Starting phenix.real_space_refine
on Tue Mar  3 11:13:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y7k_33668/03_2026/7y7k_33668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y7k_33668/03_2026/7y7k_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_33668/03_2026/7y7k_33668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y7k_33668/03_2026/7y7k_33668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y7k_33668/03_2026/7y7k_33668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y7k_33668/03_2026/7y7k_33668.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'PHE:plan': 6, 'ARG:plan': 6, 'TYR:plan': 7, 'ASP:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 4}
          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: {'TRP:plan': 3, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1}
          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: {'ASN:plan1': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 41
  Time building chain proxies: 0.86, per 1000 atoms: 0.29
  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: 0.24
  Conformation dependent library (CDL) restraints added in 128.5 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: 0.11
  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: 0.37

  Time building geometry restraints manager: 0.33 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:             5.460
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.070
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.020
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.027   0.003   ARG C  63 
 TYR   0.069   0.006   TYR C  38 
 PHE   0.024   0.003   PHE A 456 
 TRP   0.015   0.003   TRP B  49 
 HIS   0.007   0.002   HIS C  33 

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

*********************** 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  : 0.124 
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: 0.7862 (m-80) cc_final: 0.7485 (m-80)
REVERT: C   16 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.5607 (pp30)
REVERT: C   41 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8183 (tt)
  outliers start: 11
  outliers final: 2
  residues processed: 71
  average time/residue: 0.1072
  time to fit residues: 8.6071
Evaluate side-chains
  28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.060659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.052326 restraints weight = 27738.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.053584 restraints weight = 19163.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.054558 restraints weight = 14228.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.055268 restraints weight = 10973.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.055844 restraints weight = 8816.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6791
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   3009  Z= 0.256
  Angle     :  0.894   8.104   4122  Z= 0.475
  Chirality :  0.051   0.222    472
  Planarity :  0.005   0.034    540
  Dihedral  :  6.414  20.499    454
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.96 %
    Allowed  :  8.17 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  3.90 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.39), residues: 416
  helix: -2.89 (0.85), residues: 24
  sheet:  0.02 (0.46), residues: 129
  loop : -1.88 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG A 509 
 TYR   0.033   0.003   TYR C  38 
 PHE   0.013   0.003   PHE A 456 
 TRP   0.011   0.002   TRP A 353 
 HIS   0.003   0.002   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 3004)
  covalent geometry    : angle       0.89419 ( 4112)
  SS BOND              : bond        0.00657 (    5)
  SS BOND              : angle       0.90408 (   10)
  hydrogen bonds       : bond        0.04142 (  105)
  hydrogen bonds       : angle       7.87408 (  264)

*********************** 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
  35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8166 (pttp)
REVERT: B  107 TYR cc_start: 0.6293 (p90) cc_final: 0.5976 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1236
  time to fit residues: 4.9043
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  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    1.1582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.061421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.052912 restraints weight = 27759.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.054250 restraints weight = 19178.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.055257 restraints weight = 14068.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.055968 restraints weight = 10800.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.056526 restraints weight = 8659.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.4812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3009  Z= 0.146
  Angle     :  0.701   7.307   4122  Z= 0.369
  Chirality :  0.048   0.264    472
  Planarity :  0.004   0.043    540
  Dihedral  :  5.272  19.087    454
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.96 %
    Allowed  :  6.97 %
    Favored  : 92.07 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.41), residues: 416
  helix: -2.50 (0.84), residues: 25
  sheet: -0.06 (0.44), residues: 137
  loop : -1.57 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 509 
 TYR   0.022   0.001   TYR C  38 
 PHE   0.005   0.001   PHE C 102 
 TRP   0.007   0.001   TRP A 353 
 HIS   0.002   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3004)
  covalent geometry    : angle       0.69854 ( 4112)
  SS BOND              : bond        0.00837 (    5)
  SS BOND              : angle       1.36720 (   10)
  hydrogen bonds       : bond        0.03475 (  105)
  hydrogen bonds       : angle       6.87105 (  264)

*********************** 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
  32 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8105 (pttp)
REVERT: B  107 TYR cc_start: 0.6366 (p90) cc_final: 0.6029 (p90)
REVERT: C   40 GLN cc_start: 0.8544 (pt0) cc_final: 0.7829 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1122
  time to fit residues: 4.0212
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  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0060
   chunk 37 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.3402

-------------------------------------------------------------------------------
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**
** C  33 HIS ** 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 = 0.3651 r_free = 0.3651 target = 0.060983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.052517 restraints weight = 27332.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.053908 restraints weight = 18838.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.054908 restraints weight = 13736.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.055646 restraints weight = 10570.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.056193 restraints weight = 8416.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6774
moved from start:          0.5185

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= 0.145
  Angle     :  0.674   9.890   4122  Z= 0.349
  Chirality :  0.048   0.352    472
  Planarity :  0.004   0.045    540
  Dihedral  :  5.057  19.147    454
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  7.45 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.42 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.42), residues: 416
  helix: -1.76 (1.05), residues: 19
  sheet:  0.01 (0.44), residues: 138
  loop : -1.38 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  95 
 TYR   0.022   0.002   TYR C 100 
 PHE   0.008   0.001   PHE C 102 
 TRP   0.006   0.001   TRP A 353 
 HIS   0.003   0.002   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3004)
  covalent geometry    : angle       0.67367 ( 4112)
  SS BOND              : bond        0.00269 (    5)
  SS BOND              : angle       0.89960 (   10)
  hydrogen bonds       : bond        0.03219 (  105)
  hydrogen bonds       : angle       6.62487 (  264)

*********************** 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
  34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.8663 (ptpp) cc_final: 0.8051 (pttp)
REVERT: B   95 TYR cc_start: 0.8667 (m-80) cc_final: 0.8092 (m-80)
REVERT: B  107 TYR cc_start: 0.6383 (p90) cc_final: 0.6086 (p90)
REVERT: C   40 GLN cc_start: 0.8619 (pt0) cc_final: 0.7938 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1045
  time to fit residues: 4.0037
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  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 14 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0270
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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**
C  33 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.061854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.053394 restraints weight = 26616.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.054738 restraints weight = 18324.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.055718 restraints weight = 13421.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.056414 restraints weight = 10306.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.056958 restraints weight = 8279.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6705
moved from start:          0.5597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3009  Z= 0.107
  Angle     :  0.611   8.763   4122  Z= 0.314
  Chirality :  0.048   0.328    472
  Planarity :  0.004   0.047    540
  Dihedral  :  4.479  18.412    454
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  5.77 %
    Favored  : 93.51 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.41), residues: 416
  helix: -1.38 (1.18), residues: 19
  sheet:  0.27 (0.45), residues: 129
  loop : -1.52 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  95 
 TYR   0.022   0.001   TYR C 100 
 PHE   0.005   0.001   PHE A 486 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS C  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 3004)
  covalent geometry    : angle       0.61084 ( 4112)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       0.77227 (   10)
  hydrogen bonds       : bond        0.02685 (  105)
  hydrogen bonds       : angle       6.08928 (  264)

*********************** 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
  37 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.5298 (OUTLIER) cc_final: 0.4679 (m110)
REVERT: B   20 LEU cc_start: 0.8636 (pp) cc_final: 0.7922 (mm)
REVERT: B   83 LYS cc_start: 0.8660 (ptpp) cc_final: 0.8132 (pttp)
REVERT: B   95 TYR cc_start: 0.8623 (m-80) cc_final: 0.7889 (m-10)
REVERT: B  107 TYR cc_start: 0.6263 (p90) cc_final: 0.5985 (p90)
REVERT: C   40 GLN cc_start: 0.8793 (pt0) cc_final: 0.8002 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1096
  time to fit residues: 4.6503
Evaluate side-chains
  24 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0010
   chunk 28 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.9592

-------------------------------------------------------------------------------
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 = 0.3607 r_free = 0.3607 target = 0.059884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.051503 restraints weight = 27307.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.052817 restraints weight = 19083.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.053745 restraints weight = 14083.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.054487 restraints weight = 10948.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.055024 restraints weight = 8726.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.5996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3009  Z= 0.185
  Angle     :  0.668   6.460   4122  Z= 0.351
  Chirality :  0.046   0.166    472
  Planarity :  0.004   0.047    540
  Dihedral  :  5.054  19.502    454
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  6.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.42), residues: 416
  helix: -2.15 (0.92), residues: 25
  sheet:  0.16 (0.46), residues: 130
  loop : -1.67 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 509 
 TYR   0.020   0.002   TYR C 100 
 PHE   0.024   0.002   PHE A 486 
 TRP   0.009   0.002   TRP B  49 
 HIS   0.002   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3004)
  covalent geometry    : angle       0.66671 ( 4112)
  SS BOND              : bond        0.00325 (    5)
  SS BOND              : angle       1.04738 (   10)
  hydrogen bonds       : bond        0.03491 (  105)
  hydrogen bonds       : angle       6.41654 (  264)

*********************** 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
  31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 LEU cc_start: 0.8674 (pp) cc_final: 0.7980 (mm)
REVERT: B   83 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8008 (pttp)
REVERT: B   95 TYR cc_start: 0.8604 (m-80) cc_final: 0.8033 (m-80)
REVERT: B  107 TYR cc_start: 0.6397 (p90) cc_final: 0.6134 (p90)
REVERT: C   40 GLN cc_start: 0.8766 (pt0) cc_final: 0.8132 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0822
  time to fit residues: 3.0725
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  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 18 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.0582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.060511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.052059 restraints weight = 27229.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.053420 restraints weight = 18682.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.054385 restraints weight = 13660.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.055125 restraints weight = 10519.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.055659 restraints weight = 8414.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6761
moved from start:          0.6207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3009  Z= 0.121
  Angle     :  0.635   9.525   4122  Z= 0.320
  Chirality :  0.046   0.239    472
  Planarity :  0.004   0.047    540
  Dihedral  :  4.671  19.456    454
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  6.01 %
    Favored  : 93.27 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.42), residues: 416
  helix: -1.38 (1.17), residues: 19
  sheet:  0.23 (0.46), residues: 130
  loop : -1.72 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 509 
 TYR   0.019   0.001   TYR C 100 
 PHE   0.018   0.001   PHE A 486 
 TRP   0.007   0.001   TRP A 353 
 HIS   0.002   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3004)
  covalent geometry    : angle       0.63468 ( 4112)
  SS BOND              : bond        0.00320 (    5)
  SS BOND              : angle       0.72286 (   10)
  hydrogen bonds       : bond        0.02968 (  105)
  hydrogen bonds       : angle       6.22668 (  264)

*********************** 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
  27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 LEU cc_start: 0.8690 (pp) cc_final: 0.8074 (mm)
REVERT: B   83 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8086 (pttp)
REVERT: B   95 TYR cc_start: 0.8606 (m-80) cc_final: 0.8020 (m-80)
REVERT: B  107 TYR cc_start: 0.6355 (p90) cc_final: 0.6054 (p90)
REVERT: C   40 GLN cc_start: 0.8805 (pt0) cc_final: 0.8160 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0636
  time to fit residues: 2.1572
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  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.059587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.050936 restraints weight = 26993.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.052296 restraints weight = 18479.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.053319 restraints weight = 13437.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.054059 restraints weight = 10261.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.054648 restraints weight = 8189.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.6587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3009  Z= 0.155
  Angle     :  0.660   8.340   4122  Z= 0.335
  Chirality :  0.047   0.260    472
  Planarity :  0.004   0.047    540
  Dihedral  :  4.781  19.245    454
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.65 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.42 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.42), residues: 416
  helix: -2.04 (0.93), residues: 25
  sheet:  0.24 (0.46), residues: 130
  loop : -1.75 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 509 
 TYR   0.016   0.002   TYR C 100 
 PHE   0.016   0.002   PHE A 486 
 TRP   0.007   0.001   TRP A 353 
 HIS   0.002   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3004)
  covalent geometry    : angle       0.65936 ( 4112)
  SS BOND              : bond        0.00268 (    5)
  SS BOND              : angle       0.92297 (   10)
  hydrogen bonds       : bond        0.03256 (  105)
  hydrogen bonds       : angle       6.35250 (  264)

*********************** 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
  27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8543 (mp-120)
REVERT: B   20 LEU cc_start: 0.8659 (pp) cc_final: 0.8059 (mm)
REVERT: B   25 SER cc_start: 0.8625 (t) cc_final: 0.8187 (t)
REVERT: B   83 LYS cc_start: 0.8663 (ptpp) cc_final: 0.8033 (pttp)
REVERT: B   95 TYR cc_start: 0.8606 (m-80) cc_final: 0.8008 (m-80)
REVERT: B  107 TYR cc_start: 0.6349 (p90) cc_final: 0.6077 (p90)
REVERT: B  120 ASP cc_start: 0.8368 (p0) cc_final: 0.7569 (m-30)
REVERT: C   40 GLN cc_start: 0.8825 (pt0) cc_final: 0.8190 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0783
  time to fit residues: 2.5615
Evaluate side-chains
  21 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 3 optimal weight:    0.5980
   chunk 7 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    0.1980
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0070
   chunk 29 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8400

-------------------------------------------------------------------------------
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 = 0.060334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.051723 restraints weight = 27432.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.053131 restraints weight = 18885.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.054150 restraints weight = 13793.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.054898 restraints weight = 10513.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.055480 restraints weight = 8376.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.6770

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= 0.110
  Angle     :  0.604   7.660   4122  Z= 0.305
  Chirality :  0.047   0.242    472
  Planarity :  0.004   0.048    540
  Dihedral  :  4.389  18.157    454
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.01 %
    Favored  : 93.51 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.42), residues: 416
  helix: -1.25 (1.23), residues: 19
  sheet:  0.15 (0.45), residues: 141
  loop : -1.69 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 509 
 TYR   0.016   0.001   TYR C 100 
 PHE   0.013   0.001   PHE A 486 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 3004)
  covalent geometry    : angle       0.60354 ( 4112)
  SS BOND              : bond        0.00243 (    5)
  SS BOND              : angle       0.66423 (   10)
  hydrogen bonds       : bond        0.02915 (  105)
  hydrogen bonds       : angle       6.00059 (  264)

*********************** 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
  28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 LEU cc_start: 0.8619 (pp) cc_final: 0.7994 (mm)
REVERT: B   83 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8066 (pttp)
REVERT: B   95 TYR cc_start: 0.8628 (m-80) cc_final: 0.7900 (m-10)
REVERT: B  107 TYR cc_start: 0.6436 (p90) cc_final: 0.6136 (p90)
REVERT: B  120 ASP cc_start: 0.8283 (p0) cc_final: 0.7668 (m-30)
REVERT: C   40 GLN cc_start: 0.8836 (pt0) cc_final: 0.8288 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0595
  time to fit residues: 2.1459
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  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0570
   chunk 4 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0670
   chunk 33 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.6040

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.060734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.052098 restraints weight = 26955.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.053502 restraints weight = 18673.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.054547 restraints weight = 13658.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.055354 restraints weight = 10466.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.055923 restraints weight = 8270.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.6986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3009  Z= 0.101
  Angle     :  0.594   7.600   4122  Z= 0.296
  Chirality :  0.046   0.238    472
  Planarity :  0.004   0.048    540
  Dihedral  :  4.102  17.257    454
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.97 %
    Favored  : 92.55 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.42), residues: 416
  helix: -1.06 (1.25), residues: 19
  sheet:  0.22 (0.45), residues: 141
  loop : -1.71 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 102 
 TYR   0.014   0.001   TYR C 100 
 PHE   0.014   0.001   PHE A 486 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.000   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 3004)
  covalent geometry    : angle       0.59366 ( 4112)
  SS BOND              : bond        0.00227 (    5)
  SS BOND              : angle       0.76177 (   10)
  hydrogen bonds       : bond        0.02727 (  105)
  hydrogen bonds       : angle       5.71996 (  264)

********************** 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
  29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 LEU cc_start: 0.8633 (pp) cc_final: 0.7978 (mm)
REVERT: B   83 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8118 (pttp)
REVERT: B   95 TYR cc_start: 0.8647 (m-80) cc_final: 0.7923 (m-10)
REVERT: B  107 TYR cc_start: 0.6553 (p90) cc_final: 0.6201 (p90)
REVERT: C   40 GLN cc_start: 0.8799 (pt0) cc_final: 0.8249 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0725
  time to fit residues: 2.5495
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  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0060
   chunk 23 optimal weight:    0.7980
   chunk 12 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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 = 0.3656 r_free = 0.3656 target = 0.060800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.052212 restraints weight = 26070.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.053541 restraints weight = 18270.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.054516 restraints weight = 13473.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.055286 restraints weight = 10415.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.055846 restraints weight = 8327.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.7044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3009  Z= 0.106
  Angle     :  0.590   7.765   4122  Z= 0.297
  Chirality :  0.046   0.229    472
  Planarity :  0.004   0.047    540
  Dihedral  :  4.110  17.442    454
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.11
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.42), residues: 416
  helix: -0.93 (1.27), residues: 19
  sheet:  0.29 (0.46), residues: 141
  loop : -1.71 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  56 
 TYR   0.013   0.001   TYR C 100 
 PHE   0.013   0.001   PHE A 486 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3004)
  covalent geometry    : angle       0.59027 ( 4112)
  SS BOND              : bond        0.00227 (    5)
  SS BOND              : angle       0.63761 (   10)
  hydrogen bonds       : bond        0.02732 (  105)
  hydrogen bonds       : angle       5.66382 (  264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 873.24 seconds
wall clock time: 15 minutes 37.34 seconds (937.34 seconds total)