6009 (t80) cc_final: 0.5605 (t80)
REVERT: A  424 LYS cc_start: 0.9497 (tttm) cc_final: 0.9228 (tmtt)
REVERT: A  425 LEU cc_start: 0.9216 (mp) cc_final: 0.8836 (mt)
REVERT: A  444 LYS cc_start: 0.8776 (tmmt) cc_final: 0.8450 (tptt)
REVERT: A  466 ARG cc_start: 0.7502 (ttp80) cc_final: 0.6767 (ttp80)
REVERT: H   20 VAL cc_start: 0.8990 (t) cc_final: 0.8728 (t)
REVERT: H   35 GLN cc_start: 0.8824 (pt0) cc_final: 0.8454 (pt0)
REVERT: H   67 VAL cc_start: 0.7289 (p) cc_final: 0.7047 (p)
REVERT: H   83 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7896 (tpm170)
REVERT: H  105 GLN cc_start: 0.8110 (pm20) cc_final: 0.7819 (tp-100)
REVERT: L   42 GLN cc_start: 0.8763 (mp10) cc_final: 0.8477 (mp10)
REVERT: L   77 ARG cc_start: 0.6787 (mmm160) cc_final: 0.5701 (mpt180)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.1910
  time to fit residues: 24.1577
Evaluate side-chains
  77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 1 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    2.6786

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.088639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.075203 restraints weight = 14870.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.077664 restraints weight = 9486.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.079486 restraints weight = 6669.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3367  Z= 0.284
  Angle     :  0.777   9.211   4577  Z= 0.397
  Chirality :  0.047   0.266    492
  Planarity :  0.006   0.058    592
  Dihedral  :  6.136  20.552    466
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 25.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.30 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.01 %
    Favored  : 94.71 %
  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 (0.37), residues: 416
  helix: -4.20 (0.55), residues: 30
  sheet: -1.77 (0.48), residues: 105
  loop : -3.02 (0.33), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 353 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.024   0.003   PHE A 347 
 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
  101 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.6165 (t80) cc_final: 0.5825 (t80)
REVERT: A  424 LYS cc_start: 0.9509 (tttm) cc_final: 0.9163 (tmtt)
REVERT: A  471 GLU cc_start: 0.7521 (mp0) cc_final: 0.7264 (mp0)
REVERT: H   20 VAL cc_start: 0.9083 (t) cc_final: 0.8816 (t)
REVERT: H   35 GLN cc_start: 0.8908 (pt0) cc_final: 0.8385 (pt0)
REVERT: H   71 ARG cc_start: 0.8731 (ptp90) cc_final: 0.8472 (ptp-170)
REVERT: H   83 ARG cc_start: 0.8438 (ttp-110) cc_final: 0.7966 (tpm170)
REVERT: H  105 GLN cc_start: 0.8076 (pm20) cc_final: 0.7768 (tp-100)
REVERT: L   42 GLN cc_start: 0.8720 (mp10) cc_final: 0.8234 (mp10)
REVERT: L   71 PHE cc_start: 0.8559 (m-80) cc_final: 0.8231 (m-80)
REVERT: L   77 ARG cc_start: 0.6921 (mmm160) cc_final: 0.5537 (mpt180)
  outliers start: 1
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1603
  time to fit residues: 19.2589
Evaluate side-chains
  79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.089195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.075897 restraints weight = 14814.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.078395 restraints weight = 9335.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.080226 restraints weight = 6519.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    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 = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3367  Z= 0.237
  Angle     :  0.773  12.894   4577  Z= 0.385
  Chirality :  0.047   0.289    492
  Planarity :  0.006   0.057    592
  Dihedral  :  5.877  15.676    466
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  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 (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: -3.93 (0.36), residues: 416
  helix: -4.01 (0.61), residues: 30
  sheet: -1.68 (0.48), residues: 105
  loop : -3.02 (0.33), residues: 281

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   0.027   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
  101 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.6110 (t80) cc_final: 0.5744 (t80)
REVERT: A  424 LYS cc_start: 0.9542 (tttm) cc_final: 0.9162 (tmtt)
REVERT: A  471 GLU cc_start: 0.7597 (mp0) cc_final: 0.7323 (mp0)
REVERT: A  498 GLN cc_start: 0.7814 (pt0) cc_final: 0.7571 (pt0)
REVERT: H   20 VAL cc_start: 0.9049 (t) cc_final: 0.8834 (t)
REVERT: H   35 GLN cc_start: 0.8758 (pt0) cc_final: 0.8324 (pt0)
REVERT: H   83 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.7937 (tpm170)
REVERT: H  105 GLN cc_start: 0.8079 (pm20) cc_final: 0.7757 (tp-100)
REVERT: L   42 GLN cc_start: 0.8813 (mp10) cc_final: 0.8349 (mp10)
REVERT: L   49 TYR cc_start: 0.8413 (p90) cc_final: 0.8053 (p90)
REVERT: L   77 ARG cc_start: 0.6580 (mmm160) cc_final: 0.5191 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1676
  time to fit residues: 20.2611
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  : 0.368 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0970
   chunk 6 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    3.8186

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.085208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.072054 restraints weight = 15511.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.074514 restraints weight = 9739.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.076286 restraints weight = 6784.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3494
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    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 = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3367  Z= 0.357
  Angle     :  0.830   9.436   4577  Z= 0.427
  Chirality :  0.048   0.213    492
  Planarity :  0.007   0.059    592
  Dihedral  :  6.521  18.847    466
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 29.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.46 %
    Favored  : 86.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  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: -3.97 (0.36), residues: 416
  helix: -4.08 (0.58), residues: 30
  sheet: -1.72 (0.48), residues: 105
  loop : -3.04 (0.33), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 353 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.019   0.003   PHE A 497 
 TYR   0.032   0.003   TYR L  91 
 ARG   0.006   0.001   ARG A 408 

*********************** 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
  94 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.6237 (t80) cc_final: 0.5981 (t80)
REVERT: A  424 LYS cc_start: 0.9531 (tttm) cc_final: 0.9097 (tmtt)
REVERT: A  471 GLU cc_start: 0.7718 (mp0) cc_final: 0.7417 (mp0)
REVERT: A  498 GLN cc_start: 0.8145 (pt0) cc_final: 0.7871 (pt0)
REVERT: H   20 VAL cc_start: 0.9063 (t) cc_final: 0.7874 (t)
REVERT: H   35 GLN cc_start: 0.8794 (pt0) cc_final: 0.8306 (pt0)
REVERT: H   50 TRP cc_start: 0.8183 (p-90) cc_final: 0.7943 (p-90)
REVERT: H   80 MET cc_start: 0.8141 (ppp) cc_final: 0.7576 (ppp)
REVERT: H   83 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.7962 (tpm170)
REVERT: L   35 TRP cc_start: 0.7137 (m100) cc_final: 0.6788 (m100)
REVERT: L   42 GLN cc_start: 0.8813 (mp10) cc_final: 0.8391 (mp10)
REVERT: L   49 TYR cc_start: 0.8557 (p90) cc_final: 0.8138 (p90)
REVERT: L   77 ARG cc_start: 0.6861 (mmm160) cc_final: 0.5228 (mpt180)
REVERT: L   81 GLU cc_start: 0.6515 (pm20) cc_final: 0.6078 (pm20)
REVERT: L   88 CYS cc_start: 0.5136 (t) cc_final: 0.4537 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1471
  time to fit residues: 16.8693
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  : 0.346 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 28 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3732 r_free = 0.3732 target = 0.088067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.074992 restraints weight = 14807.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.077502 restraints weight = 9233.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.079350 restraints weight = 6398.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3367  Z= 0.239
  Angle     :  0.785  14.041   4577  Z= 0.393
  Chirality :  0.048   0.317    492
  Planarity :  0.006   0.068    592
  Dihedral  :  5.983  17.465    466
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 21.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  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: -3.79 (0.37), residues: 416
  helix: -4.21 (0.55), residues: 30
  sheet: -1.53 (0.49), residues: 103
  loop : -2.90 (0.33), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 353 
 HIS   0.001   0.000   HIS H 100C
 PHE   0.015   0.002   PHE A 342 
 TYR   0.030   0.002   TYR L  91 
 ARG   0.008   0.001   ARG H  71 

*********************** 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
  101 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  424 LYS cc_start: 0.9558 (tttm) cc_final: 0.9163 (tmtt)
REVERT: A  425 LEU cc_start: 0.9287 (mp) cc_final: 0.8961 (mp)
REVERT: A  471 GLU cc_start: 0.7737 (mp0) cc_final: 0.7427 (mp0)
REVERT: A  498 GLN cc_start: 0.7823 (pt0) cc_final: 0.7610 (pt0)
REVERT: A  513 LEU cc_start: 0.9232 (mp) cc_final: 0.8948 (mp)
REVERT: H   20 VAL cc_start: 0.9052 (t) cc_final: 0.7838 (t)
REVERT: H   50 TRP cc_start: 0.8057 (p-90) cc_final: 0.7714 (p-90)
REVERT: H   67 VAL cc_start: 0.7194 (p) cc_final: 0.6942 (p)
REVERT: H   80 MET cc_start: 0.8007 (ppp) cc_final: 0.7471 (ppp)
REVERT: H   83 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.7990 (tpm170)
REVERT: H  105 GLN cc_start: 0.8087 (pm20) cc_final: 0.7841 (tp-100)
REVERT: L   42 GLN cc_start: 0.8784 (mp10) cc_final: 0.8414 (mp10)
REVERT: L   49 TYR cc_start: 0.8441 (p90) cc_final: 0.8057 (p90)
REVERT: L   77 ARG cc_start: 0.6772 (mmm160) cc_final: 0.5441 (mpt180)
REVERT: L   88 CYS cc_start: 0.5043 (t) cc_final: 0.4444 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1393
  time to fit residues: 17.2482
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  : 0.347 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.092102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.079386 restraints weight = 15003.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.081907 restraints weight = 9274.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.083704 restraints weight = 6372.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3640
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3640 r_free = 0.3640    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 = 0.3640 r_free = 0.3640    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3640
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.5250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3367  Z= 0.188
  Angle     :  0.758  12.310   4577  Z= 0.379
  Chirality :  0.048   0.277    492
  Planarity :  0.006   0.070    592
  Dihedral  :  5.552  20.716    466
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 18.86
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 11.78 %
    Favored  : 87.98 %
  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: -3.47 (0.38), residues: 416
  helix: -4.17 (0.66), residues: 18
  sheet: -1.61 (0.48), residues: 107
  loop : -2.63 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP L  35 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.022   0.002   PHE A 515 
 TYR   0.020   0.002   TYR L  91 
 ARG   0.007   0.001   ARG A 509 

*********************** 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
  106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.349 
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: 0.8064 (m) cc_final: 0.7853 (p)
REVERT: A  424 LYS cc_start: 0.9515 (tttm) cc_final: 0.9223 (tmtt)
REVERT: A  425 LEU cc_start: 0.9212 (mp) cc_final: 0.8946 (mm)
REVERT: A  471 GLU cc_start: 0.7656 (mp0) cc_final: 0.7252 (mp0)
REVERT: A  509 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7550 (mtt-85)
REVERT: H   35 GLN cc_start: 0.8833 (pt0) cc_final: 0.8514 (pt0)
REVERT: H   50 TRP cc_start: 0.7966 (p-90) cc_final: 0.7721 (p-90)
REVERT: H   79 TYR cc_start: 0.8260 (m-80) cc_final: 0.8055 (m-80)
REVERT: H   80 MET cc_start: 0.8032 (ppp) cc_final: 0.7614 (ppp)
REVERT: H   83 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.8028 (tpm170)
REVERT: H  105 GLN cc_start: 0.8033 (pm20) cc_final: 0.7774 (tp-100)
REVERT: L   35 TRP cc_start: 0.6576 (m100) cc_final: 0.6262 (m100)
REVERT: L   48 ILE cc_start: 0.7999 (pt) cc_final: 0.7537 (mp)
REVERT: L   49 TYR cc_start: 0.8455 (p90) cc_final: 0.8213 (p90)
REVERT: L   77 ARG cc_start: 0.6707 (mmm160) cc_final: 0.5472 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1570
  time to fit residues: 20.0564
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  : 0.357 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.089506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.076600 restraints weight = 15368.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.079078 restraints weight = 9597.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.080891 restraints weight = 6661.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    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 = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.5291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3367  Z= 0.214
  Angle     :  0.761  11.962   4577  Z= 0.378
  Chirality :  0.046   0.272    492
  Planarity :  0.006   0.072    592
  Dihedral  :  5.605  16.264    466
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    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: -3.58 (0.37), residues: 416
  helix: -4.20 (0.52), residues: 30
  sheet: -1.58 (0.47), residues: 107
  loop : -2.66 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.004   TRP A 436 
 HIS   0.001   0.001   HIS H 100C
 PHE   0.016   0.002   PHE A 342 
 TYR   0.020   0.002   TYR A 508 
 ARG   0.005   0.001   ARG A 509 

*********************** 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
  100 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.287 
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  424 LYS cc_start: 0.9510 (tttm) cc_final: 0.9169 (tmtt)
REVERT: A  471 GLU cc_start: 0.7663 (mp0) cc_final: 0.7286 (mp0)
REVERT: H   83 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8127 (tpm170)
REVERT: H  105 GLN cc_start: 0.8031 (pm20) cc_final: 0.7808 (tp-100)
REVERT: L   48 ILE cc_start: 0.8116 (pt) cc_final: 0.7878 (mp)
REVERT: L   49 TYR cc_start: 0.8511 (p90) cc_final: 0.8255 (p90)
REVERT: L   77 ARG cc_start: 0.6699 (mmm160) cc_final: 0.5420 (mpt180)
REVERT: L   78 LEU cc_start: 0.6345 (tp) cc_final: 0.5904 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1624
  time to fit residues: 19.5116
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  : 0.355 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 39 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 13 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3790 r_free = 0.3790 target = 0.090667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.077968 restraints weight = 14695.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.080452 restraints weight = 9245.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.082283 restraints weight = 6412.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    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 = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.5465

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= 0.209
  Angle     :  0.752  11.284   4577  Z= 0.378
  Chirality :  0.046   0.259    492
  Planarity :  0.007   0.078    592
  Dihedral  :  5.548  18.038    466
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  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: -3.46 (0.38), residues: 416
  helix: -4.12 (0.61), residues: 24
  sheet: -1.64 (0.46), residues: 107
  loop : -2.56 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP H  36 
 HIS   0.001   0.001   HIS H 100C
 PHE   0.024   0.002   PHE H 100F
 TYR   0.023   0.002   TYR H  59 
 ARG   0.005   0.001   ARG A 509 

********************** 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
  102 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.342 
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  405 ASP cc_start: 0.9166 (m-30) cc_final: 0.8941 (m-30)
REVERT: A  424 LYS cc_start: 0.9529 (tttm) cc_final: 0.9176 (tmtt)
REVERT: A  471 GLU cc_start: 0.7623 (mp0) cc_final: 0.7248 (mp0)
REVERT: H   20 VAL cc_start: 0.9000 (t) cc_final: 0.8336 (t)
REVERT: H   80 MET cc_start: 0.7843 (ppp) cc_final: 0.7507 (ppp)
REVERT: H   83 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8133 (tpm170)
REVERT: L   49 TYR cc_start: 0.8567 (p90) cc_final: 0.8234 (p90)
REVERT: L   77 ARG cc_start: 0.6821 (mmm160) cc_final: 0.5657 (mpt180)
REVERT: L   78 LEU cc_start: 0.6243 (tp) cc_final: 0.5940 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1549
  time to fit residues: 18.9559
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  : 0.339 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 11 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.092802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.080204 restraints weight = 15269.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.082717 restraints weight = 9719.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.084540 restraints weight = 6747.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    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 = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.5810

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= 0.189
  Angle     :  0.730   8.702   4577  Z= 0.367
  Chirality :  0.045   0.151    492
  Planarity :  0.007   0.082    592
  Dihedral  :  5.483  20.605    466
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 19.33
  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 (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: -3.31 (0.38), residues: 416
  helix: -4.09 (0.61), residues: 24
  sheet: -1.55 (0.47), residues: 107
  loop : -2.43 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.004   TRP A 436 
 HIS   0.001   0.000   HIS H 100C
 PHE   0.014   0.002   PHE A 342 
 TYR   0.020   0.002   TYR L  91 
 ARG   0.006   0.001   ARG A 509 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1530.14 seconds
wall clock time: 27 minutes 18.81 seconds (1638.81 seconds total)