Starting phenix.real_space_refine
on Wed Sep 17 04:37:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9giu_51377/09_2025/9giu_51377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9giu_51377/09_2025/9giu_51377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9giu_51377/09_2025/9giu_51377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9giu_51377/09_2025/9giu_51377.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9giu_51377/09_2025/9giu_51377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9giu_51377/09_2025/9giu_51377.map"
  }
  resolution = 2.8
  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=  -0.000 sd=   0.031
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      29      5.16       5
     C    2742      2.51       5
     N     632      2.21       5
     O     723      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4127
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3827
          Classifications: {'peptide': 493}
          Link IDs: {'PTRANS': 18, 'TRANS': 474}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 300
          Unusual residues: {'3PE': 1, 'Y01': 7}
          Classifications: {'undetermined': 8, 'water': 17}
          Link IDs: {None: 24}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 13
  Time building chain proxies: 1.06, per 1000 atoms: 0.26
  Number of scatterers: 4127
  At special positions: 0
  Unit cell: (89.304, 68.076, 71.004, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P       1     15.00
     O     723      8.00
     N     632      7.00
     C    2742      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.38
  Conformation dependent library (CDL) restraints added in 157.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  902

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      75.7% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 80
      removed outlier: 3.527A  pdb=" N   TRP A  52 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL A  58 " --> pdb=" O   MET A  54 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   MET A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   THR A  74 " --> pdb=" O   THR A  70 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
      removed outlier: 3.508A  pdb=" N   ILE A  80 " --> pdb=" O   ILE A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 91
    Processing helix  chain 'A' and resid 92 through 111
      removed outlier: 3.682A  pdb=" N   ILE A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      Proline residue:  A 103  - end of helix
      removed outlier: 3.553A  pdb=" N   ARG A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 147
      removed outlier: 5.571A  pdb=" N   SER A 141 " --> pdb=" O   PHE A 137 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   ALA A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 187
      removed outlier: 3.964A  pdb=" N   GLU A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   GLY A 177 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.673A  pdb=" N   VAL A 186 " --> pdb=" O   TYR A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 215
    Processing helix  chain 'A' and resid 222 through 227
    Processing helix  chain 'A' and resid 229 through 251
      removed outlier: 3.503A  pdb=" N   PHE A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 454
    Processing helix  chain 'A' and resid 493 through 503
    Processing helix  chain 'A' and resid 505 through 527
    Processing helix  chain 'A' and resid 528 through 536
    Processing helix  chain 'A' and resid 548 through 584
      removed outlier: 3.561A  pdb=" N   GLN A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASP A 584 " --> pdb=" O   GLN A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 611
    Processing helix  chain 'A' and resid 613 through 621
    Processing helix  chain 'A' and resid 621 through 643
      removed outlier: 3.936A  pdb=" N   GLY A 625 " --> pdb=" O   ILE A 621 " (cutoff:3.500A)
      Proline residue:  A 635  - end of helix
      removed outlier: 3.587A  pdb=" N   GLN A 641 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 650
    Processing helix  chain 'A' and resid 659 through 690
      removed outlier: 3.718A  pdb=" N   GLN A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL A 671 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   TYR A 672 " --> pdb=" O   SER A 668 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   GLY A 683 " --> pdb=" O   ALA A 679 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   GLY A 684 " --> pdb=" O   SER A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 713
      removed outlier: 4.188A  pdb=" N   MET A 697 " --> pdb=" O   ARG A 693 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 419 through 420
      removed outlier: 6.825A  pdb=" N   TYR A 438 " --> pdb=" O   LYS A 432 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LYS A 432 " --> pdb=" O   TYR A 438 " (cutoff:3.500A)

    270 hydrogen bonds defined for protein.
    798 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: 0.69

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 658
        1.32 -     1.45: 1105
        1.45 -     1.57: 2412
        1.57 -     1.69: 2
        1.69 -     1.81: 47
  Bond restraints: 4224
  Sorted by residual:
  bond pdb=" N   VAL A 614 "
       pdb=" CA  VAL A 614 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.030 1.18e-02 7.18e+03 6.66e+00
  bond pdb=" N   GLN A 220 "
       pdb=" CA  GLN A 220 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.28e-02 6.10e+03 5.53e+00
  bond pdb=" N   GLN A 647 "
       pdb=" CA  GLN A 647 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.38e+00
  bond pdb=" N   TYR A 568 "
       pdb=" CA  TYR A 568 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.19e-02 7.06e+03 4.47e+00
  bond pdb=" N   GLU A  63 "
       pdb=" CA  GLU A  63 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.28e-02 6.10e+03 3.60e+00
  ... (remaining 4219 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 5539
        1.16 -     2.32: 187
        2.32 -     3.48: 33
        3.48 -     4.64: 8
        4.64 -     5.80: 6
  Bond angle restraints: 5773
  Sorted by residual:
  angle pdb=" CA  VAL A 614 "
        pdb=" C   VAL A 614 "
        pdb=" O   VAL A 614 "
      ideal   model   delta    sigma   weight residual
     121.29  118.29    3.00 1.07e+00 8.73e-01 7.84e+00
  angle pdb=" O   VAL A 614 "
        pdb=" C   VAL A 614 "
        pdb=" N   TYR A 615 "
      ideal   model   delta    sigma   weight residual
     121.94  124.47   -2.53 1.03e+00 9.43e-01 6.01e+00
  angle pdb=" CA  TYR A 568 "
        pdb=" C   TYR A 568 "
        pdb=" O   TYR A 568 "
      ideal   model   delta    sigma   weight residual
     120.82  118.43    2.39 1.05e+00 9.07e-01 5.18e+00
  angle pdb=" CA  GLN A 647 "
        pdb=" C   GLN A 647 "
        pdb=" O   GLN A 647 "
      ideal   model   delta    sigma   weight residual
     120.55  118.18    2.37 1.06e+00 8.90e-01 5.00e+00
  angle pdb=" O   GLN A 647 "
        pdb=" C   GLN A 647 "
        pdb=" N   TYR A 648 "
      ideal   model   delta    sigma   weight residual
     122.12  124.39   -2.27 1.06e+00 8.90e-01 4.60e+00
  ... (remaining 5768 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 2453
       17.75 -    35.50: 259
       35.50 -    53.25: 70
       53.25 -    71.00: 12
       71.00 -    88.75: 9
  Dihedral angle restraints: 2803
    sinusoidal: 1387
      harmonic: 1416
  Sorted by residual:
  dihedral pdb=" CA  ILE A 100 "
           pdb=" C   ILE A 100 "
           pdb=" N   PHE A 101 "
           pdb=" CA  PHE A 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.95  -19.05     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  TYR A 633 "
           pdb=" C   TYR A 633 "
           pdb=" N   CYS A 634 "
           pdb=" CA  CYS A 634 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.72  -17.28     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CB  GLU A 255 "
           pdb=" CG  GLU A 255 "
           pdb=" CD  GLU A 255 "
           pdb=" OE1 GLU A 255 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.84  -86.84     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 2800 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 483
       0.037 -    0.073: 151
       0.073 -    0.110: 25
       0.110 -    0.147: 10
       0.147 -    0.183: 1
  Chirality restraints: 670
  Sorted by residual:
  chirality pdb=" CA  VAL A 614 "
            pdb=" N   VAL A 614 "
            pdb=" C   VAL A 614 "
            pdb=" CB  VAL A 614 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.40e-01
  chirality pdb=" CA  THR A 102 "
            pdb=" N   THR A 102 "
            pdb=" C   THR A 102 "
            pdb=" CB  THR A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  THR A  74 "
            pdb=" N   THR A  74 "
            pdb=" C   THR A  74 "
            pdb=" CB  THR A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 667 not shown)

  Planarity restraints: 678
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  87 "   -0.007 2.00e-02 2.50e+03   1.01e-02 2.05e+00
        pdb=" CG  TYR A  87 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  87 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  87 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  87 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  87 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  87 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A  87 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 177 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.79e+00
        pdb=" N   PRO A 178 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 178 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 178 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 120 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.79e+00
        pdb=" N   PRO A 121 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 121 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 121 "    0.019 5.00e-02 4.00e+02
  ... (remaining 675 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 693
        2.76 -     3.30: 3996
        3.30 -     3.83: 6961
        3.83 -     4.37: 8567
        4.37 -     4.90: 14705
  Nonbonded interactions: 34922
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 182 "
            pdb=" O   ILE A 253 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OD1 ASP A 531 "
            pdb=" OH  TYR A 554 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ALA A 710 "
            pdb=" OH  TYR A 716 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   GLY A  98 "
            pdb=" OG1 THR A 102 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OD1 ASP A 169 "
            pdb=" O   HOH A 901 "
     model   vdw
     2.282 3.040
  ... (remaining 34917 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             7.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.070
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
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      :  0.003   0.030   4224  Z= 0.150
  Angle     :  0.534   5.795   5773  Z= 0.286
  Chirality :  0.038   0.183    670
  Planarity :  0.004   0.033    678
  Dihedral  : 15.793  88.749   1901
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.58 %
    Favored  : 81.42 %
  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 aren not related in a simple way.
  whole:  2.05 (0.38), residues: 487
  helix:  1.78 (0.27), residues: 367
  sheet:  3.09 (1.48), residues: 10
  loop : -0.15 (0.63), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.025   0.002   TYR A  87 
 PHE   0.009   0.001   PHE A  64 
 TRP   0.014   0.001   TRP A 519 
 HIS   0.004   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4224)
  covalent geometry    : angle       0.53430 ( 5773)
  hydrogen bonds       : bond        0.10249 (  270)
  hydrogen bonds       : angle       4.49325 (  798)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  454 SER cc_start: 0.8327 (p) cc_final: 0.8038 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.6286
  time to fit residues: 36.4217
Evaluate side-chains
  53 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.0020
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 197 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.168125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.142738 restraints weight = 4105.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 1.59
r_work: 0.3600 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.0630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4224  Z= 0.146
  Angle     :  0.548   7.059   5773  Z= 0.276
  Chirality :  0.040   0.147    670
  Planarity :  0.004   0.036    678
  Dihedral  : 10.543  76.870   1072
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 14.67 %
    Favored  : 81.42 %
  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 aren not related in a simple way.
  whole:  2.01 (0.38), residues: 487
  helix:  1.75 (0.26), residues: 368
  sheet:  2.77 (1.37), residues: 10
  loop : -0.14 (0.63), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 180 
 TYR   0.012   0.001   TYR A 636 
 PHE   0.012   0.001   PHE A  64 
 TRP   0.010   0.001   TRP A 519 
 HIS   0.004   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4224)
  covalent geometry    : angle       0.54829 ( 5773)
  hydrogen bonds       : bond        0.04883 (  270)
  hydrogen bonds       : angle       3.98090 (  798)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  624 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7915 (ttt)
REVERT: A  646 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6765 (tttt)
REVERT: A  647 GLN cc_start: 0.7592 (tm-30) cc_final: 0.6703 (pp30)
  outliers start: 16
  outliers final: 5
  residues processed: 60
  average time/residue: 0.5243
  time to fit residues: 32.7251
Evaluate side-chains
  57 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 28 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.169935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.144710 restraints weight = 4052.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.59
r_work: 0.3583 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.0796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4224  Z= 0.138
  Angle     :  0.532   6.140   5773  Z= 0.267
  Chirality :  0.039   0.151    670
  Planarity :  0.004   0.037    678
  Dihedral  : 10.160  75.027   1072
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 15.16 %
    Favored  : 80.20 %
  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 aren not related in a simple way.
  whole:  2.09 (0.38), residues: 487
  helix:  1.82 (0.26), residues: 368
  sheet:  2.63 (1.32), residues: 10
  loop : -0.12 (0.64), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 180 
 TYR   0.012   0.001   TYR A 636 
 PHE   0.013   0.001   PHE A  64 
 TRP   0.010   0.001   TRP A  52 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4224)
  covalent geometry    : angle       0.53150 ( 5773)
  hydrogen bonds       : bond        0.04702 (  270)
  hydrogen bonds       : angle       3.89178 (  798)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  624 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7998 (ttt)
REVERT: A  646 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6797 (tttt)
  outliers start: 19
  outliers final: 6
  residues processed: 60
  average time/residue: 0.5463
  time to fit residues: 34.0737
Evaluate side-chains
  58 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0870
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.6558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.170526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.146287 restraints weight = 3996.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 1.49
r_work: 0.3609 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3484 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.0847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4224  Z= 0.154
  Angle     :  0.552   5.905   5773  Z= 0.277
  Chirality :  0.040   0.154    670
  Planarity :  0.004   0.039    678
  Dihedral  : 10.128  73.966   1072
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 15.16 %
    Favored  : 80.68 %
  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 aren not related in a simple way.
  whole:  2.06 (0.38), residues: 487
  helix:  1.85 (0.26), residues: 362
  sheet:  2.55 (1.28), residues: 10
  loop : -0.21 (0.63), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 180 
 TYR   0.013   0.001   TYR A 636 
 PHE   0.013   0.002   PHE A  64 
 TRP   0.010   0.001   TRP A  52 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 4224)
  covalent geometry    : angle       0.55199 ( 5773)
  hydrogen bonds       : bond        0.04921 (  270)
  hydrogen bonds       : angle       3.90604 (  798)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  624 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8013 (ttt)
REVERT: A  646 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6776 (tttt)
REVERT: A  647 GLN cc_start: 0.7553 (tm-30) cc_final: 0.6634 (pp30)
  outliers start: 17
  outliers final: 8
  residues processed: 58
  average time/residue: 0.5303
  time to fit residues: 31.9944
Evaluate side-chains
  59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.169482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.144356 restraints weight = 4019.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 1.58
r_work: 0.3601 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3474 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4224  Z= 0.143
  Angle     :  0.538   5.599   5773  Z= 0.270
  Chirality :  0.039   0.154    670
  Planarity :  0.004   0.039    678
  Dihedral  :  9.955  72.507   1072
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 14.43 %
    Favored  : 81.42 %
  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 aren not related in a simple way.
  whole:  2.10 (0.38), residues: 487
  helix:  1.87 (0.26), residues: 362
  sheet:  2.57 (1.26), residues: 10
  loop : -0.21 (0.63), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 495 
 TYR   0.020   0.001   TYR A  87 
 PHE   0.011   0.002   PHE A  64 
 TRP   0.009   0.001   TRP A  52 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4224)
  covalent geometry    : angle       0.53823 ( 5773)
  hydrogen bonds       : bond        0.04787 (  270)
  hydrogen bonds       : angle       3.87056 (  798)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  624 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7988 (ttt)
REVERT: A  646 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6781 (tttt)
  outliers start: 17
  outliers final: 7
  residues processed: 57
  average time/residue: 0.5923
  time to fit residues: 35.0042
Evaluate side-chains
  57 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0870
   chunk 15 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0370
   chunk 22 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4236

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.164037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.136294 restraints weight = 4071.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.75
r_work: 0.3465 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4224  Z= 0.124
  Angle     :  0.516   5.595   5773  Z= 0.261
  Chirality :  0.038   0.153    670
  Planarity :  0.004   0.038    678
  Dihedral  :  9.678  70.286   1072
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 13.69 %
    Favored  : 81.91 %
  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 aren not related in a simple way.
  whole:  2.24 (0.38), residues: 487
  helix:  1.99 (0.27), residues: 362
  sheet:  2.47 (1.24), residues: 10
  loop : -0.17 (0.64), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 495 
 TYR   0.021   0.001   TYR A  87 
 PHE   0.010   0.001   PHE A  64 
 TRP   0.009   0.001   TRP A 519 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4224)
  covalent geometry    : angle       0.51645 ( 5773)
  hydrogen bonds       : bond        0.04450 (  270)
  hydrogen bonds       : angle       3.79432 (  798)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7376 (tp30)
REVERT: A  624 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7948 (ttt)
REVERT: A  646 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6778 (tttt)
REVERT: A  647 GLN cc_start: 0.7510 (tm-30) cc_final: 0.6769 (mp10)
  outliers start: 18
  outliers final: 9
  residues processed: 56
  average time/residue: 0.4988
  time to fit residues: 29.1137
Evaluate side-chains
  58 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  220 GLN
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  594 TYR
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 46 optimal weight:    0.3980
   chunk 3 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.162563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.135089 restraints weight = 4051.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 1.73
r_work: 0.3446 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.1001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4224  Z= 0.146
  Angle     :  0.541   5.654   5773  Z= 0.272
  Chirality :  0.039   0.154    670
  Planarity :  0.004   0.039    678
  Dihedral  :  9.775  69.572   1072
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 14.18 %
    Favored  : 81.42 %
  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 aren not related in a simple way.
  whole:  2.10 (0.38), residues: 487
  helix:  1.88 (0.27), residues: 362
  sheet:  2.52 (1.25), residues: 10
  loop : -0.19 (0.64), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 180 
 TYR   0.023   0.001   TYR A  87 
 PHE   0.013   0.002   PHE A  64 
 TRP   0.011   0.001   TRP A 519 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4224)
  covalent geometry    : angle       0.54138 ( 5773)
  hydrogen bonds       : bond        0.04793 (  270)
  hydrogen bonds       : angle       3.84807 (  798)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  521 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7712 (p)
REVERT: A  624 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7960 (ttt)
REVERT: A  647 GLN cc_start: 0.7551 (tm-30) cc_final: 0.6832 (mp10)
  outliers start: 18
  outliers final: 7
  residues processed: 58
  average time/residue: 0.5117
  time to fit residues: 30.9053
Evaluate side-chains
  57 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  521 SER
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 20 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.168161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.142889 restraints weight = 4059.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.58
r_work: 0.3453 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4224  Z= 0.160
  Angle     :  0.559   5.672   5773  Z= 0.280
  Chirality :  0.040   0.156    670
  Planarity :  0.004   0.040    678
  Dihedral  :  9.925  68.931   1072
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.40 %
    Favored  : 80.93 %
  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 aren not related in a simple way.
  whole:  2.03 (0.38), residues: 487
  helix:  1.80 (0.27), residues: 363
  sheet:  2.58 (1.24), residues: 10
  loop : -0.16 (0.65), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 495 
 TYR   0.025   0.002   TYR A  87 
 PHE   0.012   0.002   PHE A 235 
 TRP   0.011   0.001   TRP A  52 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 4224)
  covalent geometry    : angle       0.55932 ( 5773)
  hydrogen bonds       : bond        0.05013 (  270)
  hydrogen bonds       : angle       3.89070 (  798)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   68 MET cc_start: 0.7105 (mtp) cc_final: 0.6596 (mtt)
REVERT: A  521 SER cc_start: 0.7907 (OUTLIER) cc_final: 0.7669 (p)
REVERT: A  624 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7944 (ttt)
  outliers start: 15
  outliers final: 8
  residues processed: 56
  average time/residue: 0.5691
  time to fit residues: 33.0824
Evaluate side-chains
  54 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  521 SER
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  713 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.166927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.141383 restraints weight = 4121.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.59
r_work: 0.3435 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4224  Z= 0.163
  Angle     :  0.569   5.672   5773  Z= 0.285
  Chirality :  0.040   0.156    670
  Planarity :  0.004   0.040    678
  Dihedral  :  9.926  68.282   1072
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.40 %
    Favored  : 80.93 %
  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 aren not related in a simple way.
  whole:  1.99 (0.38), residues: 487
  helix:  1.78 (0.27), residues: 363
  sheet:  2.62 (1.25), residues: 10
  loop : -0.20 (0.65), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 421 
 TYR   0.026   0.002   TYR A  87 
 PHE   0.012   0.002   PHE A 235 
 TRP   0.011   0.001   TRP A 519 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 4224)
  covalent geometry    : angle       0.56947 ( 5773)
  hydrogen bonds       : bond        0.05049 (  270)
  hydrogen bonds       : angle       3.91249 (  798)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7359 (tp30)
REVERT: A   68 MET cc_start: 0.7157 (mtp) cc_final: 0.6657 (mtt)
REVERT: A  230 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6731 (tt0)
REVERT: A  521 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7673 (p)
REVERT: A  624 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7952 (ttt)
REVERT: A  647 GLN cc_start: 0.7486 (tm-30) cc_final: 0.6521 (pp30)
  outliers start: 15
  outliers final: 10
  residues processed: 56
  average time/residue: 0.5798
  time to fit residues: 33.6776
Evaluate side-chains
  60 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  230 GLN
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  521 SER
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  713 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0000
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 32 optimal weight:    0.1980
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.168013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.142475 restraints weight = 4058.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 1.59
r_work: 0.3456 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4224  Z= 0.145
  Angle     :  0.547   5.645   5773  Z= 0.275
  Chirality :  0.039   0.155    670
  Planarity :  0.004   0.040    678
  Dihedral  :  9.752  66.775   1072
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.65 %
    Favored  : 80.93 %
  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 aren not related in a simple way.
  whole:  2.09 (0.38), residues: 487
  helix:  1.87 (0.27), residues: 362
  sheet:  2.54 (1.25), residues: 10
  loop : -0.20 (0.64), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 421 
 TYR   0.025   0.002   TYR A  87 
 PHE   0.011   0.002   PHE A  64 
 TRP   0.013   0.001   TRP A 519 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4224)
  covalent geometry    : angle       0.54712 ( 5773)
  hydrogen bonds       : bond        0.04812 (  270)
  hydrogen bonds       : angle       3.86317 (  798)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7440 (tp30)
REVERT: A   68 MET cc_start: 0.7155 (mtp) cc_final: 0.6674 (mtt)
REVERT: A  230 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.6751 (tt0)
REVERT: A  521 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7727 (p)
REVERT: A  624 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7962 (ttt)
REVERT: A  647 GLN cc_start: 0.7458 (tm-30) cc_final: 0.6523 (pp30)
  outliers start: 14
  outliers final: 9
  residues processed: 56
  average time/residue: 0.5232
  time to fit residues: 30.4737
Evaluate side-chains
  58 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  230 GLN
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  521 SER
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  713 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.167981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.142612 restraints weight = 4066.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 1.59
r_work: 0.3445 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4224  Z= 0.162
  Angle     :  0.568   5.667   5773  Z= 0.285
  Chirality :  0.040   0.156    670
  Planarity :  0.004   0.041    678
  Dihedral  :  9.837  66.261   1072
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.89 %
    Favored  : 80.93 %
  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 aren not related in a simple way.
  whole:  1.98 (0.38), residues: 487
  helix:  1.78 (0.27), residues: 363
  sheet:  2.46 (1.25), residues: 10
  loop : -0.22 (0.65), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 421 
 TYR   0.026   0.002   TYR A  87 
 PHE   0.012   0.002   PHE A 235 
 TRP   0.013   0.002   TRP A 519 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4224)
  covalent geometry    : angle       0.56847 ( 5773)
  hydrogen bonds       : bond        0.05054 (  270)
  hydrogen bonds       : angle       3.91814 (  798)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1754.93 seconds
wall clock time: 30 minutes 44.22 seconds (1844.22 seconds total)