Starting phenix.real_space_refine
on Mon Feb 10 22:09:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y7k_33668/02_2025/7y7k_33668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y7k_33668/02_2025/7y7k_33668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y7k_33668/02_2025/7y7k_33668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y7k_33668/02_2025/7y7k_33668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y7k_33668/02_2025/7y7k_33668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y7k_33668/02_2025/7y7k_33668.cif"
  }
  resolution = 4.4
  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=  -0.003 sd=   0.017
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      11      5.16       5
     C    1832      2.51       5
     N     505      2.21       5
     O     594      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 2942
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1230
          Classifications: {'peptide': 179}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 9, 'TRANS': 169}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 210
          Unresolved non-hydrogen angles: 268
          Unresolved non-hydrogen dihedrals: 186
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 6, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 157
    Chain: "B"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 953
          Classifications: {'peptide': 132}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 6, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 111
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 63
    Chain: "C"
      Number of atoms: 759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 759
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 7, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 90
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 41
  Time building chain proxies: 3.12, per 1000 atoms: 1.06
  Number of scatterers: 2942
  At special positions: 0
  Unit cell: (56.58, 64.78, 104.14, 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      11     16.00
     O     594      8.00
     N     505      7.00
     C    1832      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  90 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 407.4 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:  762

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 6 sheets defined
      11.8% alpha, 30.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.118A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.651A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 65 through 67
      No H-bonds generated for 'chain 'B' and resid 65 through 67'
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'C' and resid 81 through 85
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.693A  pdb=" N   PHE B  80 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.127A  pdb=" N   TRP B  36 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER B  52 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   TRP B  38 " --> pdb=" O   ILE B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 23
    Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 50
      removed outlier: 6.235A  pdb=" N   TRP C  37 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   ASP C  34 " --> pdb=" O   TYR C  93 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   TYR C  93 " --> pdb=" O   ASP C  34 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 50
      removed outlier: 6.235A  pdb=" N   TRP C  37 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   ASP C  34 " --> pdb=" O   TYR C  93 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   TYR C  93 " --> pdb=" O   ASP C  34 " (cutoff:3.500A)

    114 hydrogen bonds defined for protein.
    264 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: 0.89 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 494
        1.28 -     1.42: 781
        1.42 -     1.55: 1715
        1.55 -     1.68: 3
        1.68 -     1.81: 11
  Bond restraints: 3004
  Sorted by residual:
  bond pdb=" C   ASN A 439 "
       pdb=" O   ASN A 439 "
    ideal  model  delta    sigma   weight residual
    1.236  1.151  0.085 1.18e-02 7.18e+03 5.20e+01
  bond pdb=" C   ARG B 102 "
       pdb=" N   SER B 103 "
    ideal  model  delta    sigma   weight residual
    1.332  1.288  0.045 1.40e-02 5.10e+03 1.01e+01
  bond pdb=" C   ASN A 439 "
       pdb=" N   ASN A 440 "
    ideal  model  delta    sigma   weight residual
    1.334  1.291  0.044 1.38e-02 5.25e+03 1.01e+01
  bond pdb=" C   LYS A 424 "
       pdb=" N   LEU A 425 "
    ideal  model  delta    sigma   weight residual
    1.335  1.265  0.070 3.04e-02 1.08e+03 5.32e+00
  bond pdb=" CA  GLU B   1 "
       pdb=" C   GLU B   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.481  0.044 2.10e-02 2.27e+03 4.49e+00
  ... (remaining 2999 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 3702
        2.41 -     4.81: 306
        4.81 -     7.22: 78
        7.22 -     9.62: 21
        9.62 -    12.03: 5
  Bond angle restraints: 4112
  Sorted by residual:
  angle pdb=" N   TYR A 489 "
        pdb=" CA  TYR A 489 "
        pdb=" C   TYR A 489 "
      ideal   model   delta    sigma   weight residual
     109.65  119.96  -10.31 1.56e+00 4.11e-01 4.37e+01
  angle pdb=" N   THR A 478 "
        pdb=" CA  THR A 478 "
        pdb=" C   THR A 478 "
      ideal   model   delta    sigma   weight residual
     109.06  119.62  -10.56 1.78e+00 3.16e-01 3.52e+01
  angle pdb=" N   TYR B 105 "
        pdb=" CA  TYR B 105 "
        pdb=" C   TYR B 105 "
      ideal   model   delta    sigma   weight residual
     110.80   98.77   12.03 2.13e+00 2.20e-01 3.19e+01
  angle pdb=" O   ARG B 102 "
        pdb=" C   ARG B 102 "
        pdb=" N   SER B 103 "
      ideal   model   delta    sigma   weight residual
     122.59  115.43    7.16 1.33e+00 5.65e-01 2.89e+01
  angle pdb=" N   PHE A 464 "
        pdb=" CA  PHE A 464 "
        pdb=" C   PHE A 464 "
      ideal   model   delta    sigma   weight residual
     110.80  121.21  -10.41 2.13e+00 2.20e-01 2.39e+01
  ... (remaining 4107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 1649
       17.46 -    34.93: 87
       34.93 -    52.39: 20
       52.39 -    69.86: 9
       69.86 -    87.32: 4
  Dihedral angle restraints: 1769
    sinusoidal: 564
      harmonic: 1205
  Sorted by residual:
  dihedral pdb=" CA  GLN C   1 "
           pdb=" C   GLN C   1 "
           pdb=" N   SER C   2 "
           pdb=" CA  SER C   2 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.81  -18.19     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  ALA C  86 "
           pdb=" C   ALA C  86 "
           pdb=" N   ASP C  87 "
           pdb=" CA  ASP C  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  ASN C  53 "
           pdb=" C   ASN C  53 "
           pdb=" N   ASN C  54 "
           pdb=" CA  ASN C  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.92  -17.08     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 1766 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 285
       0.056 -    0.112: 129
       0.112 -    0.167: 42
       0.167 -    0.223: 9
       0.223 -    0.279: 7
  Chirality restraints: 472
  Sorted by residual:
  chirality pdb=" CA  TYR A 489 "
            pdb=" N   TYR A 489 "
            pdb=" C   TYR A 489 "
            pdb=" CB  TYR A 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CA  PRO A 479 "
            pdb=" N   PRO A 479 "
            pdb=" C   PRO A 479 "
            pdb=" CB  PRO A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CB  VAL A 362 "
            pdb=" CA  VAL A 362 "
            pdb=" CG1 VAL A 362 "
            pdb=" CG2 VAL A 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 469 not shown)

  Planarity restraints: 540
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 439 "   -0.023 2.00e-02 2.50e+03   4.68e-02 2.19e+01
        pdb=" C   ASN A 439 "    0.081 2.00e-02 2.50e+03
        pdb=" O   ASN A 439 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   ASN A 440 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 490 "   -0.077 5.00e-02 4.00e+02   1.16e-01 2.14e+01
        pdb=" N   PRO A 491 "    0.200 5.00e-02 4.00e+02
        pdb=" CA  PRO A 491 "   -0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A 491 "   -0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  38 "    0.024 2.00e-02 2.50e+03   2.81e-02 1.58e+01
        pdb=" CG  TYR C  38 "   -0.069 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  38 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  38 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  38 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  38 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  38 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR C  38 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 537 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 568
        2.75 -     3.29: 2907
        3.29 -     3.83: 4888
        3.83 -     4.36: 5365
        4.36 -     4.90: 9159
  Nonbonded interactions: 22887
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  27 "
            pdb=" N   THR C  96 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   THR C   5 "
            pdb=" N   THR C  23 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   THR A 345 "
            pdb=" NH2 ARG A 509 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NE2 GLN B  41 "
            pdb=" O   LYS B  45 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" O   CYS C  90 "
            pdb=" N   GLY C 103 "
     model   vdw
     2.269 3.120
  ... (remaining 22882 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:             3.800
  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:                    0.020
  Process input model:                     12.970
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6429
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      :  0.010   0.104   3004  Z= 0.662
  Angle     :  1.632  12.028   4112  Z= 0.938
  Chirality :  0.074   0.279    472
  Planarity :  0.010   0.116    540
  Dihedral  : 13.106  87.323    992
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 33.93
  Ramachandran Plot:
    Outliers :  3.61 %
    Allowed  : 10.34 %
    Favored  : 86.06 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  :  7.09 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.50 (0.38), residues: 416
  helix: -3.92 (0.53), residues: 36
  sheet:  0.24 (0.48), residues: 126
  loop : -2.47 (0.34), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B  49 
 HIS   0.007   0.002   HIS C  33 
 PHE   0.024   0.003   PHE A 456 
 TYR   0.069   0.006   TYR C  38 
 ARG   0.027   0.003   ARG C  63 

*********************** 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
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.368 
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: symmetry clash
REVERT: B   95 TYR cc_start: 0.7862 (m-80) cc_final: 0.7483 (m-80)
REVERT: C   16 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.5606 (pp30)
REVERT: C   41 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8184 (tt)
  outliers start: 11
  outliers final: 2
  residues processed: 71
  average time/residue: 0.2212
  time to fit residues: 17.8433
Evaluate side-chains
  29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 31 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 GLN
C  33 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.062774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.054376 restraints weight = 27441.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.055635 restraints weight = 19302.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.056600 restraints weight = 14481.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3004  Z= 0.230
  Angle     :  0.794   7.863   4112  Z= 0.418
  Chirality :  0.050   0.227    472
  Planarity :  0.005   0.034    540
  Dihedral  :  5.565  19.446    454
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.96 %
    Allowed  :  7.45 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  2.48 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.87 (0.39), residues: 416
  helix: -4.56 (0.37), residues: 24
  sheet:  0.09 (0.45), residues: 135
  loop : -1.73 (0.36), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.002   0.001   HIS B 100 
 PHE   0.011   0.002   PHE A 456 
 TYR   0.029   0.002   TYR C  38 
 ARG   0.004   0.001   ARG A 509 

*********************** 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
  41 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.378 
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: B   95 TYR cc_start: 0.8609 (m-80) cc_final: 0.7871 (m-80)
REVERT: B  107 TYR cc_start: 0.6303 (p90) cc_final: 0.5994 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 41
  average time/residue: 0.3004
  time to fit residues: 13.8946
Evaluate side-chains
  23 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0870
   chunk 6 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    4.2166

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.057440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.049391 restraints weight = 27801.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.050609 restraints weight = 19292.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.051526 restraints weight = 14326.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.5649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.107   3004  Z= 0.521
  Angle     :  1.043   8.208   4112  Z= 0.556
  Chirality :  0.054   0.266    472
  Planarity :  0.007   0.047    540
  Dihedral  :  7.409  23.030    454
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 27.25
  Ramachandran Plot:
    Outliers :  0.96 %
    Allowed  : 11.30 %
    Favored  : 87.74 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  3.55 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.97 (0.39), residues: 416
  helix: -2.99 (0.69), residues: 25
  sheet: -0.07 (0.44), residues: 125
  loop : -1.86 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B  49 
 HIS   0.004   0.001   HIS B 100 
 PHE   0.019   0.002   PHE A 374 
 TYR   0.028   0.003   TYR C  38 
 ARG   0.011   0.002   ARG A 509 

*********************** 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
  28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 GLU cc_start: 0.6593 (tt0) cc_final: 0.6203 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 28
  average time/residue: 0.2180
  time to fit residues: 7.3006
Evaluate side-chains
  15 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 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 = 0.3588 r_free = 0.3588 target = 0.059229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.050700 restraints weight = 27413.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.052025 restraints weight = 18671.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.052955 restraints weight = 13745.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6868
moved from start:          0.5856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3004  Z= 0.211
  Angle     :  0.738   9.328   4112  Z= 0.384
  Chirality :  0.049   0.343    472
  Planarity :  0.004   0.048    540
  Dihedral  :  5.637  21.425    454
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  6.49 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.48 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.63 (0.41), residues: 416
  helix: -2.48 (0.77), residues: 31
  sheet:  0.11 (0.45), residues: 130
  loop : -1.62 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.004   0.001   HIS B 100 
 PHE   0.008   0.001   PHE A 338 
 TYR   0.017   0.002   TYR C  38 
 ARG   0.005   0.001   ARG C  95 

*********************** 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
  26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 LEU cc_start: 0.8365 (pp) cc_final: 0.7861 (mm)
REVERT: B   95 TYR cc_start: 0.8653 (m-80) cc_final: 0.7999 (m-80)
REVERT: B  107 TYR cc_start: 0.6200 (p90) cc_final: 0.5934 (p90)
REVERT: C   40 GLN cc_start: 0.8802 (pt0) cc_final: 0.8059 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1625
  time to fit residues: 5.2220
Evaluate side-chains
  18 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    0.2980
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.058620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.050467 restraints weight = 26925.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.051745 restraints weight = 18759.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.052696 restraints weight = 13728.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
moved from start:          0.5992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3004  Z= 0.206
  Angle     :  0.684   8.484   4112  Z= 0.354
  Chirality :  0.047   0.312    472
  Planarity :  0.004   0.049    540
  Dihedral  :  5.353  19.833    454
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  8.89 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.71 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.60 (0.41), residues: 416
  helix: -2.25 (0.93), residues: 25
  sheet:  0.06 (0.44), residues: 141
  loop : -1.67 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 353 
 HIS   0.002   0.001   HIS C  33 
 PHE   0.007   0.001   PHE A 338 
 TYR   0.027   0.002   TYR C 100 
 ARG   0.005   0.001   ARG A 509 

*********************** 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
  31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.5757 (OUTLIER) cc_final: 0.5101 (m110)
REVERT: B   20 LEU cc_start: 0.8424 (pp) cc_final: 0.7821 (mm)
REVERT: B   95 TYR cc_start: 0.8631 (m-80) cc_final: 0.7924 (m-80)
REVERT: B  107 TYR cc_start: 0.6230 (p90) cc_final: 0.5949 (p90)
REVERT: C   40 GLN cc_start: 0.8781 (pt0) cc_final: 0.8033 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1905
  time to fit residues: 7.1840
Evaluate side-chains
  20 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0770
   chunk 3 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 13 optimal weight:    0.4980
   chunk 9 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    1.2342

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.058925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.050555 restraints weight = 27239.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.051915 restraints weight = 18702.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.052908 restraints weight = 13669.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.6324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3004  Z= 0.188
  Angle     :  0.658   8.538   4112  Z= 0.339
  Chirality :  0.048   0.331    472
  Planarity :  0.004   0.048    540
  Dihedral  :  5.112  20.021    454
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  7.45 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.62 (0.41), residues: 416
  helix: -2.38 (0.92), residues: 25
  sheet:  0.22 (0.45), residues: 129
  loop : -1.70 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 353 
 HIS   0.002   0.001   HIS B 100 
 PHE   0.020   0.002   PHE A 486 
 TYR   0.023   0.002   TYR C 100 
 ARG   0.003   0.001   ARG A 509 

*********************** 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
  26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 GLU cc_start: 0.5859 (tt0) cc_final: 0.4790 (tt0)
REVERT: B   20 LEU cc_start: 0.8544 (pp) cc_final: 0.7791 (mm)
REVERT: B   95 TYR cc_start: 0.8707 (m-80) cc_final: 0.7879 (m-80)
REVERT: C   40 GLN cc_start: 0.8719 (pt0) cc_final: 0.8052 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.2137
  time to fit residues: 6.6819
Evaluate side-chains
  20 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.057605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.049580 restraints weight = 27478.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.050846 restraints weight = 18932.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.051795 restraints weight = 13703.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6891
moved from start:          0.6730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3004  Z= 0.257
  Angle     :  0.679   7.661   4112  Z= 0.354
  Chirality :  0.046   0.166    472
  Planarity :  0.005   0.048    540
  Dihedral  :  5.457  20.518    454
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.34 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.01 (0.40), residues: 416
  helix: -2.39 (0.75), residues: 37
  sheet:  0.04 (0.45), residues: 129
  loop : -2.02 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 122 
 HIS   0.002   0.001   HIS B 100 
 PHE   0.022   0.002   PHE A 486 
 TYR   0.021   0.002   TYR C 100 
 ARG   0.003   0.001   ARG C  26 

*********************** 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
  24 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   95 TYR cc_start: 0.8665 (m-80) cc_final: 0.7992 (m-80)
REVERT: C   40 GLN cc_start: 0.8743 (pt0) cc_final: 0.8078 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.2405
  time to fit residues: 6.9350
Evaluate side-chains
  19 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    0.1980
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.1980
   chunk 14 optimal weight:    0.0270
   chunk 8 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.2838

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 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 = 0.3625 r_free = 0.3625 target = 0.060158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.051456 restraints weight = 26665.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.052833 restraints weight = 18507.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.053884 restraints weight = 13557.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.6939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3004  Z= 0.135
  Angle     :  0.607   7.626   4112  Z= 0.307
  Chirality :  0.047   0.231    472
  Planarity :  0.004   0.048    540
  Dihedral  :  4.508  17.911    454
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.73 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.75 (0.41), residues: 416
  helix: -2.82 (0.80), residues: 31
  sheet:  0.44 (0.45), residues: 129
  loop : -1.91 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  49 
 HIS   0.001   0.000   HIS C  33 
 PHE   0.013   0.001   PHE A 486 
 TYR   0.020   0.001   TYR C 100 
 ARG   0.003   0.001   ARG C  17 

*********************** 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
  33 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 GLU cc_start: 0.5398 (tt0) cc_final: 0.4599 (tt0)
REVERT: B   95 TYR cc_start: 0.8722 (m-80) cc_final: 0.7916 (m-10)
REVERT: B  107 TYR cc_start: 0.6425 (p90) cc_final: 0.6119 (p90)
REVERT: B  120 ASP cc_start: 0.8355 (p0) cc_final: 0.7713 (m-30)
REVERT: C   40 GLN cc_start: 0.8762 (pt0) cc_final: 0.8238 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.2073
  time to fit residues: 8.1294
Evaluate side-chains
  25 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0770
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0970
   chunk 29 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    1.2140

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 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 = 0.3590 r_free = 0.3590 target = 0.059015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.050520 restraints weight = 26943.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.051860 restraints weight = 18347.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.052856 restraints weight = 13313.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.7072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3004  Z= 0.182
  Angle     :  0.634  10.120   4112  Z= 0.313
  Chirality :  0.046   0.218    472
  Planarity :  0.004   0.047    540
  Dihedral  :  4.641  17.563    454
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  7.93 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.77 (0.41), residues: 416
  helix: -2.69 (0.81), residues: 31
  sheet:  0.38 (0.46), residues: 129
  loop : -1.93 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.000   HIS B 100 
 PHE   0.015   0.002   PHE A 486 
 TYR   0.016   0.001   TYR C 100 
 ARG   0.003   0.001   ARG C  26 

*********************** 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
  26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 GLU cc_start: 0.5557 (tt0) cc_final: 0.4757 (tt0)
REVERT: B   20 LEU cc_start: 0.8519 (pp) cc_final: 0.7751 (mm)
REVERT: B   95 TYR cc_start: 0.8676 (m-80) cc_final: 0.7962 (m-80)
REVERT: B  120 ASP cc_start: 0.8274 (p0) cc_final: 0.7572 (m-30)
REVERT: C   40 GLN cc_start: 0.8720 (pt0) cc_final: 0.8223 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.2211
  time to fit residues: 6.9149
Evaluate side-chains
  21 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 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 = 0.3607 r_free = 0.3607 target = 0.059117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.050857 restraints weight = 27519.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.052159 restraints weight = 18935.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.053107 restraints weight = 13866.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.7185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3004  Z= 0.152
  Angle     :  0.622   9.347   4112  Z= 0.307
  Chirality :  0.046   0.209    472
  Planarity :  0.004   0.047    540
  Dihedral  :  4.524  18.203    454
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  7.21 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.74 (0.41), residues: 416
  helix: -2.60 (0.82), residues: 31
  sheet:  0.41 (0.45), residues: 129
  loop : -1.91 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  33 
 PHE   0.014   0.001   PHE A 486 
 TYR   0.017   0.001   TYR C 100 
 ARG   0.002   0.000   ARG C  63 

********************** 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
  26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 GLU cc_start: 0.5463 (tt0) cc_final: 0.4714 (tt0)
REVERT: B   20 LEU cc_start: 0.8516 (pp) cc_final: 0.7783 (mm)
REVERT: B   95 TYR cc_start: 0.8666 (m-80) cc_final: 0.8068 (m-80)
REVERT: B  107 TYR cc_start: 0.6392 (p90) cc_final: 0.6076 (p90)
REVERT: B  120 ASP cc_start: 0.8107 (p0) cc_final: 0.7586 (m-30)
REVERT: C   40 GLN cc_start: 0.8741 (pt0) cc_final: 0.8218 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1792
  time to fit residues: 5.7915
Evaluate side-chains
  22 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0870
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0000
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.4162

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 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 = 0.3639 r_free = 0.3639 target = 0.060017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.051601 restraints weight = 27074.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.052917 restraints weight = 18826.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.053874 restraints weight = 13845.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.7408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3004  Z= 0.130
  Angle     :  0.606   8.182   4112  Z= 0.295
  Chirality :  0.046   0.215    472
  Planarity :  0.004   0.047    540
  Dihedral  :  4.143  16.379    454
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.01 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.80 (0.41), residues: 416
  helix: -2.61 (0.77), residues: 37
  sheet:  0.17 (0.45), residues: 137
  loop : -1.86 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  33 
 PHE   0.015   0.001   PHE A 486 
 TYR   0.014   0.001   TYR C 100 
 ARG   0.003   0.000   ARG C  17 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1513.16 seconds
wall clock time: 27 minutes 45.00 seconds (1665.00 seconds total)