Starting phenix.real_space_refine
on Wed Jul 23 10:08:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y7k_33668/07_2025/7y7k_33668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y7k_33668/07_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_33668/07_2025/7y7k_33668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y7k_33668/07_2025/7y7k_33668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y7k_33668/07_2025/7y7k_33668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y7k_33668/07_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-5711/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: 4.88, per 1000 atoms: 1.66
  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: 0.70
  Conformation dependent library (CDL) restraints added in 477.3 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: 0.42
  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: 0.79

  Time building geometry restraints manager: 0.85 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:             4.920
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.980
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.240
-------------------------------------------------------------------------------
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   3009  Z= 0.525
  Angle     :  1.636  12.028   4122  Z= 0.939
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14705 (  105)
  hydrogen bonds       : angle      10.23875 (  264)
  SS BOND              : bond        0.00854 (    5)
  SS BOND              : angle       2.84622 (   10)
  covalent geometry    : bond        0.00994 ( 3004)
  covalent geometry    : angle       1.63150 ( 4112)

*********************** 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  : 0.322 
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: 0.2227
  time to fit residues: 17.9349
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  : 0.353 
-------------------------------------------------------------------------------
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 = 39)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.054380 restraints weight = 27441.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.055651 restraints weight = 19296.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.056613 restraints weight = 14424.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6758
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   3009  Z= 0.169
  Angle     :  0.795   7.863   4122  Z= 0.419
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  105)
  hydrogen bonds       : angle       7.43908 (  264)
  SS BOND              : bond        0.00307 (    5)
  SS BOND              : angle       1.20803 (   10)
  covalent geometry    : bond        0.00357 ( 3004)
  covalent geometry    : angle       0.79350 ( 4112)

*********************** 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  : 0.343 
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: 0.8610 (m-80) cc_final: 0.7874 (m-80)
REVERT: B  107 TYR cc_start: 0.6300 (p90) cc_final: 0.5989 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 41
  average time/residue: 0.2935
  time to fit residues: 13.5488
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  : 0.340 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   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:    4.3990

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.057154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.049097 restraints weight = 27811.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.050305 restraints weight = 19337.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.051221 restraints weight = 14346.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.5791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.105   3009  Z= 0.388
  Angle     :  1.074   8.357   4122  Z= 0.571
  Chirality :  0.055   0.265    472
  Planarity :  0.007   0.043    540
  Dihedral  :  7.588  23.923    454
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 28.51
  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: -2.04 (0.39), residues: 416
  helix: -3.00 (0.67), residues: 25
  sheet: -0.09 (0.44), residues: 125
  loop : -1.93 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP B  49 
 HIS   0.004   0.002   HIS B 100 
 PHE   0.021   0.002   PHE A 374 
 TYR   0.029   0.003   TYR C  38 
 ARG   0.011   0.002   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05853 (  105)
  hydrogen bonds       : angle       8.16887 (  264)
  SS BOND              : bond        0.00344 (    5)
  SS BOND              : angle       2.09856 (   10)
  covalent geometry    : bond        0.00786 ( 3004)
  covalent geometry    : angle       1.07008 ( 4112)

*********************** 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
  26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 26
  average time/residue: 0.2191
  time to fit residues: 6.8293
Evaluate side-chains
  16 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 21 optimal weight:    0.0570
   chunk 3 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.9704

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.058370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.050146 restraints weight = 27886.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.051422 restraints weight = 18968.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.052362 restraints weight = 13920.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.6072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3009  Z= 0.190
  Angle     :  0.786   9.436   4122  Z= 0.410
  Chirality :  0.049   0.349    472
  Planarity :  0.005   0.049    540
  Dihedral  :  6.039  22.716    454
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  6.73 %
    Favored  : 92.55 %
  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: -1.73 (0.40), residues: 416
  helix: -2.66 (0.71), residues: 31
  sheet:  0.25 (0.46), residues: 122
  loop : -1.74 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 353 
 HIS   0.005   0.002   HIS B 100 
 PHE   0.010   0.001   PHE A 338 
 TYR   0.019   0.002   TYR C  38 
 ARG   0.006   0.001   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03852 (  105)
  hydrogen bonds       : angle       7.00353 (  264)
  SS BOND              : bond        0.00344 (    5)
  SS BOND              : angle       1.22953 (   10)
  covalent geometry    : bond        0.00385 ( 3004)
  covalent geometry    : angle       0.78460 ( 4112)

*********************** 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
  25 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: B    6 GLU cc_start: 0.6019 (tt0) cc_final: 0.5797 (tt0)
REVERT: B   95 TYR cc_start: 0.8646 (m-80) cc_final: 0.8001 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1649
  time to fit residues: 5.1013
Evaluate side-chains
  16 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 37 optimal weight:   20.0000
   chunk 5 optimal weight:    0.0870
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.9964

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.057642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.049701 restraints weight = 27061.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.050985 restraints weight = 18840.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.051926 restraints weight = 13617.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.6320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3009  Z= 0.190
  Angle     :  0.734   8.662   4122  Z= 0.382
  Chirality :  0.048   0.320    472
  Planarity :  0.004   0.049    540
  Dihedral  :  5.869  21.222    454
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  : 10.34 %
    Favored  : 88.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  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 (0.40), residues: 416
  helix: -2.23 (0.92), residues: 25
  sheet:  0.19 (0.45), residues: 124
  loop : -1.86 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.003   0.002   HIS B 100 
 PHE   0.010   0.001   PHE A 338 
 TYR   0.029   0.002   TYR C 100 
 ARG   0.004   0.001   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  105)
  hydrogen bonds       : angle       6.80584 (  264)
  SS BOND              : bond        0.00321 (    5)
  SS BOND              : angle       1.18260 (   10)
  covalent geometry    : bond        0.00387 ( 3004)
  covalent geometry    : angle       0.73248 ( 4112)

*********************** 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
  28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   95 TYR cc_start: 0.8601 (m-80) cc_final: 0.7981 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.2198
  time to fit residues: 7.2863
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  : 0.318 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.6384

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.057731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.049474 restraints weight = 27246.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.050779 restraints weight = 18832.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.051766 restraints weight = 13796.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.6753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3009  Z= 0.158
  Angle     :  0.672   7.683   4122  Z= 0.347
  Chirality :  0.046   0.170    472
  Planarity :  0.004   0.046    540
  Dihedral  :  5.393  20.874    454
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  7.69 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.13 %
    Favored  : 97.52 %
  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: -1.91 (0.40), residues: 416
  helix: -2.19 (0.83), residues: 31
  sheet:  0.09 (0.45), residues: 129
  loop : -1.98 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 353 
 HIS   0.002   0.001   HIS B 100 
 PHE   0.010   0.001   PHE A 374 
 TYR   0.020   0.002   TYR C 100 
 ARG   0.006   0.001   ARG C  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03502 (  105)
  hydrogen bonds       : angle       6.46976 (  264)
  SS BOND              : bond        0.00307 (    5)
  SS BOND              : angle       1.08160 (   10)
  covalent geometry    : bond        0.00327 ( 3004)
  covalent geometry    : angle       0.67075 ( 4112)

*********************** 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
  28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.6026 (OUTLIER) cc_final: 0.5379 (m110)
REVERT: B    6 GLU cc_start: 0.5538 (tt0) cc_final: 0.4861 (tt0)
REVERT: B   95 TYR cc_start: 0.8759 (m-80) cc_final: 0.7990 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 28
  average time/residue: 0.2145
  time to fit residues: 7.1426
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  : 0.312 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   chunk 30 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.059210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.050830 restraints weight = 27475.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.052212 restraints weight = 18854.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.053218 restraints weight = 13760.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.6917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3009  Z= 0.106
  Angle     :  0.616   9.051   4122  Z= 0.315
  Chirality :  0.048   0.339    472
  Planarity :  0.004   0.047    540
  Dihedral  :  4.634  17.952    454
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.17 %
    Favored  : 91.35 %
  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: -1.70 (0.41), residues: 416
  helix: -1.92 (0.95), residues: 25
  sheet:  0.29 (0.45), residues: 129
  loop : -1.91 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 100 
 PHE   0.020   0.001   PHE A 486 
 TYR   0.018   0.001   TYR C 100 
 ARG   0.001   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02800 (  105)
  hydrogen bonds       : angle       5.94068 (  264)
  SS BOND              : bond        0.00288 (    5)
  SS BOND              : angle       0.92423 (   10)
  covalent geometry    : bond        0.00221 ( 3004)
  covalent geometry    : angle       0.61508 ( 4112)

*********************** 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
  31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 ILE cc_start: 0.7499 (mt) cc_final: 0.7278 (mp)
REVERT: B    6 GLU cc_start: 0.5292 (tt0) cc_final: 0.4611 (tt0)
REVERT: B   95 TYR cc_start: 0.8776 (m-80) cc_final: 0.8015 (m-80)
REVERT: B  120 ASP cc_start: 0.8100 (p0) cc_final: 0.7433 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1582
  time to fit residues: 6.2252
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  : 0.346 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 6 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0970
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.1980
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0040
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.3390

-------------------------------------------------------------------------------
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 = 0.3621 r_free = 0.3621 target = 0.059685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.051360 restraints weight = 27279.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.052663 restraints weight = 19165.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.053645 restraints weight = 14046.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.7119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3009  Z= 0.098
  Angle     :  0.620   9.814   4122  Z= 0.303
  Chirality :  0.047   0.281    472
  Planarity :  0.004   0.044    540
  Dihedral  :  4.186  16.613    454
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.49 %
    Favored  : 93.03 %
  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: -1.58 (0.41), residues: 416
  helix: -1.99 (0.88), residues: 31
  sheet:  0.50 (0.45), residues: 131
  loop : -1.89 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 122 
 HIS   0.000   0.000   HIS C  33 
 PHE   0.017   0.001   PHE A 486 
 TYR   0.016   0.001   TYR C 100 
 ARG   0.002   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02523 (  105)
  hydrogen bonds       : angle       5.54433 (  264)
  SS BOND              : bond        0.00228 (    5)
  SS BOND              : angle       0.86442 (   10)
  covalent geometry    : bond        0.00208 ( 3004)
  covalent geometry    : angle       0.61908 ( 4112)

*********************** 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
  31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 ILE cc_start: 0.7737 (mt) cc_final: 0.7445 (mp)
REVERT: B    6 GLU cc_start: 0.5217 (tt0) cc_final: 0.4775 (tt0)
REVERT: B   95 TYR cc_start: 0.8694 (m-80) cc_final: 0.8025 (m-80)
REVERT: B  107 TYR cc_start: 0.6359 (p90) cc_final: 0.6035 (p90)
REVERT: B  120 ASP cc_start: 0.8139 (p0) cc_final: 0.7568 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1499
  time to fit residues: 5.8288
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  : 0.308 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0060
   chunk 35 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0980
   chunk 33 optimal weight:    8.9990
   overall best weight:    0.5600

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.059531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.051244 restraints weight = 27238.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.052573 restraints weight = 18798.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.053535 restraints weight = 13821.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.7207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3009  Z= 0.096
  Angle     :  0.588   8.623   4122  Z= 0.290
  Chirality :  0.046   0.238    472
  Planarity :  0.004   0.048    540
  Dihedral  :  4.093  16.418    454
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.25 %
    Favored  : 93.27 %
  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: -1.54 (0.41), residues: 416
  helix: -1.95 (0.88), residues: 31
  sheet:  0.54 (0.45), residues: 129
  loop : -1.84 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 122 
 HIS   0.001   0.000   HIS B 100 
 PHE   0.016   0.001   PHE A 486 
 TYR   0.014   0.001   TYR C 100 
 ARG   0.002   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02510 (  105)
  hydrogen bonds       : angle       5.45078 (  264)
  SS BOND              : bond        0.00238 (    5)
  SS BOND              : angle       0.73002 (   10)
  covalent geometry    : bond        0.00205 ( 3004)
  covalent geometry    : angle       0.58735 ( 4112)

*********************** 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
  27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 ILE cc_start: 0.7708 (mt) cc_final: 0.7445 (mp)
REVERT: B    6 GLU cc_start: 0.5302 (tt0) cc_final: 0.4800 (tt0)
REVERT: B   95 TYR cc_start: 0.8736 (m-80) cc_final: 0.7967 (m-10)
REVERT: B  107 TYR cc_start: 0.6321 (p90) cc_final: 0.5958 (p90)
REVERT: B  120 ASP cc_start: 0.8150 (p0) cc_final: 0.7695 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.1723
  time to fit residues: 5.8277
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  : 0.343 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 23 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.059062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.050900 restraints weight = 27357.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.052184 restraints weight = 18886.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.053139 restraints weight = 13906.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.7275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3009  Z= 0.105
  Angle     :  0.596   8.229   4122  Z= 0.294
  Chirality :  0.046   0.229    472
  Planarity :  0.004   0.044    540
  Dihedral  :  4.153  16.912    454
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.25 %
    Favored  : 93.27 %
  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: -1.55 (0.42), residues: 416
  helix: -1.98 (0.87), residues: 31
  sheet:  0.50 (0.45), residues: 129
  loop : -1.83 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 436 
 HIS   0.000   0.000   HIS C  33 
 PHE   0.016   0.001   PHE A 486 
 TYR   0.014   0.001   TYR C 100 
 ARG   0.002   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02663 (  105)
  hydrogen bonds       : angle       5.47610 (  264)
  SS BOND              : bond        0.00244 (    5)
  SS BOND              : angle       0.79415 (   10)
  covalent geometry    : bond        0.00222 ( 3004)
  covalent geometry    : angle       0.59502 ( 4112)

********************** 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
  28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 ILE cc_start: 0.7763 (mt) cc_final: 0.7491 (mp)
REVERT: B    6 GLU cc_start: 0.5431 (tt0) cc_final: 0.4959 (tt0)
REVERT: B   95 TYR cc_start: 0.8712 (m-80) cc_final: 0.8102 (m-80)
REVERT: B  107 TYR cc_start: 0.6387 (p90) cc_final: 0.6013 (p90)
REVERT: B  120 ASP cc_start: 0.8168 (p0) cc_final: 0.7749 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1748
  time to fit residues: 6.0837
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  : 0.342 
-------------------------------------------------------------------------------
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:    0.0030
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0770
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.4348

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.059815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.051432 restraints weight = 26884.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.052760 restraints weight = 18479.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.053756 restraints weight = 13534.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.7412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3009  Z= 0.090
  Angle     :  0.564   7.346   4122  Z= 0.280
  Chirality :  0.045   0.213    472
  Planarity :  0.004   0.044    540
  Dihedral  :  3.918  16.516    454
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.49 %
    Favored  : 93.03 %
  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: -1.48 (0.42), residues: 416
  helix: -1.96 (0.88), residues: 31
  sheet:  0.60 (0.46), residues: 129
  loop : -1.81 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.000   0.000   HIS C  33 
 PHE   0.017   0.001   PHE A 486 
 TYR   0.014   0.001   TYR C 100 
 ARG   0.002   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02403 (  105)
  hydrogen bonds       : angle       5.16107 (  264)
  SS BOND              : bond        0.00205 (    5)
  SS BOND              : angle       0.70737 (   10)
  covalent geometry    : bond        0.00193 ( 3004)
  covalent geometry    : angle       0.56408 ( 4112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1629.27 seconds
wall clock time: 28 minutes 51.25 seconds (1731.25 seconds total)